Not Seeing the Grass for the Trees

I appreciate repetition.

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

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

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

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

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

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

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

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

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

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

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

References:

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

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

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

Graphic Novels & Socio-Ecological Systems

Let’s say you’ve just pulled off an innovative, interdisciplinary symposia bringing together stakeholders across socio-ecological systems in the world’s oceans. You spent a week in France with 230 ecologists, social scientists, economists, modellers, and lawyers collaborating on solutions for managing and protecting marine ecosystems. Now, how do you get the broader scientific community to read your symposium report? 

If you were clever enough to invite a professional cartoonist to the symposia, you pull together pages of fun, dynamic sketches and publish a graphic novel in the ICES Journal of Marine Science.

This is the amazing — and fun! — trick that Dr. Olivier Thébaud and Dr. Jason Link accomplished after MSEAS 2016. ‘Managing marine socio-ecological systems: picturing the future’ is a graphic novel illustrated by Bas Kohler that was published alongside Dr. Link’s traditional overview of the MSEAS 2016 Symposium. The illustrations are amazing — they pack in energy and dialogue with playful humor across an incredible range of serious, challenging subjects.

The backstory of this graphic novel contains a lesson in interdisciplinary communication. The science steering committee for MSEAS 2016 invested serious planning time into the social side of their symposium. Dr. Thébaud writes:

The idea of inviting Bas Kohler at MSEAS was initially aimed at increasing interaction between participants during the meeting, as we were bringing together folks from different disciplinary networks which do not usually meet.

Dr. Link and other steering committee members were skeptical, but MSEAS brought in cartoonist Bas Kohler through funding dedicated to the social and cultural side of the event. After Day 1, everyone at MSEAS was hooked. As Dr. Link remembers, “Kohler’s beautiful illustrations just got to the core of your talk. In fact, there was a lot of negative feedback from the day without Bas. He was wanted at every session!” After MSEAS 2016 Dr. Link says he “drew the short straw” to write the normal, boring report. But, “no one reads the boring report. We wanted to do something unique. This was a conference about social and human systems and we wanted to capture that in a different medium.” So, Dr. Link brainstormed an outline for a cartoon report. He wanted to tell a story about the state of the discipline, the meeting itself, and future directions for scientists and stakeholders. The MSEAS team looked through Kohler’s illustrations from the symposium to create the graphic novel around this outline. Dr. Link did write a straightforward report — it's published in the same issue of ICES Journal of Marine Science — but he also pitched the graphic novel to an editor at the journal. This was not a terribly risky pitch since Link was friends with the editor, but as far as he knows it is the first graphic novel published in a peer reviewed journal.

We talked a little bit about the intersection of art and science. There are many artists engaged in science communication, through most of their work is facing out towards the general public. In this case with a graphic novel in a journal*, MSEAS has Bas Kohler’s work facing inward, toward the scientific community. Link is hopeful that this “paper” will inspire other conference organizers to consider bringing artists to their symposia. He encourages others to carve out a small fraction of the conference budget, explore local artists, and ask how do we want to capture our story? “Just have it on the list,” he says. He’s following his own advice, currently working on another symposia steering committee and exploring this option again. “A lot of us have been in this game for awhile — we need to mix it up and keep it fresh.” Happy reading!

Reference:

Thébaud, Olivier, Jason S. Link, Bas Kohler, Marloes Kraan, Romain López, Jan Jaap Poos, Jörn O. Schmidt, David C. Smith, and Handling editor: Howard Browman. "Managing marine socio-ecological systems: picturing the future." ICES Journal of Marine Science 74, no. 7 (2017): 1965-1980.  

*The graphic novel & MSEAS report are open access and thus available to the general public, but still, deciding to publish in a journal is by definition looking for niche audience.

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. 

525,600 minutes, 365 papers, and 100 articles every ecologist should read

Last month, Nature Ecology & Evolution published Courchamp and Bradshaw’s ‘100 articles every ecologist should read.’ Here, Courchamp and Bradshaw attempt to compile a list of seminal papers as a foundational reading list for ecology students. To this end, they enlist the help of editorial members of a selection of ecology journals to nominate and rank papers that "each postgraduate student in ecology—regardless of their particular topic—should read by the time they finish their dissertation... [and] any ecologist should also probably read." 

Ultimately, Courchamp and Bradshaw created a list that skews heavily male through a methodology that seems designed to avoid engaging in deep reflection on unconscious bias. Many ecologists have voiced their disappointment with the list; on twitter Kelly Ramirez and Terry McGlynn started collecting nominations of favorite female-authored papers for an inclusive list of 100 articles every ecologist should read

Four of the best papers that I read in 2017 were responses to Courchamp and Bradshaw: Bruna's “Editorial board members are a non-random sample of ecological experts

Editors are indeed experts, but very few of the world’s experts are editors. Until Courchamp & Bradshaw’s survey is repeated with demographically and geographically distinct populations of qualified scientists, the extent to which the list of must-read papers they report reflects the consensus of the ecological community remains an open question.

 Baum & Martin's “It is time to overcome unconscious bias in ecology

Rather than developing a representative and inspiring list of papers for young ecologists, Courchamp & Bradshaw have presented a highly gender and racially biased list in which 97 of 100 selected articles are first-authored by white men.

 Gilbert's “Can 100 must-read papers also reflect ‘who’ is ecology?

Robert May (ten papers), Robert MacArthur (eight) and David Tilman (eight) each had more articles in the list than all female ecologists combined.

 Rameriz et al.'s “The future of ecology is collaborative, inclusive and deconstructs biases

The list continues a long-standing tradition of highlighting almost exclusively work from male scientists and perpetuates a false perception that women, people of colour and people from the Global South are new to the field of ecology. In addition, the list is restrictive in classifying what ecology is, and is not.

 These four letters to the editor at Nature Ecology & Evolution capture and articulate the most important critiques of Courchamp and Bradshaw’s list. But, I think that this one paper and its list of one hundred papers that every ecologist should read begs one more question: What does it mean to read a paper? Courchamp and Bradshaw note that we are reading more papers than before (supposedly 468 papers per year for the average science faculty member in 2012), and more efficiently (average time spent reading has decreased by one-third). They explain that we are able to keep up with this Seussian treadmill of reading more faster through strategies like ‘flick-bouncing.’ But, somehow, despite all their best flick-bouncing, the journal editorial members that voted on the 100 seminal papers ranked articles that they had not read: they marked each paper as ‘“Read it”, “Know it” or “Don’t know it”. The result: “the ranked list of articles differed substantially depending on the stringent criterion of the respondents having actually read them. Overall, only 23% of the 100 top-ranked papers in the all-article list were also in the top 100 of the read-only list. A remarkable example is the top-ranked paper in the all-article list, which is entirely absent in the read-only top 100 (in fact, it was in 325th place in the latter ranking).” 

So, what does it mean to read a paper? Is it sufficient to flick-bounce these 100 must-read papers? (Apparently it’s sufficient to not read them at all, if we go by the voters’ recommendations.) I argue for slow reading — not Courchamp and Bradshaw’s list necessarily, but in general and across a more diverse reading list. Slow reading has become one of my favorite academic activities, and a practice I will forever associate with new parenthood. As I was preparing to return to my dissertation research at the end of my maternity leave, I stumbled on a series of blog posts about #365papers. It was late December 2015, and many of my academic heroes were reflecting on a year in which they had challenged themselves to read a paper a day. In 2015 I was decidedly not on top of the literature: that year I had navigated committee meetings & pregnant fieldwork, presented my research at 35 weeks pregnant and with an eight-week-old baby, I had learned how to install a carseat, but I had not kept up with reading papers. But, I was inspired by the lists, the #365papers hashtag, and the honesty in the recaps. Anne Jefferson's post especially resonated with me: she wrote of her experience reading with a newborn and I thought I could do thatMeghan Duffy at Dynamic Ecology wrote about how she defined a #365papers paper: 

Overall, I read 181 “papers” – though what to count was not always clear. I counted only papers that I read thoroughly and completely – say, at the level that I read something for a lab meeting. This meant that a lot of things that I read didn’t get counted, because I didn’t read the whole thing or only skimmed parts of it. I decided to count manuscripts and grant proposals that I was reviewing, as well as individual chapters of books and dissertations.

 The thorough and complete requirement intrigued me — I had spent my first few years in graduate school perfecting the art of the skim. I often read an abstract, the opening paragraphs of the introduction or discussion, and some figure captions, and then considered myself prepared for class discussion. I didn’t really do deep dives, especially in papers that weren’t directly related to my research. But I liked the idea, as Josh Drew wrote, that this resolution would give “me an excuse to read papers that were outside of my field.” So, I began #365papers in 2016.

In those early exhausting months of parenthood, I could at the very least read one paper each day and feel like I had accomplished something academic. I may have spilled every ounce of milk I pumped, I may have fallen asleep at my desk at office hours, I may have posted the wrong grading rubric for my class, or applied for a field permit for the wrong GPS coordinates, but I was reading! Reading slowly in 2016, I worked my way through the literature behind four chapters of my dissertation and two sets of revisions on my first paper. I re-read the papers that were the cornerstones of my fieldwork methods, I set up google scholar alerts on my field site, I pulled out my copy of Foundations of Ecology, I collected recommendations from folks on twitter, I identified which journals I consistently turned to and started systematically scouring their tables of contents. I came out of the experience with a deeper appreciation for good writing. My reviewing and writing skills improved as I gained confidence in my expertise in both ecology and syntax.

In 2016, I averaged a paper a day for eleven months — I took a break in October — and I loved it. I’ve been less consistent in 2017, but I jumped back into #365papers this October and I’m ending the year on a solid three-month streak. I still skim abstracts (though often those papers end up in my To-Read list for #365papers) and I engage in my share of flick-bouncing. But the papers that shape my thinking — the ones that spark new ideas & stick in my brain for weeks — are slow reads.

As a freshly-minted ecology PhD, I’m not convinced that we need a single list of ‘must-read’ papers. I think instead we need to learn how to read slowly, to build our own systems for collecting pdfs and organizing our stacks of papers, to practice carving out time in our busy days to dig into the literature and think deeply. My favorite slow reads of the year:

  • The four letters to the editor in response to Courchamp & Bradshaw.

  • Kueppers et al. 2017. Warming and provenance limit tree recruitment across and beyond the elevation range of subalpine forest. Global Change Biology.

  • Hudson et al. 2017. Phenoseasonal subcanopy light dynamics & the effects of light on the physiological ecology of common understory shrub, L benzoin. PLOS ONE.

  • Frederickson, ME. 2017. Mutualism are not on the verge of breakdown. Trends in Ecology & Evolution.

  • Ogilvie, et al. 2017. Interannual bumble bee abundance is driven by indirect climate effects on floral resource phenology. Ecology Letters.

  • Toomey, Knight & Barlow. 2017. Navigating the space between research and implementation in conservation. Conservation Letters.

  • Nelson et al. 2017. Signaling Safety: Characterizing Fieldwork Experiences and Their Implications for Career Trajectories. American Anthropologist.

  • Rabinowitz D. 1981. Seven forms of rarity. In The Biological Aspects of Rare Plants Conservation.

  • Graae et al. 2017. Stay or go — how topographic complexity influences alpine plant population and community responses to climate change. Perspectives in Plant Ecology, Evolution and Systematics.

And one more recommendation — it’s not related to scientific literature at all, but I titled this blog post so I could link to David Rakoff’s radio essay on Rent. He felt as salty about Rent as I feel about '100 articles every ecologist should read'.Here’s to the 525,600 minutes awaiting us in 2018 — to daylights, sunsets, midnights, cups of coffee and 365 papers next year.

Australian Students Grapple with Citizen Science

Tis the season for student projects! 

As a postdoc I’m not teaching this year and I’m not pining for a pile of grading, but this is a bit of the academia-phenology that I miss. I’ve found myself idly re-listening to my favorite student-created podcast on alpine heath snowbank communities from a final project last spring. But while I mire in the nostalgia of the ghosts of student projects past, a recent PLoS ONE paper presents an innovative partnership of student projects and citizen science in Australia. Here, Nicola Mitchell and her colleagues showcase the Journal Project — a semester-long project for first year students in large (266-586 students) introductory biology classes that incorporates natural history, data analysis, and writing peer-reviewed papers. Mitchell, a senior lecturer at the University of Western Australia, has led the Journal Project since its inception in 2011.

After reading this paper, I’m torn between two equally strong urges. Should I pose as a freshman Never-Been-Kissed-style and join Mitchell’s class or wholesale borrow this project design and teach a Journal Project with an American citizen science program? Citizen science describes programs that involve non-scientists (ie the citizens, though recently organizations like The Audubon Society have moved toward the term ‘community science’) in some (or all) aspect(s) of study design, data collection or data analysis. The most common model of citizen science draws on volunteer-collect data to expand the spatial or temporal scale of observations, while scientists determine the questions, analysis, and interpretation of the data. 

Earlier this month Ferris Jabr published a wonderful essay in New York Times Magazine on the citizen science app iNaturalist. With iNaturalist, you can snap a photo of an organism and receive identification help almost immediately, placing a name in the palm of your hand. Jabr writes: “Learning the names of wild things changes the way we look at nature and the way we think about it… [It] is an exercise in perspective and empathy, transforming the outdoors from a pastoral backdrop into a world of parallel societies inhabited by diverse creatures, each with its own character and career.” This sentiment so beautifully matches the advice of one of my favorite botanical heroes: “never be content with the common name only. Search, inquire, study, until you have discovered the title by which science recognizes your favorite. There are dozens of swamp pinks; there is only one Arethusa bulbosa; there are scores of Mayflowers, but only one Epigaea repens.” This is from Annie Sawyer Downs, and though she was a 19th century botanist, I believe she would have enjoyed iNaturalist for the same reasons that Jabr does. Just last weekend iNaturalist recorded its 7 millionth observation; the app has become a repository, archiving our human encounters (smartphone in hand) with the natural world over the last nine years. 

The Journal Project is linked to the Australian phenology citizen science program ClimateWatch. ClimateWatch, like iNaturalist, depends on volunteer-collected data. It is specifically focused on documenting changes in seasonal events (budding, leafing, flowering) and behavior (nesting, breeding, migration) for a suite of common species — the phenologies of these species are tracked as indicators of climate change. The Journal Project first requires students to collect data for ClimateWatch, and then assess the program’s volunteer-collected data. I genuinely love the requirement to collect data — in her paper Mitchell includes this quote from a student about their experience collecting ClimateWatch data: “it creat[ed] awareness of the different kinds of plants and birds. They are not just trees, they are now jacarandas and banksia and birds are not black-tail bird or crows they are willie wagtails and magpie lark etc.” This naming is the Jabr & Saywer Downs effect, and I’m so impressed that a large intro bio class was able to facilitate this kind of natural history engagement through citizen science. But, the data collection is just the beginning: early in the semester students are divided into teams and given a raw dataset — all of the records (i.e. no data quality checks) for a given species that have been submitted to ClimateWatch since the launch of its website in 2009.

Assessing the quality of volunteer-collected data can be thorny: were the volunteers where they say they were? Did they actually see what they said they saw? I emailed with Emily Bennett, a recent student who participated in the Journal Project, and asked which part of the experienced was more challenging, making her own observations or assessing the quality of others’ observations. Bennett writes: 

Contrary to my initial expectations before undertaking the Journal Project, I found that assessing the quality of others' observations was one of the most challenging components of the Journal Project; the quantity of observations provided by ClimateWatch Citizen Scientists and combined with the need to generate extensive and yet efficient criteria posed a significant challenge to my group, especially when we realised that the majority of the observations provided did not meet our specified criteria needed to be deemed reliable…After considering criteria for evaluating research from other scientists, I found that making my own observations was a much easier task, and that I was actively seeking ways to improve my observations in both detail and accuracy to ensure that it would meet the criteria for data quality and be of use to other scientists.

 (I am beyond impressed by Bennett and her fellow students here: I assessed the quality of volunteer-collected phenology data in New Hampshire as a M.S. student, and if you want to know more, you should definitely cite McDonough MacKenzie et al. 2017). 

The Journal Project presents students with real data and asks them to engage in two big real-world questions: Does their data provide evidence of phenological or distributional shifts? Does citizen science produce reliable data? Each Journal Project group writes a paper that grapples with one or both of these questions, and then submits this paper to the peer-review process. Peers (other student) review the papers, but so ‘Subject Editors’ (PhD students and postdocs). Revisions are re-submitted and the best articles are published in an online student journal Cygnus on the final day of semester. 

I emailed with two Subject Editors because I wanted to hear more about their role in the class and how closely the Journal Project mirrored the reality of writing a peer-reviewed paper. Mavra Grimonprez explained: “Subject editing…is a very interesting process: we do not have contact with the students [aside from] email and reading their articles, exactly as peer-reviewers do. So we are not biased in any way while marking as we can just assess the quality of the work submitted to us...though we still get a good picture of the writers' personality through reading. It is a thrilling adventure to watch the students improve, see who is responsive to feedback, who is not, watch the groups' dynamics unfold, etc.” When I asked what the Subject Editors received from the experience, Grimonprez said, “I was writing my own article when I applied to be a subject editor: all the guidance and advice I had received from my supervisor, I could in turn provide it to the students and a lot of it made suddenly even more sense as I was in the reviewer's shoes!” She also said that serving as a Subject Editor improved her own writing, a sentiment echoed by Jamie Tedeschi, who wrote “Serving as Subject Editor has not only improved my own manuscript writing, but [gave] me confidence as a manuscript reviewer…I have become a better critic of scientific writing, and have learned how to give valuable and constructive feedback to my peers of all stages in their careers, whether they be undergraduate students, colleagues or supervisors.” 

Another side beneficiary of the Journal Project is ClimateWatch. Mitchell and her coauthors report that by November 2014, 41% of the ClimateWatch records were from University of Western Australia students. Citizen science programs are generally inundated with retirees volunteering to collect data, but often struggle to engage younger audiences. The Journal Project exposes students to citizen science, but it also flips the script as the participants analyze their own data and grapple with data quality in a volunteer-based program. As Mitchell told me, “I guess, like the students, I was pretty shocked to discover how many errors are in the data (some datasets more so than others) – basically the citizen scientists frequently record the wrong species. That said, there IS a lot of good data in each species dataset, and now that ClimateWatch has matured to seven years old, the largest datasets would be valuable for phenological research once erroneous data are removed.” Mitchell’s students are engaged in natural history, data assessment and data analysis, paper writing, peer review, and publishing — an ambitious, broad, and inquiry-based experience that produces both incredible projects and well-trained scientists. Mitchell shared some recent student reflections with me, including these two heart-warmers: 

“Participating in ClimateWatch and the Journal Project have change[d] my perspective of science and affirmed to me that I am on the right path regarding careers…The Journal project was very intimidating, but the experience was rewarding and taught so much more than just learning from a syllabus.” — Emma Kuzminski

“We would like to thank you for the submission of our paper to the Cygnus journal. This has made our day. Being in a scientific peer reviewed journal, where people can see our paper and use it for further research is an amazing start to all of our careers… For a team that was petrified at the start of the year, this has filled us with confidence.” —Sean Davey (and team)

 I encourage you to cuddle up with a copy of Mitchell’s PLOS One paper this winter. You’ll drift off to sleep with visions of student engagement dancing in your heads… Happy holidays!

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

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

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

Impacts of rock climbing on plant communities.

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

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

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

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

Cross country skiing and meadow vegetation

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

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

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

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

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

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

Wildland recreation disturbance at broader scales: hiking & wildlife

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

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

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

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

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

References:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

References:

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

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

A Little Light Reading

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

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

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

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

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

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

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

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

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

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

Ada Lovelace Day

In honor of Ada Lovelace Day, I’m reflecting on the power of naming women in STEM. Ada Lovelace Day aims to “increase the profile of women in STEM and, in doing so, create new role models who will encourage more girls into STEM careers.” There are many biases, systemic and unconscious, that hamper the success of women in STEM or gatekeep against their entry all together. This can make it easy to be cynical of efforts like Ada Lovelace Day — knowing Ada’s name does not impart a force field against rampant sexism in tech; knowing of Rosalind Franklin doesn’t shield one from sexual harassment in the lab or field. And yet, throughout September I kept bumping against examples of the power of naming women in STEM. Reading scientific literature, scrolling through twitter, participating in a TEDx event*: I continued to find myself engaged in conversations about institutions and individuals honoring specific women, and the next generation of women in STEM identifying their own role models.

For example… 

NASA’s Katherine G. Johnson Computational Research Facility officially opened last month. The mathematician, whose story was made famous in the book and film Hidden Figures was one of the human computers whose calculations made early spaceflight possible. I thought about this as I navigated a new campus in my first weeks as a postdoc. I have studied science in many buildings and while not all of them were named for men in STEM, I can’t think of a single building in my career that’s been named to honor a woman in STEM. 

At TEDx Piscataqua in early September, seventeen-year-old Lidia Balanovich shared her perspective as an early-early-career woman in STEM. She spoke of her experience as the lone woman in an AP Physics class — instead of despairing when her personal research on careers revealed examples of STEM’s leaky pipeline, Lidia began a science club for elementary aged kids with the goal of engaging young girls in STEM. Her science activities at local libraries are open to boys and girls, but intentionally highlight the contributions of women in STEM. I was impressed that Lidia’s reaction to the data on the challenges facing women pursuing careers in STEM was to open the path to the generation behind her. She immediately recognized the power of naming women in STEM — both for herself and for the kids with whom she engaged. 

On twitter, @JacquelynGill recognized Phyllis Draper, the first scientist to reconstruct past vegetation from pollen in North America. Jacquelyn, Assistant Professor of Paleoecology and Plant Ecology at University of Maine and an established palynologist in her own right, wrote of her general recognition that historically many women contributed to the field, their names now lost to history. That such an eminent scientist and feminist could not know about a foundational figure in her own field is astounding. For women in STEM, our historic role models are there — analyzing pollen in 1929 — but we have to excavate their stories and bring their names to light. This is work for the whole STEM community — to bring recognition to the history of our fields, to highlight the work that our research and theory is built on, and to reflect on the progress of our efforts to create equity and inclusion and the challenges that still remain embedded in our labs and field sites.

Finally, eight-year-old Sophia Spencer co-authored a paper in the Annals of the Entomological Society of America. She writes with Dr. Morgan Jackson about the power of the #BugsR4Girls hashtag. Sophia’s mom reached out to the Entomological Society of Canada when Sophia, an avid bug enthusiast, was teased for liking bugs. This letter inspired #BugsR4Girls, and suddenly twitter was full of entomologists exclaiming that of course bugs are for girls! Sophia expresses her reaction to this outpouring in her paper: “After my mom sent the message and showed me all the responses, I was happy. I felt like I was famous. Because I was! It felt good to have so many people support me, and it was cool to see other girls and grown-ups studying bugs. It made me feel like I could do it too, and I definitely, definitely, definitely want to study bugs when I grow up, probably grasshoppers.” 

Happy Ada Lovelace Day! Here’s to women in STEM — may we be them, may we raise them, may we recognize their contributions both historical and modern, and may we name more buildings after them! 

*After reflection, I realized that in my own TEDx talk, I was also naming a woman in STEM. I shared the story of Annie Sawyer Downs, a 19th century botanist, mostly forgotten, who mentored the young Edward L Rand as her compiled the Flora of Mount Desert Island, Maine. A part of my inspiration for this talk: Rand’s data and field notes made it into my dissertation, but despite years of searching I’ve never found Annie’s journals or raw botanical records. I uncovered the pieces of a fascinating life — she grew up botanizing with Thoreau, she was a school teacher who published natural history essays in magazines, she founded a library on Mount Desert Island — but none of this story made it into my PhD defense talk.

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

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

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

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

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

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

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

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

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

References:

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

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

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

Science Communication, Simple Words, and Story Telling at ESA 2016

A guest post from PLOS Ecology Reporting Fellow, Caitlin McDonough, on research from the Ecological Society of America Scientific Meeting in Ft. Lauderdale, Florida, August 7-11, 2016.

On Tuesday afternoon at the Ecological Society of America 2016 Conference in Ft. Lauderdale, FL, amid the many Latin species names and varied sub-discipline jargon, it was possible to stumble upon a session of talks about blue flyers, spring pretty flowers, God’s creatures, and animals with six legs and no bone in their back. The audience fell in love with black back wood hitters, cheered for flying friends with six legs and four wings that like sweet things and help plants with sex and was touched by the sentiment that the land had memory made up of things in the dirtand much of the memory was lost. 

This was the Up Goer Five Ignite Session, where seven brave scientists took on the challenge made famous by xkcd comic author Randall Munroe and his Thing Explainer book and presented their research using only the 1,000 most common words in the English language, originating from Munroe’s eponymous example. In the ESA session, the phylogeny of grassland plants was reduced to grasses, grasssish, smells fresh, sun flowers, fixers, and roses and climate change was described as the whole earth surface is getting more and more hot. The presenters approached their talks with a high level of creativity and humor, and the audience responded with enthusiasm, empathy, and #UpGoESA tweets.

Rebecca Barak opened the session with a high-energy summary of grassland restoration research. Her talk featured the poetic land memory line and the hilariously simplified grass phylogeny, as well as the explanation that one piece of equipment used to study seeds was the special machine that doctors use to look inside of you.

Nick Haddad asked Can I light a fire to save those damn butter flies? With surprising dexterity he wove the story of Icarus and Daedalus into his research on fire adaptation and complex species interactions. Here, we noticed how difficult it is to mark temporal change and population dynamics of a butterfly species with only the 1,000 most common words: over five tens of years the numbers of these plants have gone down to zero. The stark phrasing that people may need to kill these animals to save them was very powerful in this pared down vocabulary.

Margaret Lowman may have smuggled in a few extra words, but her talk about working with priests in Ethiopia to save sacred forests (birds eye view of trees: in the center is a round house called a church) was a refreshing reminder that there are whole communities that ecologists traditionally neglect to engage with, and these have the potential to be fruitful partnerships.

David Inouye shared research from his field site (or where he spends his time playing while not teaching) and explained phenology models by asking the audience Can we guess when that will happen? His talk featured the memorably phrased description of his Colorado field site location as the place where people over 21 can buy grass to get high. Samuel Cowell regaled us with tales of the nesting behavior of blue flyers — their propensity for stealing some wood hitter homes, but also their territorial protection of other wood hitter homes, ultimately summarizing their complex interactions as blue flyers are bad and good to the wood hitters.

Jeff Atkins’s visuals — drawings commissioned from his and his colleagues’ children — strongly resonated with the audience. Pairing crayons and construction paper with the big green stuff and the small green stuff, in the mountains and the not so flat ground was a brilliant take on the simplified vocabulary.

Finally, Elizabeth Waring closed the session with her comparison of Old Green Things and New Green Things. The crowd loved her terms for nitrogen deposition (extra ground food to make green things for humans grow harder faster stronger) and greenhouse experiments (grown in a hot box, I changed how hot the grass got).

Science communication, language, and accessibility were at the center of the post-presentations discussion. Across all of the talks, the most memorable and successful Up Goer Five phrases didn’t just substitute simple words for scientific jargon, they were emotional and evocative compositions. Distilling one’s science into the 1,000 most common words was described as an opportunity to influence the connotation of common (but not top 1,000 words common) phrases with thoughtful word choice. The direct vocabulary has a sharp impact. As one audience member noted, this was not just an exercise in how good are you at using a thesaurus — the speakers found ways to be poetic, expressive, and clear.

Restricting word choice to the 1000 most common words highlights how few of our common words are ecological terms. In a way, this highlights the difficulty of science communication with the general public: our vocabularies do not always intersect. Meg Lowman wondered aloud if we could add 125 of “our words” back to the common vernacular. The loss of nature words from the Oxford Children’s Dictionary and our vocabulary in general has been noted. Is this a crusade for ecologists? What are the 125 words that we most miss? And what can we do to reintroduce these into words so that the next generation of Up Goer Five ecologists has the ability to say “trees”? 

Great story telling was not limited to the Up Goer Five session. At the Wednesday night Special Session “Engaging with the Wider World True Tales Told Live” four ecologists were given the whole range of the English language to speak to their experiences in diverse forms of engagement. During his tale Matthew Williamson confessed to fellow story-teller and ESA President Monica Turner that years ago, in a punk rock phase, he had joined her field team as kid with a Mohawk and a bad attitude. The narratives tracked births, deaths, career changes, and community building; they reflected on intersections of creativity, courage and advocacy. There were funny moments — Monica Turner admitted “I am not Stephen Colbert!” — and deeply poignant personal stories. In beautifully crafted prose, Annaliese Hettinger described the joy, isolation, and exhaustion she found in finishing her Ph.D. within a year of the birth of her son, while caring for her dying mother who, decades before, had defended her own Ph.D. when Annaliese was an infant. There was a real sense of craving in the audience as we watched these ecologists talking about science communication. We want more examples of successful science communication, and more opportunities to practice these skills ourselves. These opportunities are at ESA; among our ranks are excellent science communicators, our meetings feature multiple workshops focused on diverse engagement opportunities, and the Up Goer Five audience passionately embraced the idea of an annual Ignite Session. Hopefully this is an areas where we can continue to build and grow. 

Caitlin McDonough MacKenzie is a PhD candidate in the Primack Lab in the Biology Department at Boston University. She spends her field seasons in Acadia National Park, Maine studying leaf out and flowering phenology and patterns of historical species loss across plant communities. Her field methods include three ridge transects that are conveniently located adjacent to beautiful running trails and carriage roads. Away from Acadia’s granite ridges, she’s interested in underutilized sources of historical ecology data including herbarium specimens, field notebooks, photographs, and old floras; the potential for citizen science in phenology research; and the intersection of science and policy.  (Follow Caitlin on Twitter @CaitlinInMaine)

Leveraging the Power of Biodiversity Specimen Data for Ecological Research

A guest post from PLOS Ecology Reporting Fellow, Caitlin McDonough, on research from the Ecological Society of America Scientific Meeting in Ft. Lauderdale, Florida, August 7-11, 2016.

Leveraging the Power of Biodiversity Specimen Data for Ecological Research at ESA 2016 While ecologists spend their graduate days troubleshooting code, writing manuscripts, and fighting with dataloggers, they often trace their roots back to a love of natural history--an acknowledgement of a childhood curiosity sparked by museums, camping trips, and backyard bug collections. This curiosity ties us ecologists to a long line of scientists, taxonomists, and collectors; we imagine that we could have sailed on the Beagle, or climbed Chimborazo, or that we would have happily canoed the wild Allagash River to botanize with Kate Furbish. On Wednesday morning, a group of 21st century ecologists presented a modern twist on these natural history dreams, with research in collaboration with these taxonomists, botanists, and collectors of the past. (A video of the session will be posted here.) 

iDigBio (Integrated Digitized Biocollections) organized this session, which brought together a diverse array of ecologists who have leveraged the power of biodiversity specimen data to approach 21st century problems in taxonomy, conservation biology, and climate change research. Each project relied on some form of biodiversity specimen data — from herbarium specimens to insect collections to marine collections — for applications ranging from restoration ecology to unraveling cryptic speciation, or creating species distribution models to tracking patterns in phenology. Recent efforts to digitize biological specimen data have sparked a renaissance in their use — pressed plants and pinned bees that once sat neglected in a dusty corner are now accessible to researchers thousands of miles away. In many cases, the 19th century collectors would likely recognize these research goals as they too were interested in species distributions,  recorded phenological events, and made observations about interactions between herbivores and plants. But, Thoreau did not geotag his field notes, and Linneaus might be surprised to find his herbarium specimen available as a jpeg. The importance of making biodiversity specimen data digitally accessible was clear from the start of the session.

Pamela Soltis noted that there are over 1,600 natural history collections in the U.S. with somewhere between one and two billion specimens. But iDigBio estimates that only 10% of biodiversity specimens are digitized. Throughout the session, presenters noted both the benefits of accessing the digitized data and the challenges of working with taxa and trophic levels that were underrepresented in the digital specimen world. Katja Seltmann lamented the lack of digitized parisitoids collections, and called out a bias towards plants and pollinators. Joan Meiners, who uses digital natural history collection specimens to investigate native bee conservation, showed a graphic of the low proportion of digitized bee specimens at major U.S. insect collections. The next speaker, Francois Michonneau, topped both of their complaints with an example of a historic sea cucumber collection that had been preserved in pieces, the equivalent of an ornithologist placing a beak and talons in a glass bottle and calling it a bird collection.  It is clear that the biodiversity specimens that are digitized are inspiring new research. Emily Meineke shared the origin story of her herbaria research: her project began in her kitchen. While flipping through old specimen data online during a procrastination jag, she noticed herbivory damage captured in one of Linnaeus’ specimens. With a little more digging, she found evidence of herbivory in many specimens — leaf mines, chewing damage, and galls — as well as actual insects preserved in the old leaves. Another example of unintentional data captured in herbarium specimens is Amanda Gallinat’s fruit phenology study. She found over 3,000 specimens comprising 55 species in seven major New England herbaria that contained mature fruit pressed among the plant material. Just as Meineke realized that herbaria offer unprecedented opportunities to understand what factors drive herbivory rates across large spatial and temporal scales, Gallinat was able to assess patterns in fruiting across native and invasive species at a regional scale from the 19th century to the present. Meineke has begun surveying for herbivory damage in the Harvard University Herbarium collection, but she is also working to make this a citizen science project called Bite Marks in the Zooniverse. Soon everyone will have the opportunity to look at herbivory damage while procrastinating in their kitchens! 

In addition to the diverse research that has emerged from digitized biological specimens, this session provided some practical advice for all ecologists. Pamela Soltis presented Charlotte Germain-Aubrey’s project “Using museum data for species distribution modeling: The case of plants in Florida” and provided a thoughtful behind-the-scenes look at the building of a maximum entropy model. She deliberately explored the process behind decisions about climate data (e.g. average climate vs. climate data from the year of collection for each specimen), the area in which the model trains, smoothing response curves, and the number of background points. François Michonneau closed his talk with a great overview of his best practices for instituting data quality checks in R code workflow. While these skills are typically missing from our training, he stressed the importance of building a culture of documentation and replication, recommending courses from datacarpentry.org. Katelin Pearson showed that the collector community — a group that is regularly in the field, well-trained to recognize patterns and norms, and communicate with other experts — currently lacks the protocols and the semantics to document outliers in a consistent, meaningful way. This community has great potential to detect outliers in phenology, distribution, ecology, behavior, morphology, but at the present there is no direct feed between the collectors and ecologists who are tracking changes or outliers.

Finally, Libby Ellwood closed the session with an overview of iDigBio’s citizen science projects to engage the public in the work of digitizing the many, many biological specimens that are not yet a part of the digital record. 

Caitlin McDonough MacKenzie is a PhD candidate in the Primack Lab in the Biology Department at Boston University. She spends her field seasons in Acadia National Park, Maine studying leaf out and flowering phenology and patterns of historical species loss across plant communities. Her field methods include three ridge transects that are conveniently located adjacent to beautiful running trails and carriage roads. Away from Acadia’s granite ridges, she’s interested in underutilized sources of historical ecology data including herbarium specimens, field notebooks, photographs, and old floras; the potential for citizen science in phenology research; and the intersection of science and policy.  (Follow Caitlin on Twitter @CaitlinInMaine

Common Gardens For All Your Climate Change Needs

A guest post from PLOS Ecology Reporting Fellows, Caitlin McDonough MacKenzie & Daniel E. Winkler, on research from the Ecological Society of America Scientific Meeting in Ft. Lauderdale, Florida, August 7-11, 2016. 

Experimental gardens are an old-school methodology. In perhaps the best known example in the 1930s and 1940s Clausen, Keck, and Hiesey transplanted Potentilla glandulosa across their range in the Sierras to explore the roles of environment and genetics played in determining growth form. Clausen, Keck, and Hiesey’s classic methodology of reciprocal transplanting has a contemporary application in climate change studies, whereby researchers relocate a plant (or seed) from its home and current climate to a transplant garden and new (and perhaps future) climate. Seven decades later, the Ecological Society of America’s 2016 Annual Meeting features experimental gardens that include species ranging from alpine forbs to douglas fir trees to a dune-loving annual—collected along latitudinal, elevation, and habitat gradients. 

Nicole Rafferty opened the Climate Change: Ranges & Phenology I session presenting her research on patterns of bumblebee visitation at the Rocky Mountain Biological Laboratory. As a part of this project, she installed a reciprocal transplant experiment with seeds from three elevations planted at 12 plots per elevation site. She wanted to test how alpine plant-pollinator relationships might change as plant communities experience new microclimates (for example, if a species is transplanted to a warmer site at a lower elevation). Unfortunately, the first year of this study coincided with a dry summer and low germination rates — as a result, in 2016 she switched to seedlings. In her 2015 seed study, the glacier lily seeds from mid-elevation had the lowest success in the transplants, suggesting that mid-elevation might be a barrier to plant migrations upslope for this species.  

Range shifts and phenological are also on the minds of researchers at the U.S. Forest Service. This time with an applied focus aimed at aiding land managers who will likely need to develop strategies to make Forest Service lands more resilient to climate change impacts. Sheel Bansal at the U.S. Forest Service’s Pacific Northwest Research Station and colleagues carried out a large-scale common garden study aptly named the Douglas-fire Seed-Source Movement trial. Their experiment used seeds from 60 sources throughout the species range in Washington, Oregon, and California and grew trees from each of the sources in 9 climatically-divergent field sites and also used artificial freeze experiments to test the impacts of changing environmental queues on Douglas fir cold hardiness and associated genetic linkages. They found strong differences in cold hardiness, with minimum winter temperatures and fall frosts as major predictors of cold hardiness based on seed source. Their results have important implications for the ability of species to shift their ranges by tracking climate envelopes, and further extend to land management efforts to maintain healthy forests experiencing future climates.

In the Great Lakes region, Elizabeth LaRue from the Emery Lab at the University of Colorado Boulder used a common garden to explore dispersal traits in American sea rocket (Cakile edentula var. lacustris). She knew that dispersal traits like pericarp, or seed wall, thickness and wet mass varied across the Cakile edentula range, but it was unclear if the variability was caused by environmental or genetic differences. Collecting seeds from across the range, and growing them together in a common garden isolated the role of genetic differences and revealed lower dispersal traits at the range edges. This data was used to inform species distribution models with different scenarios for starting dispersal genetics for Cakile edentula under climate change.

Kennedy Rubert-Nason in the Department of Entomology at the University of Wisconsin-Madison and his colleagues looked at the role of vernal freezes in determining aspen phenology and growth. They planted 6 aspen genotypes into common gardens at varying temperatures and examined a number of biological responses.  The number of days it took aspen to break bud accelerated in trees that experienced freeze-damage. Freeze-damaged trees were also stunted in their second year of growth when they experienced a freeze event during their first year. Defense compounds were also dramatically impacted, potentially indicating the negative effects of freeze events and the associated ability of the trees to defend against herbivores during their most vulnerable life stage. Their study nicely highlights the importance of the timing of environmental queues in dictating species susceptibility to a changing climate. 

Caitlin McDonough MacKenzie is a PhD candidate in the Primack Lab in the Biology Department at Boston University. She spends her field seasons in Acadia National Park, Maine studying leaf out and flowering phenology and patterns of historical species loss across plant communities. Her field methods include three ridge transects that are conveniently located adjacent to beautiful running trails and carriage roads. Away from Acadia’s granite ridges, she’s interested in underutilized sources of historical ecology data including herbarium specimens, field notebooks, photographs, and old floras; the potential for citizen science in phenology research; and the intersection of science and policy.  (Follow Caitlin on Twitter @CaitlinInMaine

Daniel Winkler is a PhD candidate at the University of California, Irvine and a recent National Park Service Young Leader in Climate Change. Daniel is a plant ecophysiologist interested in invasive species, evolutionary ecology, and climate change impacts on native communities in “extreme” environments. His field sites include much of the desert southwest, alpine regions of Colorado, the subalpine forests of Baja California, and the tundra of northern Japan. All of Daniel’s research focuses on climate change impacts on native systems, with an emphasis on parks and protected areas. You can follow him on Twitter @DanielEWinkler, his research on Facebook at www.facebook.com/GeoMustard/, or find more information on his website at www.winklerde.com.