Category Archives: my research

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].

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.

Queer in STEM survey of LGBTQ science professionals now published

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The first peer-reviewed paper from the Queer in STEM survey of lesbian, gay, bisexual, trans, and queer scientists, engineers, and research professionals is now online ahead of print in the Journal of Homosexuality. It’s the first big, nationwide study of LGBTQ career experiences in the sciences — a potentially important resource to inform the policies of scientific employers and professional organizations.

Some of the most important points in the paper, which I wrote with collaborator Allison Mattheis, are

  • There are a lot of LGBTQ folks working in science, technology, engineering, and mathematics (STEM) — we had more than 1400 responses from STEM professionals across the United States, and in several other countries. (Edited to add: Does this mean LGBTQ folks are well represented, as a proportion of everyone working in STEM? We can’t tell from this dataset — but that’s something we hope to work on in a follow-up study.)
  • Most survey participants reported being completely open about their LGBTQ identity with their friends and family, but a large subset of them were not open at all with their colleagues or coworkers. (This is similar to the results of a survey of U.S. workers released by the Human Rights Campaign last year.)
  • Participants were more likely to be open to their colleagues or coworkers if they described their workplace as safe and welcoming.
  • Participants were more likely to be open to their colleagues or coworkers if they worked in a STEM field with better representation of women (see the figure below). This suggests that in fields with poor gender balance, the climate may be less comfortable for anyone who fails to conform to a straight male gender presentation.
Queer in STEM participants were more likely to be open to colleagues if they worked in STEM fields with better representation of women, as estimated from the U.S. National Science Board's Science and Engineering Indicators (SEI) report. Regression with all STEM fields (solid line), p = 0.31; with Psychology excluded (dashed line), p = 0.02.

Queer in STEM participants were more likely to be open to colleagues if they worked in STEM fields with better representation of women, as estimated from the U.S. National Science Board’s Science and Engineering Indicators (SEI) report. Regression with all STEM fields (solid line), p = 0.31;
with Psychology excluded (dashed line), p = 0.02.

You can find the full paper on the website of the Journal of Homosexuality, or download an easier-to-read PDF copy of the manuscript here.

New place, new project

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Lodgepole Pine, Pinus contorta

Lodgepole pine, up close. (Flickr: J. Maughn)

I’m very excited to announce that I’ve accepted a new postdoctoral position as part of the AdapTree project at the University of British Columbia, starting in mid-August. The work I’ll be doing with AdapTree is a dramatic extension of the landscape genomic research I’ve done with Medicago truncatula, studying the genetic basis of adaptation to different environmental conditions. For AdapTree, the focal species are lodgepole pine — Pinus contorta ssp. latifolia — and two species of spruce — Picea glauca, P. engelmanni, and hybrids between them. Using genetic data from thousands of trees at hundreds of sites across British Columbia and Alberta, and growth and performance measurements in big climate-controlled experiments, I’ll get to help figure out what it all means for the future of northern forests.

Apart from the sheer awesomeness of the data, it’s going to be fantastic working with the AdapTree collaborators, which include many biologists whose work I’ve long known and admired: Sally Aitken, Michael Whitlock, Loren Rieseberg, Jason Holliday, Katie Lotterhos, and Sam Yeaman, among others. On top of all that, I get to do it at UBC, one of the premier North American universities for evolutionary ecology, and in Vancouver, one of the most beautiful cities I’ve ever visited. Really, this will be a return to the northern Pacific coast community of biologists where I “grew up” as a graduate student at the University of Idaho, but I’ll be coming back with four years of great experience and learning from my time at Minnesota.

I can’t wait to get started.

My #Evol2014 talk on population genomic “scans” for local adaptation

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This year at the Evolution meetings, for the very first time, the conference organizers offered presenters the option of having our talks filmed by graduate student volunteers. Naturally, I had to try this out—and the result isn’t half bad!

If only I’d pointed myself at the microphone more consistently. And said “umm” about three times less frequently. And maybe worn a nicer shirt …

The Molecular Ecologist: Scanning the genome for local adaptation

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The collection locations for plant lines sampled in my analysis. Figure 1 from Yoder et al. (2014).

This week at The Molecular Ecologist, I’ve just posted a new discussion of the latest publication to come out of my postdoctoral research with the Medicago HapMap Project. It’s an attempt to find genome regions that might be important for adaptation to climate, by scanning through a whole lot of genetic data from plants collected in different climates.

This is what’s known as a “reverse ecology” approach—it skips over the process of identifying specific traits that are important for surviving changing climates, and instead uses population genetic patterns to infer what’s going on. One approach for such a scan is presented in my latest paper, which is in this month’s issue of Genetics. Essentially I think of this as what you can do, given a lot of genetic data for a geographically distributed sample—in this case for barrel medick, or Medicago truncatula. Medicago truncatula is a model legume species, which has been used in a great deal of laboratory and greenhouse experimentation—but in this project, I tried to treat M. truncatula as a “field model” organism.

For a run-down of what I did, and what I found, go read the whole post—or check out the paper itself [PDF].◼

One of these moths is not like the other … but does that matter to Joshua trees?

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A Joshua tree flower, up close
A Joshua tree flower, up close

Cross-posted from Nothing in Biology Makes Sense!

A huge diversity of flowering plants rely on animals to carry pollen from one flower to another, ensuring healthy, more genetically diverse offpsring. These animal-pollinated species are in a somewhat unique position, from an evolutionary perspective: they can become reproductively isolated, and form new species, as a result of evolutionary or ecological change in an entirely different species.

Evolutionary biologists have had good reason to think that pollinators often play a role in the formation of new plant species since at least the middle of the 20th century, when Verne Grant observed that animal-pollinated plant species are more likely to differ in their floral characteristics than plants that move pollen around via wind. More recently, biologists have gone as far as to dissect the genetic basis of traits that determine which pollinator species are attracted to a flower—and thus, which flowers can trade pollen.

However, while it’s very well established that pollinators can maintain isolation between plant populations, we have much less evidence that interactions with pollinators help to create that isolation in the first place. One likely candidate for such pollinator-mediated speciation is Joshua tree, the iconic plant of the Mojave Desert.

Continue reading →

Queer in STEM on Autostraddle

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My collaborator on the Queer in STEM project and I are flattered to be the subjects of an entire profile over at Autostraddle, part of the great series on “Queered Science” by Vivian Underhill, who also gave us a nice nod in an article for Bitch Magazine. The Autostraddle article gets into the genesis of the project:

Allison had done some work on queer issues previously, on “discrimination in school settings, transnational queer migration, and identity development.” So Jeremy asked Allison what she thought about the idea of a survey of a nation-wide sample of queer scientists – as a social scientist, did she think results like that would be publishable? “I responded, ‘are you asking me to teach you about doing research with human subjects? Sure!'”

There’s even an artist’s rendering of us hard at work in the field:

You should definitely go read the whole thing.◼

Postdoc in genetics of complex traits

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2012.10.22 - Medicago truncatula Your new favorite plant? Photo by jby.

Do you like evolution, genetics, and evolutionary genetics? Would you like to think of things to do with a whole lot of genetic data and a flagship model legume? Well, my boss, Peter Tiffin, is looking for another postdoc. Here’s the post description from EvolDir:

I have available a post-doctoral position to work on association and evolutionary genomics of the model legume Medicago truncatula. Collaborators and I have recently collected genome sequence for > 200 accessions and have used these data for GWAS and population genomic analyses. We are currently working to refine our understanding of genomic variation segregating within this species and are particularly interested in the evolutionary genetics of the symbiosis between Medicago and Sinorhizobia. The successful applicant will have considerable freedom to develop research in their area of interest.

The deadline for submissions is 15 September 2013, so get in touch with Peter pronto if you’re interested. (See the full ad for contact information and the application package requirements—it’s standard stuff.) Benefits of the position include working with population genomic data from the cutting edge of current technology in a collegial lab with some very smart people (and me) in the midst of a fantastic community of biologists at the University of Minnesota—as well as living in the Twin Cities, which are empirically awesome. Yes, even in winter.◼