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!

Writing and Publishing: Mentos, Manatees, and Sinkholes

I’ve been reflecting on my own writing. Today, I picked up three bound booklets from my local copy shop. These are the ‘after’ picture of my PhD dissertation — the pdfs of the peer-reviewed papers that grew out of my ‘before’ dissertation chapters. The volume is sleeker than my official hardcover ProQuest dissertation copy, the figures are more refined, and the writing inside is much better.

I was so excited to share this news that I lost control of grammar and hit ‘send tweet’ with this: “Just picked up bound copies of my PhD’s final outputs for my and my mentors — the four peer-reviewed papers that came out of my dissertation chapters!” which I quickly followed with “**me and my mentors? Or myself and my mentors? I guess my typo split the difference?” My former labmate, Dr. Amanda Gallinat, shot back the brilliant response: “My mentos and their manatee*”

My dissertation was fine — I graduated! — but I am so proud of these papers and I appreciate how much work my mentors (my mentos) put into the polishing the writer (me, their manatee) in the years before and after I graduated. I am thinking in this framing — about my luck as a well-polished manatee — because I just read Stephen Heard’s blog post ‘Edit to polish the writing, or edit to polish the writer?’ Heard talks about the evolution of his feedback to early career writers, from full on track-changes to more restrained, but open-ended comments. He writes, “I now try to explain what writing problem I see and suggest fixes that the ECR might choose to pursue – that is, my intent is to edit to polish the writer, rather than to polish the writing.”

Last year I had the honor of serving as an advisor for a senior capstone project, supervising a student while she wrote the equivalent of a senior thesis. Her final paper was outstanding. Over the summer, we began revising that paper for submission to a conservation journal. Looking back, I recognize the tension I felt between polishing my student and polishing our paper. At the time, I didn’t have the framework to explain this feeling — Heard captures it with beautiful simplicity — but I remember the effort of reigning in my copyediting instincts. This student and I spent a few days together in July when I visited the research station where she was working on a field crew. I was fresh off of sending in proofs for my last dissertation chapter manuscript, and it seemed very important to step out of the mindset where I was the manatee, and shift into the role of being her mento on this paper. The adjustment was both imperceptible and enormous.* 

My sleek, beautifully bound booklet of dissertation papers is less homogenous than my original dissertation. Without an introduction and conclusion, it’s still fairly cohesive — the first three papers are centered on Acadia National Park and clearly riff on each other’s datasets. But, there is a visible shift from paper to paper. The American Journal of Botany has columns, Rhodora does not; Ecosphere has a smaller font size than Northeastern Naturalist. When I place my booklet next to my dissertation, the inconsistencies in formatting are striking. Intriguingly, PLoS ONE just published ‘Scientific sinkhole: The pernicious price of formatting,’ a paper that quantifies the cost associated with formatting research papers for publication in peer-reviewed journals. Dr. Allana LeBlanc and her coauthors surveyed research scientists on the time they invested in their manuscripts outside of analysis, writing, and editing — in other words, how long did they spend formatting the body of the manuscript, figures, tables, supplementary files, and references? LeBlanc concludes, “our results suggest that each manuscript costs 14 hours, or US$477 to format for publication in a peer reviewed journal. This represented a loss of 52 hours or a cost of US$1908 per person-year.”

While I agree that re-formatting a manuscript for a new journal is a pain (the researchers in LeBlanc’s survey reported that their manuscripts required a median of two attempts per accepted paper), I’m not sure that all 52 hours are a ‘sinkhole.’ The first 14 hours — the original formatting — won’t completely disappear even if journals adopt more open formatting standards. Maybe there will be less stress associated with meeting the approved journal abbreviations in your literature cited section or table dimensions, but you will still need to generate a literature cited section and you will still need to create the table. I’m not arguing that we keep arcane formatting rules — how is there not yet a common app of manuscript submissions?! — just that we acknowledge the non-writing hours that will always be required in manuscript preparation. Especially since, as we become the mentos, it’s likely our manatees will be the ones engaged in the frustrating work of formatting the manuscripts we helped them to polish. 

And finally, I wanted to mention some lovely science writing advice for all the mentos and their manatees. In the Nature Career Column last week Van Savage and Pamela Yeh compiled the generous advice that they have received from a Pulitzer-prize winning writer. ‘Novelist Cormac McCarthy’s tips on how to write a great science paper,’ is a powerhouse advice paper. I especially love: “Dashes should emphasize the clauses you consider most important — without using bold or italics — and not only for defining terms. (Parentheses can present clauses more quietly and gently than commas.) Don’t lean on semicolons as a crutch to join loosely linked ideas. This only encourages bad writing.” I’m a big fan of dashes — I love them more than I love absurd manatee riffs — and I'm working on my semicolon crutches. 

McCarthy’s last tip is to “try to write the best version of your paper: the one that you like.” I look at my booklet of PhD papers and I like these papers. The heart-swelling pride that I feel holding them all at once is part spite — I published new research about the impacts of climate change in a national park during the Trump Administration** — but also a recognition of personal and professional growth. These papers are the best version of my dissertation chapters. My mentos and their manatee did that — we took a decent dissertation and produced four really great peer-reviewed papers. It feels good. 

*This code-switching between mentos and manatees could be, I think, one of Meghan Duffy's less obvious signs of reaching a new career stage. My whole post-doc has been this mash up of mentoring and being mentored that seems to shift from day to day. Britney Spears can relate.

**I explored the angst and intensity around publishing climate change research in 2018 last year. Writing about Castillo Vardaro's research on pikas in the Rocky Mountains, I said "we both finished our dissertation field work in National Parks before the 2016 election. Her work could inform whether pikas are listed as endangered or threatened under the Endangered Species Act; my research supported a climate change vulnerability assessment; and after our halcyon days as PhD students under the Obama administration, we are now watching an administration and Secretary of the Interior generally disregard the National Park Service expertise on these issues. I told Castillo Vardaro that I feel an extra sense of urgency in publishing my Acadia papers now — especially in open access venues. I wondered if this was a personal quirk or if she felt a similar sense of responsibility for her field sites and study species." 

References:

Novelist Cormac McCarthy’s tips on how to write a great science paper. Nature Career Column. https://www.nature.com/articles/d41586-019-02918-5

LeBlanc AG, Barnes JD, Saunders TJ, Tremblay MS, Chaput J-P (2019) Scientific sinkhole: The pernicious price of formatting. PLoS ONE 14(9): e0223116. https://doi.org/10.1371/journal.pone.0223116 

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 

Looking for Human-Nature Connections in Seasonal Wikipedia Searches

Recently, I was wrapping up some revisions on a phenology paper and to comply with the journal’s style for taxonomy, I needed to know the authority on a species of white violets that a Maine hunting guide had noted in his diaries in the mid-twentieth century. Obviously, I turned to Wikipedia.

Ecologists who study phenology (or anything!) use Wikipedia all the time, but Dr. John C. Mittermeier and his coauthors take this practice to a whole new level in their paper A season for all things: Phenological imprints in Wikipedia usage and their relevance to conservation. This study, published in PLoS Biology earlier this month, uses Wikipedia page views to trace when humans show seasonal interest in the natural world. For over 30,000 species in 245 languages —which amassed 2.33 billion pageviews between July 2015 and June 2018 — they found some strong seasonal signals linking how and when people interact with plants and animals online.

“The idea for this study happened somewhat by chance to be honest,” Dr. Mittermeier confides. “I was collecting Wikipedia pageview data on different animals as part of another study (hopefully this should be published soon!) and on a whim I decided to plot a time-series of daily views to see what it looked like.” As an ornithologist, he was drawn to migratory bird data and his whimsical time-series plot for migratory bird page views peaked near its ecological migration season. This was the prototype for a figure in the PLoS Biology paper. Mittermeier says, “this [plot] made me curious as what other plants and animals might show seasonality in their views and how widespread these patterns might be in general.”

While searching for migratory birds on Wikipedia seems categorically different from actual birding, Mittermeier and his colleagues found strong correlations between these two activities. They compared trends in Wikipedia page views to eBird records. In this analysis, eBird frequency records are like “outdoor pageviews” of bird species. “It was easy to match the eBird taxonomy to the taxonomy used by Wikipedia,” Mittermeier says, “and the way in which seasonal abundance information was structured in eBird is very accessible.”

Birders, like Wikipedia users, are surprisingly great at generating big data. Just under half of the bird species in the dataset had page view patterns correlated with seasonal eBird records. But, for species that occurred in more than one of the four language/countries (Italy, Germany, Sweden, and the U.S.), just over a third showed a significant positive relationship between eBird frequency and pageviews across multiple languages. All of the countries in this analysis are in the northern hemisphere and experiencing basically the same seasons, so I asked Mittermeier if this result indicated that some birds are more "seasonally famous" in one location? He agreed that “some species do seem to be more “seasonally famous” than others, meaning that certain species may be viewed more as seasonal indicators. This could be a result of the behavior of the species (i.e. something about their seasonality is particularly visible and obvious), some sort of cultural context (maybe the species featured in a well known book or fairy tale and had a seasonal association there, for example), or some sort of combination of both of these. Comparing how seasonal indicator species are similar or different across languages would be a great way to gain insight into what leads to a species acquiring this significance. I think this is a fascinating question and one that would be very interesting to explore further.” 

But, the paper is not limited to birds, and human interest in animal and plant Wikipedia pages is not always aligned with ecological events. Figure 2 shows a spike in shark species page views that aligns with Shark Week. There are cultural drivers to the phenology of when humans search out certain species on Wikipedia. Mittermeier shares that, “The Wild Turkey was actually the first page that I looked at in relation to cultural events. Turkeys have such a powerful association with the Thanksgiving holiday in the United States I was curious as to whether this would impact people’s online searches (it does as we show in the figure!)” When the turkey hunch worked out, Mittermeier started brainstorming other cultural or marketing events associated with plants or animals that could impact online interest. “This was right around the time that Shark Week was going on over the summer and that’s why I decided to check if that had an impact on pageviews for Great Whites.”  

While the eBird community is full of self-proclaimed bird nerds, and eBird datahas been used inpeer-reviewed papers for over a decade, the programming around Shark Week has a decidedly different relationship to science and natural history. Dr. David Shiffman, a Liber Ero Postdoctoral Fellow in Conservation Biology at Simon Fraser University, studying how information related to sharks is spread on the internet, notes, “Shark Week has a well documented problematic relationship with the truth, spreading nonsense to its massive audience that I and other scientists have to spend years correcting.” I asked him what he thought about the Wikipedia-Shark Week connection that Mittermeier and coauthors uncovered. He says, “the temporary spike in public interest in sharks that Shark Week causes is something that the marine biology community takes advantage of to spread actual facts. This paper provides further evidence that scientists wishing to engage in public outreach about their area of expertise need to know their audience, and know that there are times of year when people are more likely to be receptive to learning about that topic!” Indeed, these seasonal patterns in interest — whether for migratory birds, Thanksgiving turkeys, or sharks — can be leveraged by conservation practitioners to affect policy and outreach.

Research into the public attitudes about species, including how they rise and fall seasonally, is important. Mittermeier and his coauthors write: “Seasonal changes in human interest in plants and animals can have an important role in conservation in at least three ways: (a) by identifying species for which phenology forms a component of their “value,” (b) by helping to reveal differences or similarities in how species are valued across cultural groups, and (c) by providing temporal awareness to help maximize the effectiveness of conservation marketing campaigns.” I’ve experienced this myself in a small way: when I publish papers on spring wildflowers in the dead of winter, the press releases don’t get much traction. 

And finally, I had to address the paradox of scholarly work based on Wikipedia. I’ve TA-ed intro Biology labs and scrawled “not peer-reviewed” next to many Wikipedia-base citations in lab reports. Mittermeier laughed with me, “My mother used to teach junior high school and was always telling her students not to cite Wikipedia and now here I am using it as the source for my research.” 

Reference:

Mittermeier JC, Roll U, Matthews TJ, Grenyer R (2019) A season for all things: Phenological imprints in Wikipedia usage and their relevance to conservation. PLoS Biol 17(3): e3000146. https://doi.org/10.1371/journal.pbio.3000146 

Bumble and Bumble: what’s black and yellow and maybe more than one species?

During the dark afternoons of December in New England, I like to scroll through my old field photos and think of all the green, growing things I’ve measured in beautiful places during those long-ago long-lit seasons. Yesterday I flipped through a couple field photos from a friend — “Photos of younger Jon! :)” he wrote in the email — and the same sunny feelings flooded in.

As a master’s student*, Dr. Jon Koch and his insect net chased bumble bees all over the western United States. He was studying bumble bee decline, but hit weird hurdle: a messy species boundary between two bumble bees. Taxonomists and field guides were torn on whether Bombus fervidus was or was not Bombus californicus. These two “species” in the Bombus fervidus species complex were nearly morphologically identical, except for their color patterns: B. fervidus is noted as usually mostly yellow with a little black, while B. californicus sports mostly black with some yellow in variable detail. They were maybe different species, maybe hybridizing, or maybe the same thing with different color morphs. As Jon explained to me, “If we don’t know what the species are, how will we manage them? Bumble bees are differentially sensitive to land use change, disease, etc. The bumble bees in the Bombus fervidus species complex are found to be impacted by one disease, Nosema bombi, but perhaps differently. Therefore, it is important to recognize what the species boundaries are because estimates of infection prevalence might be not be done correctly due to the inability to tell the species apart.” 

Jon wanted to bring some clarity to the species complex by providing some new molecular evidence with broader taxa sampling. His new PLoS ONE paper, “Phylogeny and population genetic analyses reveals cryptic speciation in the Bombus fervidus species complex (Hymenoptera: Apidae)” delivers on the broader taxa sampling — 320 specimens from 53 sites — but the clarity is a bit of a cliff hanger. During the fieldwork, Jon and his coauthors keyed out identifications for their bees based on the setal color, and also took a tarsal clipping from the mid-leg for DNA extraction and microsatellite genotyping. When they compared field identification to the genotypes, they had an ID rate of just under 94%. Jon and I agree that that’s a pretty good record for fieldwork with cryptic species** but he adds, “it’s also cool to think that 6.2% of the time we were wrong! These bees are great at fooling us.” 

The bees that were fooling Jon were B. fervidus dressed as B californicus and vice versa. In Pinnacles and Yosemite National Parks there were ten mostly black bees (the typical B. californicus look) that turned out to belong to the genetic cluster that usually wears mostly yellow. The rest of the bees with black setal coloration belonged to another clade based on genotype, though this clade also included some bees in yellow. I asked Jon, “What is going on with the bee costume parties in Pinnacles and Yosemite?” His wild speculation is that little black dress is the dominant phenotype for bees in these parks, and the typically-yellow-genotype wears black here because everyone else is doing it: “bumble bees are notorious for converging on a local phenotype, which can even make it very hard to tell distantly related species apart.” However, in the sites where both genetic clusters of the B. fervidus species complex overlap, they usually do not look alike, so they aren’t mimicking each other. 

Ultimately, Jon’s team determined that the species complex comprised two lineages, but that both lineages exhibit the yellow and black phenotypes depending on geography. So while the B. fervidus species complex is not a single species, B. fervidus and B. californicus are not NOT conspecifics. Jon explains, “those names [B. fervidus and B. californicus] might not even be valid! The holotype of B. californicus happens to be where the genotype assigned to the “B. fervidus” was collected in the Sierra Nevada.” In short, the original bee that taxonomists knew as B. californicus may actually be genetically on the B. fervidus side of the lineage, and eventually one or both names might need to be thrown out.

This “it’s complicated” conclusion might be depressing news for someone who dedicated so much time and energy towards disentangling the species complex, but Jon closes his email to me with a happy emoji “nature has so many surprises, and science is an ongoing process :)” In the meantime, this paper points out that even if we don’t have the right names in place, we know enough to recommend that managers use Jon’s non-lethal method of clipping a bit of mid-leg for genotyping, and monitor the two clades of the B. fervidus complex separately. This is a great reminder for all of us in conservation research: we need to keep the ongoing process in perspective, while also delivering our findings, however not-quite-as-clear-as-we-hoped or maybe-unnamed as they may be, to our partners in management and policy. 

References:Koch JB, Rodriguez J, Pitts JP, Strange JP (2018) Phylogeny and population genetic analyses reveals cryptic speciation in the Bombus fervidus species complex (Hymenoptera: Apidae). PLoS ONE 13(11): e0207080. 

*Now, old Jon and old Caitlin are David H. Smith postdoctoral fellows together :)

**see McDonough MacKenzie et al. 2017 — When I was a master’s student working with volunteer-collected data I would have killed for a 93.8% identification rate. One my species, Labrador tea, was correctly identified 27.3% of the time. This is not a cryptic species; it doesn't sometimes dress up as Diapensia. 

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

Family and the Field

 Over the weekend I submitted a grant proposal, wrote a quippy tweet, and read a paper. The paper was Dr. Christopher Lynn’s ‘Family and the field: Expectations of a field- based research career affect researcher family planning decisions’, published last month in PLoS ONE. The tweet was:

At bedtime I told my three-year-old I had to stay up to submit a grant proposal.

Her: Just do it in the morning.

Me: I can’t, it’s due at midnight.

Her: Oh. I’m gonna do mine in the morning.

I bet she gets funded over me.

The grant was a proposal to do more field work away from my family. 

Though Dr. Lynn and his coauthors were focused on anthropology fieldwork, I found myself nodding along emphatically at each response to their survey of anthropologists. Ecology, like anthropology, has a long tradition of field-based careers, and high proportions of women in undergraduate and graduate programs which are not reflected in the gender breakdown of later career stages (though see this Dynamic Ecology post on recent tenure track hires).

Even as I’ve openly tweeted and blogged about it — you know my older kid is funny, you know I have a new baby — I’ve been reluctant to share much of my deeper experience as a parent in ecology. The gritty details are full of the tensions that Lynn captures in his paper. I’m nervous about how parenthood will impact my quest for a tenure track job, but I want to normalize academic parenthood for the students behind me. I want credit for the hard work that I’ve put into carving out this balance, but I know my experience is grounded in the intersections of incredible privilege.

At breakfast on Friday, while I enjoyed a latte served in a beer stein and my baby napped in the stroller and my partner covered our toddler’s preschool drop off, I told a friend that I didn’t know how to write this post. “So you want to have a baby in grad school? Just get an NSF grant that doesn’t exist anymore, then have a healthy infant who sleeps through the night, and have your partner use their paid parental leave to uproot their life and come into the field with you.” It’s disingenuous to package my experience as pithy advice. But Lynn’s paper provides a framework for talking about parenthood and fieldwork in an honest and meaningful way. 

The prominence of fieldwork in careers like anthropology and ecology reinforces stereotypes of lone practitioners who can afford to drop everything at home to spend weeks at a remote site totally immersed in gathering data. Lynn and his coauthors explain that this expectation “systematically overlooks the significant social and financial responsibilities experienced by many professionals and trainees, including dependent family members (children, elderly parents, etc.), and household expenses (rent, car payments, student loan bills, tuition, credit card bills), and may act to systematically privilege those without these pressures.”

Lynn surveyed nearly one thousand anthropologists to explore the relationships between fieldwork and family. My own experiences as an ecologist and mom mirrored so much of the results reported in this paper. Lynn’s work clearly identifies the privileges that enable parents like me to balance fieldwork and family — here, I reflect on how the anecdotes of my life align with the survey of anthropologists. The responses to Lynn’s survey were nearly evenly split between professionals and students; most identified as women (80%), and white (82%). Aside from my field, my background fits the profile of the typical anthropologist who filled out Lynn’s online survey. I’m a white woman, I’m married (like 72.5% of professional respondents) with 1+ children (67%), I was raised in and I live in North America (82.6%; 80.9%). I’m from an educationally privileged, high-status family; in other words, my parents both went to graduate school and I married a lawyer. 

“Regardless of gender or career stage, the majority of those with children (56%) indicated that parenthood did not impact their decision to pursue a career in anthropology.”

I think I fall into the 44%; I realized early on in parental leave that I was not cut out to be a stay-at-home parent. This was not a surprise — I had very much planned on finishing my PhD — but, I did not expect to miss science so much. The weeks that I spent at home with my first child — those long, monotonous, and lonely weeks — solidly reinforced my decision to pursue a career in ecology. Having kids also made me more hopeful, and more committed to applied conservation research so that I might contribute something towards improving the state of the world they would inherit. 

“Women were less likely to have conducted field-based research since having a child. When they did, women were dependent on support from their parents more than their male peers were…who were more dependent on spousal support…Support from family and academic peers has a significant impact on individual abilities to conduct extended stretches of fieldwork, the places where fieldwork can be conducted (safety, distance, etc.), and possibly the quality of the work that can be conducted, which echoes findings on family-career balance in academia in general.”

 As a PhD student, I spent six field seasons in Acadia National Park; I was pregnant during my fifth and my daughter joined me for my sixth. The next year, when she was almost two and no longer nursing, I left her behind for a two-week field course and then a two-month trip to my postdoc home campus, which included a week of fieldwork. When she was two and a half, I left her again for a week of fieldwork; her sister came with me though, because I was 11 weeks pregnant. Except for my most recent week of field work (Baxter), my postpartum fieldwork is based in a cushy tourist town (Bar Harbor). I’ve had decent cell phone service and ice cream shops with bougie flavors like blueberry sour cream crumble and Maine sea salt caramel. I started working in Acadia before I had kids — in fact compared to the rest of my lab, my field site was wild and remote — but the location of my dissertation work definitely made it easier to consider having kids while I was in graduate school. 

“Women and men used a variety of resources for childcare while in the field, though men tended to rely exclusively on a co-parent or combination of childcare options, whereas women more often utilized grandparents and non-relatives (p = .01). The majority of those who had taken their kids to the field reported it as a good experience for the children (87%), though half (51%) also reported that it made fieldwork more difficult.”

 My childcare while in the field spanned the gamut — my mom, my husband, a college kid that once upon a time had been my camper at summer camp when I was soccer counselor. We pieced together twelve weeks of childcare for my last dissertation field season in an effort that felt both shoestring and super-privileged. I think it was a good experience for my eight-month-old, mostly because it extended her breastfeeding and she loved eating. Among the challenges that I faced during my dissertation fieldwork, having my kid with me ranked well below a government shutdown closing my National Park, a government sequester closing access roads to my field site, and a controlled burn burning my control plots. I found being pregnant in the field more difficult than being a mom in the field: the heartburn, the achy ligaments, and the visibility were tough. As a mom in the field I carried my kid in a backpack a few times, but mostly I was out there on my own and it was refreshing to get away from the unfamiliar challenges of parenthood (where I often felt totally inept) and jump into the familiar challenges of fieldwork (where I often felt like my most capable self). When you are pregnant, it is much harder to compartmentalize fieldwork and family — you can’t leave the pregnancy symptoms at home. 

“Having a partner who is also in academia significantly increases stress, as do negative employment status and, curiously, planning not or being unsure about future children. Among students, being white was significantly associated with a positive sense of family-career balance, as was positive employment status. There was a significant relationship between a low career impact on family planning and a positive sense of family-career balance.”

 I don’t know if have a partner outside of academia has significantly decreased my stress. However, I do not find it curious that uncertainty about future children increases stress; in retrospect, I think I was more stressed in the years that we were thinking about kids, or trying to have a kid, than I am now with two children. It’s a huge decision to grow your family — and once you decide, you have so little control over the process. Trying to conceive while attending endless women-in-science panels full of audience questions about disapproving advisors and maternity gaps in CVs is a very unsettling experience. Finally, if I were confident that my decision to have children “early” had a low impact on my career, then I think I would have an extremely positive view of my family-career balance. The truth is, as a postdoc, I don’t yet know the impact on my career trajectory though I think that it’s worth noting the irony in my experience this summer when I was considered both early career and just months shy of being a geriatric prenatal patient. My self-assessed family-career balance is this: I’m too tired to think that I’m doing a bad job. If I am this tired, I must be getting sh*t done. 

“Family planning decisions of women were significantly more likely to be affected by concerns with conducting fieldwork, getting tenure, impacts on promotion, preconceived notions of peers, and disappointing their advisors than in men.”

 Step One: Paid parental leave for everyone.

I started thinking about this post after my tweet about post-bedtime grant writing went science-twitter-viral. A Syracuse PhD candidate replied “Your ‘Dr. Mom’ tweets keep me going.” The forward-facing social media projection of my ‘Dr. Mom’ life is built on a scaffolding of duct tape, socioeconomic privilege, and falling asleep as soon as the toddler is at preschool. There’s also the luck of landing at the right university (with paid parental leave for graduate students) and the right postdoc fellowship (the orientation featured a powerpoint of all the babies born to fellows during their time in the fellowship). I wasn’t specifically looking for family-friendly programs during my applications, but the visible examples of successful parents in my field allayed (most of) my fears about having one child, and then having a second.

The ‘Dr. Mom’ tweets are a part of this visibility, but they also obscure the daily grind of parenthood and the many, many toddler conversations that are way more frustrating and way less quotable. I’ve had every advantage in this game from socioeconomic status to health to living near extended family and it’s still scrape-me-off-the-floor-at-the-end-of-the-day hard. Lynn’s research on expectations of a field-based career provides this framework for parents like me to contextualize our experiences, recognize our privileges, and then work to make our fields more inclusive for all parents, professionals, and trainees. 

One last note: this is only the first paper from Lynn’s survey. I’m excited to see where this research goes as they “explore the role of ethnicity, status of first-generation college students in accessing an anthropological career, and how anthropology fares in supporting breastfeeding and maternal and paternal leave, among other workplace issues.”

Pikas Meet Cute: Two Subspecies, One National Park

The National Park Service is wrapping up celebrations on its 102nd anniversary this August. I’m unabashedly biased towards park science: my dissertation and my postdoc research are both Acadia-based, while cleaning out old papers last week I actually paused for a moment before recycling a torn up, coffee-stained copy of a National Park research permit from 2013. (Don't worry, the original pdf is safely stored on an external hard drive.)

I’d report on the hybridization of pikas in Rocky Mountain National Park even without the excuse of a belated happy birthday to the National Park Service, but clearly covering research on pikas and #poopscience is the perfect way to honor the stewards of our public lands. There are charismatic megafauna (mini-fauna?) and there are charismatic landscapes, and the scientists who study pikas in the western National Parks enviably have cornered the market on both. Dr. Jessica Castillo Vardaro just published new research on the population genetics of American pikas in PLoS ONE last month. In “Identification of a contact zone and hybridization for two subspecies of the American pika (Ochotona princeps) within a single protected area” Castillo Vardaro and coauthors analyze the DNA in pika poop to pinpoint where the northern and southern Rocky Mountain lineages of these rabbit relatives meet. Their pika #poopscience spanned samples from Grand Teton National Park, Great Sand Dunes National Park, and Rocky Mountain National Park.

Before Castillo Vardaro’s work, there was some evidence that the northern and southern Rocky Mountain pika subspecies had a historic contact zone somewhere near-ish Rocky Mountain National Park. However, Castillo Vardaro wasn’t looking for a contact zone or hybrid pikas when she began working on the Pikas in Peril (PIP) project — a team of National Park Service staff and academic researchers. Pikas are a bit of poster child for climate change vulnerability — “a climate indicator species” — because they cannot tolerate prolonged exposure to high temperatures. Castillo Vardaro’s initial genetic analyses of pika populations in western National Parks focused on signals of isolation by distance (IBD). She explains, “the further individuals are apart geographically, the less related they are genetically. Since pikas typically establish territories close to where they were born and mate with their neighbors, I expected to see strong signals of IBD. I did in all of my study sites except Rocky Mountain National Park (ROMO).” Comparisons of the pika samples and their sequences to Genbank showed that there were two genetic lineages represented in ROMO — Northern and Southern. Then, at a pika meeting (could there be a cuter meeting?) Castillo Vardaro met Preston Somers, a researcher who studied pika dialect in the Rockies in the 1970's. She notes, “His work suggested there might be a contact zone, but we were the first to actually show it and evidence of contemporary gene flow. So, we weren't initially interested in studying ROMO as a potential contact zone, but we are now.” The analyses in this research are steeped in #poopscience, or what the paper refers to as “fecal samples…through a combination of random, targeted, and opportunistic sampling.” I asked Castillo Vardaro about the trade offs of #poopscience versus tissue samples. As a plant ecologist, my Methods have never included gems like, “We avoided collecting old fecal pellets by preferentially collecting pellets with green plant material inside to avoid degraded DNA” — but I was curious to hear more. Castillo Vardaro expounded,

Fecal DNA is essentially the mucus and cells lining the digestive tract that then coat the fecal pellet as it passes through. There are very few cells compared to tissue (organ tissue or ear clips), there are other things present that can inhibit the PCR process like plant secondary compounds, and the feces has been sitting around outside for an unknown amount of time so the DNA can degrade. Each sample has to be genotyped multiple times to overcome the errors resulting from low quality/quantity DNA. My genotyping success rate was 50% - 75%, after removing samples that failed, contaminated samples, and multiple samples collected from the same individual unknowingly. That's a lot of work in the lab.

But, the #poopscience lab work pays off if you need lots of samples across a broad geographic area:

In contrast, I just got back from a week in Montana where I was helping my coauthor Chris Ray trap pikas at a site she has been monitoring for 30 years. In four days of effort (two trap days, but it takes a day to set up traps and a day to check traps/process pikas) we trapped 5 pikas. One person can collect 10-25 quality fecal samples in a day, plus anyone can collect fecal samples for genetic analyses after about 10 minutes of training. So while I would have preferred to have worked with tissue, there is no way to sample the number of individual pikas necessary for 10 high resolution genetic analyses if you had to trap every animal.

The collaborative nature of Castillo Vardaro’s research and the Pikas in Peril reminded me of an earlier blog post I wrote about the Biological Conservation paper “The importance of non-academic coauthors in bridging the conservation genetics gap.”  I noticed that Castillo Vardaro’s PLoS coauthors were all academics, but she pointed out that her coauthor and grad mentor, Clint Epps, designed the PIP project alongside National Park Service personnel and other academic researchers. “The questions, goals, and desired products were explicit from the beginning. These included National Park Service reports, summaries, briefs (publications on the web and available at the parks themselves), spatial data, and research that could be utilized in each of the parks.”

While Castillo Vardaro was doing field work, she worked with National Park Service and US Fish and Wildlife Service biologists, interns, and volunteers. She noted, “we worked with interpretive staff to prepare the park specific resource briefs. We (myself, Clint Epps, and Doni Schwalm) also wrote a note on the potential effects of a proposed quarry site in Grand Teton National Park on the pika populations there, which was provided to resource managers there.” Basically, this work (one of Castillo Vardaro’s dissertation chapters) is the exception that proves the rule to the non-academic coauthors paper: here, the coauthor list belies the strong partnerships with non-academic scientists and managers, and if you didn’t know about Pikas in Peril, you might think wow, these academics really know how to put together explicit management implications single-handedly! 

Finally, in Castillo Vardaro’s research I saw a mirror of my own dissertation work. I had no pikas or fecal DNA, but we both finished our dissertation field work in National Parks before the 2016 election. Her work could inform whether pikas are listed as endangered or threatened under the Endangered Species Act; my research supported a climate change vulnerability assessment; and after our halcyon days as PhD students under the Obama administration, we are now watching an administration and Secretary of the Interior generally disregard the National Park Service expertise on these issues.

I told Castillo Vardaro that I feel an extra sense of urgency in publishing my Acadia papers now — especially in open access venues. I wondered if this was a personal quirk or if she felt a similar sense of responsibility for her field sites and study species. She agreed that highlighting the work that we are doing on public and federally managed lands is even more important in the current political climate. “One of the main reasons I chose to publish in PLOS ONE was because I wanted the manuscript to be accessible (open access).” She also noted that, “the PIP project was funded as part of the NPS Climate Change Response Program. I do worry about continued funding for similar projects and initiatives under Zinke and the Trump administration. Pikas tend to live in places that aren't as directly impacted by development as other ecosystems (it would be difficult to put a subdivision on the steep, rocky, side of a mountain), but the policies and proposed changes to the Endangered Species Act under the current administration to make it easier for development and resource extraction on public lands could definitely impact pikas.” 

The flipside of non-academic coauthors bridging a conservation gap is this: when the federal government is hostile towards non-extractive natural resource management, the academic coauthors in these partnerships will continue to publish our findings, piling up the evidence to support our field sites and our study species. For those of us in academia who completed National Park fieldwork in what seems like another era, getting the writing done can seem both daunting and futile. It's not. Traditionally, the first wedding anniversary is the “paper” anniversary, but for the National Park Service’s 102nd I think papers are still an appropriate — and important — gift. 

References:

Castillo Vardaro JA, Epps CW, Frable BW, Ray C (2018) Identification of a contact zone and hybridization for two subspecies of the American pika (Ochotona princeps) within a single protected area. PLoS ONE 13(7): e0199032.

The Hidden Gems of Data Accessibility Statements

Sometimes the best part of reading a scientific paper is an unexpected moment of recognition — not in the science, but in the humanity of the scientists. It’s reassuring in a way to find small departures from the staid scientific formula: a note that falls outside of the expected syntax of Abstract-Introduction-Methods-Results-Discussion. As an early career scientist who is very much in the middle of sculpting dissertation chapters into manuscripts, it’s nice to remember that the #365papers I read are the products of authors who, like me, struggled through revisions and goofed off with coauthors and found bleak humor in the dark moments. 

Ecology blogs, twitter, and the wider media also love noting the whimsical titles, funny (and serious) acknowledgements, memorable figures, and unique determinations of co-authorship order that have appeared in the pages of scientific journals.

I enjoy stumbling on these moments of levity in my TO READ file; last spring I procrastinated formatting my dissertation by avidly reading the Acknowledgements section of anyone I’d even vaguely overlapped with in my PhD program. One place I have not thought to look for serendipitous science humor: the Data Availability Statement. As it turns out, I have been missing an interesting story.

A recent PLOS ONE paper set out to analyze the Data Availability Statements of nearly 50,000 recent PLOS ONE papers. This may sound like a dull topic, but Lisa Federer and coauthors' work is surprisingly engaging, topical, and thought provoking. In March 2014 PLOS unveiled a data policy requiring Research Articles to include a Data Availability Statement providing readers with details on how to access the relevant data for each paper. But, as Federer et al point out “‘availability’ can be interpreted in ways that have vastly different practical outcomes in terms of who can access the data and how.” 

Why do Data Availability Statements matter? In ecology, open data advocates make the case for reproducibility and re-use. So many of us work on small study areas and amass isolated spreadsheets of data, and then publish on our system, maybe throwing a subset of the data we collected into a supplementary file. But big picture questions that look across scales, ecosystems, and approaches rely on big data — and big data is often an amalgam of many small datasets from a wide array of scientists. Small (or any size) datasets that are publicly available, and easy to access in data repositories instead of old lab notebooks or defunct lab computers, are much more likely to have legs, to get re-used and re-tested, and contribute to the field at large.

While PLOS was on the vanguard of Data Accessibility Statements among peer-reviewed journals, Federer’s review of the contents of these Data Availability Statements makes it clear that we are not yet in the shiny future of Open Data. PLOS’ Data Accessibility policy “strongly recommends” that data be deposited in a public repository; Federer found that only 18.2% of PLOS papers named a specific repository or source where data were available. Most Data Accessibility Statements direct the reader to the paper itself or supplementary information. Even among the data repository articles, some Data Accessibility Statements indicated a repository but failed to include a URL, DOI, or accession number — basically sending readers on a wild goose chase to locate their data within the repository. 

Other statements seem to have been entered as placeholders, potentially intended to be replaced upon publication of the article, such as “All raw data are available from the XXX [sic] database (accession number(s) XXX, XXX [sic])” or “The data and the full set of experimental instructions from this study can be found at <repository name>. [This link will be made publically [sic] accessible upon publication of this article.]” These two articles, published in 2016 and 2015, respectively, still contain this placeholder text as of this writing.

 These examples of placeholders that made it into publication are embarrassing, but human, and as Federer points out, Data Accessibility Statements should be reviewed by editors and peer reviewers with the same scrutiny that we apply to study design, statistical analyses, and citations. I have worked on meta-analyses and projects that depend on data from existing digital archives. The frustration of chasing down supplementary information, Dryad DOIs, and GitHub addresses only to find a dead end or a broken corresponding author email address is a feeling akin to discovering squirrels chewing through temperature logger wires halfway through the field season. Federer notes that the tide is turning towards open data: after a rocky start in 2014 — Federer’s team parsed many papers likely submitted before (but published after) the Data Availability policy went into effect — 2015 and 2016 saw the percent of papers that lacked a Data Availability Statement drop dramatically. Over the same time period, Federer notes slight increases in the number of statements referring to data in a repository and fewer that claim the data is in the paper or — shudder — available upon request.

At a broader level, open data is a newly politicized topic. The EPA recently proposed new standards that would ban scientific studies from informing regulatory purposes unless all the raw data was widely available in public and could be reproduced. This is not so much a gold standard as a gag rule.

In a PLOS editorial, John P. A. Ioannidis points out that while “making scientific data, methods, protocols, software, and scripts widely available is an exciting, worthy aspiration” in eliminating all but so-called perfect science from the regulatory process, the EPA is committing to making decisions that “depend uniquely on opinion and whim.” Most of the raw data from past studies are not publicly available — and as Federer’s research shows, even in an age of required Data Availability Statements, open data is still a work in progress. And so we beat on — scientists against anti-science Environmental Protection Agency administrators, borne back ceaselessly in support of publishing accessible, open data as a kind of green light to past research. 

References:

Federer LM, Belter CW, Joubert DJ, Livinski A, Lu Y-L, Snyders LN, et al. (2018) Data sharing in PLOS ONE: An analysis of Data Availability Statements. PLoS ONE 13(5): e0194768. https://doi.org/10.1371/journal. pone.0194768 

Ioannidis JPA (2018) All science should inform policy and regulation. PLoS Med 15(5): e1002576. https://doi.org/10.1371/journal.pmed.1002576 

National Parks are for the Birds

Happy National Parks week!While I tend to plan trips around plants — Thuja plicata in Olympic National Park, Lathyrus japonicas at Cape Cod National Seashore — I understand the draw of non-botanical Park residents: the iconic bison in Yellowstone, the wolves and moose of Isle Royale, the bald eagles cruising the coast of Acadia. 

Birds are among the most beloved park wildlife, and people — regular visitors, rangers and researchers alike — have been studying birds in National Parks for decades. Bird watchers are among the most consistent and prolific citizen scientists and their observations from National Parks to backyards comprise some of the largest and oldest community-based science research in the country. The most famous datasets of this kind are the Christmas Bird Count and the Breeding Bird Survey. These two datasets — covering a huge spatial area, a long species list, and over three decades of observations — allowed the National Park Service and the National Audubon Society to project bird responses to climate change across the National Park System.

Imagine you are standing in a National Park (I always imagine I am standing in Acadia). Take a moment to identify the avifauna — aka the birds — in this park. Now, zoom into the future, sometimes between 2041 and 2070. What birds are in your National Park now? Has your species list changed? Grown? Shrunk? Park managers, researchers, and bird watchers would all love to know the results from this time traveling exercise. Now, thanks to Dr. Joanna Wu and colleagues, we have these projections available! In a recent PLoS ONE paper, Wu and coauthors use the Christmas Bird Count and Breeding Bird Survey to model climate suitability for over 500 bird species. Then, they zoom into the future and look around at the projected climatic changes in 274 National Park. From this perspective in the future, they write a new species list for each park: which birds are disappearing, and which new colonizers are expected to move in. They find that most parks are likely to become more bird-y — potential colonizations will exceed extirpations, especially in the winter. 

The models of summer and winter distributions were trained on two big, old citizen science projects — the Breeding Bird Survey and the Christmas Bird Count. I asked Wu if it was coincidence that this research was grounded in community-based science, since both Audubon and the National Park Service depend on the general public for support. She writes, “these data sets were the only ones done with survey rigor at a large enough of a spatial scale to allow us to map out bird occupancy across the entire North America. It was certainly meaningful for Audubon as the compilers of the Christmas Bird Count data to rely on our community science products in a scientific study.” This shared enthusiasm between Audubon and the community of birders is reflected in the beautiful website that presents Wu's findings to the public: you can watch species turnover, click on specific parks, and look at national trends.And it’s not just that birds are charismatic fauna with huge fan bases that are obsessed with making lists (I’m looking at you, birdwatchers). Wu notes, “birds are important ecological indicators because they travel much larger distances on an annual basis (as a whole) than plants or mammals, and may thus be able to track climate better than other taxa.” So, when Wu and her colleagues project changes in bird communities at the National Parks, they are looking at the frontline of ecological changes under anthropogenic climate change.

“Though plants and mammals are shifting too, birds are indicators as they’re likely to respond first and more drastically. Of course this leads to a potential mismatch in resource availability as plants, insects, etc. respond at a different rate to climate change, leading to unforeseeable consequences.” 

Finally, I asked Wu what we can do if we live and/or work outside of a National Park. Unfortunately, Acadia is not actually home, and I wanted to know how my actual backyard fit into the bigger picture here. “Our research does show that birds are going to be on the move and the corridors between parks are important to support this change. State parks, wildlife sanctuaries, and even back yards are going to be increasingly important places for birds moving to new areas in light of climate change. One of the things we can do is planting native plants to provide resources for birds as they face unprecedented change to the climates and habitats they evolved in in the coming decades.” 

Enjoy National Park Week! Happy birding! 

Reference:

Wu JX, Wilsey CB, Taylor L, Schuurman GW (2018) Projected avifaunal responses to climate change across the U.S. National Park System. PLoS ONE 13(3): e0190557. https://doi. org/10.1371/journal.pone.0190557

An Epic Joshua Tree Roadtrip & the Reproductive Ecology of an Iconic Southwest Plant

Think of your most amazing four-state roadtrip. How much data did you collect between stops at Disney Land and the hotel pool? Did you stargaze in the Mojave Desert or were you too exhausted after a day of running transects through Joshua Tree National Park? Did you look at the famous Joshua trees with wonder and awe, or did you keep your head down and count individual flowers on these episodic bloomers then hastily move on to the next site to keep tallying reproductive metrics? Did you come home to your computer and upload slideshows of vacation snapshots or did you immediately begin writing up notes like:

Despite its prominence in plant communities of the Mojave Desert, surprisingly little has been published on its reproductive and structural ecology. The majority of research on Joshua tree has focused on its highly coevolved pollination relationship with the Yucca moth. Outside its pollination biology only a few studies have been published on its reproductive ecology.

Thanks to one amazing roadtrip — with a little help from Disney World and Denny’s — new research is shedding some light on patterns of flowering, fruit production, and stand structure of Joshua trees across the Mojave Desert. I did not realize how “hashtag blessed” my own phenology research was until I read Samuel St. Clair and Joshua Hoines’ new PLoS ONE paper on the reproductive ecology of Joshua trees.

My research is a steady annual routine: I study flowering in plant populations that consistently bloom every spring when I arrive in Maine to record them. St. Clair does not have this luxury with Joshua trees — he writes: “episodic blooms make it hard to anticipate a study of its reproduction.” Early in 2013, St. Clair saw Joshua trees blooming at his field sites and called around — the trees seemed to be blooming across their range, he “even heard reports of blooming in Las Vegas and Phoenix yards.” As it became clear that 2013 was a rare opportunity to study reproductive ecology for an unpredictable study organism, St. Clair jumped to take advantage.

“Obviously there was little time to spare. I mapped out a range wide survey of populations, put a travel map together and booked hotels. Took my two sons out of school (ages 10 and 9) for field help in early May and promised them a stop at the Adventure Dome in Las Vegas and a day at Disneyland. We jumped in our car and were off.” St. Clair, a professor at BYU, and Hoines, at the National Park Service, split the fieldwork and covered ten study sites across four states in May and June 2013.

At each site they collected data on the population characteristics (population density, tree height, trunk diameter) and reproduction (number of inflorescences and total fruits, percent of trees in bloom, fruit mass, seed number) of 120 Joshua trees. That’s 1200 trees — from 60 100-meter transects! — in under two months. St. Clair shared some memorable moments, “A grasshopper outbreak at Lytle Rach that had the boys in tears, Kids eat free at Denny’s at least 4 or 5 nights and Disney Land was awesome. The boys still talk about the trip fondly.” The opportunistic rush for reproductive data revealed interesting patterns across the climate gradient of the Joshua tree’s range. At warmer sites, the Joshua trees produced more flowers and seeds, but stand density was lower, while at cooler sites, there were more Joshua trees but fewer flowers and fruit per tree. So while warming temperatures may be good news for reproductive success, the establishment of new Joshua trees seems constrained by warmer temperatures. I asked St. Clair what these results meant for Joshua trees facing climate change. “I think the bigger limitations moving forward will probably be in the seedling establishment and recruitment phases of development.  The fruiting success suggests that the pollinator populations are intact which is good—we’ve see pollination failure due to a lack of yucca moth in populations of Banana Yucca in a recent paper we published.” 

The future of Joshua trees in Joshua Tree National Park is not just a concern for scientists. The official twitter account of the Park (@JoshuaTreeNPS) garned five minutes of fame last November when they began tweeting about the potential effects of climate change on the park’s biodiversity. Secretary of the Interior Zinke apparently reprimanded the Joshua Tree National Park superintendant for these social media science lessons.The idea that a national park should be dissuaded from sharing research on the natural and cultural resources — including, the namesake of that park — with visitors and general public is truly absurd.

I think this means that it is our responsibility to tweet out the results and implications of St Clair and Hoines’ new paper and continue the conversation that @JoshuaTreeNPS started. 

Reference:

St. Clair SB, Hoines J (2018) Reproductive ecology and stand structure of Joshua tree forests across climate gradients of the Mojave Desert. PLoS ONE 13(2): e0193248. https://doi.org/10.1371/journal.pone.0193248

Not Seeing the Grass for the Trees

I appreciate repetition.

My favorite class in high school was AP Chemistry, but I think I owe most of my AP success to the previous year's slog through regular Chemistry. By the time I took AP Chem, all the basics were finally settled in my mind and I could hit the higher-level concepts that I’d only whiffed at the year before.

The second time I ran a marathon I had so much more fun — and so much more left in the tank for that last, terrible 10K.

The second time I read a paper from a new-to-me sub-discipline, or with specific, sophisticated statistical methods, I get a similar boost of adrenaline and understanding. These déjà vu methods* are often serendipitous — it’s hard to consciously search for them — but they are so rewarding when I stumble into them. Déjà vu methods struck PLoS ONE this winter in the form of land cover change captured in Landsat images. The Landsat program has been capturing satellite images of Earth since the 1970s, and researchers can compare decades of Landsat images to tell a time-lapse story of changing land cover at a high resolution. Two great papers used this method to explore trends in forest cover on opposite sides of the globe: New England in the United States and the Western Ghats in India. 

As I read Thompson et al.’s ‘Forest loss in New England: A projection of recent trends’ I could imagine the last twenty years of land cover change in my mind’s eye before even glancing at the figures. I’ve lived in New England nearly my entire life; I went to grad school in one of the three case study sub-regions, and worked college summers in another. The third case study sub-region is a long stretch of coastal Maine that I drove through every field season on my way to Acadia National Park. I’ve collaborated on remote sensing work, but it’s not my wheelhouse, so reading Thompson’s paper allowed me to enter this world in a really intuitive way because the results and projections already felt familiar to me. 

And then I read ‘Not seeing the grass for the trees: Timber plantations and agriculture shrink tropical montane grassland by two-thirds over four decades in the Palani Hills, a Western Ghats Sky Island.’ Here, Dr. Arasumani and a team of academic and non-academic researchers used four decades of Landsat images to quantify patterns of land cover change in grasslands, forests, plantations and agriculture in a region of southern India called the Palani Hills. This is a landscape that I could not imagine — fortunately Arasumani’s team collaborated with photographer Prasenjeet Yadav who created an amazing 4-minute film. This video is a fantastic introduction to the ecosystem with beautiful footage of the shola grasslands and shola forests. ‘Not seeing the grass for the trees’ is a response to the local perception that timber plantations have replaced shola forests in the sky island of the Palani Hills. Local conservation policies center on restoring shola forest trees, with little focus on the shola grasslands. So, a group of scientists began using Landsat to challenge the current conservation view. As Dr. Milind Bunyan and Dr. Robin Vijayan write, 

“The popular discourse that timber plantations are invading shola forests runs deep and wide, but there are exceptions to this observation. In the state of Kerala for instance, there is growing appreciation that it is the grasslands that have been lost to plantations and not the forests. The state that holds a majority of this ecosystem both in original and modified states (viz. Tamil Nadu) however, largely believes that plantations have invaded forests (although there are individuals in the state forest department who now recognize the loss of grasslands).”

Coauthor Robert Stewart and his late wife Tanya Balcar had been working in the Palani Hills since the 1980s: their Vattakanal Conservation Trust focused on forest and grassland conservation and they were among the first to notice that the grasslands were disappearing. The story of how Tanya Balcar’s observations snowballed into this paper is a lovely peek behind the curtain of conservation research: the collaborations, the shoestring budget, the surprises, and the great food all ring true to my experiences working with NGOs and government agencies in New England. Bunyan and Vijayan gave me a long version to edit down, but I love the details too much.

“[Tanya and Robert] convinced some of us who were working on different projects in this landscape including Ian Lockwood, a two-generation resident of Palani Hills, and a friend of Tanya & Bob. Using his skills as a geographer, Ian conducted a preliminary GIS analysis, which revealed the dramatic changes that had occurred during his lifetime; he then published these results on his blog. This caught our attention when we realized that much of the change in the landscape had occurred very recently, and providentially within the period of LANDSAT imageries.Anil and Sunayana Choudhary from INTACH Kodaikanal (listed in the acknowledgements) were the people who really made the project happen. They generated INTACH funding for the project to conduct fieldwork, and to hire a technician to do the GIS and ground-truthing. As with most research projects however, we did not stick to the script and ended up hiring two technicians (one for the lab and the other for the field), despite uncertainties at the time on how we would support both of them. Of these, Danish Khan came with a tremendous wanderlust and was therefore, the natural choice for our field component, and Arasumani M., who graduated at top of his class, was the lab person conducting the GIS analyses.The only thread that binds all of us is a desire to work in the landscape, albeit on varied aspects, and understand and document the threats and changes in this landscape, which required a baseline that we could use for future studies. This was an extremely frugal study, and most of us contributed significant amounts of time (and in some instances, money) to the project in different ways. With different roles on the project, we found working together relatively easy and complementary. A lot of our work also involved working different physical locations (including putting these responses to your questions together), and used cloud-platforms like Google Docs. We’re also proud to say that our meetings were almost like large family gatherings, full of great food (supplied generously by the Choudharies), and travelling through the landscape.”

Through Landsat images and ground-truthing, this team found that shola grasslands — the dominant cover type forty years ago — had been invaded by agriculture and plantations. Agriculture and plantations overran shola grasslands with different spatial patterns of replacement and degradation: agriculture takes over in “large, compact, and spatially aggregated patches” while plantations puncture the landscape with small, irregular-shaped patches as invasive plantation species spread into the ecosystem. This analysis also found that only half of the existing grasslands are currently included in the Kodaikanal Wildlife Sanctuary; they identified eight additional grasslands along cliff edges or bordering abandoned agricultural areas to include in this sanctuary.

Finally, the authors conclude with four specific conservation recommendations: (1) identify and conserve core grasslands (2) check invasion in sparsely invaded grasslands (3) review indiscriminate removal of mature plantations (4) contain agriculture. I asked Bunyan and Vijayan how these recommendations have been received by the Kodaikanal Wildlife Sanctuary and the local communities. They write “In addition to our town hall meetings, we have had several interactions with forest department staff of the KWS to disseminate our conservation recommendations. We opine that the Forest Department is positive, and we hope to work with them to be able to achieve the goals stated in the paper. The publicity that this article has generated, which has been covered in the national media and now internationally, will go a long way in promoting these recommendations.” 

I wish good luck to them as they continue this important work! And thank you for enriching my winter with beautiful images of the shola grassland!

References:

Arasumani M, Khan D, Das A, Lockwood I, Stewart R, Kiran RA, et al. (2018) Not seeing the grass for the trees: Timber plantations and agriculture shrink tropical montane grassland by two-thirds over four decades in the Palani Hills, a Western Ghats Sky Island. PLoS ONE 13(1): e0190003. https://doi.org/10.1371/journal. pone.0190003 

Thompson JR, Plisinski JS, Olofsson P, Holden CE, Duveneck MJ (2017) Forest loss in New England: A projection of recent trends. PLoS ONE 12(12): e0189636. https://doi.org/10.1371/ journal.pone.0189636    

* To expand on déjà vu methods, I present the thylacine. Last November I read a preprint of a paper on thylacine extinction; I don’t actually know anything about thylacines, but my friend Kevin Burgio was a coauthor, I had studied abroad in Australia when I was in college, and I thought it sounded cool. This thylacine paper introduced me to Bayesian Extinction Estimators and less than a month later, my PhD advisor published ‘A statistical estimator for determining the limits of contemporary and historic phenology’ — a paper that repurposed Bayesian extinction estimators for historical and herbaria-based phenology data. Reading the thylacine paper serendipitously primed me to fully understand this methodological approach for my own field (plant phenology). I'm not the brightest crayon in the box, but if I just keep reading déjà vu methods, I'll make it to razzmatazz.

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.”