Category Archives: science

New paper: Conflict and communication in mutualism

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Medicago truncatula, or barrel clover, a member of the legume family that hosts bacteria in its roots. The bacteria transform nitrogen gas from the atmosphere into fertilizer for their host plant, and the host feeds the bacteria with sugar. Experiments with barrel clover and its mutualists have shown that signals between the plant and the bacteria are important in this interaction, and provide an inspiration for the evolutionary models built by Yoder and Tiffin. (Flickr: jby)

I’m very excited to see this in virtual print — it’s a new model of coevolution between mutualists that takes into account signals between the partners as well as the benefits they provide each other (or don’t).

Yoder JB and P Tiffin. 2017. Sanctions, partner recognition, and variation in mutualism. American Naturalist doi: 10.1086/693472.

I’ll try to write about this in more depth at some point, but here’s the lay summary at the American Naturalist website:

Mutually beneficial relationships between species, or mutualisms, are ubiquitous in the living world, with examples ranging from flowering plants that rely on animal pollinators to fish that clean the teeth and scales of other fish. Mutualisms are often imperfect — one partner or the other varies in the quality of the help it provides. Evolutionary theory predicts that this should break up the relationship, but most mutualisms hold together in spite of partners that take the benefits of mutualism without properly paying them back.

This paradox may be explained by the fact that there’s more to mutualism than trading goods or services. This is a key result of mathematical evolutionary models published in the American Naturalist by Jeremy Yoder and Peter Tiffin, biologists at the University of British Columbia and the University of Minnesota. Yoder and Tiffin built a mathematical evolutionary model of mutualists that communicate before trading resources, and compared it to simpler models with only resource-trading or only communication. In the model with communication and resource-trading, host could “sanction” by cutting off resources to prevent poor quality partners from taking over, but evolution of the signals sent by partners and the hosts’ response to those signals maintained variation over time. Neither of the simpler models could do this. With only resource-trading, sanctions eliminated all poor-quality partners, and all variation; with only communication, poor-quality partners took over the mutualism.

The Yoder Lab opens in fall 2017

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I’m very excited to announce that I’ve accepted a faculty position with the Department of Biology at California State University Northridge, starting this coming fall.

CSUN is about as close as possible to the ideal place to do the kind of science and scholarship I want to do — a large, diverse public university with strong support for teaching and research, and great colleagues studying ecology, evolution, and every aspect of the living world. Campus is located within half an hour’s drive (well, maybe an hour with traffic) from sites where I studied Joshua trees as a graduate student, and it has good facilities and an excellent climate for growing my favorite legume, too. (I’d be remiss if I failed to mention, as well, that CSUN should be familiar to fellow fans of “Crazy Ex-Girlfriend” as the alma mater of one Joshua Felix Chan.)

To extend a metaphor I used in an essay about being a postdoc last year, I feel like I’ve finally been called up to the big leagues. I’ve already submitted my first pre-proposal for NSF research funding with CSUN affiliation, with collaborators from the Joshua Tree Genome Project, and I’m making plans to hit the ground running with that project and others when I officially arrive on campus later this summer.

I also have a lab website and Twitter feed set up, and I’m looking for graduate students to start in the fall. The deadline to apply to the CSUN Biology Master’s program is coming up fast — interested students can find out the details here and drop me a line.

We’re in challenging times for teaching science and doing basic research, but I firmly beleive that the challenges scientists and educators now face make our work all the more important. There’s a lot of exciting science to be done, and I can’t wait to start.

New paper: Understanding mutualism with population genomics

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Comparing metrics of diversity (x axis) and geographic differentiation (y axis) for thousands of genes in the Medicago truncatula genome (gray points) reveals that some symbiosis genes (red points) are genome-wide outliers — but they are not all the same kind of outlier (crosses and triangles). Yoder (2016), Figure 1.

Comparing metrics of diversity (x axis) and geographic differentiation (y axis) for thousands of genes in the Medicago truncatula genome (gray points) reveals that some symbiosis genes (red points, crosses, and triangles) are genome-wide outliers — but they are not all the same kind of outlier. Yoder (2016), Figure 1.

My very latest scientific publication is now online at the American Journal of Botany. It’s sort of an odd paper — something of a review, or an opinion piece, discussing how population genomic data can help us understand why mutualisms stay stable [PDF] in spite of the risk of “cheating” by partners, with a “worked example” with data from the Medicago HapMap Project. Here’s some key bits from the abstract:

Different hypothesized models of mutualism stability predict different forms of coevolutionary selection, and emerging high-throughput sequencing methods allow examination of the selective histories of mutualism genes and, thereby, the form of selection acting on those genes. … As an example of the possibilities offered by genomic data, I analyze genes with roles in the symbiosis of Medicago truncatula and nitrogen-fixing rhizobial bacteria, the first classic mutualism in which extensive genomic resources have been developed for both partners. Medicago truncatula symbiosis genes, as a group, differ from the rest of the genome, but they vary in the form of selection indicated by their diversity and differentiation — some show signs of selection expected from roles in sanctioning noncooperative symbionts, while others show evidence of balancing selection expected from coevolution with symbiont signaling factors.

The paper is my contribution to a Special Section on “The Ecology, Genetics, and Coevolution of Intimate Mutualisms”, which I co-edited with Jim Leebens-Mack. You can view the whole Special Section here, and download my paper here [PDF].

My review of Lab Girl for the LA Review of Books

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How should I illustrate a review of Lab Girl? Let's go with a cool plant. This is bunchberry, Cornus canadensis (Flickr: jbyoder)

How should I illustrate a review of Lab Girl? Let’s go with a cool plant. This is bunchberry, Cornus canadensis. (Flickr: jbyoder)

You have surely, by now, heard all about Hope Jahren’s terrific scientific memoir Lab Girl, including as one of my “bookshelf” recommendations for Chronicle Vitae. My full-length review of Lab Girl is now online at the LA Review of Books, and it is, as you might expect, very positive — Jahren writes beautifully about the process of scientific discovery and the daily miracles of the natural world. As a postdoc still scrabbling for purchase on the lower rungs of the tenure track, though, Lab Girl managed to simultaneously tweak my anxieties and give me hope:

The world is heating up, and it often seems that the intellectual luxuries afforded to scientists of the past — Darwin’s leisurely publication schedule, Haldane’s dalliances with radical politics — are gone. Lab Girl’s rendition of the daily institutional frustrations of research marks it as a different kind of scientific memoir — but also as a product of twenty-first century science. If you navigate among scientists’ blogs or scroll through their Twitter feeds, you’ll quickly find the same fears and vexations and injustices Jahren describes, intertwined with accounts of the work that excites scientists’ passions. … Jahren does not makes science look like an easy career choice, but it isn’t her job to do so — and if Lab Girl chronicles the real and substantial barriers to becoming a successful scientist, it also makes that life compelling: she shows the fruit that can still grow from the rocky soil of a research career.

I do hope you’ll read the whole review, and pick up a copy of Lab Girl if you somehow haven’t already.

A new Queer in STEM starts soon!

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There’s big news today at the Queer in STEM project site: we’re about to launch a new iteration of our online survey. Queer in STEM 2.0 is happening thanks to Joey Nelson, a PhD candidate in geosciences at Stanford, who approached us last fall about developing a new study to build on what we’ve learned from the first Queer in STEM survey. He had some great ideas for new questions to tackle:

Do LGBTQ-identified people remain in the closet in STEM workplaces mainly because they feel a lack of support, or because STEM workplace cultures discourage discussion of personal lives outside the lab? How do LGBTQ-identified colleagues, mentors, and role models affect their careers? Does being “out” in the workplace affect their research productivity?

Queer in STEM 2.0 aims to answer these questions with a new online survey designed for more specific hypothesis testing. We hope to hear again from participants in the original Queer in STEM survey, and to achieve an even bigger sample from LGBTQ-identified STEM professionals across the U.S. and Canada. Finally, in our biggest innovation from the original study, we will also ask STEM professionals who don’t identify as LGBTQ to answer many of the same questions we will ask LGBTQ-identified participants, to provide a powerful new tool for understanding the survey results: a control sample.

Joey’s taken the lead in developing a new, more focused questionnaire that adjusts the questions it presents based on initial responses — so, hopefully, it’ll be a smaller time commitment for participants. We’ve also had help and input from Daniel Cruz-Ramirez de Arellano, a chemist at the University of South Florida who’s already worked with Allison to analyze one-on-one interviews from the first study. We’re also grateful to have the continued support of NOGLSTP, and now oSTEM, too.

As an aside: We’d originally planned to announce the new study on Monday, but we held off for a bit in the wake of the horrific mass killing at the Pulse nightclub in Orlando. It’s hard to think that a project like Queer in STEM matters much, in the face of that kind of hatred. I do believe, though, that working to understand individual queer experiences — the nitty gritty details of our lives and careers — is part of the much bigger project of making society kinder to all people. The Pulse massacre is only the latest act of anti-queer violence to add to the fears that LGBTQ-identified folks carry with us every day — including in our laboratories and classrooms. I know I speak for all my collaborators when I say that we hope Queer in STEM can help to make those spaces feel safer.

We’ll officially open the new survey for responses on Monday, 20 June — look for notice here, on the study site, or on social media.

Chapter on coevolution in the Encyclopedia of Evolutionary Biology

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Grant (1949).

My visualization of key data from Verne Grant’s 1949 paper showing that floral traits are more likely to be important in the taxonomic descriptions of plant species when those species are pollinated by animals — which suggests that those plant-pollinator interactions play a role in the formation of new species.

I got word this morning that the Encyclopedia of Evolutionary Biology, a huge compendium of current knowledge on evolution, systematics, and ecology, is now online. That’s exciting in and of itself, but it’s particularly so because it means you can finally see my contribution, the introduction to the topic of coevolution. Here’s the opening paragraph, of which I’m rather fond:

No organism is an island. Every living thing contends with predators, parasites, and competitors, and most also receive benefits from mutualists (Table 1). These interactions with other species exert natural selection—and predators, parasites, competitors, and mutualists may also experience selection in return. The mutual evolutionary change that results from this reciprocal selection is ‘coevolution’ (Janzen 1980; Thompson 2005).

The rest of the Encyclopedia includes contributions from a tremendous array of other authors, and I’m grateful to subject editor Andrew Forbes for the invitation to contribute. You can browse the whole thing on the publisher’s website, and download a manuscript-format PDF of the final text of my chapter here.

STEM employers in North Carolina: Time to put your money where your mouths are

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Morehead Planetarium on the campus of UNC Chapel Hill (Flickr: William Yeung)

Morehead Planetarium on the campus of UNC Chapel Hill (Flickr: William Yeung)

North Carolina’s got a shiny new law legalizing antigay discrimination and legislating where trans folk can pee. (More specifically, it forbids the state’s cities and municipalities from passing nondiscrimination laws that protect sexual orientation and gender identity, which some have done.) It’s probably in violation of current Federal regulations and the Constitution, but it could be years before that’s sorted out in court.

H2 was written, passed in a special legislative session, and signed into law in about 10 hours — so quickly that some Democrats walked out of the state Senate in protest of the procedural chicanery. There was effectively no time to mount any public campaign against the law before it became law. Which is a pity, because a similar law under consideration in Georgia is now literally up against Mary Poppins and Captain America: the Walt Disney Company and its subsidiary Marvel Entertainment are threatening to pull operations from the state if the bill passes.

I’m not aware that North Carolina has much of an economic stake in making superhero science fiction, but I do happen to know that the state is deeply invested in actual science. The Research Triangle is a development region created in a public-private partnership to foster science, engineering, technology, and mathematics (STEM) businesses with close ties to Duke University, the University of North Carolina, and North Carolina State University. It was named one of the “Top 10 Biopharma Clusters” last year. So this seems like it might be a problem for the academic side of all that partnership:

As interpreted by the Department of Education, Title IX of the Education Amendments of 1972 forbids discrimination against trans students in any school that receives federal funding. These schools are prohibited from excluding trans students from the bathroom consistent with their gender identity. The new North Carolina law, dubbed H2, rebukes this federal mandate by forbidding public schools from allowing trans students to use the correct bathroom. That jeopardizes the more than $4.5 billion in federal education funding that North Carolina expected to receive in 2016.

Continue reading →

Coming soon: Crowd-funding a Joshua tree genome

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Joshua trees at Tikaboo Valley, Nevada (Flickr: jby)

Joshua trees at Tikaboo Valley, Nevada (Flickr: jby)

I’m very excited to announce a new project, with a new model for doing science: The Joshua Tree Genome Project, in which I’m working with a bunch of smart, accomplished folks to sequence the genome of my favourite spiky desert plant. A sequenced Joshua tree genome will provide the framework to understand how coevolution with highly specialized pollinators has shaped the history of Joshua trees, and to use the landscape genomics skills I’ve developed with the Medicago HapMap Project and AdapTree to understand how the trees cope with extreme desert climates — and how to ensure they have a future in a climate-changed world.

Perhaps most excitingly (terrifyingly?) we’re going to raise some of the funds to do the genome sequencing by crowdfunding, using the Experiment.com platform. So please keep an eye on the project site, follow our Twitter feed, and Like our Facebook page to make sure you don’t miss your chance to help understand Joshua trees’ evolutionary past and ensure their future.

In 2016, keeping an eye on the numbers

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(Flickr: An&)

(Flickr: An&)

Whether or not it makes any sense, the start of a new year is traditionally when we come up with lists of things we wish we did more, or less, or at all. At least it’s a chance to place a psychological flag in the sands of time and say, now is when I start keeping track of whether or not I do this thing. Reading other folks’ academic resolutions for 2016, I’ve seen some things I’d like to work on for my own sanity and scholarly productivity, and there’s a meta-resolution that ties them all together: counting.

I’ve long had a skeptical relationship to resolutions about achieving specific numbers of things — losing pounds, reading papers, writing pages. It seems like a lot of cognitive load for payback that is nebulous, at best. But as I look back on years past, I have to admit that what I count is what I get done.

I’ve run eight marathons in the last seven years, and most of my actual training has been simply aiming to run at least 30 miles a week. Over last year that added up to 1,882 miles — I’ve run upwards of 1,500 miles every year since 2010. I don’t fret about pacing or getting in just the right mood or the specific route I take — I just make sure I get to 30 every week. When I got my first activity-tracking wristband (I currently have a Fitbit) and started logging calories, I actually did find myself making small, sensible changes — walking more, eating more vegetables — to keep my daily numbers above 10,000 steps and below an activity-adjusted calorie count. Tracking my reading on GoodReads hasn’t gotten me to a goal of 20 books in a year yet, but it’s definitely gotten me doing more pleasure reading than I was before I kept count. And on the career front, I started out the 2015-2016 hiring season by building a spreadsheet to track my applications for faculty jobs—and I will, in fact, manage to get to 60 submissions. (Which have led to a non-zero number of interviews, about which I will say nothing further in any public venue lest I jinx something.)

In conclusion, counting a thing is a good way to help (me, at least) get more of that thing done. So, in 2016, I might as well count some other things that I would like to do more. Two things that have fallen by the wayside while I’ve moved across the continent and done all that job-applying are keeping up with the scientific literature (apart from what I read in the course of grant- and paper-writing) and writing rapidly and often. So I’m signing on for 365papers and 50posts. And here’s hoping for a non-stop new year.

https://www.youtube.com/watch?v=Slt18JWkdj4

Social Evolution Forum: Evolution in response to ecological conditions changes ecological conditions

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Daphnia magna adult and juvenile. (Flickr: NTNU Faculty of Natural Sciences and Technology)

Daphnia magna adult and juvenile. (Flickr: NTNU Faculty of Natural Sciences and Technology)

I am very happy to be among the members of the Evolution Institute’s new community blog, the Social Evolution Forum. The team includes a bunch of terrific geneticists and anthropologists and people with more social-science-y backgrounds … and me, with a publication record that’s easily 90% research on plants, which do not have societies in any meaningful sense, and interactions between plants and other things that are not really very social, either — moths, or bacteria. Still, nothing in biology makes sense except in the light of evolution, and evolution is very much what I study, and I have written about the biology of the most quintessentially social species, Homo sapiens quite a bit in the past.

All the same, for my inaugural post to SEF, I’m leaning into my role as the generalized evolutionary ecologist with a kind of post I haven’t written in some time, it feels like: a brief discussion of a cool new experiment in rapid evolutionary change and its ecological consequences.

Evolution in response to natural selection over a few weeks or months may not seem like it could matter much, but a recent experiment with one tiny evolutionary champion shows that it can, in fact, have measurable effects on a whole community of interacting species. The communities in question are the kinds found in ponds all over the world, in which swarms of small crustaceans compete to graze and prey on algae and other microorganisms, and evade death in the gaping maws of minnows and sticklebacks. One of these crustaceans is Daphnia magna, the common water flea, which has a life cycle that turns out to be quite convenient for scientists who want to watch evolutionary change in real time.

As you’ll find if you read the whole thing, Jelena H. Pantel and her coauthors raised clonally-reproducing Daphnia in artificial environments with communities of competing crustaceans for about three months — ten water-flea generations or so. They then used individuals sampled from those evolved populations to colonize new communities, and compared what happened to those communities to ones started with Daphnia that hadn’t had time to evolve. It’s a nice experiment in ecological consequences of evolutionary change — and how that change can actually feed back to alter the conditions that caused it in the first place.

And, when you’re done with that, check out great opening articles by Arun Sethuraman, Lee Alan Dugatkin, Jennifer Raff, and Anthony Biglan — that should give a pretty good sense of the variety of voices and expertise you can expect at SEF.