Wrapped and Read: A Reading Advent Update

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

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

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

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

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

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

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

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

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

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

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 

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

References:

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

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

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 

Hiking with Reviewer 2

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

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

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

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

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

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

Before the first observation and after the last

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

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

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

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

The pregnant field season

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

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

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

The phenology of phenology monitoring

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

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

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

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

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

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

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

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

National Parks are Hot Spots

In this space, I’ve often shared my love for National Park-based research. I count myself among the researchers devoting time and energy to documenting how climate change affects the ecosystems and natural resources in U.S. National Parks; we study everything from pikas to forests, Joshua trees to birds. But, the underlying rate of warming in these National Parks was not on my radar and I had not given much thought to the climate exposure of National Parks versus the rest of the United States. It turns out, the parks are literal hotspots on the landscape.

Last fall, Dr. Patrick Gonzalez and coauthors from the University of Wisconsin published ‘Disproportionate magnitude of climate change in United States national parks’ in Environmental Research Letters. This study looked at historical and projected temperature and precipitation across all 417 U.S. National Parks. Between 1895 and 2010, mean annual temperature of the national park area increased at double the U.S. rate — parks warmed by 1.0°C (±0.2°C) per century, the rest of the U.S. land area by 0.5 °C.Dr. Gonzalez is a forest ecologist and Associate Adjunct Professor at the University of California, Berkeley. He is also the Principal Climate Change Scientist of the U.S. National Park Service, but he answered my questions here under his Berkeley affiliation, not for the Park Service.

I asked why he wanted to study a spatial analysis of historical and projected climate across all 417 US National Parks. What was the motivation for expanding on the earlier work of researchers who presented similar findings for the 289 large parks in the National Park System system?

“Up until our research, the severity of climate change across all the US national parks was unknown.” Gonzalez writes. “The previous work had only looked at subsets of parks. I work at a national level and it is important for me to give national policy-makers scientific information that is robust and comprehensive. The time-consuming parts of the work were the individual analyses by park and the computational tasks of downscaling all available general circulation model output of future climate projections to 800 m spatial resolution, which had not previously been accomplished for the U.S.”

In addition to the climate exposure of National Parks, Gonzalez and his team considered climate velocities. Climate velocity is the speed at which a plant or animal will need to move, migrate, or disperse — usually north or upslope — to “catch up” to their climate as it changes. Gonzalez found an interesting paradox in climate velocities: the park lands have experienced extreme temperature and precipitation shifts, but they also show lower climate velocity than the U.S. as a whole. They point out that this does not mean that plants and animals in National Parks are not in peril: “The lower climate velocities in the national park area are an artifact of that indicator being calculated as horizontal movement of areas of constant climate. Climate velocity can underestimate exposure in mountains.”

The National Parks are more mountainous than the rest of the United States. This is a reflection of our unsystematic history of serendipitous-style protection; we collect the pretty places as national parks, without considering the underlying biophysical diversity, and mountains are very pretty places. So while moving a couple meters upslope might seem easier than moving hundred of meters north to track a suitable climate, this is often an oversimplification. “Despite the computational artifact, our results indicate that projected climate velocities in national parks could exceed maximum natural dispersal capabilities of many trees, small mammals, and herbaceous plants.” Gonzalez elaborates, “Any new protection of natural areas, whether close to or far from national parks, can add to global conservation of ecosystems for biodiversity and human well-being.”

I asked Gonzalez if he had any thoughts on how the research could be interpreted for park visitors. I wanted to know if there is an effort to get this work not just to park managers on the ground, but to interpretive staff as well. “For national park interpreters, I’ve given many presentations directly to staff in individual parks, including interpreters,” he says. “I encourage all U.S. National Park Service staff to speak about the robust science of climate change and its human cause, which points us to solutions to saving America’s most special places.”

Finally, I noticed that both this paper and the earlier National Park System climate exposure study, which covered 289 large parks, were published in open access journals. I asked if this was an intentional pattern and these research teams were hoping to reach managers who may not have access to peer-reviewed journal articles.

Gonzalez confirmed that, “the open access of the journal of course enabled a much larger audience to directly download and read the original work. This greatly benefited national park staff and other natural resource managers, to whom we aimed to provide information useful for conservation under climate change. Intense interest immediately developed – people downloaded the pdf file more than once a minute in the first 24 hours of publication.”

But their outreach was not limited to open access journals. Gonzalez points out, “public media published over 40 individual stories, including in the Washington Post, on page 1 of the San Francisco Chronicle, on public radio stations, and on television." Gonzalez also wrote a concise summary for the website the Conversation. He says that the University of California, Berkeley, has greatly helped in the effort to reach natural resource managers by publicly posting the spatial data, and he directly provided customized analyses and maps for numerous individual national parks.

Finally, Gonzalez writes, "I just presented the results to the U.S. Congress in a hearing where I testified on human-caused climate change in U.S. national parks. The open access of the journal was critical, but we engaged a broader effort to widely communicate the science.”

Thank you to Dr. Gonzalez and his colleagues for providing the climate data that underlies so much ecological research across the National Park System! And thank you for modeling effective outreach and impressive science communication*! 

References:

Gonzalez, P., Wang, F., Notaro, M., Vimont, D. J., & Williams, J. W. (2018). Disproportionate magnitude of climate change in United States national parks. Environmental Research Letters, 13(10), 104001–13. http://doi.org/10.1088/1748-9326/aade09

Monahan WB, Fisichelli NA (2014) Climate Exposure of US National Parks in a New Era of Change. PLoS ONE 9(7): e101302. https://doi.org/10.1371/journal.pone.0101302 Banner image: photos by Jodi Kurtz, Via Tsuji, and Gabriel Millos, Creative Commons 

*if I ever publish a paper that averages one pdf download every minute, I will throw the biggest party and give everyone temporary tattoos of the figures.

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.”

Summer Reading (Part 2)

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

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

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

Plant Mysteries

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

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

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

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

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

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

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

Best Practices

Do this…

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

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

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

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

Happy Fall Reading! 

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 Rollercoaster of Exploding Pollen

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

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

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

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

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

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

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

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

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

References:

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

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

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

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

Science Twitter and the Secretly Super-rare Saxifragaceae

During one of the coolest experiences of my PhD, I had the opportunity to work as a field assistant on a flora for an iconic park in Maine. The Plants of Baxter State Park is a beautiful book and, if you turn to page 135, there’s a stunning photograph of a carpet of Empetrum atropurpureum, red crowberry — okay, full disclosure it’s my photograph. 

Reflecting on my small contributions to this wonderful book, I remember the sunburns, the crystal clear ponds, the apple cider doughnuts, the black flies, the incredibly cushy shower in one of our crew cabins, and the incredible love I developed for this rugged, cut-over landscape. These expansive memories are tied up in 477 printed pages that sit in a place of honor on my desk. The flora is a snapshot of a place and time: Baxter State Park in 2016. It is already outdated; when I returned to Baxter in Spring 2018 for new research, I heard from the rangers that hikers and botanists had recently found a population of a species we thought was lost from the park —it was in a new, downslope location from its historical site. The limitations of published flora — and the fun of the internet — have led some 21st century botanists to embrace new, technologically innovative tools. In one outstanding example, YouTube, twitter, and iNaturalist played a major role in the discovery of a globally imperiled plant species in Pennsylvania.

Dr. Scott Schuette and coauthors published this finding in a paper that merges social media with early 20th century herbarium specimens, and a gorgeously produced YouTube series with a serious NatureServe Conservation Rank Assessment. They write: “This discovery may also serve as a cautionary tale of relying entirely for plant identification on floras which, through no fault of their own, become incomplete or ‘static’ over time.” “The hidden Heuchera: How science Twitter uncovered a globally imperiled species in Pennsylvania, USA,” published in PhytoKeys in April 2018, is the peer-reviewed version of corresponding author Dr. Chris Martine’s March 2018 YouTube video “Rappelling Scientists Find Rare Species Hiding for 100+ Years.” If you need a break from #365papers, if your ‘To Read’ folder is overflowing with pdfs, if you lost your reading glasses — seriously, it’s summer vacay, you don’t need an excuse — watch the video! 

The episode starts as a quest to re-locate a historical population of the state-endangered plant golden corydalis. Martine, a professor at Bucknell and host of the YouTube series Plants Are Cool, Too! interviews Schuette while botanists in climbing gear rappel down the shale cliff faces of Shikellamy Bluffs above the Susequehanna River*.

After three days, they finally locate the elusive golden corydalis by climbing up from the base of the bluffs. Martine and Schuette shake hands in a classic wrap up scene. And then — record-scratch sound effect, the frame freezes and tilts, and a voiceover exclaims, “normally this is where our episode would end, but this story took another amazing turn…” Martine flashes back to stills from earlier in the episode and sports-commentator-style circles a Saxifragaceae species with coral bell-shaped flowers that had blended into the background as the climbers searched for golden corydalis. 

Throughout the survey, the team — and Martine on twitter — had identified this as the common plant Heuchera americana, American alumroot. A tweet reply from Heuchera expert Dr. Ryan Folk revealed their common plant was very, very uncommon. It was Heuchera alba, a globally imperiled wildflower, endemic to the mountains of West Virginia and Virginia — a plant never before recorded in Pennsylvania. Ultimately, Schuette, Folk, Martine, and coauthor Dr. Jason Cantley found eight populations of H. alba in Pennsylvania, as well as historical evidence that the plant had been there, hidden, for at least a century. When they re-examined herbarium specimens of the two known Pennsylvania Heuchera species, they found four specimens collected between 1905 and 1949 that were actually H. alba.

One of those specimens — housed in Bucknell’s Wayne E. Manning Herbarium — was collected at Shikellamy Bluffs in 1946. By W. Manning. Even the guy who got the herbarium named after himself missed this identification! As the paper title notes, the credit goes to “Science twitter,” a resource that Manning unfortunately did not have when he was botanizing the Shikellamy Bluffs. I asked Schuette and Martine about their social media habits. While all of the paper’s authors had met IRL (in real life), the Plants Are Cool, Too! episode and twitter conversation around H. alba sparked this research through virtual collaboration. Martine says, “I use Twitter nearly every day and see it as part of my job as a scientist and academic. It is my go-to source for keeping up with the latest findings in my disciplines and the most pressing issues in higher education.” Schuette admits that his twitter check-ins were less frequent, “but certainly picked up a bit after the H. alba discovery.” Schuette is active on iNaturalist — parallel to Martine’s twitter mis-identification, Schuette had a similar social-media moment when his iNaturalist post of a Heuchera in Pennsylvania turned out to be H. alba. He explains, “I started on iNaturalist when I started my position with the Pennsylvania Natural Heritage Program at the Western Pennsylvania Conservancy. I viewed my work as a great opportunity to share the diversity that I see on a day to day basis with the larger naturalist community.” Both Schuette and Martine work in Pennsylvania and their standard botanical reference, the Plants of Pennsylvania flora, lists H. americana and H. pubescens as the only Heuchera species present in the state. Earlier botanists were working under the same assumptions, no one expected to find H. alba in the state — the difference is that in 1946 you couldn’t upload your herbarium specimen to a network of naturalists across a broad geographic range and receive instant feedback on your identification.Martine muses,

“I just saw a Tweet from a scientist saying that she had been told by a senior colleague that "no one who matters" is using Twitter. That is totally false, of course, but I would also say that we are fast approaching a time where it might even be more true to say the opposite: Everyone who matters is using Twitter. They are equally silly statements, really, but my point is that on-line communities like Twitter are now where scientists do a lot of their networking, sharing, and, as shown by our study, collaborating. If you ain't there, you are missing out.”

Schuette echoes this perspective on the great potential for social media in scientific research:

“I think that as field botanists we are constrained by the prevailing taxonomic concepts of the times and places where we work. However with the immense availability of information through online databases and social media outlets, we are in a unique position in history to really increase our understanding of biodiversity at several different scales ranging from local parks to EPA Ecoregions. The fact that H. albahas been here under our noses raises some really interesting biodiversity questions that we can now explore in detail.”

 Finally, I just loved that they were able to name-check “science twitter” in the title of a peer-reviewed paper. I asked if they had received any pushback from the journal. I didn’t know anything about PhytoKeys before this paper appeared in my own twitter feed; for the similarly uninitiated, it is “a peer-reviewed, open access, rapidly published journal, launched to accelerate research and free information exchange in taxonomy, phylogeny, biogeography and evolution of plants.” Martine assured me that it was a smooth process; he had experience publishing new species descriptions in the journal and he had a hunch it would be a good fit for the paper. He says, “In working with [PhytoKeys] I have come to appreciate how progressive they are when it comes to promoting their articles online, including via social media - so we weren't especially surprised when they accepted our title. Personally, I think it was the smart thing to do!”

The metrics on PhytoKeys’ website show that the article has received over 670 unique views and 153 pdf downloads. Martine and Schuette agree that the social media buzz around the paper has been positive and congratulatory. As Martine notes, “people who believe in social media as a way to engage with both the public and one's broader scientific community see it as a confirmation; meanwhile, even people who might poo-poo Twitter as a waste of time for scientists have to admit that it led to a pretty cool discovery in this case.” 

References:Schuette S, Folk RA, Cantley JT, Martine CT (2018) The hidden Heuchera: How science Twitter uncovered a globally imperiled species in Pennsylvania, USA. PhytoKeys 96: 87-97. https://doi.org/10.3897/phytokeys.96.23667

*I do love rock-climbing botanists!

**I'm also a big fan of Rosemary Mosco!

Hidden in Plain Sight: the Secret Tree Diversity of Cultural National Parks in the East

Last summer, my daughter received All Aboard! National Parks, a whimsical board book that devotes full-page spreads of colorful, kid-friendly illustrations to nine National Parks along a fictional railroad route. The National Parks skew western — Olympic, Yosemite, Yellowstone, Grand Canyon — with Acadia and Great Smoky Mountains representing the entire eastern half of the U.S. But, the book is a skewed representation of the National Park System in another way too: it only showcases the large, iconic, and “wild” national parks. Where are the National Battlefields, the National Recreation Areas, the National Scenic Rivers, and the National Historic Sites?

A recent paper from Forest Ecology and Management has me thinking that the cultural parks of the east that fall under the National Park Service umbrella deserve their own board book!

In the eastern United States, our National Parks dot the landscape as constellations of historic battlefields, homes of important historical figures, and wild islands of nature scattered across an eastern seaboard of cities, development, and fragmentation. But, it turns out that these small, cultural protected areas are harboring incredible tree species diversity. Dr. Kathryn Miller and colleagues from the National Park Service and University of Maine published “Eastern National Parks protect greater tree species diversity than unprotected matrix forests” after comparing tree species diversity measured in National Park Service Inventory & Monitoring plots to the species diversity recorded in nearby US Forest Service Forest Inventory and Analysis plots. Miller considered five metrics of diversity in each plot — number of individuals, tree species richness (how many species were in each plot?), Shannon evenness (are the species in the plot relatively as abundant as each other or are some super common and others very rare?), McNaughton Dominance (what is the relative abundance of the two most abundant species?), and Percent Rare N/S (what percent of species in a plot have fewer individuals than the average species abundance in that plot?).

The title of Miller's paper is a spoiler alert — the parks were more diverse than the matrix (non-park) forests — with park forests comprising higher species richness and a more even, less dominated distribution of abundance across species. She found this pattern of higher species diversity across the majority of the parks in the study, but it was most consistent in the lower latitude parks. Over a decade of publicly available data from the National Park Service’s Inventory & Monitoring plots and the Forest Service Forest Inventory and Analysis plots allowed Miller and her team to explore tree species diversity across 39 eastern National Parks, each containing between 4 (Sagamore Hill National Historic Site) and 171 (Acadia National Park) forest plots. Before Dr. Miller began her PhD at UMaine, she led field crews that collected some of the data in the National Park Service Inventory and Monitoring Program. Miller told me, “My field experience sampling and hiking around eastern forests has definitely helped me frame the types of research questions to ask, and interpret whether the results are meaningful. When I started this study, I suspected that at least some of our parks, particularly the larger ones (e.g. Delaware Water Gap National Recreation Area, New River Gorge National River), would have greater tree diversity. I was surprised, however, to find out that many of our cultural parks, which tend to be smaller and haven't been protected as long, also have greater stand-level tree diversity than matrix forests.”

Miller’s results are both expected and unexpected. First, there’s a general understanding among ecologists that eastern US forests today are smaller, younger, and more homogenous than they were before centuries of European settlement, land clearing, and timber harvesting. And, we know on a basic level that forests in US National Parks are largely protected from development and harvesting. So, it shouldn’t be shocking to find that forests managed by an agency that is dedicated to promoting ecological integrity and natural disturbance regimes are full of lots of species — not just the early successional ones. But, on the other hand, we often don’t imagine Minute Man Historical National Park — a battlefield replete with actors in Revolutionary War costumes — as bastion of biodiversity. Or, in the case of All Aboard! National Parks, we don’t imagine these cultural parks as national parks at all. So how did Miller land on this question — what made her interested in comparing the tree species diversity in parks and unprotected forests in the east? She muses that “this research question in particular was a follow-up to [our 2016 Ecosphere paper] "National parks in the eastern United States harbor important older forest structure compared with matrix forests" which compared metrics of forest structure in eastern national parks with surrounding matrix forests.” In that study, she found that “parks, regardless of park designation (e.g. National Park, National Recreation Area, or National Historical Park), had consistently older forest structure than matrix forests.” Were these older forests also more diverse? The same forest plot databases could answer that question as well! 

I asked Miller if her research changed her view of the ecological value of cultural national parks. “For me, the results of this study were very encouraging, and confirmed that our efforts to monitor and keep even the smallest parks' forests healthy are worthwhile. I am hopeful that the results of these studies are empowering to the resource managers in our cultural parks, and lead to stronger emphasis and additional resources for maintaining healthy forests in these parks. Ultimately our research also makes a strong case for the importance of protected areas in preserving forest biodiversity, even small urban parks.”

This research seems relevant to managers outside of National Parks as well — and Miller hopes that private landowners, state parks, and NGOs take note. She recognizes that resilience to global change is a big contemporary concern for many land managers. “In forests, tree diversity and structural complexity are important components of resilience, and our results demonstrate the positive influence that protection, particularly protection from logging, can have on forest resilience. In addition, park managers often receive pressure from well-meaning members of the public, and even other park staff to "clean up" forests after natural disturbances. In fact, this was typical management practice in the early days of national parks before we knew better.” She tied together her species diversity and forest structure research and reflected that, “coarse woody debris, dead and dying trees, and blow-downs all contribute to the overall diversity of a forest, and our research has shown that protected forests have more of these features than unprotected forests. Hopefully our research can help inform and support managers' decisions not to clean up after disturbances unless there is a concern about human safety (e.g. hazard trees).” Miller and I both work in Acadia — the kind of classic wild National Park that appears in our imaginations and children’s books as an iconic protected landscape. But as Miller points out, “Interestingly, Acadia National Park did not come out as being more diverse than surrounding matrix forests, particularly because the park has more extensive late successional forests that are largely dominated by red spruce.” She explains, “this isn't necessarily a bad thing, but it does suggest that the forests in Acadia may be more vulnerable to stressors than matrix forests, particularly stressors that could impact red spruce. While this isn't the greatest news, this is important information for park managers to know.”

Like many folks in the greater Boston area, I drive hours to Acadia and feel like I am stepping into a wilder, more biodiverse ecosystem when I lace up my hiking boots at the trailhead to Cadillac Mountain. But, there are pockets of protected tree species diversity hidden in plain sight across the eastern US. Miller’s research makes me rethink my summer road tripping plans — perhaps I should seek out some of those old, diverse forests in National Recreation Areas and Historical Parks, maybe some are actually accessible by railroad... I'm going all in on my research for the All Aboard! Cultural National Parks of the East board book pitch! 

References:Miller, K.M., McGill, B.J., Mitchell, B.R., Comiskey, J., Dieffenbach, F.W., Matthews, E.R., Perles, S.J., Schmit, J.P. and Weed, A.S., 2018. Eastern national parks protect greater tree species diversity than unprotected matrix forests. Forest Ecology and Management, 414, pp.74-84.

Miller, K.M., Dieffenbach, F.W., Campbell, J.P., Cass, W.B., Comiskey, J.A., Matthews, E.R., McGill, B.J., Mitchell, B.R., Perles, S.J., Sanders, S. and Schmit, J.P., 2016. National parks in the eastern United States harbor important older forest structure compared with matrix forests. Ecosphere, 7(7).  

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 

Conservations Genetics, Non-academic Coauthors & Erdős Numbers

I spent a week in Washington DC about two weeks before the government shutdown. Part of my conservation science postdoc fellowship involves professional development retreats and this winter we were in DC for policy training. Over three days, panels of government scientists, NGO staff, and legislative staffers repeated this message: publishing peer-reviewed papers is not enough to impact policy. I remember sitting at the bar one evening and lamenting the standard “these results suggest conservation managers should…” sentence near the end of each of my dissertation chapters.

As early-career scientists, we all felt a little stuck — what could we do to make our research more policy-relevant and accessible? Well, for one, we could write papers with non-academic coauthors. 

A recent study in Biological Conservation reports that papers with non-academic coauthors better link conservation genetics and genomics research to policy and conservation outcomes. Britt et al. assert that conservation genetics faces an application crisis: while many peer-reviewed publications tout the importance of conservation genetics, there has been limited integration of genetic data into management. Dr. Aaron Shafer at Trent University speculated that this “conservation genetics gap” was not a case of managers lacking access to expertise and funding, but driven instead by academics under pressure to publish who were framing genetic studies in conservation buzzwords. He thought the swell of conservation genetics in the literature might not match the needs of managers on the ground — thus, managers reading the peer-reviewed lit would be unlikely to find relevant conservation genetics research, and instead focus limited resources on old school methods like radio-collaring. Shafer shared this hunch with an undergrad and she hit the ground running — lead author Meghan Britt led a meta-analysis of conservation genetic and genomic studies to uncover the causes behind the conservation research-implementation gap. 

Britt and Shafer’s paper, ‘The importance of non-academic coauthors in bridging the conservation genetics gap,’ found three thought-provoking trends after reviewing 300 publications. First, the majority of these papers were focused on “species of low conservation concern or species yet to be assessed.” So, conservation genetics was often centered on species that were not top priorities according the IUCN RedList or NatureServe. Second, less than 40% of the papers contained specific conservation recommendations. They write, “an article was ranked as having a specific conservation recommendation if there was a clear course of action suggested, stated implementation methods, or policy changes that were advocated for.” The generic “we propose maintaining genetic diversity of the species to ensure long-term viability” did not count: there’s no clear or readily transferable application. Finally, a non-academic coauthor was associated with a 2.5-fold increase in the odds of a publication making a specific recommendation. Basically, non-academic coauthors seem to bring a heightened understanding of policy and on-the-ground needs to conservation genetics projects, and the result is a more management-forward paper. 

I’m not a geneticist, so I asked Shafer, isn’t this just good practice for conservation research in general? Shouldn’t we all seek out non-academic collaborations if we want our research to have real-world applications? His answer: Yes!

“We try to get out of the bubble, but it’s hard. We need to make that effort. We don't know the regulations and laws. There are people that understand these organisms on the ground, stakeholders who live with these animals. We think that we are always the knowledge providers, but really it is a two-way street.”

 Shafer has a long history of working with Alaska Fish and Game, dedicating many years to building good relationships with researchers and managers. I asked if these collaborations might also alleviate another side of the conservation genetics-implementation gap by increasing managers’ access to expertise and funding. He sees a lot of benefits for management in these partnerships: “Arguably we have more freedom on the academic side to try different protocols, whereas it's more rigid for management, and our flexibility can help bridge this. But, to have real world impact it needs to be guided by the managers.” He noted that academics often wear blinders to the on-the-ground needs of managers or the policy implications of their work. “In academia we can have samples in the freezer and yet we’ve never seen that animal in the wild.” We often think of the “gap” in conservation implementation as a fault of managers and policy-makers not listening to the science, but it is unrealistic and out of touch to see the gap is as a part of a linear model of conservation scientists delivering the empirical solutions.* 

Finally this paper made me think about Erdős numbers. In academia, a person’s Erdős number is a Kevin-Bacon-like metric of the “collaborative distance” between themselves and prolific mathematician Paul Erdős. Instead of counting the number of co-stars between yourself and Kevin Bacon, you count the number of coauthors between yourself and Paul Erdős. Stephen Heard recently blogged a bit about his absurdly low Erdős number. Since Heard is an ecologist, and Erdős was a mathematician, this low number shows the cross-disciplinary reach of their work. But, Britt’s paper led me to wonder if conservation scientists need a new Erdős number. What if we scored our collaborations outside of academia, or thought of a clever name for collecting coauthors from different agencies, from different levels of government, or from a range of NGOs? What if we celebrated these partnerships with the same cute, tongue-in-cheek competition that we do for Erdős numbers? I wrote one paper with an NGO during my master’s and my dissertation committee includes a National Park Service employee, so I think my “Britt Number” is a solid 2. 

Reference:

Britt, M., Haworth, S.E., Johnson, J.B., Martchenko, D. and Shafer, A.B., 2018. The importance of non-academic coauthors in bridging the conservation genetics gap. Biological Conservation, 218, pp.118-123. 

*For more on how to conceptualize the space between conservation research and implementation, I recommend Toomey et al.'s paper 'Navigating the Space between Research and Implementation in Conservation' in Conservation Letters. Britt et al. consistently describe the 'conservation genetics implementation gap' but Toomey has me now questioning is this a gap? what is a gap? which is kind of a weird but rewarding rabbit hole. 

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

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

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

Impacts of rock climbing on plant communities.

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

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

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

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

Cross country skiing and meadow vegetation

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

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

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

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

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

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

Wildland recreation disturbance at broader scales: hiking & wildlife

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

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

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

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

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

References:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

References:

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

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