Wrapped and Read: A Reading Advent Update

Spotify just told me that Superfruit was my artist of the year. “You discovered 265 new artists this year, but you really vibed with Superfruit,” Spotify Wrapped announced*. Google Scholar has not released a comparable look back at my year; there is no sleek graphic design of my year in citations. And Google Sheets is equally lagging on a social-media-sharable data visualization of my admittedly haphazard #365papers record keeping. I guess I will have to manually reflect on my reading the old-fashioned way — through blogging. 

To kick off December, I created a list of twelve 2019 papers that I had really meant to read this year, but by late November were still kicking around in my ‘To Read Pile.’ Each business day in December, I’ve carved out a little time to curl up with a mug of tea, don a cozy sweatshirt, light a little candle, and read one of these papers. The ritual is so lovely. I expected this — I knew the reading itself would be a kind of reward. The challenge lay mostly in creating the list: wading through the debris of my ‘To Read Pile’ after prepping for summer conferences and fall teaching hobbled, and then assassinated, my reading habits. But once you have a list, you just have to brew the tea and show up in sweats — the paper is chosen and waiting. It is the meal prep of staying on top of the literature: a dozen tupperwares of perfectly portioned pasta, a standing line of freezer bags with curried squash soup that were frozen lying on their sides on baking pans and now stack perfectly in the freezer, a double-batch of zucchini-corn-black bean empañadas made from scratch. I will tell you from experience that those foil-wrapped freezer empañadas are doubly amazing: they are delicious and some previous version of yourself already decided what’s for dinner. I knew that making the reading list for my advent of ecological literature would be the hardest part of the 12 Days of Reading; I did not expect that I would love the gift of having a list so much.

I picked some pretty great papers — see the reviews below — but even more fundamental than the quality of the papers is the fact that they are listed and for the last seven and the next five business days I don’t need exert any mental energy on choosing what to read. I cannot recommend the act of listing enough. 

If you are looking for papers to add to your list, here are some recommendations from my list: If you want to bone up on reading that will help you practice inclusion in your classroom and research, read On reporting scientific and racial history and An alternative hypothesis for the evolution of same-sex sexual behaviour in animals. 

If you want to reflect on active learning in your teaching and how to help students understand the benefits of feeling uncomfortable in active learning, read Measuring actual learning versus feeling of learning in response to being actively engaged in the classroom. 

If you want to think BIG about ecology and evolution across geologic time scales, read Why mountains matter for biodiversity. 

If you want to think small about local extinctions and species traits over the past century and really dig into what we can learn from historical ecological data, read Species characteristics affect local extinctions. 

If you are early career and you just feel like maybe you don’t have enough imposter syndrome in your life, read Postdocs’ lab engagement predicts trajectories of PhD students’ skill development. It is extremely hard to read this paper, in which a cohort of graduate students are judged annually on a single piece of academic writing, and not try to imagine the trajectory of your own skill development. The paper models how students transition among skill levels from year to year. Honestly, I do not self-identify as a person with a simple, positive linear growth over time. I think I was among the oddball 13.1% of students that apparently decreased in skill level and then increased. But aside from the general cloud of existential reflection, I struggled with this paper because I could not reconcile the results (“PIs’ laboratory and mentoring activities do not significantly predict students’ skill development trajectories”) with the discussion’s complete lack of accountability for PIs. If a postdoc’s attendance at lab discussions is a more powerful predictor of PhD students’ skill development than the PI’s mentoring, I don’t see this as a feel-good story about the power of postdocs. (Obviously postdocs are awesome and we work wicked hard and we deserve only good things.) Postdocs are also a reflection of the PI’s mentoring; the idea that “postdocs participating in laboratory discussions” is somehow a predictor that is independent of the PI’s mentorship or lab culture seems fundamentally flawed. I was particularly put off by the suggestion that, pursuant to these results, postdocs should receive training in effective mentoring practices. In literally the next sentence, the authors admit “postdocs are underpaid relative to the value they contribute to scholarly productivity” and yet instead of a call to better compensate postdocs, they would like to add to our responsibilities.

Finally, this recommendation may be a tad over-specific, but if you want to really understand the question your committee member was working to articulate during the closed session of your dissertation defense while you made confused faces and pointed to the literature on phenological sensitivity, read On quantifying the apparent temperature sensitivity of plant phenology. (The middle author was my committee member; I totally understand his question now and it is a really freaking good one.) Happy Reading! 

*Thanks for the introduction to this band, Dr. Becky Barak & the amazing group text of the Plant Love Stories team.

Thanksgiving Reading List

Last November, Binghamton Unversity-SUNY’s WHRW station shared this message as part of their program ‘Broadcasting World Literature’: “Today, since it’s Thanksgiving week, I thought it would be good to start off with a reading or just do a reading of a native scholar’s take on giving thanks.” Daimys Garcia explains before she begins reading from Robin Wall Kimmerer’s Brading Sweetgrass,“It’s important to remember that Thanksgiving has history that’s rooted in genocide, colonization, and oppression of native peoples on this land so I thought it’d be great to read a piece by a native scholar who is thinking about thanksgiving not as the holiday but in the act of giving thanks.”

Garcia’s reading of the chapter ‘Allegiance to Gratitude’ is so beautiful — I cannot recommend listening to this episode of 'Broadcasting World Literature' enough. I echo Garcia’s sentiments that in Thanksgiving week, and Native American Heritage Month, we remember the history of this landscape, the indigenous people who were here and live here still, and the food that we’ve done our best to re-brand as thoroughly Americanized. 

Whether your preparations for Thanksgiving break involve long lists of ingredients for baking marathons, hamstring stretches for turkey trots, or stacks of lab reports for grade-a-thons, somehow we have arrived in late November. I pulled together a list of on-theme academic papers to keep your cocktail hour anecdotes accurate and your sidebars over the side dishes peer-reviewed.

Here is a totally non-thorough, mostly-ecological literature review of turkeys (and the extinct poultry you might expect on a more or less accurate Thanksgiving spread), cranberries, sweet potatoes, and…ptarmigan. But — before you dig into this feast of a reading list, remember Rule 7: Respect working hours, public holidays, and vacations. This is from the recent PLoS Computational Biology paper, Ten simple rules towards healthier research labs. “Working rules commonly in place in labs around the world often mean that academics work all day long, on weekends, and even during holidays,” the author, Dr. Fernando Maestre, writes. “The stress associated with this excessive work without a life outside the lab is one of the main reasons behind the increase in mental problems in academia, particularly among early career researchers and young PIs.”

You, my friend, are ahead of the game. Relaxing with a little blog reading before Thanksgiving and making excellent life choices. Well done! 

First, Americans check out turkeys on Wikipedia in November in alarming numbers. Dr. John Mittermeier and coauthors report that “pageviews for wild turkey Meleagris gallopavo show a seasonal peak in the spring and a sharp peak during the Thanksgiving holiday in the US.” This idea — that Americans are reading up on Thanksgiving turkeys year after year — was part of the inspiration behind Mittermeier’s PLOS Biology paper A season for all things: Phenological imprints in Wikipedia usage and their relevance to conservation.

If you aren’t convinced of the cultural relevance of turkeys, or question how much Americans love to look up turkeys on the internet, consider the fact that a recent PNAS paper, Characterizing the cultural niches of North American birds, had to treat google searches of turkeys as an outlier. In the Methods, they report, “After assembling estimates of relative interest for all 622 species, we normalized values so that bald eagle, the second most popular search topic, was assigned a value of 100, and all other taxa were assigned values proportionally. Wild turkey was the focus of more interest than bald eagle, but we considered the species an outlier (i.e., it received more than an order of magnitude more searches than bald eagle) and did not include it in our core analyses.” 

This turkey obsession is interesting in part because it begs the question, what are we learning from Wikipedia? I recently found this tidbit on the Wikipedia page for heath hens (Tympanuchus cupido cupido) “Heath hens were extremely common in their habitat during Colonial times, but being a gallinaceous bird, they were hunted by settlers extensively for food. In fact, many have speculated that the Pilgrims' first Thanksgiving dinner featured heath hens and not wild turkey.” Here’s the deal though: heath hens were about two pounds. The last population of heath hens lived (& died) on Martha’s Vineyard. I as wrote last month, I have a long-buried ecological connection to Cape Cod and its offshore islands, so while most college kids bring the emotional baggage of Pysch 101 to the Thanksgiving table, I was the know-it-all who threw down random historical ecological nuggets such as, it is unlikely that heath hens or their grassland habitats were as common in early colonial Massachusetts as some historical sources would have you believe. The story that servants refused to eat them multiple times a week is probably apocryphal. You see, I had read Interpreting and conserving the openland habitats of coastal New England: insights from landscape history in Forest Ecology and Management and — this was likely more influential since I was legitimately bad at reading papers until late in grad school — taken a seminar with the author Dr. David Foster. The paleoecological evidence does not support extensive openland vegetation in coastal New England until after European arrival. The landscape was mostly forest, and according to the preeminent expert on heath hens (here Foster and Motzkin throw in a wonderful citation from a 1928 Memoirs of the Boston Society of Natural History, definitely going in my #ToReadPile), the birds actually preferred, “open sandy woods and scrub oak barrens rather than grassland.” I love roping my family into this kind of argument and I am a lot of fun at parties. 

But back to turkeys — I found two more great turkey papers when I searched through my records in Papers (my reference software of choice). I was a bit confused when the results included a 1943 paper in The Condor titled, “Birds Observed between Point Barrow and Herschel Island on the Arctic Coast of Alaska.” It turns out that the author, Dr. Joseph S. Dixon, was comparing male ptarmigans to turkeys: “Ptarmigan were a most important food item after a winter of fresh meat starvation. By May 13, 1914, at Humphrey Point, the males were in full breeding plumage. They cackled and strutted about like diminutive turkey gobblers. From far and near their calls were heard over the snowy plain between the sea coast and the foothills.” 

If you want to go on a fascinating deep dive into the history of turkey husbandry before European settlers arrived to kick off a genocide, barely survive a winter, and two hundred years later get a national holiday declared during the Civil War, I recommend Dr. Erin Kennedy Thornton’s 2012 PLoS ONE paper Earliest Mexican Turkeys (Meleagris gallopavo) in the Maya Region: Implications for Pre-Hispanic Animal Trade and the Timing of Turkey Domestication. Thornton and her coauthors leverage archaeological, zooarchaeological, and ancient DNA evidence to confirm that Mayans in present-day Guatamala were raising domesticated turkeys. These turkey remains were discovered well south of the natural geographic range of the Mexican turkey, Meleagris gallopavo, which is the wild progenitor of what we know today the turkey on the Wikipedia page we check out every November — indicating that northern Mesoamerica and Maya cultural regions were engaged in animal trade as early as 300 BC–AD 100. They write, “prior information on Preclassic exchange comes primarily from non-perishable goods such as obsidian and ceramics so the non-local turkeys at El Mirador also expand our understanding of the types of goods that were exchanged long distances during this early period of Maya history.” Traveling long distances for turkey dinner is not a new idea. Mayan culture was holding it down well before the Spanish arrived and they didn’t even need to refer to a Wikipedia page each fall to get it done. 

If you are looking for a paper to pair with your ancient turkeys, consider Historical collections reveal patterns of diffusion of sweet potato in Oceania obscured by modern plant movements and recombination. In this 2013 PNAS paper, Dr. Caroline Roullier and her coauthors assessed genetic diversity in modern and herbarium samples of sweet potato (Ipomoea batatas) and confirmed that well before Columbus' time, Polynesian and South American peoples were sharing sweet potatoes. I love the subsection, “Did Genes and Names Disperse Together?” and the idea that linguistics is a kind of sleeper science — that names can keep information even while recombined genotypes and colonialism obscure the data. This is another powerful story of culture and food enduring; the spread on our dinner table for a celebration of settler colonialism can also be a story of resistance and resilience. 

Don’t forget the cranberry sauce! It’s mountain cranberry actually, since I’m an alpine ecologist. Mountain cranberry, Vaccinium vitis-idaea, is the berry behind the beloved Ikea treat, lingonberry preserves. According to a 2017 study in Biological Conservation by McDonough MacKenzie et al. (yes, that's me), volunteers struggle to identify mountain cranberry in a citizen science project recording flowering phenology above treeline. If you want to brush up on your plant ID skills before you hit the dinner table this year, check out the supplementary materials from Lessons from Citizen Science: Assessing volunteer-collected plant phenology data with Mountain Watch — it’s a page of photos of alpine plant species and their look-alikes. Honestly, if you have a laminator lying around this could be a really beautiful Thanksgiving placemat*. Do you think google scholar counts placemats towards your h-index? 

One last Thanksgiving resource. If you are struggling with how to talk to your family about climate change, Katharine Hayhoe has a webinar for you. Seriously, let's talk about climate change. This is tougher than checking out the wikipedia page for turkeys, but definitely a more meaningful discussion than the twenty-two-year-old at the table trying to school you about a heath hen you have never heard of and never claimed to be at the first thanksgiving anyway. Man, I am so much fun at parties. 

References:

Dixon, J. S. (1943). Birds Observed between Point Barrow and Herschel Island on the Arctic Coast of Alaska. The Condor, 45(2), 49–57. http://doi.org/10.2307/1364377

Foster, D. R., & Motzkin, G. (2003). Interpreting and conserving the openland habitats of coastal New England: insights from landscape history. Forest Ecology and Management, 185(1-2), 127–150. http://doi.org/10.1016/S0378-1127(03)00251-2

Garcia, Daimys, "Episode 9: Rethinking Thanksgiving: A Reading of "Allegiance to Gratitude" by Robin Wall Kimmerer" (2018). Broadcasting World Literature. https://orb.binghamton.edu/broadcasting_world_literature/9

Maestre, F. T. (2019). Ten simple rules towards healthier research labs. PLOS Computational Biology, 15(4), e1006914–8. http://doi.org/10.1371/journal.pcbi.1006914

McDonough MacKenzie, Caitlin, Georgia Murray, Richard Primack, and Doug Weihrauch. 2017. Lessons from Citizen Science: Assessing volunteer-collected plant phenology data with Mountain Watch. Biological Conservation, 208, 121-126. http://dx.doi.org/10.1016/j.biocon.2016.07.027

Mittermeier, J. C., Roll, U., Matthews, T. J., & Grenyer, R. (2019). A season for all things: Phenological imprints in Wikipedia usage and their relevance to conservation. PLOS Biology, 17(3), e3000146–12. http://doi.org/10.1371/journal.pbio.3000146

Roullier, C., Benoit, L., the, D. M. P. O., 2013. Historical collections reveal patterns of diffusion of sweet potato in Oceania obscured by modern plant movements and recombination. PNAS. http://doi.org/10.5061/dryad.77148

Schuetz, J. G., & Johnston, A. (2019). Characterizing the cultural niches of North American birds. PNAS, 205, 201820670–6. http://doi.org/10.1073/pnas.1820670116

Thornton, E. K., Emery, K. F., Steadman, D. W., Speller, C., Matheny, R., & Yang, D. (2012). Earliest Mexican Turkeys (Meleagris gallopavo) in the Maya Region: Implications for Pre-Hispanic Animal Trade and the Timing of Turkey Domestication. PloS One, 7(8), e42630–8. http://doi.org/10.1371/journal.pone.0042630 

*In putting together this post, I found an error in my supplementary materials! If you can find this mistake on your placemat, send me an email and I'll reward you with a Plant Love Stories sticker!

A Drought By Any Other Name

What is a drought? I know I don’t know — I live in the temperate northeastern United States and my field site is frequently wrapped in fog — but I get the feeling that I am not alone. According to a paper born from a Colorado State University graduate student seminar on ecology and drought, we should all be asking ourselves this question.

Drought seems to have lost its meaning for ecologists, and not in the semantic satiation way, where if you say a word over and over again it become aural nonsense. Ingrid J. Slette and her co-authors published ‘How ecologists define drought, and why we should do better’ in Global Change Biology this summer. As Slette tells it, “This project grew out of discussions during a grad student seminar course about ecology and drought. Everyone in the class approached drought from a different perspective, and when we looked to the literature to find a definition of drought that we could all agree on as a starting point for the class, we couldn't find one.” The class decided they needed to take a step back, and they shifted from synthesizing the impacts of drought to simply defining it. This might seem like a trivial point of semantics, but as they write in their paper, “Failure to define or characterize drought conditions in the published literature challenges out ability to advance ecological understanding.” You can’t compare studies, or compile a meta-analysis without understanding the idiosyncratic environmental conditions hidden under the catch-all term ‘drought.’

Perhaps we should not be surprised that ecologists can’t agree on drought; as I discovered while reading Slette’s paper, meteorologists and climatologists also struggle to define drought. But, the sticking point is not that we don’t have a clear definition of drought, it’s that ecologists use the term ‘drought’ in the literature as if we do. When Slette and her team surveyed 564 publications from the last fifty years of drought research, less than a third of the papers explicitly defined drought or cited a definition of drought. In addition, they report: “ecologists most often use the term drought as a synonym for generally dry conditions (~30% of papers). In other words, authors state they are studying drought without quantifying and/or contextualizing how dry conditions are relative to normal (e.g., by reporting stardardized index values, or some measure of deviation from average conditions).”

But wait, it gets even juicer — it turns out that hand-waving about drought may be distracting ecologists from noticing the actual climatic conditions at their study sites.Slette and her coauthors selected a subset of studies from their review that were (a) bad at defining drought, but (b) good at providing details about their geographic location. They pulled the location coordinates and timeframes of these studies to calculate Standardized Precipitation Evapotranspiration Index (SPEI) values using the Global SPEI database. Only half of the droughts in this subset were characterized by especially dry SPEI values, outside the range of normal climate variability for their ecosystem. They found that 87% of the drought studies took place during times that were drier than average for the study site, but 13% of these “drought” studies were from periods that were slightly wetter than average based on estimated SPEI values. And while there may have been extremely local conditions that were truly dry at some of these "wet-droughts", we don't know because the authors did not report on them or place them within the context of the local long-term climate records. 

I asked Slette about the review process for this paper. I had seen on twitter that it was her first publication as a lead author, and I wondered if journal editors had recognized the importance of this topic. I assumed that Slette may have faced the same challenges as authors of ‘advice papers’ who struggled to find the right home for their work. Both this paper and Dyson et al’s advice for urban ecologists working on private property had origin stories in graduate students creating the resources that they were searching for early in their careers. Slette and her seminar wanted a straightforward ecological definition on drought and couldn’t find it. Slette wrote, “I anticipated that it would be quite difficult to get this paper published, but I was actually pleasantly surprised by how well the editors and reviewers received it. Choosing to submit this paper as an Opinion was an important decision in terms of finding a good home for it, I think that turned out to be a better fit for it than as a primary research article.” Then, I asked her about her own research, aside from writing sharp reviews of ecological literature. I wanted to know what definition of drought she used and how it had changed since writing her definition paper. Slette is a PhD candidate at CSU, and she answered, “I study how changing precipitation amounts and variability affect plant production. Specifically, I have been studying how experimentally-imposed extreme droughts affect plant root production and aboveground vs. belowground resource allocation in Central U.S. grasslands. For these experiments, drought was defined as a reduction in precipitation similar to what this area experienced during the Dust Bowl, about a 2/3 reduction from average. After writing this review paper, I am much more cognizant of all drought definitions, including my own. In every paper that I write from now on, I am definitely going to include more detail about the conditions of the drought itself, not just about its impacts.”

Finally, I asked her if the process of mining hundreds of papers for definitions of drought has made her a tougher reviewer or raised her standards for precise language from other ecologists. “I will definitely become a tougher reviewer now! I'm going to evaluate for precise wording and ask for lots of information about study design and justification.” I think that anyone who reads Slette’s paper will walk away with similar raised standards. And those of use who work in wet ecosystems should think about this too — we need to evaluate how we define our own work and what assumptions are hidden in our terms and jargon. As Slette notes, “I hope that the positive feedback and acceptance of this paper signals increased interest in (re)evaluating how ecologists define their work.”   

References:

Slette, I.J., Post, A.K., Awad, M., Even, T., Punzalan, A., Williams, S., Smith, M.D. and Knapp, A.K., 2019. How ecologists define drought, and why we should do better. Global Change Biology. 25(10), pp.3193-3200.

Looking Closer at Look at Your Fish

“In science, I concluded, even in fields as apparently apolitical as ichthyology and glaciology, the story always involves more than a fish in a tin pan or lines etched on bedrock. Culture, history, and beliefs about humans determine, now as in the nineteenth century, who exactly is invited into the science laboratory to “look and look again” at the fish in the pan, and who exactly has the leisure and means to take a trip to Maine.”— Marion K. McInnes, “Looking for Louis Agassiz: A Story of Rocks and Race in Maine” 

Less than a week after I published a blog post that referenced Louis Agassiz and the Look-at-Your-Fish-school-of-natural-history-instruction, I stumbled upon an essay that upended my perception of Agassiz, glaciers, and the apocryphal fish. “Looking for Louis Agassiz: A Story of Rocks and Race in Maine” flashed on my radar via my google scholar alert for Acadia National Park and Dr. Marion McInnes pulled me down a history of science rabbit hole to face my own field site and writing in an unforgiving mirror. 

McInnes weaves together the geologic history of Mount Desert Island, Maine, Agassiz’s well-founded theories on glaciers, and his illegitimate theories on race in an astounding piece that’s part archival detective story, part cultural criticism. This essay is engaging and thought-provoking and scathing. I did not escape unscathed. Because, here’s the thing: I elided Agassiz’s racism when I quoted Look at Your Fish. I knew better — I read Chrisoph Irmscher’s 2013 biography Louis Agassiz: Creator of American Science and half-remembered Agassiz’s spurious writing on superior and inferior races even as I was typing up pithy takes on his pedagogical style. 

Both McInnes’ essay and Irmscher’s Agassiz biography cover the breadth of Agassiz’s career as a scientist and teacher. In the mid-19th century, Agassiz leveraged his position as a public intellectual to expound on race: his writing and lectures added scientific credence to the idea of the white superiority. He was an abolitionist and a champion of glaciers over the biblical Noah’s flood as a geologic force. He also rejected Darwin and believed in a theory of multiple creations, which included separate creations for different human races, the “newest” and best model being white Europeans like himself. My personal brand is loving 19th century naturalists, and my historical ecology research makes it clear that all my favs are problematic. This essay reinforces the important point that glossing over these problems, especially if they were cultural norms, is itself problematic. 

McInnes’ essay centers on her quest to find the Agassiz Outcrop, a site that, at the outset, she believes is a National Historic Landmark in Maine celebrating an outcrop of 510 million-year-old Ellsworth Schist bedrock bearing glacial striations and Agassiz’s name. Except she discovers that the Agassiz Outcrop is unmarked, half-hidden beside a parking lot, and its status has actually been inflated by a mistake on Maine.gov — it’s on the National Register of Historic Places, added in 2003, but it is not a capital ‘L’ Landmark. Ellsworth is on the mainland side of the bridge to Mount Desert Island; it’s where I do my grocery shopping on my way to my field housing each spring and boasts the Home Depot where I’ve spent thousands of dollars of grant money on corner gutter pieces, zip ties, cloth weed barrier, and various other field ecology supplies.

As I read McInnes’ essay, I could picture most of the geological formations she references — the pink granite, the glacial erratics — but I had never heard of the Agassiz Outcrop. Then, I saw her photo and I immediately recognized the parking lot.

I’m a pretty curious person with a stubborn streak in research projects, but I’m not sure I would have followed the threads that McInnes plucks from here; I think I might have let the project die in that parking lot of underwhelming landmark status and disappointment. I am genuinely amazed by what McInnes has crafted from the ashes* of the Agassiz Outcrop anecdote, and her dedication to unwinding the story of Agassiz, this outcrop, and the cultural moments they connect. As she writes in her introduction, “when I started this project I thought I was taking a trip back to the Palaeozoic and pre-Cambrian Eras, but in fact I landed squarely in the nineteenth century.” 

Among my favorite moments in this essay is when McInnes reads Agassiz’s ‘Glacial Phenoma of Maine’ from a bound copy of the year-end edition of Atlantic Monthly in her college library: “When I took down volume XIX to look for Agassiz’s articles on Maine, the leather spine tore along the seam; red dust coated my fingers and stained my clothes. All the better: this was the volume published in 1867, here in my hands, and not on a sterile computer screen.” A more recent paper on Maine glaciology looms large too: Smith and Borns’ “Louis Agassiz, the Great Deluge, and Early Maine Geology” published in Northeastern Naturalist nineteen years ago. Smith and Borns turn out to be the catalyst behind the Agassiz Outcrop’s listing on the National Register of Historic Places; it was their recommendation that landed the site this honor. But McInnes is more interested in what Smith and Borns’ left out of their writing on Agassiz: race. 

“In their article for Northeastern Naturalist in 2000, Smith and Borns sidestep the issue of Agassiz’s racism; they simply do not refer to his views on race at all. One might argue that they wrote this piece, after all, for an audience interested in geology, not social history…Yet this reasoning does not suffice. In the last section of their article, Smith and Borns consider Agassiz’s legacy outside of his contributions to glacial theory; they highlight his contributions to science education, his skill as a mentor of future brilliant scientists, and his support of women…I can understand their quandary as writers, and I continue to appreciate the research Smith and Borns have done on nineteenth-century geologists, including Agassiz, who studied bedrock in Maine. But if Agassiz’s enlightened views of women are relevant to the case they make for his being ‘one of the world’s preeminent natural historians,’ then so are his views on race.” 

Here, McInnes cuts through a thousand thorny arguments with incredible clarity. Why did I feel so guilty reading this after publishing a blog post that conveniently forgot to mention Agassiz’s racism? I think McInnes nails this sin of omission. In her writing on stripping memorials of problematic namesakes she plucks a perfect metaphor from the google map view of the road that passes by the Agassiz Outcrop: a ‘FILL WANTED’ sign. “This alternative, it seems to me, calls for research and interpretive work rather than erasure of the past. We want and need the full story of science history: we need to fill in what has been left out of geology textbook chapters on Agassiz’s Ice Age Theory; and “FILL” could usefully be added to the signage in the galleries of what once was the Agassiz Museum of Comparative Zoology.” 

I cannot recommend this essay enough. When I teach Field Natural History, I will assign it in tandem with Look At Your Fish; the two pieces are now inseparable in my mind.

It is amazing how this improbable connection came together: an essay written by a Professor Emerita of English at DePauw University, published in the latest issue of Mosaic, an interdisciplinary critical journal that I’d never heard of before. This is, by all accounts, a paper I should never have read. But, the practice of reading a paper a day can be expansive and magical; it can allow for opportunities to read broadly and cast a wide net, or an interdisciplinary Acadia-sized-net. For these reasons, I’m just sort of charmed that my off-again on-again dedication to #365papers became a conduit for the universe to reach out and smack me for letting Agassiz’s racism slide unchecked in the year of our goddess 2019. I will do better. 

*terrible wordplay here — Ellsworth Schist is not igneous rock. 

Reference:

McInnes, Marion K. 2019. Looking for Louis Agassiz: A Story of Rocks and Race in Maine. Mosaic: a Journal for the Interdisciplinary Study of Literature. 52(2): 35-56. 

Drawn to Learning

This post is a short attempt to peel back the curtain on my “bad at pollen” process.

Since my very first pollen clinic in the BEAST Lab at University of Maine I’ve been instructed to sketch the pollen as I see it on reference slides and create my own kind of visual library. This approach makes sense — I remember drawing carex perigynia and fern pinnae in my first field botany course, filling my Rite-in-the-Rain notebook with pages of half-erased sepals and efforts to capture anther angles.

I’m not a practicing sketch-book type of scientist — my field books from my PhD research are mostly long tables dotted with squashed mosquitos and lists of taxa — but I don’t vehemently claim that “I just can't draw”. When I was a master’s student, I took at print-making class at Burlington City Arts and got off campus and out of my head for a couple hours each week. I couldn’t completely stop thinking about my research, but I could redirect that energy towards creating screen prints of my study species. I poured over my photographs from my field season and sketched each of the six flowers over and over again.After I graduated, and moved to Chicago, I took a class at the Lillstreet Art Center and did it again — creating a new alpine plant screen from a new series of sketches of the same six species.

But, I knew those plants (even if, as it turns out, our volunteers maybe didn’t know them?), and drawing familiar flowers repeatedly is perhaps a different game from sketching pollen grains and lining the margins with notes like “cute tennis ball” (Fraxinus) and “I think this is a margo” (Acer).

A recent paper in Journal of Biological Education reinforces the idea that drawing plants — or in my case, pollen — can help us develop botanical knowledge. The paper, “A comparison of descriptive writing and drawing of plants for the development of adult novices’ botanical knowledge,” presents a case study that supports the sketch-to-learn model, or at least the sketch-to-better-capture-the-details-in-your-notes model. Drs. Bethan C. Stagg and Michael F. Verde led half-day wildflower events where students filled notebooks with either descriptive writing or labelled drawing for a suite of plants. Later, the students were given an identification test (labeling plants from the learning activities with their common name or noting ‘look-alike’ for trick question species that were not a part of the learning activities) and a morphology test (true/false questions about diagnostic characters of the study species).

These were all self-described novice botanists — “the event announcement stated that participants should not be able to identify more than twenty common native plants.” The writers and drawers scored equally well on the tests, but Stagg and Verde found that the sketches captured more recognizable diagnostic characters for each species than the written descriptions.

“Drawing in biology develops students’ observational skills by engaging the learner in close, detailed study of the focal organism,” Stagg and Verde write in the Introduction. They reel off a list of citations, but this connection between drawing and observing in biology has a long tradition in natural history training. In the classic essay “Look at Your Fish,” a prospective entomology student joins Louis Agassiz’s lab in the 19th century and is given a jarred haemulon fish specimen and instructed to study it.

Slowly I drew forth that hideous fish, and with a feeling of desperation again looked at it. I might not use a magnifying glass; instruments of all kinds were interdicted. My two hands, my two eyes, and the fish: it seemed a most limited field. I pushed my finger down its throat to feel how sharp the teeth were. I began to count the scales in the different rows until I was convinced that that was nonsense. At last a happy thought struck me—I would draw the fish, and now with surprise, I began to discover new features in the creature. Just then the professor returned."That is right," said he; "a pencil is one of the best of eyes."

Ultimately the student spends three days observing this fish and sporadically fielding questions from Professor Agassiz in what sounds like one of the most stressful and bewildering orientation exercises. Agassiz is never satisfied and leaves every interaction cryptically instructing him to “look at your fish” before disappearing for an unspecified period of time.

The pedagogical style is outdated, kind of. While none of my PIs pulled a straight Agassiz on me, the essay has been assigned as a reading in natural history courses twice in my career.

My fish is a box of pollen slides. But my fish is also a stack of literature, palynology and conservation paleobiology papers in a field where I am very much still sketching the outlines and learning the vocabulary. Is it possible to bring that pencil-is-one-of-the-best-of-eyes attention to detail to reading indoors instead of botanizing outdoors or pollen-counting under a microscope?

The amazing botanical illustrator and comic artist Liz Anna Kozik inspired me to think about this last month.

She tweeted, “I'm going to do quick TLDRs for the articles I read~!” and posted a handwritten summary of the 2003 paper Keeping the Academics in Service Learning Projects, or Teaching Environmental History to Tree Planters with an illustration of a student sitting by a freshly-planted seedling asking “What did I just do + what does it mean?” Liz usually creates artwork that centers the prairie plants she studies, but here, she's sharing digital sketches of the academic literature. She beautifully distills the papers into these concise take-away nuggets framed by her simple, striking art. Each TLDR page is inviting and memorable —and the process creates so much more meaning than my haphazardly highlighted pdf pages and marginalia from my folder of #365papers.

I love exploring prairie ecosystems through Kozik’s eyes, but now I can’t wait to see more of her TLDR and follow her reading! To circle back, I’ve been trying to apply Stagg and Verde’s advice to my pollen sketches — “Participants were encouraged to be undeterred by drawing ability or botanical knowledge and were advised to create their own terms for unknown morphological features.” I’m not quite at the level of sketching paleoecology papers, but my “light freckles, three-cornered popcorn kernel” is slowly becoming “surface psilate, exine indistinctly tectate, sub-triangular to spherical, pores aspidate.” 

Reference:

Stagg, B. C., & Verde, M. F. (2018). A comparison of descriptive writing and drawing of plants for the development of adult novices’ botanical knowledge. Journal of Biological Education, 28(2), 1–16. http://doi.org/10.1080/00219266.2017.1420683

An ornithologist and an entomologist go into the kīpuka...

There is something magical about reading a well-written, remarkable paper from outside of your sub-discipline — the echoes of familiarity in methodology, the unpredictable overlaps, the serendipity of finding the research in the first place.

I recently found this magic in Vertical foraging shifts in Hawaiian forest birds in response to invasive rat removal, published in PLoS ONE in September 2018. Co-first-authors Dr. Erin E. Wilson Rankin and Dr. Jessie L. Knowlton transported me to the northeast slope of Mauna Loa Volcano for a bird-watching and bug-counting adventure through a network of half rat-eradicated kīpuka — a jigsaw puzzle of fragmented forest pieces dissected by lava flows. 

By most measures, I should never have read this paper. It came out while I was staggering though the first weeks of parental leave last fall. My invasive species are plants (not rats); there’s really no vertical space available (the trees are too short!) for shifts in arthropods or their predators in my plant communities at treeline; my island study site (downeast Maine) hasn’t seen volcanic activity for hundreds of millions of years (Hawaii’s kīpuka are created when volcanic lava flows move through native forests). For reasons I can’t explain, earlier this month I clicked on a link to The Wildlife Society’s — a society I’m not a part of and don’t actually follow on social media — Wildlife Publication Awards 2019 shortlist announcement. At the end of the Journal Paper category, this Hawaii study caught my eye, because I’m planning a trip there in the fall and recently spent three early morning hours driving through Iowa and Minnesota with my friend who is a postdoc at the University of Hawaii, Hilo.

Despite the winding the path to get this paper into my To Read Folder, there was a straight line from my final scroll through the Conclusions to the “compose” button on my email. I had to hear more from Drs. Wilson Rankin and Knowlton.

Here is what my initial google searches turned up: stunning photographs of kīpuka; and the discovery that the two first authors, now faculty at UC Riverside and Wheaton College, were postdocs on this project who first came to the kīpuka from the subfields of entomology (Dr. Wilson Rankin) and ornithology (Dr. Knowlton) back in 2011. The invasive rat removal efforts in their paper was a part of a larger study: 16 kīpuka fragments were methodically outfitted with trapping grids and compared to another 18 kīpuka without rat traps. “The larger study has examined how impacts by invasive predators (rats) change across a gradient of ecosystem size,” Wilson Rankin and Knowlton explained to me. “The kīpuka are a patchwork of forest fragments that were created when volcanic lava flows moved through native forests. The result is a landscape dotted with naturally fragmented forest patches that range in size from very small (<0.1 ha) to very large (>12 ha). This study system allowed us to tease apart the effects of invasive rats and the effects of ecosystem (or forest patch size) in order to better understand the forces that shape communities.” 

I asked how an entomologist and an ornithologist from different universities on the US mainland ended up working together in Hawaii. “The kīpuka project was a highly collaborative project among PIs at Stanford University, University of Maryland, Michigan Tech, and the US Forest Service that integrated multiple research fields to examine the effects of an invader on native communities.” They confirmed what google had hinted about their origin story. “We both joined this project early on as post-docs, one focusing on quantifying invasion impacts on the arthropod communities and the other focusing on the responses of native forest birds. By bringing together a research team with diverse backgrounds and expertise, the kīpuka project was able to develop a broad and in-depth understanding of how rats shape the invaded communities and alter the interactions among native species.” They ultimately found that the presence of invasive rats altered the foraging behavior of native birds — in rat-filled fragments the birds foraged higher in the canopy. The rats are not found above 6 m in the forest, but they seem to control the arthropod biomass below 6 m, suppressing the resources available for birds, especially insectivores and frugivores. In sites without rats, there was more arthropod biomass below 6 m and birds foraged at lower mean heights compared to higher foraging heights in control kīpuka.

These kīpuka are like the matryoshka dolls of island biogeography, a model system in a model system. The forest fragments are islands of habitat, and these in turn are contained within the island of Hawai‘i. I asked Wilson Rankin and Knowlton what they hoped managers in other systems could learn from this work. They write, “The fact that the kīpuka are fragments of habitat within a less hospitable matrix makes them comparable to other fragmented systems, which, as we all know, are increasingly common as human development continues to expand through natural habitats.” The kīpuka islands within islands system is special, but can still contribute to our understanding about invasive species in general. “While Hawaii is unique because of its high number of endemic species and long isolation from mammalian predators, many fragmented habitats are having to contend with extinctions of native species and invasions of nonnative species, even on the mainland. Our work shows that these invaders can alter whole trophic systems, either directly or via shifts in species’ behavior. This work helps to highlight the importance of considering the synergistic and sometimes unpredictable effects that habitat fragmentation and invasive species together can have on native food webs. We hope that both factors will be taken into account when planning restoration or conservation actions.” 

Finally, I just loved the opportunity to write about two women in STEM and their postdoc work. And I told Wilson Rankin and Knowlton that I appreciated reading a new paper covering fieldwork that concluded six years ago. My own dissertation researchfrom 2011-2013ish just reaching publication now too. As they write, “Patience and persistence are the two key words when it comes to getting your research published.” Wilson Rankin and Knowlton shared this reflection on the triumphs and low points of the journey from fieldwork to award-winning publication: “We both came onto this project as postdocs, and supervised the data collection for the three years of field research. After that we both went on to other positions, and thus had to balance writing up manuscripts from this research with the demands of new positions. Once submitted, this manuscript went through the revision process, which took some time but we are all pleased with the end product. In general, our advice to others would be to not be discouraged during the review process or its pace, as you can always improve a manuscript and the reviews are meant to help you improve your work.”

Somehow, this magical paper also brought some timely advice into my email inbox as I head into a summer of writing up first drafts of my own postdoc papers. I welcome this nice reminder to keep grinding, and to keep working with some of my fabulous peer-collaborators as they embark on new adventures and new jobs in the coming years. And of course, I am now more excited than ever to spend some time in Hawaii with conservation researchers this fall!

Reference:

Wilson Rankin EE, Knowlton JL, Gruner DS, Flaspohler DJ, Giardina CP, Leopold DR, et al. (2018) Vertical foraging shifts in Hawaiian forest birds in response to invasive rat removal. PLoS ONE 13(9): e0202869. https://doi.org/10.1371/journal.pone.0202869 

All I Really Need to Know I Learned From Peer-Reviewed Papers (Part 2)

How to Write About the Science You (and Others) Did

I bought Stephen B. Heard’s The Scientist’s Guide to Writing at ESA in 2016. I was a soon-to-be sixth year PhD student with one publication (my master’s thesis) and zero written dissertation chapters. Maybe not exactly zero — there were chunks of methods paragraphs from grant proposals, and a super-rough-draft of chapter 1 shared with collaborators from another university — but close enough that my plans to defend in the spring were borderline comical. I needed writing advice and a structured plan: The Scientist’s Guide to Writing was my magical guidebook, my used Potions textbook annotated by the Half-Blood Prince. I read it methodically, one chapter at a time, and it worked — by March I had four chapters and a viable defense date. I received other lucky breaks besides the perfect reading material: a postdoc fellowship provided motivation to finish the PhD, my parents hosted a writing retreat for my last chapter; there were awesome babysitters, baristas who slipped me extra shots of espresso, and committee members who provided prompt and constructive feedback along the way. But, I still turn to reading when I need help writing.

Earlier this month I covered my favorite new advice papers on How to Do the Science. This week — my favorite recent papers on How to Write About the Science You (and Others) Did: Dr. Scott Hotaling’s Publishing papers while keeping everything in balance: Practical advice for a productive graduate school experience and Dr. Emma Sayer’s The anatomy of an excellent review paper. I like the contrasting perspectives here: Hotaling as a newly minted PhD explains the context for getting the writing done — creating a habit of writing and organizing tasks — while Sayer provides critical advice for the writing that must be accomplished once you have achieved Hotaling’s headspace and you are deep into drafting a review paper. Hotaling’s system will get you to the desk; Sayer’s will polish the word document that’s languishing in your Review Paper file.

Hotaling’s Publishing papers while keeping everything in balance: Practical advice for a productive graduate school experience began as an informal pep talk: he was a postdoc with a good publishing record and grad students in his new department turned to him for advice. “I realized that, like me in graduate school, the students knew they needed to be writing papers (or their thesis) but they didn’t know where to start from a practical standpoint,” he explains. “So, I decided to write down my approach to working to at least give students a jumping off point. When I started looking in the literature, I realized that much of the existing advice came for more senior academics and was often much more cynical than I felt was necessary. Ultimately, I felt I could fill a need by offering my own positive, but realistic, take on how to be productive in graduate school. Once I began writing it, I realized that it should really be a more holistic perspective with advice for being productive mixed with good practices for developing (and maintaining!) collaborations, taking care of your mental health, etc.”

Though Hotaling offers advice that seems more universal and traditional (journals have been publishing writing advice to grad students for a long time) than how to do urban ecology work on private property, I wondered if he ran into the same resistance (3x rejected) from journal editors that Dyson had experienced. “It was difficult!” Hotaling agreed. “I reached out to a number of journal editors and received replies that varied from encouraging rejections to one editor who essentially asked why I wasted my time writing something so useless. Ideas in Ecology & Evolution was the first journal I formally submitted the manuscript to and it wound up being a great home for it.”

Sayer’s advice paper zooms in on writing an excellent review paper. She wrote to me: “To give you a bit of background – I’m a big advocate for the importance of effective science communication. I do a lot of work with early-career researchers on presenting science in various formats to different audiences.” Sayer’s advice paper is built on a deep history of this work. “I started creating guides for the British Ecological Society when I was a postdoc – I’ve written guides on giving talks at conferences and designing science posters (the latter is now used as the society’s guidelines). Within a couple of years of starting my own research group, I had students and postdocs from 7 different countries and many of them struggled with the same aspects of science writing. I compiled a short guide for them, which turned into The British Ecological Society Short Guide to Scientific Writing (and will be published formally in Functional Ecology this year). In the meantime, I had taken on the role of reviews editor for Functional Ecology. Based on the success of the “Short Guide” and my experience in handling review papers from different subdisciplines, the other editors asked if I would try to write a guide for review papers...”

Most of the authors I talked with for this blog post wrote their advice papers as grad students — they were writing the paper they wanted to read early in their careers — but Sayer writes from a more established point in her career. I asked if she thought writing review papers is just a topic that requires more experience. “In this case, yes, having greater experience certainly helped. I’ve always preferred reviews that synthesise information and create something new from the published literature, but it wasn’t until I became Reviews Editor for Functional Ecology that I realised how useful a set of guidelines would be. We learn to summarise information but synthesising it is much harder and is quite an abstract concept to explain to someone.” I too have noticed this steep learning curve between being able to summarize the literature, and being able to add something to the conversation. I first read the short and sweet (three pages!) The anatomy of an excellent review paper early in the group-writing phase of my own review paper (Berend et al. 2019, accepted!). I found myself returning to our google doc with new eyes (which, in an inside joke to myself, I named “Box 1-tinted glasses”) and re-structured our outline around central concepts.

In Part 1 of this series Dr. Ziter had reflected, “I started out thinking this is the paper I wish I had been able to read as a graduate student, and of course by the time the paper came out I was starting my own lab, so now I think I'm so excited that MY grad students will be able to read this before they start fieldwork.” Similarly, Sayer wrote The anatomy of an excellent review paper from the perspective of a PI reminiscing on resources she wished she could have had earlier. “I initially wrote the Short Guide to Scientific Writing for my research group – partly because it described the kind of research papers I wanted to read, but also because I would have loved something like that when I started writing.”

Both Hotaling and Sayer felt that the peer-review process added value and reach to their advice. Hotaling writes, “I chose to publish it as a peer-reviewed paper for two reasons. First, I wanted reviewer input on the paper. I received extensive feedback from my lab and academic friends, but it was important that it also be reviewed by people outside of my day-to-day sphere. It’s a very a personal paper and I needed to know that people who didn’t know me personally still found value in the paper. I’d like to add that the reviewers of the paper (Drs. Meryl Mims and Robert Denton) were exceptional and their feedback greatly strengthened the final paper. And second, from a more practical perspective, it was better for my own career that it be published as a peer-reviewed article.” Sayer echoes, “First and foremost, [peer review] ensures quality – the content has been scrutinised and improved in response to feedback, which gives the reader more confidence in the advice. Then there’s the question of recognition – a lot of work goes into writing guidelines, and thousands of authors have downloaded the paper. It may not attract citations, but it’s still important that the contribution is acknowledged. Last but not least, publishing guidelines as a peer-reviewed paper or editorial makes them much easier to find.”

Since Sayer’s advice emphasizes how to structure a paper, I asked if she had leaned on other advice papers for guidance on structure or tone — essentially, what peer-reviewed advice influenced her presentation of peer-reviewed advice. “There are quite a few papers about writing reviews in other subject areas that I cited in the guidelines.” Here, I need to point out that the short references section in Sayer’s paper is an excellent resource for nerds like me that strive to read their way into better writing. Sayer notes that all of the references contain great advice, but no single paper contained all the information she wanted — that’s why she wrote hers! Her own favorite/favourite advice paper is subject-specific: “I give all my students the 1991 paper by Eberhardt and Thomas on Designing Environmental Field Studies (Ecological Monographs 61:53-73) – it gives a great overview of experimental design and introduces lots of important considerations for developing field work. My other favourite is a book, rather than a paper, but it’s a great read and incredibly useful for communicating research: Made to Stick by Heath and Heath (Random House).”

I asked Hotaling about his favorite advice papers too. We have similar learning styles — he says, “I read a lot of similar papers while writing my own. I particular enjoyed John Smol’s 2016 Some advice to early career scientists: Personal perspectives on surviving in a complex world for its clear, conversational perspective and that paper was a big reason why I ultimately submitted my article to the same journal (Ideas in Ecology and Evolution). Beyond academia, I also drew inspiration from Stephen King’s 2000 memoir “On Writing” and specifically his approach to a regular, ritualistic writing routine. If there’s one takeaway from my paper that I hope early career scientists will try out, it would be developing a regular, daily writing habitat. It’s staggering what such a simple practice can yield in terms of productivity and, at least for me, satisfaction with my work. By writing every day, I feel far less stressed about finishing things and more able to balance my work and life in a healthy way.”

I’m drawn to advice papers, in part, because they can ameliorate imposter syndrome; they say, of course you don’t know this yet, but here, I have given you a guide and you can quietly take this pdf to your favorite chair, curl up with a mug of tea, and have an introvert’s field day. Good advice papers can be a kind of pensieve — the instrument in Dumbledore’s office that allowed wizards in Harry Potter to share their memories, and immerse themselves in each others' past experiences. I love these particular pensieves and the stories behind their publication — thank you so much to Drs. Dyson, Ziter, Broman, Hotaling, and Sayer! 

References:

Sayer, E. J. (2018). The anatomy of an excellent review paper. Functional Ecology, 32(10), 2278–2281. http://doi.org/10.1111/1365-2435.13207

Hotaling, S. (2018). Publishing papers while keeping everything in balance: Practical advice for a productive graduate school experience. Ideas in Ecology and Evolution, 11, 1–12. http://doi.org/10.4033/iee.2018.11.5.f

All I Really Need to Know I Learned From Peer-Reviewed Papers (Part 1)

I remember feeling a spark of urgent curiosity when I found a copy of All I Really Need to Know I Learned in Kindergarten on a shelf in the guest bedroom. I was 11. And though I had made it to middle school, I had never attended kindergarten. This book contained information that I lacked and needed. I hid under the guest bed and read it cover-to-cover.

This character trait — this drive to read my way into knowledge — is still going strong in my life as an early career ecologist. Recently, I turned to Dr. Marieke Frassl’s 2018 Ten simple rules for collaboratively writing a multi-authored paper as I took on a leadership role writing a paper with my postdoc cohort. Reading this guide for collaborative writing gave me a new sense of focus and energized me for the ensuing work of organizing notes, framing our paper, and planning for an upcoming writing retreat.

I’m a reader, and so it shouldn’t be surprising that I seek paper-based advice in the stacks of my #365papers To Read Pile. Reflecting on the helpful scaffolding that I found in Ten simple rules for collaboratively writing a multi-authored paper, I pulled out my favorite Advice Papers from the last year. Flipping through the pdfs, I wondered, Why do we publish advice in journals? Why did these papers, which often echo advice I’ve already received in person or on twitter, resonate so much for me? What does it mean to offer your advice via peer-reviewed papers?

One of the major perks of writing for PLoS Ecology is the opportunity to cold-email scientists (or work-email scientist-friends) and pick their brains about their papers on exploding pollen, unexpected biodiversity hotspots on historic battlefields, and epic fieldwork roadtrips. So, I started writing to the authors of my favorite Advice Papers. This exercise took on a life of its own as Advice authors shared their stories, and their advice, with me. At the same time, I started collaborating on my own Advice Paper with coauthors. The project of selecting the year’s top Advice Papers has expanded beyond my initial curiosity and grown way too long for a single blog post. Here is the first of a two-part series on the best recent Advice Papers in ecology — Part One: How to Do the Science.

The two best papers I read on doing science were Broman and Woo’s 2018 Data Organization in Spreadsheets in The American Statistician and Dyson et al’s 2019 Conducting urban ecology research on private property: advice for new urban ecologists in Journal of Urban Ecology. I ranked Data Organization in Spreadsheets as one of my top-ten Summer 2018 papers, and I continue to stan this lovely guide to foundational data management. While my research is largely National Parks-based and urban ecology on private property seems to fall outside of my wheelhouse, I appreciate the framework for planning urban fieldwork in Dyson’s paper, and my friend Carly Ziter is a coauthor. When the paper came out, Carly tweeted “A few of us ECR urban ecologists got together and wrote the paper we wish we had been able to read before starting private property research.” At the time, I was hip-deep in revisions with a few alpine ECR ecologists on the paper that we wished we had been able to read before starting common garden research. I had to read someone else’s version of the paper they’d wished they’d been able to read and see that this process could be completed. 

Dr. Karen Dyson explained, “During my first (urban) field season I realized very quickly that I had had no idea what I was getting myself into.” She was surprised by the time commitment needed for communicating with private property owners to set up site visits and experienced the gamut of hospitality from having security called on her to being subject to overly-friendly non-stop talkers. “Basic things like bathroom breaks required more planning than you would expect. If I recall correctly, it was this last point that I was commiserating with my co-author Tracy about when the first idea for this paper came about.” Second author Dr. Carly Ziter agreed, “Like Karen, I didn't know many people working on private land when I started my PhD fieldwork, and I really just muddled through it pretty naively.” Private property is an important part of the urban ecological landscape, but the challenges of working on private property mean that urban ecology research is often conducted through remote sensing or from a sidewalk. Dyson wrote, “You’re never going to understand ecology in cities if you don’t engage with people—and not just park administrators, but the individuals who make myriad decisions each day on every parcel about what trees to cut down, what shrubs to plant, etc. All this is critical to furthering the field, and we wanted to see more of it, done well, with sensitivity to the people whose lives we’re intruding on.”

Dyson put together a workshop on the topic for ESA 2016, and Ziter attended. She remembers thinking, “finally, other people who get what this is like!” Dyson interviewed Ziter for the paper, and as Ziter remembers, “at some point, I think I more or less invited myself onto the team (thanks Karen et al!). I started out thinking this is the paper I wish I had been able to read as a graduate student, and of course by the time the paper came out I was starting my own lab, so now I think I'm so excited that MY grad students will be able to read this before they start fieldwork.”

I asked Ziter and Dyson why they decided that this advice needed to be presented in a peer-reviewed paper. Ziter notes that “Urban ecology is growing really quickly right now. And as the field grows, there are more and more students collecting urban data whose advisors/labmates are not trained in urban ecology or urban field methods (e.g. in my case, I was the only urban-focused grad student in my lab). So there isn't that passed-down or institutionalized knowledge present within research groups to help students get started.” And, as Dyson recognizes, “Peer-review is more permanent and has gravitas, and can be cited as a reason for doing something. We also wanted open source, since it’s accessible to those without library connections. Also, this is a serious subject that needs to be treated seriously, and often isn’t… which is also why we interviewed almost 30 people from as many countries as we could and went searching outside the discipline for role models.” There’s definitely some field site pride on the line. Carly explains the exasperation of hearing, “oh you do urban ecology? Your fieldwork must be so easy.” “Really the logistics are often more challenging than working in traditional field sites. So it was personally really rewarding to be able to help Karen and the team articulate in a more formal way that hey, this isn't just in our heads, there really are unique and pervasive challenges inherent in this kind of work (just as there are challenges inherent in more remote field ecology that we don't face!)”

The origin story behind Data Organization in Spreadsheets is a bit different from Dyson’s work to build a coalition dedicated to capturing and publishing best practices for field work on private property. Dr. Karl Broman’s website on organizing data in spreadsheets — “largely a response to a particularly badly organized set of data from a collaborator” — already existed when Jenny Bryan and Hadley Wickham were organizing a special issue on Data Science for the journal The American Statistician. He admits that, “it seemed unnecessary to write an article when I could already point people to the website,” and he backed out of his promise to contribute to the special issue. But, he reports, “Jenny didn't want me to back out and asked several friends if they'd help me to write the article, and Kara Woo agreed to do that and did the bulk of the work of rearranging the content in the form of an article and adding an introduction citing relevant literature.”

The peer review process for Data Organization in Spreadsheets was fairly straightforward. Broman writes, “every article solicited for the issue was assigned two reviewers from among the authors of other articles. The reviews were constructive and helpful. After the review, the article was published at PeerJ Preprints and also formally submitted to American Statistician...American Statistician is paywalled; available to most statisticians but not many others. I paid some huge fee (like $3500) to make it open access, since the target audience for the paper is much broader. I hemmed and hawed about whether to pay to make it OA; the fee seemed way too high, and the material was already available both at PeerJ Preprints and as a website. But I did pay and I'm glad I did, because I think way more people have read the paper, as a consequence of it being free. If people find the paper and it's available, they'll read it, but I think if they get a paywall, they're not likely to look further to find a free version.”

In contrast, the urban ecology peer review process was long and winding, though it also included a PeerJ Preprint. When it was finally published, Dyson shared the journey in a twitter thread. “It was desk rejected from Landscape and Urban Planning and Methods in Ecology and Evolution and rejected after review from Urban Ecosystems.” She remained dedicated to the paper throughout: “Since I ran the workshop at ESA 2016 and a well-attended poster at ESA 2107, we knew there was a need for it among students…We also put it in PeerJ preprints and it was one of the top five read/visited papers of 2018. So despite getting very frustrated with the process, we didn’t really lose faith in the manuscript—though we did give it complete reorganization after the rejection from Urban Ecosystems. We saw Journal of Urban Ecology was doing a free open access as they got started and decided ‘why not?’ since they’d also published Pickett and McDonnell’s The art and science of writing a publishable article. They’ve been lovely throughout the process—and have been great about re-tweeting and promoting the paper. It’s now one of their most read articles.” Here, Ziter chimed in to say, “I should disclose that I am sometimes the thumbs behind that twitter account. So that's why it got good twitter press ;). But I have no other role in the journal decisions or review process - so the rest of the loveliness is on them!”

Finally, I asked Broman and Dyson if they had any favorite Advice Papers. Dyson answered with an enthusiastic “Yes! In general, I love advice papers and papers that compare methodology, so I enjoyed putting this one together and hope to do more!” (I agree — we should write an urban-alpine ecology crossover!). She highlighted, “Hilty and Merenlender’s 2003 paper that deals with many of these issues (though not as in depth) on rural private property… [and] we used a few papers as models when we were writing (and re-writing) our manuscript, including Harrison’s Getting started with meta‐analysis; Goldberg et al’s Critical considerations for the application of environmental DNA methods to detect aquatic species; and particularly Clancy et al’s Survey of Academic Field Experiences (SAFE): Trainees Report Harassment and Assault.”

Broman writes that he didn't seek out any advice papers for guidance/structure while writing Spreadsheets. He muses, “I think the main advice papers I'm familiar with are those "ten tips for ..." [sic] at PLoS Computational Biology, which have been really useful though I think the formula has become a bit grating. I also really like Bill Noble's paper on organizing projects.”

Thanks to Broman, Dyson and Ziter for sharing their advice and adding to my reading list. Both of these papers are well-written and offer tangible, useful advice. I’ve found myself ruminating on them as I plan future fieldwork, and definitely wishing I could have read them much earlier as I wrap up old projects and wrestle with my old data.Stay tuned for Part Two: How to Write About the Science You (and Others) Did.

References:

Dyson, K., Ziter, C., Fuentes, T. L., & Patterson, M. S. (2019). Conducting urban ecology research on private property: advice for new urban ecologists. Journal of Urban Ecology, 5(1), 48–10. http://doi.org/10.1093/jue/juz001

Broman, K. W., & Woo, K. H. (2018). Data Organization in Spreadsheets. The American Statistician, 72(1), 1–10. http://doi.org/10.1080/00031305.2017.1375989 

Hiking with Reviewer 2

This is a deep dive into my own research — the backstory behind a single line in a recently published paper and the data-driven trip down memory lane that was spurred by an innocent question from Reviewer 2. 

This research took place on Wabanaki land. I want to respectfully acknowledge the Maliseet, Micmac, Penobscot, and Passamaquoddy tribes, who have stewarded this land throughout the generations. I am certainly not the first person to devote time and energy to tracking seasonal changes on Mount Desert Island. 

This week one of my dissertation chapters, Trails-as-transects: phenology monitoring across heterogeneous microclimates in Acadia National Park, Maine, was published in the journal Ecosphere. In this project, I pulled the space-for-time trick and hiked three mountains repeatedly to collect a lot of phenology observations across diverse microclimates. The mountains in Acadia are not huge — these granite ridges roll up from the Gulf of Maine and top out at 466 m — but my transect hikes were between 4.8 km and 9.7 km each, and I wore out a pair of trail runners each season. I took to heart Richard Nelson’s advice: “There may be more to learn by climbing the same mountain a hundred times than by climbing a hundred different mountains.” 

A couple months ago, in our second round of reviews, Reviewer 2 noted, “I think that it would be useful for those wanting to replicate your transect-as-trails approach (especially land managers) to know approximately how many person hours it took to complete a transect observation, here in the main text or in the appendix.” I had a magnet (which is apparently also available as a coaster) hanging next to my desk in grad school: over a silhouette of a golden retriever with three tennis balls in its mouth, it reads: “If it’s worth doing…it’s worth overdoing.” This magnet perfectly describes my response to Reviewer 2. I sent a back-of-the-envelope estimate to my coauthors, but I couldn’t shake the feeling that the precise person hours per transect was a knowable statistic. In addition to my field notes scribbled into weatherproof notebooks, I had collected my data via fulcrum, a smartphone app that automatically recorded the time of each observation. From my cache of fulcrum csv and xlsx files, I should be able to automatically pull the time of the first and last observation of each transect. The 10.7 MB of data in my fulcrum files represented four years of field work, hours and hours on the trails, slogging through rain, snow, and sun, training field assistants, combing through patches of lowbush blueberry and mountain cranberry for the first, hidden open flower.

I became obsessed with the idea of seriously calculating person hours per transect, but I was increasingly convinced that a single number would be meaningless. I also realized that I lacked the coding chops to deal with my messy raw data: 171 files, each with 77 columns, usually containing data from a single transect, but occasionally comprising half a transect (when we had to bail due to weather) or more than one transect (when I ran ambitious double-days, or my field assistants and I split up). I turned to Porzana Solutions, and Auriel Fournier expertly helped me unlock my person hours data.Over 177 the hikes in my fulcrum files, the mean time between first and last observation is 3.51 hours.

Three and a half hours does not even begin to tell the story. This blog post is my second supplemental appendix. Here is the story of person hours per transect — the lead time, the pregnant field season, and the phenology of phenology monitoring. 

Before the first observation and after the last

There is a lead time in every transect hike. After rolling out of bed, pulling on the same old running shorts, race tshirt, and powder blue sunglasses, after packing the same handful of granola bars, dried papaya, and sharp cheddar, zipping my phone into its waterproof case, and slinging my backpack into the passenger seat, after driving to the trailhead and placing my research permit on my dashboard, there’s still a gap between the start of the fieldwork and the first official observation of the day. Especially as the summer crowds began arriving in June, I had to get out early to grab a spot at the limited parking by the north or the south end of Pemetic, or else add some extra miles from a spillover lot*. Even at the best parking spot, the approach to the Sargent South Ridge trailhead requires navigating 0.7 miles of carriage roads between the car and the trail on every hike. When I started the project in 2013, the Sequester kept Park Loop Road closed late into the spring season. For the first six weeks of fieldwork, I walked along the empty road to access Cadillac North Ridge, and Pemetic North and South Ridge.

The transect hikes were 4.8 km (Pemetic), 9.2 km (Cadillac), and 9.7 km (Sargent) up the North Ridge and down the South Ridge or vice versa (all of the mountains had uncreatively named north and south ridge trails). So at the end of a transect, I was 4.8, 9.2, or 9.7 km away from my car. I could run the carriage roads to connect the trailheads after Sargent or Pemetic (a 6.6 km run post-Sargent, and 7.2 km run post-Pemetic). From Cadillac South Ridge, a run up Route 3 to park loop road got me back to the north ridge trailhead in 10 km. Sometimes I arranged rides with friends to skip the run, and when I had funding for field assistants in 2015 and 2016 we often carpooled to drop a car at the finish line for each other. (There were some benefits to this running routine — in 2014 I won free ice cream after placing third in my age group in the Acadia Half Marathon.)

The person hours per transect statistic is limited because not every transect was a straight shot. Sometimes we had to bail 3km into a hike due to bad weather and finish the transect another day. Once, one of my field assistants took a wrong turn and recorded phenology observations on the wrong trail down Pemetic, and so I went back, retraced her steps, and picked up the right trail the next day. Once, I did a wild two-a-day and in the middle of Cadillac, I ran down the Canon Brook Trail, looped through the Pemetic transect, and then ran back up the Cadillac West Face Trail to finish Cadillac. Once, I had a friend in town and we caught a ride to the summit of Cadillac and then enjoyed the leisurely hike down the south ridge with my eight-month-old in the baby backpack.

While the time between first and last observation averaged just over 4 hours for Cadillac, 2.5 hours for Pemetic, and 3 hours and 40 minutes for Sargent, those times discount the bookends of the hikes. As much as I’m railing against the answer to my query here, the process of working with Porzana Solutions to calculate these times has been incredibly rewarding. I feel like I’m getting to know my both raw data and the tidyverse in a weirdly intimate way that goes way beyond a standard tutorial. 

The pregnant field season

In 2015 I was 17 weeks pregnant at the start of my field season. In addition to my daughter, I was also joined in the field by two field assistants. According to the Porzana analysis, I hiked less than half as many transects in 2015 (15) compared to each of the two previous years (2013: 35** hikes, 2014: 37 hikes). I actually hiked 20 transects that year — my assistants were entering the data (and getting credit for the hike in fulcrum) while we hiked together in the beginning of the season***. On my solo transects in 2015, I felt sloooooow. I averaged thirty minutes slower than 2013 and 2014 on Cadillac, 50 minutes slower on Pemetic, and 22 minutes slower on Sargent. On top of this, I was covering less ground — in 2013 and 2014 I had monitored phenology in off-trail Northeast Temperate Network plots near my transects in an effort to compare trail-side phenology with forested sites that was ultimately cut from my dissertation. In 2015, I stuck to the trails.

I remember feeling pretty terrible at the beginning of most hikes that year. I had one favorite spruce tree on the south ridge of Sargent, and I can picture myself looking up through the needles on more than one occasion from my lie-down-spot while I tried to decide if a bite of granola bar would make me feel more or less nauseous. As I climbed above treeline and into the breeze the fog of morning sickness would lift, and as I hiked downhill, my daughter would do this funny little fetus-roll and kick in a way that I interpreted to be happy.

Hiking while pregnant was hard, but it felt easier than grappling with the looming challenges of becoming a parent. I liked the hard of fieldwork, it was the kind of hard that I felt capable of conquering. I also loved being pregnant in Bar Harbor. It was my fifth field season in Acadia and I had this wonderful community of supportive colleagues and mentors at the park service and in town. I had a favorite yoga class, a favorite milkshake, a favorite iced chai and blueberry muffin spot. I also had two field assistants — my pregnancy fortuitously aligned with NSF funding! — and working with Ella and Natasha that season was great. The person hours per transect figure obscures my field assistants, folding us into each other and masking the time we spent training together on the ridges. It also hides my pregnancy in the averages. I want to recognize those extra 22-50 minutes: they were some of the best worst minutes of my PhD.

The phenology of phenology monitoring

The person hours per transect average doesn’t show the sprint finishes of June. I monitored thirty species (the paper highlights the 9 most common taxa) of spring-flowering plants. On the transect hikes, I recorded leaf out and flowering phenology. In April, this was a bit of a scavenger hunt, and I’d pour over thickets of shrub stems for the first sign of bud break, then in May I’d peek into each curled Canada mayflower leaf for flower buds. By early June, my plants had leafed out, and the flowering season was winding down. I knew the trails by heart, and the location of each focal taxa along the ridge was bright in my mental map; each transect became a point-to-point trail run between the last phenological hold outs. Did the rhodora finish flowering on Cadillac? Had the last sheep’s laurel buds opened on Pemetic? Were the blueberries beginning to ripen below Sargent’s summit?

As I followed the spring phenology, I grew faster, my calf muscles more defined, my appetite more voracious. Acadia’s steep climbs will whip you into shape. I remember in 2013 arriving in the field a month after passing my comps and feeling so sluggish after a winter of studying instead of running. In comparison, I ran hard in the winter of 2013-2014, set a personal best half marathon time in a trail race in March, and just cruised through the early season field work in 2014. Even in 2015, as I grew rounder each week, I also grew more comfortable with the trails. Hiking while pregnant became easier over the season, although I’m happy it ended when it did, because that trend was not sustainable into the third trimester. 

I think about Reviewer #2 and I want to ask: do you mean the person hours per transect in April? Or at the end of June? What kind of mileage were you averaging before the start of the field season? Do you have any old hamstring injuries? Tell me about your field assistants. Do you like to stop for lunch at the summit or are you an on-the-go-snacker? Did you pack a couple bucks to buy a Harbor Bar at the Cadillac souvenir shop? Are you saving your energy for the 10k run at the end of the transect? Is the National Park Service well-funded in this year’s federal budget? How do you feel about stopping for a swim in Sargent Mountain Pond?

I love these questions because each one pulls on a thread winding through my Acadia memories. I hiked upwards of 125 transects between 2013 and 2016, and now that the paper is done, I’m a little sad to be shelving the fieldnotes for good. The trail runners that I wore are long gone, my field hat fell apart, most of my baggy race tshirts carried me through my second pregnancy and suffered for it.

In the end, the idiosyncrasies of the hikes were smoothed and flattened into the sentence, “Each transect could be completed in under 6 person-hours.” This is both true and wildly circumscribed. Not unlike a well done chapter of a PhD dissertation.

*Acadia National Park actually closed the lot by the Pemetic North Ridge trailhead in 2017 and it’s now exclusively a bus stop for the island explorer, the free bus that begins running right as my season wraps up at the end of June.

**This doesn’t include hikes before I had figured out the fulcrum platform. There was "no" data on those hikes (nothing was leafing or blooming, no signs of budburst) and they only exist in my field note books.

***I hired three field assistants for this project and, concurrently, a common garden experiment. In 2014, Paul was my garden guy, but we also hiked two transects together and he hiked two solo. In 2015, Ella, Natasha, and I split the transect and garden work. Ella came back for most of the 2016 season and then I finished the two projects solo in June 2016.

For Love of Ecology

Happy Valentine's Day! A shortlist of loves.

• I loved this episode of Major Revisions podcast— PLoS Ecology Community Editor Jeff Atkins interviews Rob Nowicki. Their conversation covers Nowicki's analysis of keywords in ecology papers over the past three decades which finds that ecologists today are centering management, and thinking about predictions to a greater degree than their 90s predecessors. Jeff & Rob also compare their fears of bears (the marine ecologist's fear) and sharks (the forest ecologist's fear) and talk about the decline of taxonomists and their own personal failings as naturalists in their study systems. (This honesty is so refreshing! I feel like I am a pretty good naturalist in a very narrow study system, and my skills drop off dramatically as I hike away from the alpine zone, or into southern New England.) Great episode of a fun podcast.

• Earlier this month, K. Taylor PhD wrote a wonderful twitter thread highlighting historic black women in STEM from Diann Jordan's Sisters in Science: Conversations with Black Women Scientists on Race, Gender, and Their Passion for Science. Required reading.

• Some adorable ecology Valentines! Plant Love Stories (hot tip: #PlantHeartArt artist Rosemary Mosco has some additional romanticc omics on her website birdandmoon.com), Maine Audubon & McHenry County Conservation District

• And #ValentineASpecies has been a super fun twitter hashtag.

Sex ≠ Gender

A guest post from Talia Young, Ph.D., David H. Smith Conservation Postdoctoral Fellow, Princeton University & Director of Fishadelphia

I recently saw another ecology talk refer to “gender ratios” of fish. I’d like to talk about the difference between sex and gender, and why ecologists should care about this topic.  

DefinitionsThe words “sex” and “gender” are often used interchangeably in colloquial contexts, but they have different meanings that are relevant to our work in ecology.

“Sex” refers to categories based on a combination of biological and physical characteristics, such as body organs, chromosomes, and hormones (WHO 2011, APA 2015). Sex is commonly assigned on the basis of external genitalia at birth and is often assumed to be only male or female, but scientists have identified at least five different groupings of human sex chromosomes, anatomy, and hormone physiology (Fausto-Sterling 1993).  Other terms that relate to sex include intersex, freemartin, and hermaphrodite. (Note that hermaphrodite is a term currently used for animals but considered outdated and rude when used to describe humans; the preferred contemporary term for humans is intersex.)  (“Sex” can also refer to activity among one or more individuals that may or may not result in sexual arousal and/or genetic recombination. I’m not addressing this meaning of the word in this piece.)

“Gender” refers to identities and categories based on social or cultural characteristics (WHO 2011, APA 2015). Gender is both internal (gender identity, which is each person’s innate sense of their own gender), and external (gender expression, which is how each person expresses their gender identity). Woman, man, masculine, and feminine are all terms that can refer to gender. Transgender is a term used to describe a person whose gender identity is different from the sex they were assigned at birth. Gender is primarily a human and social term, and it is not usually relevant for non-human animals or plants.

When we observe biological and physical aspects of our study organisms, those observations tell us about the sex of those individuals, not the gender. When we interact with other humans, we usually know more about their gender rather than their sex: for example, we often know about their clothing and hairstyles but not very much about their body organs, chromosomes, or hormones.  (Furthermore, and this fact may be obvious, but clothing and hairstyles are not necessarily signifiers of any particular gender identity.)  Among humans, sex and gender may be related, but they are not equivalent. In other words, female and woman are often thought to be synonymous, but in reality, female refers to different characteristics than woman does. It also seems worth noting that both of these sets of categories (sex and gender) are imperfect systems that we have developed in an attempt to describe the world we live in.  As with all categorization systems (such as species, or developmental stages), the world is more complicated than our words can capture.

Usage

1. If (a) you work with plants or animals, and (b) you are interested in categories such as female and male, and (c) those categories are determined by biological or physical criteria (such as presence of sexual organs or gonads, sexually dimorphic coloring, or hormone levels), the accurate term to use is “sex,” not “gender.” See examples in Table 1.

1. If you (a) are talking about scientists and (b) interested in categories such as “women” and “men,” it’s more polite to use gender rather than sex categories. Why? In professional contexts, we may think we know what gender our colleagues present themselves as (e.g., women, men), but probably don’t know very much about the biological sex of our colleagues (e.g., chromosomes, body organs, hormones). It’s odd and inappropriate to make assumptions about other people’s bodies, especially in a professional context. See examples in Table 2. It’s also worth noting that it’s polite to ask people how they prefer to be described. For example, you might ask, “What are the best pronouns to use for you?”

Why is this language important?

1. Accuracy. As ecologists, we are a profession dedicated to describing our beautiful but chaotic and messy world with the best accuracy we can muster. Using language correctly and appropriately is one important part of that work. If you have ever made a distinction between a substantial and significant difference, or taught a student that a single data point is singular while data are collectively plural, the difference between “sex” and “gender” is just one more way to increase the accuracy of our language and our work.

2. Respect. Using gender rather than sex categories when talking about humans means that we do not make intrusive assumptions about other people’s bodies.

Take-homes

• Language matters. Using accurate language is important both in our work and in our community. Being careful with our language helps us improve the quality of our science and allows us to describe our world with greater accuracy. It also helps us build a considerate and thoughtful community of scientists.

• Improving the accuracy of our language is a lifelong process. None of us started out understanding the difference between a substantial and a significant change, or an individual’s sex and gender. But one of the gifts of being scientists is that we are constantly learning new things about our world. Doing so helps us become both better scientists and better people.

Questions?  Comments? I’d love to hear them. Email me at talia.young@princeton.edu. #sexvsgenderinecology

Acknowledgments

Thanks to K. Baker, H. Batson, S. Borrelle, N. EtShalom, Y. EtShalom, S. Fox, S. Kassabian, E. Kaufman, and C. McDonough MacKenzie for suggestions and improvements to this piece.  All errors are mine.

References

• World Health Organization, Gender Mainstreaming for Health Workers, 2011. https://www.who.int/gender-equity-rights/knowledge/glossary/en/

• APA dictionary of psychology (2nd ed.). American Psychological Association. (2015). https://www.apa.org/pi/lgbt/resources/sexuality-definitions.pdf

• Fausto-Sterling, A. 1993. “The Five Sexes: Why Male and Female are Not Enough.” The Sciences. https://www.fd.unl.pt/docentes_docs/ma/TPB_MA_5937.pdf

Other resources

• Krieger, N. 2003. Genders, sexes, and health: what are the connections—and why does it matter? International Journal of Epidemiology, 32(4), 652–7, https://doi.org/10.1093/ije/dyg156

• Fausto-Sterling A. 2000. Sexing the Body: Gender Politics and the Construction of Sexuality. New York, NY: Basic Books.

Banner image photo credits: Mimi Kessler and Don Young

Up All Night

 As a parent to a newborn, I was drawn to the recent PLoS ONE paper ‘Creeping in the Night.’ I’m creeping in the night all the time — but I don’t get the excitement of working with mongoose, full moons, and unexpected den visits.

Drs. Carol Anne Nichols and Kathleen Alexander documented nocturnal behavior in a diurnal species when their camera traps captured some surprising late-night activity. Their paper, Creeping in the night: What might ecologists be missing? is part natural-history-note and part call-to-action for ecologists to shake off our perceptions of how animals partition their days and nights. As a reader, I came for the sleepwalking mongoose, but I stayed for the existential questions of how we structure our research activities and when binary traits might actually be blinders. 

Nichols and Alexander have been studying banded mongoose behavior in Northern Botswana for years. The project began in 2000, Alexander joined as a field ecologist in 2014, and in 2016 they began camera trap research as a means to study behavior without observer presence. I asked if the den site selection for the camera traps, which spanned urban areas and natural habitats, was serendipitous or it they had intentionally radio-collared urban and country mongooses. They told me that they studied mongoose troops in “town” (ie urban areas of Kasane and Kazungula) and “park” (Chobe National Park) habitats to “understand how different landscapes influence wildlife behavior and potential impacts that could impose on pathogen transmission dynamics.” Within a month of deploying the camera traps, they caught a mongoose outside of a den at night on film.

“It was certainly an amusing discovery to find so early in the project,” says Nichols. “We were excited to see if more nocturnal detection were to come, or if, as we joked, that first mongoose was just sleepwalking.” After 215 trap days, they had photographs of mongooses at night from 7 trap days. Among these photographs, there was no pattern of more night-activity among town (vs. park) habitats or moonlit (vs. dark) nights. In at least two photos, a mongoose appears to be sneaking around a den of another troop. In a scene that could be the trailer for a mongoose-version of COPS, a series of photos captures one mongoose approaching a den at night, another mongoose emerging from the den, the ensuing chase, and hours later, a single mongoose returns.

Nichols and Alexander say they are now deploying more cameras in hopes of understanding ringed mongoose nighttime behvavior. “This discovery has changed the way we thinking about mongoose,” they write. “There is much more happening! This discovery has made us question all our assumptions. The mystery continues!”

In the same month that Nichols and Alexander published Creeping in the Night, Dr. Kaitlyn Gaynor and colleagues published the meta-analysis The influence of human disturbance on wildlife nocturnality in Science. Gaynor compiled 76 studies comprising 62 mammal species from across the globe to explore how daily patterns of wildlife activity responded to different types of human disturbance, including vehicles, resource harvesting, development, and recreation. Each study in the meta-analysis included data on animal nocturnality under conditions of low and high human disturbance. They found that across all the different types of human impacts, the mammals showed a significant increase in nocturnal activity compared to mammals in low-impact habitats.

This contrasts with the ringed mongoose — Nichols and Alexander’s data were not included in the meta-analysis, but they found no difference between the human-impacted town den sits and the park sites in mongoose night time activity. Nevertheless, at least in habitats marked by human disturbance, mongoose might not be the only so-called diurnal mammals creeping in night. This pattern of nocturnal behavior among mammals that we thought were diurnal calls into question the traditional dichotomy between day-time animals and night-time animals. In their Discussion, Nichols and Alexander write that this “limited approach [only looking at day time behavior] may fail to capture data critical to understanding the ecology, biology of a species, and the temporal nature of space use.” As she reviewed their photos, Alexander recalled Samuel Sneiders’ “The theory of ecology” — “specifically that heterogeneity was an underlying phenomenon of ecology. In our writing, we wanted to emphasize that these unexpected events are really the interesting nuggets of new discovery!”

The Discussion encourages ecologists to be open to temporal heterogeneity with references to classic ecological work in spatial heterogeneity. This connection made me think of a recent essay in Current Biology: Are the ghosts of nature’s past haunting ecology today? Here, Dr. Brian Silliman and coauthors explore trends of rebounding populations of large-bodied consumers. These species —for example, sea otters and alligators — seem to be expanding into habitats that ecologists thought were beyond their niche space. Often this is beause we decimated their populations before thoroughly studying their original ranges, and we’re working with incomplete baseline data. In both cases — spatially with rebounding sea otters and alligators and temporally with ringed mongoose — this limits our ability to provide recommendations for management and conservation. As Nichols and Alexander write, “This work emphasizes the idea that you don’t know what you don’t know.” They encourage researchers to:

Push the envelope and see what you find. It might make all the difference in your approach to management and effective conservation of a species. With mongoose, we realize that between group dynamics and contacts are more complicated than we thought with these nighttime excursions and we need to understand the drivers of this behavior to understand disease transmission in this population — a critically important management objective.

For me, during those rough 4 am feedings, it's weirdly comforting to think, maybe there's a mongoose out there who is also awake right now. But, as I look forward to returning to my own research next semester, I will be thinking about Nichols and Alexander's big question What might ecologists be missing? and working to better define the edge of my assumptions around my study system, species, and methods. 

References:

Nichols, C. A., & Alexander, K. (2018). Creeping in the night: What might ecologists be missing? PloS One, 13(6), e0198277–7. http://doi.org/10.1371/journal.pone.0198277

Gaynor, K.M., Hojnowski, C.E., Carter, N.H. and Brashares, J.S. (2018). The influence of human disturbance on wildlife nocturnality. Science, 360(6394), pp.1232-1235.

Silliman, B. R., Hughes, B. B., Gaskins, L. C., He, Q., Tinker, M. T., Read, A., et al. (2018). Are the ghosts of nature’s past haunting ecology today? Current Biology, 28(9), R532–R537. http://doi.org/10.1016/j.cub.2018.04.002

Summer Reading (Part 2)

Last week I wrote about my favorite new papers on mountains and phenology after a summer of scientific reading. In the second half of my top ten list, I’m highlighting some plant mysteries and best practices of 2018. 

“Plant mysteries” is a label that I’m using to lump together three plant papers that I can’t stop thinking about. They cover some of my favorite methodological quirks — historical field notes, herbarium digitization, citizen science — and two genera that I think are cool — Sibbaldia and Erythronium. The mysteries range from: Is this still here? to Why is this here in two colors?  to Can I get this specimen to tell me what else grew here? without much thematic overlap, but all three papers tell gripping stories. If nothing else, they share a strong natural history foundation and well-executed scientific writing that made for lovely hammock-reading.

“Best practices” are just that — descriptions of how we can improve our science as individuals and collectively. We can design better spreadsheets for our data and we can support gender equity in our scientific societies. I strongly recommend that all ecologists read up on both. 

Plant Mysteries

I didn’t particularly notice [trophy collecting/associated taxa/pollen color polymorphism] before, but now I can’t not see it…

1. Sperduto, D.D., Jones, M.T. and Willey, L.L., 2018. Decline of Sibbaldia procumbens (Rosaceae) on Mount Washington, White Mountains, NH, USA. Rhodora, 120 (981), pp.65-75.

I love this deep dive into the history of snowbank community alpine plant that occurs in exactly one ravine in New England (though it’s globally widespread across Northern Hemisphere arctic-alpine habitats). Over the past four decades, surveys in Tuckerman’s Ravine have documented a continuous decline in the abundance of creeping sibbaldia, and recently researchers have been unable to find it at all. This would make creeping sibbaldia the first documented extirpation of an alpine vascular plant in New England. Dr. Daniel Sperduto and coauthors revisit the photographs and notes from contemporary surveys and find that mountain alders are encroaching on the creeping sibbaldia’s snowbank habitats. These notes also include anecdotes of local disturbances like turf slumping at the sites where creeping sibbaldia used to be found. In herbaria across New England, Sperduto and coauthors discovered sheets covered with dozens of specimens — this “trophy collection activity” in the 19th century led them to calculate that “there are more than three times as many plants with roots at the seven herbaria examined than the maximum number of plants counted in the field within the last 100 years.” I am obviously partial to New England alpine plants, and I got to see Sperduto present this research as a part of an engaging plenary session at the Northeast Alpine Stewardship Gathering in April, so you could write this off as a niche interest. Despite this, I see creeping sibbaldia as a lens for considering the universal mysteries of population decline and extirpation, and the challenges of tying extirpation to concrete cause-and-effect stories. 

2. Pearson, K.D., 2018. Rapid enhancement of biodiversity occurrence records using unconventional specimen data. Biodiversity and Conservation, pp.1-12.

Leveraging herbarium data for plant research is so hot right now. But what if you could squeeze even more information from a specimen label? For example, many collectors note “associated taxa” along with the date and location of collection. The associated taxa are plants that were seen nearby, but not collected — a kind of ghostly palimpsest of the community that grew around the chosen specimen. Herbaria across the globe have spent the past decades digitizing specimens and uploading photographs of their pressed plants. In this process, the associated taxa on specimen labels are often stored in a ‘habitat’ database field. In this impressive single-author paper, Dr. Kaitlin Pearson extracts the associated taxa data from Florida State University’s Robert K. Godfrey Herbarium database with elegant code that can recognize abbreviated binomial names and identify misspellings. She then compared the county-level distributions of the associated taxa database with their known county-level distribution from floras and herbarium specimens. Incredibly “the cleaned associated taxon dataset contained 247 new county records for 217 Florida plant species when compared to the Atlas of Florida Plants.” There are plenty of caveats: the associated taxa can’t be evaluated for misidentification the way a specimen can, and lists of associated taxa are obviously subject to the same spatial biases as herbarium specimens. But this is clearly a clever study with a beautifully simple conclusion: “broadening our knowledge of species distributions and improving data- and specimen-collection practices may be as simple as examining the data we already have.” 

3. Austen, E.J., Lin, S.Y. and Forrest, J.R., 2018. On the ecological significance of pollen color: a case study in American trout lily (Erythronium americanum). Ecology, 99(4), pp.926-937.

Did you read Gelman and Hill’s Data Analysis Using Regression and Multilevel/Hierarchical Modelsin a seminar and think, this seems like an amazing resource but I’m an ecologist and examples about school children watching Sesame Street or election outcomes and incumbency for US congressional election races just don’t resonate with me? The ecological and evolutionary mystery of red/yellow pollen polymorphism is super interesting in its own right and Dr. Emily Austen and coauthors thoroughly attack this question. For me — and I’ve admitted here before that I am the kind of learner who benefits from repetition  — Austen’s statistical methods are the star. Austen demonstrates glm best practices and brings stunningly clear plant ecology examples to the Gelman and Hill framework. I would probably teach this paper in a field botany course (trout lilies are charismatic! look at this fun map of pollen color polymorphism!), but I would absolutely prefer to assign it in a statistical methods course, especially as a supplement/set of alternative exercises to Gelman and Hill. 

Best Practices

Do this…

1. Potvin, D.A., Burdfield-Steel, E., Potvin, J.M. and Heap, S.M., 2018. Diversity begets diversity: A global perspective on gender equality in scientific society leadership. PloS one, 13(5), p.e0197280.

Gender equality in biology dramatically decreases as you look up the ladder in academia — compare the gender breakdown in the population of graduate students to tenured professors and gender disparity is stark. Leadership in our field is still heavily male skewed. Dr. Dominique Potvin and her coauthors asked, is this true in scientific societies too? Scientific societies are generally more open than academic departments, and there is more transparency in the process of electing governing boards and leadership positions. Potvin and coauthors leveraged these traits to ask: what is the role of scientific societies in rectifying gender inequity? why are some societies better than others at promoting women in leadership? After considering 202 societies in the zoological sciences, they found that the culture of the society — the age of the society age, size of its board and whether or not a it had an outward commitment or statement of equality — was the best predictor of equality in the gender ratio of society boards and leadership positions. This “outward commitment or statement of equality” covered anything published on the society website — a statement, committee, or other form of affirmative action program — that “implies that the society is dedicated to increasing diversity or improving gender equality.” Of the 202 societies they studied, only 39 (19.3%) had one of these visible commitments to equality. Whether societies with high proportions of female board members were more likely to draft and publish these statements, or whether societies that invested time and energy in producing such commitments attracted more women to leadership positions is a bit of a chicken-and-egg riddle. Societies looking to reflect on their own state of gender equality can take advantage of the resource presented in Table 6: “Health checklist for scientific societies aiming for gender equality.” Assessing gender equality is kind of a low hanging fruit — and the authors encourage societies to reflect on intersectionality and race, age, ethnicity, sexuality, religion and income level as well. Basically, if a scientific society is struggling to support white women in 2018, there’s an excellent chance it is failing its brown, LGTBQ, and first-generation members to a much greater extent.

2. Broman, K.W. and Woo, K.H., 2018. Data organization in spreadsheets. The American Statistician, 72(1), pp. 2-10.

If I could send a paper in a time machine, I would immediately launch Broman and Woo’s set of principles for spreadsheet data entry and storage back to 2009, when I started my master’s project. Reading through this list of best practices made me realize how many lessons I learned the hard way — how many times have I violated the commandments to “be consistent”, “choose good names for things”, or “do not use font color or highlighting as data”? Way too many! Eventually, I pulled it together and developed a data entry system of spreadsheets that mostly conforms to the rules outlined in this paper. But, if I’d read this first, I would have skipped a lot of heartache and saved a lot of time. This is an invaluable resource for students as they prepare for field seasons and dissertation projects. Thank you Broman and Woo, for putting these simple rules together in one place with intuitive and memorable examples! 

Happy Fall Reading! 

Summer Reading (Part 1)

We’re rushing out of the dog days of summer and into the start of a new semester — or in my case the start of parental leave, which is a little bit like embarking on a new semester at an unknown campus and while I completed the newborn syllabus three years ago, I have this sinking feeling that I don’t even know which classes I’m enrolled in yet. Regardless, I’m reflecting on my summer reading.

Over June, July, and August, I was all in on #365papers and I have a top ten list of scientific papers from these long summer days of slow reading. Because my “semester” might start at any moment, I’m breaking this post into two parts. First up: my favorite hot-off-the-press summer reads on mountains and phenology.

On Mountains

Think globally & way into the past…

1. Iglesias, V., Whitlock, C., Krause, T.R., Baker, R.G., 2018. Past vegetation dynamics in the Yellowstone region highlight the vulnerability of mountain systems to climate change. Journal of Biogeography 45, 1768–1780. doi:10.1111/jbi.13364

Fifteen pollen records covering 16,000 years and the 80,000 km2 mountainous Greater Yellowstone Ecosystem create an incredible review of elevational patterns of vegetation change in an iconic mountainous region. In this paper, Dr. Virginia Iglesias lays out the challenges of quanitifying pollen-vegetation relationships in mountain regions (aka what I didn’t know when I proposed my postdoc research) and then pulls in a staggering amount of modern and fossil pollen data to recreate the history of Yellowstone’s dominant conifers. These are stories of both stability and rapid change through past climatic changes with conservation implications for managers facing anthropogenic climate change. My favorite line: “The current vegetation distribution is, at best, a short and rather anomalous baseline for evaluating ecological responses to future climate change.” 

2. Elsen, P.R., Monahan, W.B., Merenlender, A.M., 2018. Global patterns of protection of elevational gradients in mountain ranges. PNAS 115, 6004–6009. doi:10.1073/pnas.1720141115

This study has it all: mountain biodiversity love, protected area planning, big data analysis, and beautifully designed maps of “elevational protection” across the globe. Full disclosure: Dr. Paul Elsen is a fellow Smith Fellow and I also got to see this paper as a speed talk at the North American Congress for Conservation Biology in July. The bottom line is this: when you zoom out, most of the world’s mountain ranges are narrowly protected — we need conservation across elevation gradients to effectively protect species under climate change. 

On Phenology 

Wherever you get your phenology data (maybe from TV?) scientists are asking some really interesting questions about community composition, temporal dynamics, and the implications of climate change on interspecific relationships…

3. Carter, S.K., Saenz, D., Rudolf, V.H.W., 2018. Shifts in phenological distributions reshape interaction potential in natural communities. Ecology Letters 30, 133–9. doi:10.1111/ele.13081

Amphibian breeding phenology is not the kind of phenology that I study — I don’t install recorders at ponds to capture EPs of overnight breeding calls, I don’t log hours listening to the audio to identify twelve different amphibian species and record the number of individuals per species calling during each recording session, and I certainly have not done this tirelessly for fifteen years. But I’m so glad that Dr. Shannon Carter and her colleagues did because their ingenuous analysis of changes in the timing of calling between pairs of amphibian species has huge implications for how we — plant phenology people included! — study phenological mismatch. The overlap (or "phenological distributions") of amphibian breeding calls has shifted in weird and non-uniform ways, and metrics like ‘first day of calling’ or ‘median call date’ don’t capture these changes well. This is just a great analysis of a grinder ball dataset (8 ponds in Northeast Texas, monitored consistently over 15 years) which opens up a window to these big questions — How do we monitor phenology? What information do we need to know that temporal mismatch is occurring?

4. De Frenne, P., Van Langenhove, L., Van Driessche, A., Bertrand, C., Verheyen, K., Vangansbeke, P., 2018. Using archived television video footage to quantify phenology responses to climate change. Methods Ecol Evol 149, 1791–9. doi:10.1111/2041-210X.13024

Dr. Pieter De Frenne and his coauthors have received tons of press coverage (best sub-headline: "ignore the lycra—look at the flowers") for this incredibly photogenic work. They basically watched 200 hours of TV (old coverage of the Tour of Flanders), justified this as “research” by grabbing screen shots of 46 shrubs and trees from along the cycling course, and found surprisingly strong advances in the timing of spring leaf out and flowering in these plants over the years. This is, on one level, the opposite of Carter et al listening to frog calls for fifteen years — the phenology monitoring here is opportunistic and there is only a single metric each year (what was happening on the day they filmed the Tour). But as De Frenne points out at the end of the paper: “Probably the most promising way forward for phenology research is to better integrate all types of phenology data…observational time series, experimental manipulations of climate, herbarium records, historical surveys of vegetation, historical maps, repeat photographs and other, yet unexploited, sources such as television video footage from broadcast archives.” 

5. Winkler, D.E., Butz, R.J., Germino, M.J., Reinhardt, K., Kueppers, L.M., 2018. Snowmelt Timing Regulates Community Composition, Phenology, and Physiological Performance of Alpine Plants. Front. Plant Sci. 9, 631–13. doi:10.3389/fpls.2018.01140 

Dr. Daniel Winkler, PLoS ESA Reporting Fellow 2016, tweeted out his new paper in July and he had me at “community composition, phenology, and physiological performance of alpine plants.” My “alpine-ish” communities include true alpine on Katahdin, but also Cadillac Mountain in Acadia, which is a whopping 1,530’ and more accurately described as ‘Northern Appalachian-Acadian Rocky Heath Outcrop’ by NatureServe. I’m definitely interested in the differences between alpine-restricted species and wide-ranging species. Winkler’s team recorded species diversity, flowering phenology, and physiological measurements including gas exchange, net CO2 assimilation, and stomatal conductance across plots along an elevation and aspect gradient in the Colorado Rockies. Two results jumped out at me: the alpine-specialists displayed less flexible flowering phenologies than the wide-ranging species, but there were not strong differences between these groups in physiology. This is the kind of paper that inspires mad grant writing — I'm interested but skeptical, will this hold up in my pet region/ecosystem/study system? I want to replicate this kind of research in the Northeast — and across a gradient of sites where phenology is tied to snowmelt (true alpine areas of Katahdin and the Presidential range), and where the two are (I think) decoupled (Cadillac Mountain). Winkler and I wrote a blog post together in 2016, I think I can convince him to collaborate on a larger scale — and get him to New England! 

Bonus “Reads”

Recent podcast episodes tangentially related to recent blogging

• This American Life covers The Feather Thief. My review of the book.

• Outside/In reports on underrepresentation in outdoor gear (aka 'shrink it and pink it' does not make women happy shoppers, especially when we can't find our sizes, preferred styles, or performance level). This touches on some of the same themes — inclusion & diversity in the outdoors — as my response to “Have Ecologists Lost Their Senses? Walking and Reflection as Ecological Method”

The Rollercoaster of Exploding Pollen

When I think about reading peer-reviewed natural history papers — including contemporary articles in a ‘Natural History Miscellany Note’ or ‘The Scientific Naturalist’ section — I imagine them mostly as a classic throwback: just a scientist, a hand lens, and a notebook. I generally do not think about employing $50,000 of high-speed video recording equipment to test dueling hypotheses about pollination modes from the 1860s. I’m clearly missing out. 

The American Naturalist recently published a mash-up of 19th century natural history observations and 21st century tech: in “Dispensing Pollen Via Catapult: Explosive Pollen Release in Mountain Laurel (Kalmia latifolia)” Dr. Callin Switzer and coauthors present speed records, specialized weaponry vocabulary, and plot twists. 

The Speed Records: Mountain laurel is well known for its explosive pollination — a great botanical cocktail party conversation starter*, but an adaptive function that has remained a mystery since the 19thcentury. Back in 2005 fans of understory plants of the temperate deciduous forest and speed records** were wowed by bunchberry — researchers from Williams College clocked this explosive pollinator launching pollen grains at 3.1 meters/second, and accelerating pollen at 24,000 meters/second2.Switzer’s research at the most basic level sought to record the speed and acceleration of mountain laurel’s explosive pollen. The mechanisms behind the explosion were well documented by the 1990s (pollen on the mountain laurel anthers are tucked into “pockets” in the petals and held under tension by curved filaments — when the anther is released from the pocket, the pollen is launched into the air), but the speed was still unrecorded. Switzer explains, “The paper was inspired by walking around the Arnold Arboretum with several of the faculty there. Robin Hopkins (my PhD advisor) and Ned Friedman both knew that I had done some high-speed video projects in the past, and they suggested that I should take a look at the mountain laurels. I first had the high-speed videography background, and then Robin pointed me to the 19th century literature.” From the high-speed videos, Switzerfound that mountain laurels launched pollen at 3.5 meters/second for an average maximum speed and achieved average maximum acceleration at 4,100 meters/second2. Mountain laurels thus have “one of the fastest-moving floral parts recorded”! But why? In 1867 The American Naturalist published competing hypotheses for the adaptive function of explosive pollination in mountain laurels. Was the pollen aimed at the stigma for incredibly efficient self-pollination? Or is the pollen catapulted on to visiting bees for cross-fertilization? These 19th century natural history observations sat at the heart of Switzer’s interest in quantifying the speed of mountain laurels — a chance to unravel this species’ mythology of adaptive explanations. “I think of natural history as a part of biology that starts with curiosity about the natural world.” Switzer reflects. “Naturalists tend to get ideas for projects simply by going out into the field with a hand lens and a notebook -- with all the new technology available, however, naturalists can do a lot more interesting and quantitative studies.”

Before revealing the speed-pollen’s adaptive function, I just need to acknowledge the weird side effect of reading about explosive pollen — I learned a ton about the physics and vocabulary of medieval weapons…

Specialized Weaponry Vocabulary: The next time you are struggling to articulate the difference between a regular catapult and a medieval trebuchet, just think about the difference between a mountain laurel and a bunchberry. While both flowers have filaments under tension and fling pollen from the tips of their anthers, on bunchberry anthers there is a hinge connecting the anther to the filament tip. The bunchberry trebuchet is a specialized catapult: the payload is attached to the throwing arm by a hinge. Mountain laurels may be standard issue catapults — without the hinge that propels bunchberry pollen with incredible acceleration — but mountain laurel pollen grains are structurally designed to be their own weapon. The mountain laurel’s pollen grains “form tetrads connected with viscin threads…causing each anther to release several stringy aggregations of pollen when it is triggered.” Switzer hypothesizes that these stringy aggregations may act as a bola— hitting a target/pollinator and then wrapping around to attach itself tightly. Both the bunchberry and mountain laurel papers weaponize their flowers, making explosive pollination seem explicitly conflict-driven. I asked Switzer, “Are plants at war with their pollinators?” He responded, “plants and pollinators are in evolutionary conflict -- they have different "goals", and both are constantly evolving to suit their own goals.  If you'll excuse the anthropomorphizing, plants "want" bees to keep pollen on their bodies and transfer it among flowers, but bees "want" to collect the maximal amount of resources, without wasting energy carrying pollen among flowers.” When we look closely at the world around us, the metaphors of natural harmony and balance blur and fade: petals are architects of secret triggers, flowers a minefield of exploding pollen. 

The Plot Twists: Switzer filmed 69 mountain laurel pollen explosions outdoors at the Arnold Arboretum to capture the insect visitors and causes of catapulting pollen. Bees — mostly bumble bees — triggered the anther catapults, while appearing to search for nectar. During this fieldwork, and in the playbacks of the high-speed videos, Switzer watched pollen fly past the bees. It seemed like the catapults were missing their target. Maybe this was an elaborate, Rube Goldberg-esque set up to have a bee trigger a catapult to self-fertilize a flower via an extremely fast but weirdly complicated mechanism?A second set of high-speed videos, recorded in the lab, allowed Switzer to calculate pollen trajectories in 3-D space. In these videos, the flower is set in profile to the camera and half the petals have been removed to give a clear view of the flower parts: stigma, style, anther pocket and filament. The catapult is manually triggered by a needle. When the pollen trajectories are traced and modeled into 3-D space, it’s clear that most of the time the catapulted pollen crosses the central axis of the flower at just about bee-height. Switzer admits, “I was very surprised when I made observations with only my eyes, and I saw pollen flying past the bees. I came up with all kinds of interesting explanations in my head, until I collected the high-speed videos and saw what was really happening.” In the Discussion of the pollen catapult paper, there is a refreshing transparency about this plot-twist moment: “Only with detailed experimentation and observations were we able to better understand the adaptive significance of explosive pollination—we realized that field-based observations did not allow us to see how much pollen actually hit the bee (because the bee’s body often blocked the view).”

The story of the research — stretching back to those 19th century naturalists and the mythology of adaptive explanations — is so clear here. We thought we saw something. We tested it from another angle and saw something else. 

As Switzer explains, “This was indeed a gut-check moment, and it did help me have more empathy for 19th century naturalists as well as present day naturalists. Doing good science with good statistics is hard -- it can be so easy for scientists (myself included) to convince themselves of something that is not true.  For me, it's really helpful to get constructive feedback from others to help me find those 'blind spots.'”

Switzer’s ultimate contribution — beyond allowing mountain laurel to rest on its speed laurels, side by side with bunchberry in the Fast Plants Hall of Fame — is this effort to keep looking: to bring in two high speed cameras, half-dissected flowers in a lab setting, and 3-D modeling, and shed light on the unknowns with every tool in his 21st century natural history toolbox.

References:

Callin M. Switzer, Stacey A. Combes, and Robin Hopkins, "Dispensing Pollen via Catapult: Explosive Pollen Release in Mountain Laurel (Kalmia latifolia)," The American Naturalist 191, no. 6 (June 2018): 767-776. https://doi.org/10.1086/697220 

Edwards, J., Whitaker, D., Klionsky, S., & Laskowski, M. J. (2005). A record-breaking pollen catapult. Nature,435(7039), 164–164. http://doi.org/10.1038/435164a    

*Botanical cocktail party conversation starters are definitely a thing. Just read Amy Stewart’s The Drunken Botanist.

**There are many fans of understory plants of the temperate deciduous forest and speed records. Just think of all the trail-runners you know who are also ecologists and/or iNaturalist enthusiasts. We generally have two speeds: extremely slow (botanical observations) and extremely quick (peak bagging). We pack lots of snacks. We have favorite races based on the phenology of the date and the beta-diversity of natural communities along the course. We like to poke things.

Reading, Walking, Wishing

June in New England is a long stretch of long-lit days. When I was a PhD student, my Junes were the peak of my field season and I spent the long days logging miles up and down Cadillac, Sargent, and Pemetic mountains. For four years, my Junes were hiking ridges, recording data, wearing holes in the toes of my trailrunners. Now, I’m revising the papers that were written on the heels of those leg muscles and it’s weird to be indoors in June, sitting at a computer, without the tight hamstrings or blackfly bites.

After a long slog through a cold spring, this June I’ve returned to reading, picking up #365papers again in earnest after slacking off on the literature for a few months. Last week, I read Liam Heneghan’s essay “Have Ecologists Lost Their Senses? Walking and Reflection as Ecological Method” in Trends in Ecology & Evolution. I was indoors, at my desk, with the AC whirring, reading about walking. I felt like a fish out of water, or more aptly a field ecologist out of nature. In the essay, Henegham makes the distinction between ecologists and naturalists, comparing word counts in the anthologies The Essential Naturalist: Timeless Readings in Natural History (2011) and Foundations of Ecology: Classic Papers with Commentaries (2012).

“Although the two disciplines ‘observe’ and ‘see’ things in equal measure, natural historians nonetheless report engaging all of their senses in the pursuit of observations of nature to a greater degree. Natural historians report touching, feeling, hearing, and smelling the things of the world to an extent that scientific ecologists do not. Indeed, ecologists, if this small sample is representative, have abandoned smelling in its entirety. Moreover, natural historians ‘walk’, ‘roam’, ‘climb’, ‘sniff’, and ‘listen’ to a degree their ecological colleagues do not.”

I am a roaming, climbing, sniffing ecologist. But I bristled at the thought that ecologists as a whole should be compelled to walk to prove some kind of connection to the true core of the discipline. Heneghan does not outrightly demand that all ecologists walk, roam, and climb — his main argument seems to be the gentle conjecture “ecologists may have overlooked the fact that scrutinizing nature can benefit from an engagement of all the senses” — but he doesn’t leave much space within the discipline for non-field ecologists.

Perhaps Heneghan’s essay title is misleading and he isn’t worried about all ecologists losing their senses, just the outdoor ones. The field-based, nose-to-the-ground, perambulatory science that Heneghan and I practice is clearly not universal to ecology — and it shouldn’t be! We need modelers and theorists and lab scientists! But I fell for this essay hard. I am the target audience. When I started as a master’s student at the University of Vermont’s Field Naturalist and Ecological Planning program, my Botany 311 class, the Fall Field Practicum series of weekly full-day field trips, listed 7 goals on the syllabus. Goal #7: “Visit bakeries and enjoy spending the day outdoors.” In Heneghan’s analysis of word counts in the Ecology vs. Natural History texts, “Breakfast” receives 0.72 mentions per page in The Essential Naturalist; it does not appear at all in Foundations in Ecology*. Just digging out my Fall Field Practicum syllabus conjured up memories of cider donuts and eskers, travel mugs of maple-syrup-sweetened coffee and ombrotrophic bogs. My UVM experience was steeped in the kind of sensory details that Heneghan would appreciate and savor.

‘Walking and Reflection as Ecological Method’ reminded me of a similar paper I’d read in another (sadly non-bakery-centered) UVM class: Craig Loehle’s 1990 ‘A guide to increased creativity in research — inspiration or perspiration?’ Loehle also identifies the benefits of walking as a part of the scientific process when he encourages students to “get bored” as a work habit. This is recommended alongside running, procrastinating, and surfing — allegories for carving out time to think deeply and engage in non-productive, non-routine activities. These pursuits, Loehle promises, will facilitate creative problem solving. When I went back to re-read Loehle this week, I was surprised to find the advice “Don’t read the literature” under his list of methods for releasing creativity. I am, traditionally, a big fan of reading the literature. I’m a reader: when I was asked to review a Tansley Insight manuscript for The New Phytologist, my first move was to download and read the 2015 editorial “Introducing Tansley Insights – short and timely, focussed reviews within the plant sciences.” I won’t admit how many other Tansley Insights I downloaded after. A lot, okay? Maybe all of them. But Loehle’s “Don’t read the literature” is not a blanket statement; he clarifies that the first step as a scientist begins mulling over a new idea should not be to run to Web of Science (or whatever researchers used to find papers back in the dark ages of 1990), but to work through it a bit on your own.

“[Reading the literature] channels your thoughts too much into well-worn grooves. Second, a germ of an idea can easily seem insignificant in comparison to finished studies. Third, the sheer volume of material to read may intimidate you to abandoning any work in a new area.”

I agree with Loehle on all three points, but I’d add that the habit of reading broadly in the literature — taking recommendations from twitter**, searching outside of the Table of Contents of your subdiscipline’s favorite journal, checking out how your pet methodology is applied in another country or ecosystem, or seeking out papers with your field site as a keyword by researchers who are not in your field — is a kind of antidote to the well-worn grooves.

This month I read papers from Agricultural and Forest Meteorology, Alpine Botany, Bioscience, Conservation Biology, Current Biology, Ecology, Ecosphere, Frontiers in Ecology and the Environment, Integrative and Comparative Biology, Journal of Applied Ecology, Journal of Geophysical Research: Biogeosciences, Nature Geoscience, New Phytologist, Ocean & Coastal Management, Palynology, Proceedings of the National Academy of Sciences, and Trends in Ecology & Evolution. I am a broadly trained field ecologist — thanks UVM! — but as my career has progressed I’ve naturally found myself engaged in narrower research pursuits, and reading broadly keeps me centered, provides context for the tedium of slicing a 4.09 m core of lake sediment into half centimeter subsamples, and makes my work feel connected to society, policy, and big-picture conservation.

I’ll likely never publish in Ocean & Coastal Management, but reading “‘Back off, man, I’m a scientist!’ When marine conservation science meets policy”*** resonated with my own experiences writing public comments and meeting with congressional staffers. In a way, reading broadly is a kind of indoor-walking for restless ecologists who are prone to wandering.

Loehle and Heneghan’s essays are endlessly quotable for natural history students. But while they strive to expand how scientists engage in the world — Shake off your routine! Get outside! Smell! — they present an ironically narrow picture of role models. The patron saints of creative, roaming researchers, name-checked by both Loehle and Heneghan, are Darwin and MacAthur. I feel very strongly that if your argument around what’s needed in the “culture of ecology” can be reduced to “be more like this white man who had the privilege to travel freely and comfortably in the outdoors” you are fundamentally wrong. In Heneghan’s case, in 2018, there’s no excuse for whitewashing field ecology. Priya Shukla’s amazing piece in Bay Nature Magazine beautifully lays out the importance of representation in contemporary ecology, and the urgent need to uncover and share the ways in which wild landscapes are not empty areas that blankly awaited manifest destiny and reflect only Anglo-European stories. She writes “We need an act of revisionist natural history to color in the environmental and conservation movements. We should remind every hiker, biker, birder, citizen scientist, and field researcher that innumerable diverse people have shaped our natural spaces.” In a series of profiles of diverse voices in outdoor recreation, James Edward Mills writes in Outside, “Organizations like Outdoor Afro, Latino Outdoors, and Out There Adventures have begun stripping away the presumption of a white, male, heterosexual experience. Even more importantly, by unapologetically presenting their unique points of view, they’ve shined a light on a rich heritage of adventure and environmental stewardship that has been there for generations.”

This diversity exists in field ecology and natural history writing too, and it is not hard to find. Sure, Darwin and MacArthur were great at walking and writing about walking with wonderful sensory detail — but have you read J. Drew Lanham’s essay ‘Birding While Black’ or his book The Home Place? Robin Wall Kimmerer’s Braiding Sweetgrass? Janisse Ray’s Ecology of a Cracker Childhood****? Hope Jahren’s Lab Girl —in which the titular "girl" (Jahren) spends long stretches outside of the lab writing lyrically about working in the outdoors?

Heneghan begins his essay in a bog, but his call to arms (hiking boots?) is not simply an #OptOutside manifesto. He follows his walking naturalists — his long list of old white men: Irish botanist Robert Lloyd Praeger, Henry David Thoreau, Charles Darwin, Robert McArthur, and E. O. Wilson — indoors to their writing desks. At the end of the piece, Heneghan is in the archives, reading Praeger’s papers and reflecting on his prodigious writing. “A day’s walk can furnish long hours back at the desk.” Heneghan muses, “Thus for every insight into nature, there is a hidden process by which that insight was achieved; every active life contains a hidden core of repose.”

So this is my indoor June, my hidden core of repose. My trailrunners lie neglected, but the writing & reading continues, as I adventure through the memories and field notes and spreadsheets on the heels of the illustrious white men, and the many, many equally bold, sure-footed, and thoughtful unnamed white women and people of color who have trod this path before me.

References:

Heneghan, L., 2018. Have Ecologists Lost Their Senses? Walking and Reflection as Ecological Method. Trends in Ecology & Evolution 1–4. doi:10.1016/j.tree.2018.04.016 

Loehle, Craig. 1990. "A guide to increased creativity in research: inspiration or perspiration?." Bioscience 40.2: 123-129.  

*I have a confession to make here. I read most of Foundations in Ecology while I was a PhD student. I had not even heard of The Essential Naturalist until I read this paper. So maybe I’m not such a great naturalist after all? ...Or maybe I’m an amazing naturalist, always outside tromping around, and I don’t have time to read natural history anthologies because I’m too busy smelling nature?

**I found Heneghan’s essay by way of @ChelskiLittle’s prolific #365papers tweets. Thanks Chelsea!

***I found this paper by way of @Drew_Lab’s #365papers tweets. Thanks Josh!

****I cannot say enough about Milkweed Editions. This independent, nonprofit literary powerhouse in Minneapolis publishes incredible environmental writing. My husband gifted me a Milkweed book subscription years ago and it's my absolute favorite piece of mail every month. Maybe 30% of my love for LacCore & the science they do there is a side effect of the fact that every time I visit LacCore, I get to take a side trip to Milkweed. 

Are we playing (or hiking or skiing or climbing) too hard? Recreation, Ecology, and Recreation Ecology

In two consecutive years of my PhD, I spent the weekend before Thanksgiving 300 miles away from my family, fighting with temperature loggers in a National Park. This was not so much “opting outside” as desperately trying to install soil probes in raised beds that were basically garden-sized popsicles. But looking back, I perversely treasure those November trips to Maine and the chance to spend a quiet day on the mountain before the bell lap on the fall semester rushed through December. These last-minute-get-the-equipment-in-the-ground-before-the-snow-falls trips occurred in the years before REI created the #OptOutside hashtag, and on the wrong side of Thanksgiving anyway, since we are corporately encouraged #OptOutside instead of shopping on Black Friday. Regardless, this is the image in my head when I think about #OptOutside: standing alone below the summit of Cadillac Mountain under a grey Maine sky, snow flurries dotting my datasheet as the bare branches of the birches and maples and shadbush below fade to purple against the granite. It is rare to have Cadillac to yourself. Acadia is crawling with people opting outside year round: hiking, rock climbing, cross country skiing.

My research on plant communities was recreation-adjacent — I monitored phenology on hiking trails — but this fall I read four interesting papers exploring recreation ecology itself. Recreation ecology is the study of human impacts on landscapes where we play; this subfield is decades old with some foundational books (including Wildlife and Recreationists: coexistence through management and research and Wildland Recreation: ecology and management), but it is often neglected when we ecologists think about conservation (our prevailing views on conservation historically exclude people) or the top 100 papers in our field. Matthew Klingle wrote an excellent essay examining #OptOutside from the cultural and consumerism perspectives, critiquing the socio-economic assumptions about who gets to opt outside and where they get the gear they are hauling into the woods and artfully arranging for their instagrams. I am writing this post as the ecological companion piece: what are the impacts of our recreational activities on the plant and animal communities we hope to conserve? In honor of opt outside day — or for folks who are opting to read about the outside world — here are my top four 2017 papers on recreational ecology. 

Impacts of rock climbing on plant communities.

 Research on the ecological impacts of rock climbing received some press this year from the Sierra Club’s magazine. In a short piece, Diana Crow outlined recent findings that indicate climbing routes support less plant cover and lower biodiversity than unclimbed cliffs. Among these studies is a PLoS ONE paper from Juan Lorite on the Mediterranean limestone cliffs. Dr. Lorite told me that he did not approach the study of cliff flora from the perspective of a rock climber — “I have tried [climbing] but I would rather prefer to keep my feet staying on the ground” — however, “two students (Fabio Serrano and Adrian Lorenzo co-authors of this work) contacted me to do their master's thesis and end-of-degree project respectively, on the impact of climbing rock over plants. Both were biologists and also climbers and were worried about the impact of this activity.” Lorite and his colleagues paired unclimbed cliff transects with climbed transects across three levels of climbing use and used photographs to compare the plant cover and biodiversity on these cliffs.

Laura Boggess and co-authors used a similar methodology in Big South Fork National River and Recreation Area, Tennessee to survey the cliff flora of sandstone cliffs. Here, they carried 1mx1m quadrats into the field and visually estimated percent cover as they rappelled down, collecting plants, lichens, and mosses from either side of the vertical transect. Boggess, a mountaineer, got started climbing as a master’s student when the grant for this research was funded. She stressed the importance of studying the impacts of climbing from inside the climbing community: “it’s nice to have participation in the activity when you study its impacts, it improves communication across groups.” While the Sierra Club article generalizes that “few ecologists have enough climbing experience to do the work”, Boggess points out that the field work is not technically rock climbing up, it’s rappelling down. Often the hardest part was actually bushwalking to the tops of the cliffs. In addition, the Boggess’ coauthor, Gary L Walker, and his lab at Appalachian State, have been surveying cliff flora and writing reports for many years using standardized methods; they don’t often publish peer-reviewed literature and they were not included in the Sierra Club article. 

The “cliff” notes comparison of Lorite and Boggess’ results: climbed routes supported significantly less plant cover and diversity in the Mediterranean, but there was no difference in climbed and unclimbed routes in Big South Fork. Looking deeper, Lorite found that the more heavily used and overcrowded climbing routes were the most impacted; the more specialized (and less crowded) routes experienced relatively little damage. Boggess points out that Big South Fork generally receives low levels of climbing traffic — it’s routes are remote and undeveloped and it is located between two nationally recognized climbing areas in the Obed River Gorge and Red River Gorge. But, rock climbing is gaining in popularity nearly everywhere, including Big South Fork, and Boggess told me that anecdotally there do seem to be more climbers in Big South Fork since she conducted her fieldwork. In fact, part of her analysis included a creating a spatial model of the cliffs across the park: “we added a simple layer of climbing attractiveness to further specify which cliffs climbers may prefer to develop.”

One of the critiques of rock climbing studies in general is an oft-repeated maxim that climbers self-select routes with lower diversity because it’s easier to climb on bare rock. If this is the case, then comparing climbed routes to unclimbed routes is a biased methodology: the unclimbed routes aren’t a control and monitoring ideally should be before-after control-impact. Here, Boggess might have just published the ‘before’: her work identifies cliffs that are likely to become climbing routes and her results are a prime candidate for re-surveying to assess the impacts of increased climbing pressure in the future. Additionally, Boggess is very clear that the face of the cliff is not her main concern: “it hurts my heart to see trampled moss mats at the top of a cliff.” Her research found interesting and sensitive vegetation along the cliff tops, and she urges climbers to used fixed anchors instead of “topping out” and climbing over the edge of cliffs. Lorite also has advice for climbers hoping to minimize their impacts. “Some common practices are very harmful and should be abandoned, for example the conditioning process for a new route establishment usually consist of removing all the plants and to brush the rock surface removing all the mosses and lichens attached to the rock. Surprisingly this activity is called in the jargon as ‘gardening’ causing a high impact on plant community.” 

Cross country skiing and meadow vegetation

What about our recreation during the plants’ dormant season? A research group from Germany has a paper in press in Basic and Applied Ecology that explores the ecological impacts of cross country skiing on meadow vegetation. Manuel Steinbauer and colleagues looked at cross country ski tracks in the Fichtelgebirge, in northeast Bavaria; since floodlights were installed in 1979 for night skiing, the heavy grooming machinery has covered the same 84 km of tracks for over 30 years. I was unable to arrange an interview with Dr. Steinbauer or his coauthors, but I talked to Chelsea Little, a PhD candidate at the University of Zurich in Switzerland and editor-at-large for FasterSkier.com about this paper. Chelsea and I both read this paper last month when it was first available online as an accepted manuscript; we were intrigued by the paper’s bold title “Positive sport-biosphere interactions? − Cross-country skiing delays spring phenology of meadow vegetation.” First, we recognized that the conditions at the study site were somewhat unique in the heterogeneous world of cross country ski tracks. Chelsea writes: 

I think one thing to think about is that this doesn't necessarily mean that there is overall more maintenance of these trails than the non-lighted trails - the lighting is somewhat independent of the degree of other management. Also, they aren't, like, football stadium lights. They are fairly weak in a lot of places. It does mean that light pollution is a relevant question though! And also, having skiers moving around when it is dark probably has very different effects on wildlife, for example, than places where skiers are only out during the day...

I guess that this brings up one question I had about the study. There is a huge gradient in terms of how intensively ski trails are managed. Some very minimally, and they are only skied when there's enough snow to cover everything. On the other hand, I worked at a place in Vermont where we often scraped and graded the trails during the summer, used crowbars to pry out rocks, and reseeded the trails with grass, all with the purpose of making it possible to ski even when there's just a little bit of snow. Given the current climate, more and more cross-country ski areas are also investing in snowmaking. This will result in bigger and bigger mismatches in growing season length between the ski trails and surrounding areas, and also even bigger differences in water and soil moisture conditions.

 Steinbauer and his colleagues collected an incredible array of data on the vegetation and the conditions in plots on and off the tracks (similar to the climbed/unclimbed transects): flowering phenology, above-ground biomass, species composition, snow cover, soil frost, soil moisture, soil density, daily radiation, and detailed interviews with the landowners! Ultimately, they found no significant difference in plant species richness or biomass production between the ski trails and the off-trail plots. However, flowering phenology was delayed by almost two days on the ski track. They conclude that on these trails — which are lit and groomed but receive no artificial snow — the impact of ski trails on the meadow vegetation is minimal, and may be seen as a “positive” because they add environmental heterogeneity. Both Chelsea and I were wary of this broad conclusion. From my background in plant phenology, I wanted to know more about this delayed flowering: what were the pollinators doing? Was there gene flow between the on- and off-trail plant populations? Chelsea took a hard look at environmental heterogeneity: 

It seemed rare to me that creating environmental heterogeneity where there was none before would be considered a positive outcome. I totally understand that heterogeneity can be great in promoting metacommunity stability, for example. In my mind, however, when trying to apply this in a conservation setting, it would be more about trying to stem the homogenization of habitats that comes with development, large-scale agriculture, or some managed forestry…But in this case of this paper, it seemed like they are talking about doing the opposite: taking an intact-ish piece of habitat (although it is a set of meadows which are mowed by the landowners, so not exactly pristine), and making it more heterogeneous.

 Ultimately, the ecological impacts of ski trails depend on the local management decisions and the vegetation is not the only aspect of the environment that may be affected. Last summer Chelsea wrote at piece for FasterSkier.com about the impacts of skiing on wildlife. She reflects: “It was interesting to see the reaction from skiers - this is a demographic that in general is fairly environmentally conscious (after all, they spend a lot of time outdoors), but I would say that overall they did not seem impressed that we should change our trail design/layout for the benefit of wildlife, as it is felt that cross-country skiing is a very low-impact activity compared to many others (i.e. snowmobiling, downhill skiing). But I hope that people will start being more thoughtful about how we fragment the forest even with these seemingly low-impact trails, and leave some big chunks of habitat undisturbed.” 

Wildland recreation disturbance at broader scales: hiking & wildlife

 Finally, the cover picture of the November issue of Frontiers in Ecology and the Environment features a line of photographers angling for a shot of a bison. Inside, Kevin Gutzwiller and coauthors explore the impacts of wildland recreation (like hiking and wildlife photography) at a broad scales — think entire parks instead of individual cliff faces — through GIS and statistical approaches. I talked to Gutzwiller and his coauthor Ashley D’Antonio about this paper and the field of recreation ecology in general.

Gutzwiller literally wrote the book (Wildlife and Recreationists) on recreation impacts on wildlife. When comparing impacts on plants and animals, he says it’s “fundamentally an issue of movement. Plants ten feet off of a trail may be safe from trampling. Wildlife can move but that doesn’t mean they are less susceptible. It’s harder to link the impacts to disturbance.” D’Antonio echoed: “wildlife impacts are hard to measure at the population level: if you flush a bird, how does that affect the bird populations? A lot of recreation ecology studies are very site specific…this is a smaller scale than that at which wildlife actually function and live in the ecosystem. This is a major constraint to studying wildlife impacts.” Their paper aims to help conservation managers scale up and look at recreation as another layer on the landscape. They both stressed that the field of recreation ecology wants to get people outside: they want their research to provide opportunities to enjoy the landscape, while minimizing impacts. Here, they hope their conceptual paper can get managers thinking about what they already do — using GPS techniques to see how visitors interact with resources — and adding two statistical approaches to quantify disturbances and model them across landscapes.

I asked Gutzwiller and D’Antonio about the intersection of their recreation ecology research and their personal outdoor recreation hobbies. Gutzwiller is an all-around outdoorsman who enjoys cross country skiing, snowshoeing, hiking, fly fishing, and hunting. “Getting out into remote wild areas is what I live for — I'd love to be there almost all of the time. You get insights out there you can’t get from looking at walls.” He says that knowing the literature, “knowing how subtle disturbances can affect animals influences how I recreate.” D’Antonio, an avid hiker — “it’s pretty much what I study too, mostly-foot-based recreation, boots on the ground type of impact” — worries that she’s becoming an annoying hiking companion between pointing out the social trails and stopping for photographs of signage instead of views. She says that though it can feel like work “because I can’t turn off seeing the impacts,” work and play can overlap a lot in recreation ecology. Getting outside is “an opportunity to clear your head, do the deep work, and think creatively.”

Throughout my interviews for this post scientists told me this repeatedly: getting outside improved their work. The #OutdoorsyScientist hashtag in September 2017 made it pretty clear that many scientists on twitter — from the recreation ecologists to the lab-bound biologists and indoor modelers — find restoration, renewed energy, and stress release in the great outdoors. Those scientists who have dug into the research on recreation impacts, or who are actively engaged in the studies themselves, seem universally conscientious of their footprints, ski trails, and climbing routes. I hope their work and their thoughtfulness ripple out across the outdoor communities as we opt outside today and in the future. 

Finally, I want to share Gutzwiller’s enthusiasm for working on this 2017 wildland recreation paper: “I had a blast working with Ashley [D’Antonio] and Chris [Monz]! They’re fabulous. I wish they worked down the hall from me!” This conversation made my heart grow three sizes a la the grinch. My holiday wish is that we all end up with coauthors who gush this way about us.

References:

Gutzwiller, Kevin J, Ashely L D’Antonio, and Christopher A Monz. 2017. Wildland recreation disturbance: broad-scale spatial analysis and management. Frontiers in Ecology and the Environment. 15(9): 517-524, doi: 10.1002/fee.1631

Boggess, Laura M, Gary L Walker, and Michael D Madritch. 2017. Cliff flora of the Big South Fork National River and Recreation Area. Natural Areas. 37(2):200-211.

Lorite, Juan, Fabio Serrano, Adrian Lorenzo, Eva M. Cañadas, Miguel Ballesteros, and Julio Peñas. 2017. Rock climbing alters plant species composition, cover, and richness in Mediterranean limestone cliffs. PLoS ONE. 12(8) https://doi.org/10.1371/ journal.pone.0182414

Steinbauer, M.J., Kreyling, J., Stöhr, C. and Audorff, V., 2017. Positive sport-biosphere interactions?− Cross-country skiing delays spring phenology of meadow vegetation. Basic and Applied Ecology.   

Biodiversity Patterns in Melanesian Coral Reef Fish: New Research with Old Naturalists

Old naturalists are my jam. I dedicated my PhD dissertation to a 19th century botanist who had spent her childhood following Thoreau around the Concord woods. I have a soft spot for research that draws on the work of older ecologists, for data that was handwritten before the advent of ballpoint pens, for 21st century papers based on museum natural history collections. This nostalgia is well-timed: museum collections are increasingly digitized and freely available online, and the Biodiversity Heritage Library is doing the same for scientific literature on biodiversity.

Just as my kind of fieldwork no longer requires taking the steamship to downeast Maine and a buckboard on wild roads between logging communities, my scholarship is not dependent on scouring the library stacks for a particular volume or traveling to the archives of a natural history collection to comb through specimens for just the right sample. In the 21st century it is significantly easier to be an armchair laptop historical ecologist. Easier, but not easy.

“Natural history and collections seem to be a bit of a hard sell when it comes to the ecological literature, which surprised me,” says Dr. Kathryn L. Amatangelo. She and Dr. Joshua Drew just published a PLOS ONE paper using coral reef fish data from museum collections records, peer reviewed literature including fish check lists, and biological inventories. The biodiversity pattern they were attempting to analyze and understand — that reef fish diversity in the Indo-West Pacific decreases along a longitudinal gradient from species-rich Papua New Guinea to species-poor American Samoa — was described in 1906.

Amatangelo laments, “It seems almost passé to look at old collections and think about how and why long-dead historians collected their data. When you try to combine that with statistics and scientific analyses people seem to get a little squirrely.”

Drew and Amatangelo’s paper “Community Assembly of Coral Reef Fishes Along the Melanesian Biodiversity Gradient” applies modern ecological theory and big data statistical tools to observations recorded by David Starr Jordan, a Victorian-era ichthyologist who was both the founding president of Stanford University and a suspect in the possible murder of Jane Stanford. If that legacy is not problematic enough, he was also into eugenics.

Thanks to the efforts of Biodiversity Heritage Library (BHL), we can read Jordan’s 1906 paper “On a Collection of Fishes from Fiji” where he notes the diminishing diversity of fish as you travel across Melanesia. Drew remarks, “historical ecologists are always looking for old species lists, and it was super cool to find that he worked in my study system in Fiji.” Drew describes a Jordan as “an ichthyological hero of mine, a complex and not unproblematic figure”: Jordan’s writing on ichthyological biogeography and community change, his system for organizing ichthyological collections and his service on the US Fish Commission, a precursor of NOAA, provide a foundation for the kind of work that Drew and Amatangelo so beautifully execute here.

In the pursuit of quantitatively describing this biodiversity gradient, Drew and Amatangelo compiled presence/absence records for 396 fish species in five taxa across 7 countries. As Drew describes it, this dataset was created from “a massive literature search from collections-based and peer-review based lists that were then double-checked with FishBase.” They looked for agreement across all three datasets (collections, literature, and FishBase), which gave them more confidence in the data since it was not susceptible to the biases present in only one dataset. Amatangelo is a community ecologist with a plant background, she partnered with Josh Drew through a twitter connection, bringing statistical savvy to these new-to-her taxa and ecosystems. I asked her what it was like to work with unfamiliar study species in this project. “One downside was that things that were intuitive to Josh, such as why some traits are important, was a bit of a mystery to me. That could also be considered a positive, though, because it meant that Josh had to be able to explain WHY they were important, which helped in writing the paper.”

The paper’s ultimate goal was to illuminate the processes behind the reef fish biodiversity pattern to inform conservation efforts. Drew acknowledges that their conclusions are not ground-shattering — the biodiversity gradient was described 110 years ago, and likely broadly known before then in local communities. “But it’s nice to put a p-value on it,” he says. “Natural history and traditional ecological knowledge are not always recognized because they don’t come with a p-value, so here we did that. We probably could have told you the same result before, but this adds weight to the management recommendations.” Those management recommendations include collaborations across Melanesia to more efficiently share resources and partition the region into functional biodiversity groups.

Through the power of twitter, digitization, and online collections two modern ecologists were able to build on a paper from 1906 and study Melanesian coral reef fish diversity from their laptop screens in the United States. So much of this data would be instantly recognizable to Jordan, but so little of the actual process of collaborating, compiling and analyzing data, and writing a paper has remained constant since 1906.

Drew reflects on this revolution in his recent correspondence to Nature Ecology and Evolution: “Digitization of museum collections holds the potential to enhance researcher diversity.” He and coauthors write that “the advent of digitization (open access to images and specimen data) now makes a wealth of biodiversity information broadly available…Digitization allows access to museum holdings to those for whom collections have typically been out of reach.” The concentration of collections in the Global North is a reflection of our discipline’s role in the history of exploration and colonialism. Untangling this broader context of past research is perhaps the most impressive, thoughtful work that a historical ecologist could pursue.

In two papers this fall Drew has managed to both uphold the ichthyological legacy of Jordan, and articulately argue that the museum collections Jordan once organized in his spare time from being abhorrently racist, could be, in digital form, a force for increasing diversity in science. 

References:

Drew, Joshua A., and Kathryn L. Amatangelo. "Community assembly of coral reef fishes along the Melanesian biodiversity gradient." PloS one 12, no. 10 (2017): e0186123.

Drew, Joshua A., Corrie S. Moreau, and Melanie L. J. Stiassny. "Digitization of museum collections holds the potential to enhance researcher diversity." Nature Ecology & Evolution (2017):10.1038/s41559-017-0401-6

A Little Light Reading

As the leaves fall this October and the canopies bare their skeletal limbs, there’s suddenly more light filtering across the riverside trails in Maine and I’m wearing sunglasses on runs where I used to be totally engulfed in the shade. It’s hot toddy season, pumpkin spice season, submit-your-GRFP season. When the weather finally chills we’ll get into ugly sweater season, rush-to-take-family-photos-for-a-holiday-cards season, and grading-endless-finals season. Culturally, we humans divide the year into more than just autumn-winter-spring-fall. A recent PLOS ONE paper makes the case that understory plants probably do this too.

Janice Hudson and her coauthors explored the seasonal dynamics of sunlight in a temperate deciduous forest and the ecology of the common shade-tolerant shrub, spicebush. They were inspired, in part, by a relatively obscure 1977 Ecological Monographs paper* with the unassuming title “The Distribution of Solar Radiation within a Deciduous Forest,” in which the authors, Boyd A. Hutchison and Detlef R. Matt, outline the concept of phenoseasons.  

Get ready to update your calendars — the seven phenoseasons for life under a forest canopy are: winter leafless, spring leafless, spring leafing, summer leafing, summer fully-leafed, autumnal fully-leafed, autumnal partially-leafed. I only wish that Hutchison and Matt had dined with Tolkien. Imagine the invitation: “Let’s meet for second breakfast to celebrate the end of spring leafless.” [Insert ent joke here.] Hudson was interested in how changes in light availability affected understory plants like spicebush. As Hudson explains “broadly, this study was an attempt to better understand the pre-existing conditions of the forest…[are] light conditions...a controlling factor in the distribution and presence of plant species?” The phenoseason construct hasn’t taken off in ecology and the annual cycle of subcanopy light exposure is not well understood. Hudson and her coauthors stumbled on Hutchinson and Matt while working on a literature review, but the idea of phenoseasons — now update-able with a high-tech piece of equipment called line quantum sensors — seemed ecologically intriguing. Hudson’s background is in eco-hydrology and the link between seasonal changes in light and phenology had immediate implications for her. She wanted to know “how understory plants acclimate…[and] plant contributions to nutrient and water cycling during individual phenoseasons, and yet, the literature on the subject of phenoseasons is scant.”

Hudson’s team combined a year of intense field measurements with experimentally manipulated light conditions in growth chambers to explore light intensity through the phenoseasons. At Fair Hill Natural Resource Management Area in Maryland, Hudson and her team carried a light sensor through the forest of American beech and yellow poplar trees to measure light conditions above, within, and under the spicebush canopy, compiling over 4,500 measurements in a year across 26 sites (25 in the forest, one open area just outside the forest for comparison). 

When Hudson talks about light, she talks about photosynthetically active radiation (PAR) and, for this study, subcanopy photosynthetic photon flux density (PPFD), which is a measure of PAR. Unsurprisingly, the highest PPFD values under the beech and poplar canopy occur in spring leafing — the days are growing longer, the northern hemisphere is tilted toward the Sun, the trees are still mostly bare. During summer leafing, the subcanopy PPFD values drop, and continue to decrease into summer and autumnal fully-leafed, before a slight bump for the autumnal partially-leafed phenoseason. In a nod to Hutchison and Matt, Hudson recreates their 1977 figure mapping the contours of PPFD through the year at different canopy levels with her own data. It’s the scientific equivalent of siblings re-staging family photos as adults.

But what does it mean to be a spicebush living in the light environment depicted in these figures? In general, Hudson found that there’s almost 10 times more subcanopy light available during the leafless seasons than the leafing and leafed seasons. During the leafing and leafed seasons there are high-energy sun flecks and hot spots — think of a sun-dappled forest floor — which contribute to the variability of light measurements throughout the phenoseasons. But, mostly the understory species must make proverbial hay (read: Germinate! Flower! Leaf out! Photosynthesize like crazy!) while the sun shines in the short leafing seasons. Even in the leafless seasons, the open site received much more PPFD than the subcanopy: the woody surfaces of the trees were intercepting plenty of winter and early spring light.

The spicebush plants in the field and in the growth chambers grew best under the highest PPFD conditions found in the Maryland woods. This is the light niche. In the growth chambers, plants that received higher PPFD conditions were actually less healthy, produced fewer leaves and less biomass. Hudson wrote a beautiful explanation of this when we emailed and I have to let this paragraph speak for itself:

We know that all organisms have an ecological sweet spot, but very rarely are all conditions ideal. Canopy species are "less limited" in the sense that they may experience some shading by neighbors but are primarily subject to changes in light due to latitude, season, and sky conditions. This "light intensity niche" is especially important for shade-adapted and shade-loving plant species when you consider spectral filtration (one way that plants "communicate" with each other and adapt growth direction and strategy) and temporal sequences of incident radiation at both long and short time scales (the timing and amount of light availability is crucial for physiological and biochemical processes for these species). It puts a sort of "ceiling" on the amount of light that is useful for the understory plant, whereas for canopy species there really isn't such a thing as too much light – their growth is primarily limited by the lower boundaries of light availability.

 Finally, this study’s implications for climate change research are quite interesting. In the decades while the ‘phenoseasons’ concept was languishing, research in phenology has taken off: the timing of seasonal events like leaf out and flowering are almost universally creeping earlier in response to warming temperatures. This advancing spring phenology has been definitively tracked in temperate deciduous forests like Hudson’s study site. As the climate changes, leafing phenoseasons may bite into the leafless phenoseasons. The density of the canopy may change as the species composition, size, and height of canopy trees changes. As Hudson wrote, these are the pre-existing conditions in the forest from the perspective of an understory species. We often think about species migrations and no-analog communities when we talk about the ecological effects of climate change: now I think I’ll imagine the reshuffling of the pre-existing conditions, and the interactions between biotic and abiotic factors that create the “ecological sweet spots” that we study. And now, as we enter the autumn leafless, I’ll soak up the sun on my unseasonably warm October runs. 

*This paper’s obscurity is not helped by the fact that the google scholar pdf link takes you to a 627-page annual report hot off the mimeograph with old-timey typer-writer kerning; Hutchison and Matt’s paper is buried in this report (just scroll to page 327), though much easier to find via JSTOR.

Flying Foxes and Lilford’s Wall Lizards: At Your (Seed Dispersal) Service

I'm Dr. Caitlin McDonough MacKenzie, a new PLOS Ecology Community Editor. Last summer I was a PLOS Ecology Reporting Fellow at the 2016 Ecological Society of America meeting and I'm excited to join the team year-round! My first post as a Community Editor has me reflecting on my field site in the "off season", #poopscience, and the under-appreciated role of seed dispersers in ecology and conservation. Two papers dig into the seed dispersal services provided by charismatic megafauna in island ecosystems, and in both cases it's not much of an exaggeration to say: 'Save the Seed Disperser, Save the World.' 

I study plant phenology, specifically leaf out and flowering, on an island in Maine. I leave my field site just as flowers are senescing and unripe fruits are developing, and return again in early spring to catch the last patches of snow before the first green shoots emerge. I hardly ever think about what my plants are doing from July through April, but of course the ecological processes in these months — fruiting, seed dispersal, germination — underlie a fundamental assumption of my fieldwork: that there will be new plants each year when I return. I depart Maine and the seeds are just developing in green fruits, I arrive and new green stems are popping out of the soil, but in between seed dispersal was quietly a crucial, and perhaps overlooked, part of this circle of life. 

Two recentpapers in PLOS One highlight the seed dispersal services of charismatic megafauna in different study systems with implications for island conservation and habitat restoration. Both studies focused on the relationship between an animal seed disperser and a plant that prefers to grow in open, sunny environments. In Sa Dragonera Natural Park, on an islet in the Mediterranean off the coast of Mallorca, Dr. Constanza Neghme and her coauthors studied Ephedra fragilis, an evergreen shrub that produces pseudo-flowers and pseudo cones. E. fragilis is an early successional shrub, colonizing new areas and establishing in open ground without a “nurse” (for example, another plant) to provide shade and minimize water loss. So, E. fragilis seeds need to get to these open areas, away from the shade of their parents. In fact, seeds that were not dispersed, and landed below the parent plant, did not survive in Neghme’s study.

Dr. Ryszard Oleksy and collaborators worked in three forests in varying states of fragmentation and degradation across Madagascar, with a focus on fig trees: Ficus polita, F. grevei and F. lutea. These are all pioneer species, able to survive in degraded areas, and as their root systems penetrate hard substrates, they can improve aeration and drainage of the soil, facilitating the establishment of other plants. Fruiting fig trees depend on frugivores (fruit-eating animals) for seed dispersal, but rapid deforestation in Madagascar has decimated native wildlife populations, dramatically reducing animal-mediated seed dispersal. Dr. Neghme’s E. fragilis and Dr. Oleksy Ficus have particularly charismatic seed dispersers: wall lizards and flying foxes. The Lilford’s wall lizards (Podarcis lilfordi) are “superabundant” on Dragonera islet; they are endemic to the Balearic islands, but now extinct on nearby Mallorca and Menorca. Neghme reports that they are the only known seed dispersers of E. fragilis on the islet. In Oleksy’s research, the Madagascan flying fox (Pteropus rufus) is studied as a potential long-distance fig seed disperser. Madagascan flying foxes are the largest bat species on Madagascar. These frugivores crush fruit in their mouths to devour the fruit juice and soft parts (often including seeds), then spit out the fibrous fruit coating, not unlike my two-year-old eating blackberries. I’m sure she would love to eat figs with flying foxes if given the chance.

Both of these studies depend heavily on #poopscience. The #poopscience hashtag is popular among a certain segment of ecologists on twitter, and though the authors were unfamiliar with this term when I contacted them, they were universally enthusiastic to talk about their experiences in #poopscience. Neghme told me: “ My first time with poop science was when I was doing my bachelor thesis with lizard in high mountain ecosystems, I was helping a post doc and he encourage me to do questions by my own, then I saw the lizard poops carrying seed, and after reading an article from lizards as pollinators and seed dispersers in island ecosystems I started the journey in to poop.” Dr. Gareth Jones, the corresponding author on Oleksy’s paper, said that he’s “been into #poopscience for ages, initially using microscopic analyses to analyse prey of insectivorous bats, more recently using DNA barcoding to identify insects in poop to species level.”

To know what a seed disperser is eating, and to test the germination success of what Oleksy euphemistically calls “bat-processed seeds”, scientists collect and pick through lizard and bat faeces. Both studies planted “undispersed” (read: collected from parent plant) and dispersed (read: found in poop) seeds and tracked seedling emergence and seedling survival in a range of microhabitats. For both E. fragilis and the Ficus species, the “processed” seeds won. Lizard-dispersed and bat-dispersed seeds were much more likely to germinate, emerge, and survive as seedlings than the undispersed (non-faecal) seeds. Logically, the next question is where are the lizards and bats taking these seeds? We know you proverbially should not poop where you eat, but how far apart are the eating and pooping places of these lizards and bats? Neghme estimated how much time the lizards spent in different microhabitats on the islet, assuming that the proportion of time spent in each place would determine the probability of seed dispersal to those microhabitats. She and her colleagues walked transects and recorded if the lizards they spotted were in open areas, under Ephedra, or under other plants. The lizards spent most of their time in open habitats, and, unsurprisingly, this is where Neghme found the most lizard poop.

In Madagascar, 11 bats were outfitted with GPS devices, which tracked their movements overnight. These GPS tracks were combined with information about the bats’ gut retention time from a captive bat experiment. Basically, captured bats were fed a known quantity of fig seeds on banana slices and then researchers recorded the length of time between feeding and pooping, while counting the fig seeds present in each pooping event. (Ecology research can be especially glamorous.) Oleksy’s team then modeled the “seed shadow” of the bats’ flights — which is a nice way of saying they created a map showing where the bats were most likely to have pooped on the landscape. These “probable poop maps” confirm that Madagascan flying foxes are important long distance seed dispersers, and they frequently disperse seeds in degraded habitats as they fly between forest fragments. I love that both Neghme and Oleksy created sophisticated stochastic models of seed dispersal, and then ground-truthed them by walking through their field sites* and saying, “Yes. This is where the poop is.”

The ecosystem services provided by the E. fragilis shrubs on Dragonera and the Ficus fig trees on Madagascar are so important to habitat restoration and conservation. These early-successional species colonize open and degraded areas, and facilitate the growth and success of other, less-hardy plant species. But without their seed dispersers, they cannot access these open habitats and their seeds languish in the shade of parent plants. The Madagascan flying fox is listed as ‘Vulnerable’ in the IUCN Red List; Lilford’s wall lizard is ‘Endangered’. These seed-dispersing animals can act as super-conservationists: naturally maintaining and regenerating habitat through their poop. Neghme explained to me that the lizards are threatened by introduced predators and habitat loss, both “usual[ly] happen in island ecosystems to build tourist resorts.” In Madagascar flying foxes are legally hunted, and Oleksy notes that the “best protection would be to ensure that no one is allowed to hunt between August and December. Also no hunting at the roosting trees…Education would be a key to ensure local communit[ies] understand the role and importan[ce] of the bats.” The parallels between the lizards and the bats, the open-grown shrubs on Dragonera and pioneering fig trees in degraded Madagascan forests, run through these papers from study design to conservation implications. These strong relationships between plants and their animal seed dispersers highlight the importance of conserving species interactions for biodiversity maintenance and ecosystem functioning. Or as twitter might say: #poopscience can inform conservation! 

References:

Neghme C, Santamar ́ıa L, Calviño-Cancela M (2017) Strong dependence of a pioneer shrub on seed dispersal services provided by an endemic endangered lizard in a Mediterranean island ecosystem. PLoS ONE 12(8): e0183072. https:// doi.org/10.1371/journal.pone.0183072

Oleksy R, Giuggioli L, McKetterick TJ, Racey PA, Jones G (2017) Flying foxes create extensive seed shadows and enhance germination success of pioneer plant species in deforested Madagascan landscapes. PLoS ONE 12(9): e0184023. https://doi.org/10.1371/journal. pone.0184023 

*Note that ground truthing was limited by violence in Oleksy’s study. He explains: “at the time of the study south of Madagascar was at war with local rebels. I was based at Berenty Reserve which was rather safe, however due to the war we were not allowed to leave the reserve. We would still capture bats beyond its boundaries accompanied by a guard and ground truth in nearby areas. However, the more distant places to which bats flew were too dangerous to visit…Fortunately, we got enough data to analyse the GPS.”