New publication: A genetic fingerprint of coevolutionary diversification

A red milkweed beetle, Tetraopes tertophthalmus, on its host plant (jby)

A new paper from the lab — coauthored with all three of the Yoder Lab’s graduate student alumni — is now online ahead of print in the journal Evolution Letters. In it, we analyze population genetic data from 20 pairs of plants and herbivores, parasites, and mutualists that live intimately on those plants to test for evidence that the associate species’ population genetic structure aligns with that of their host plants. This is an expected result if adaptation to the host plant drives diversification of the associates — and we found that it is indeed a recurring pattern. This is a pretty neat result, and, I think, a nice contribution to a long-established literature on how intimate associations with plants has driven the diversification of groups like butterflies and beetles.

The variety of queer scientists in The Queer Variable

Shaun O’Boyle and Alfredo Carpineti have spent the last two years interviewing LGBTQ+ folks working in the sciences, and the result is now available today on the website of Pride in STEM: an e-book compilation of 40 edited interviews, The Queer Variable. I’m very glad to have been included, as just one voice in an impressively international (if necessarily Anglophone) chorus. The book is something of an oral history, not of a single event or project, but of the career trajectories of the interviewees and how their queer identities have intersected and shaped their work — a topic addressed in a more systematic (dry) manner in the second Queer in STEM paper [PDF]:

Three key processes emerged from our analysis of participant experiences and provide an explanatory framework for how queer STEM workplace identities are shaped by a combination of internal and external influences (see Figure 1). Defining explains how these individuals come to understand and name themselves as queer in terms of gender and/or sexuality; Forming refers to their construction of specific STEM identities; and Navigating describes how the interplay of professional and personal influences impacts expression of identity in places of work and study.

The Queer Variable effectively samples the wide range of ways LGBTQ folks have defined their queer identities, formed their place in a STEM field, and navigated the challenges of a career that incorporates both. Go download the free e-book and have a look.

On making the local news

This is a bit of a rehash from the social media platform whose name I will not utter here, but earlier this month I made my first TV appearance as an “expert” on Joshua trees, talking about the Joshua Tree Genome Project common garden experiments as a first step towards assisted gene flow to help the trees cope with climate change. It was a weird experience! The reporter emailed to arrange things and I agreed to an interview on Zoom, but I didn’t fully realize I was being recorded for broadcast until we were wrapping up. Mercifully, he selected the most coherent bits of what I told him and I didn’t make too many weird faces.

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New paper: How flowers’ symmetry may affect pollinator diversity

I’m delighted to announce a new paper published today in the Biology Letters, coauthored with Colin Carlson at Georgetown University and a CSUN undergrad researcher, Gio Gomez. In it, we examine a big collection of floral visitation records and find a pattern that pollination biologists have talked about but never quite directly demonstrated: the symmetry of flowers seems to shape the diversity of animals that visit them, and potentially provide pollination services. Here’s a brief “lay summary” we wrote to accompany the article:

For centuries, botanists have understood that the symmetry of flowers — whether or not they are “zygomorphic”, with a single line of symmetry — shapes how they attract and interact with pollinators. We examined 53,609 records of animal visits to flowers in 159 communities around the world, and found that zygomorphic flowers are visited by fewer potential pollinator species. This may explain broad patterns in the diversity of flowering plants, in which zygomorphic flowers are associated with faster formation of new species. It also suggests that plant species with zygomorphic flowers may be at greater risk of extinction due to pollinator loss.

We released this work as a preprint on bioRxiv awhile ago, but you can now find the final “official” version of the peer-reviewed paper on the Biology Letters website.

This is an exciting paper because it’s my first foray into pollination ecology proper, and because of its place in that broader field of research — and also because it’s the first paper I’ve published with a student coauthor since starting on faculty at CSUN. On top of all that, the project has been a really nice bridge between my interests (mutualism) and Colin’s (host-associate community ecology), and it’s kicked off a collaboration that has produced some even more exciting results, coming soon to a preprint server near you.

New paper: Meta-analysis of local adaptation experiments compares sources of natural selection

Low clouds surround mountaintops in the San Gabriel Mountains. The analysis in the new paper suggests that selection by abiotic factors like high-elevation conditions may often be weaker than selection created by interactions between species. (Flickr: Jeremy Yoder)

Local adaptation, in which populations of a species become better able to survive and thrive in their home environment than in conditions found elsewhere in the species’ range, is a widespread pattern that evolutionary biologists have long used to study the causes and consequences of natural selection. My newest paper, which is now online ahead of print in The American Naturalist, combines data across many studies of local adaptation to answer a persistent question about the history of life on Earth — has evolution been influenced more by selection arising from environmental conditions, or by interactions among living things?

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2018 photos: Fieldwork (and tourism) in Spain and France

2018.06.20 - Gruissan
Gruissan, a coastal village near Narbonne.

If I’m really going to take my digital life off Facebook, I have to get serious about tending to a more distributed version of that site’s functions. Exhibit A is my Flickr account, which I’ve gotten lax with updating — I was almost a year behind with uploading images there! The holidays have been a good chance to catch up, though, and I’ve finished updating through a trip to Spain and France for fieldwork last June.

I was there to take samples of Medicago truncatula along the Spanish and French Mediterranean coasts — ridiculously pretty territory, even when a snafu with my car rental meant I had to do a fair bit of collecting by mass transit and rental bike. I flew into Madrid (with a layover in London), then to the Spanish coastal town of Málaga; then I spent most of a week in and around Narbonne, France, and finished with a day in Paris before flying home (again via London). It was my first time in both Spain and France, and my first time in Europe in more than a decade.

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New paper: Conflict and communication in mutualism

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

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

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

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.