Category Archives: my research

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.◼

Queer in STEM, one month in

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rainbow flag : banner, harvey milk plaza, castro, san francisco (2012) Happy Pride! Have some data. Photo by torbakhopper.

Over at the blog for the Queer in STEM study, I’ve just posted an update on the project’s progress about a month after we first launched it. In short: it’s going really amazingly well.

Back on May 7, we opened an online survey of folks working in science, technology, engineering, and mathematics who identify as lesbian, gay, bisexual, trans*, and queer. As of today, 1,523 people have answered the call—out of which, 1,180 participants have completed the key survey questions on their identity and experience.

Our “snowball sampling” method of asking participants to pass along links to the study has been extremely successful: we know that the survey has been mentioned in at least 185 tweets, recommended 467 times on Facebook, and shared 20 times on Google+. We’ve been linked from websites we know well—like It’s Okay to Be Smart and Minority Postdoc—and also from new friends like Geek Feminism, The Asexual Agenda, the University of North Carolina at Charlotte, Lab and Field, and many, many folks on Tumblr.

To find out what’s next for the project, and to help spread the word (or even answer the questionnaire, if by some tiny chance you haven’t yet), go read the whole thing.◼

New project: Surveying LGBTQ folks working in science

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Rainbow leds Photo by Julio Martinez.

I’m pleased and excited to announce that a project I’ve been working on for the last few months is finally ready to launch: A new, nationwide survey of queer folks working in science, technology, engineering, and mathematics.

You may recall that back when I hosted the first Pride Month edition of the Diversity in Science Carnival, one of the recurring themes was that, although we know lesbians, gay men, and bisexual and trans* folks work in STEM fields, our presence isn’t very visible. A few months ago, I started poking around the peer-reviewed literature, looking for studies of LGBT folks in science. I didn’t find much. Studies of LGBT folks in academia either focus primarily on undergraduate students, or consider faculty and staff across all academic disciplines as a group, or they consider very small, localized samples. And careers in STEM extend well beyond the campuses of research universities—what about folks outside the ivory tower?

I brought this up with my friend Allison Mattheis, who just happens to be the perfect person to talk to about this kind of thing: she’s just finished a Ph.D. in Organizational Leadership, Policy, and Development, and who is starting a faculty position in the College of Education at California State University Los Angeles this fall. Together we decided that, yes, there’s a real gap in the existing literature—and we want to close that gap.

So, in our not-very-considerable spare time, Alli and I have been putting together the first stage of a study to answer the questions we have about queer folks in STEM: who we are, what we study, and how our identities have shaped our interest in science and our experiences of working in research. That first stage is an online survey, which we’re hoping to distribute as widely as possible using a strategy called (heh) “snowball sampling”—asking folks who take the survey to pass it on to their friends and colleagues.

As of today, that survey is live and accepting responses at a dedicated website, QueerSTEM.org. If you’re lesbian, gay, bisexual, or trans*, have at least a Bachelor’s or technical degree, and are currently working in a STEM field in any capacity—from grad school to tenure-track faculty to corporate R&D to government employees to teachers—then we want to hear from you. Go take the survey, and then help us spread the word by sharing the short-link http://bit.ly/queerSTEM on Facebook and Google Plus, tweeting it (with the hashtag #QueerSTEM, if you please), or e-mailing it to folks who should contribute.

The plan is to leave the survey open for sampling until we’re satisified that we’ve collected a large, thorough sample of queer folks working in STEM in the U.S. I’ll share prelminary results as they become available—both here and on the blog at QueerSTEM.org—and, with any luck, we’ll ultimately publish what we find in an appropriate scholarly journal. We’re very excited to see the picture of sexual diversity in scientific careers that emerges from this work.◼

Nothing in Biology Makes Sense: Making sense of gene tree conflict across an entire genome

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The only illustration in The Origin of Species. Image via Wikimedia Commons.

This week at Nothing in Biology Makes Sense, I discuss my latest research paper, which has just been published online ahead of print in Systematic Biology. In it, my coauthors and I use a genome-wide data set to reconstruct relationships among a couple dozen species in the genus Medicago—a data set that proved to be kind of a challenge.

Using that data, we identified some 87,000 individual DNA bases that varied among the sampled species—single-nucleotide polymorphisms, or SNPs. That’s not a lot in terms of actual sequence data—but considering that every one of those 87,000 SNPs is a variable character, and that most of them were probably spread far enough across the genome to have independent evolutionary histories, it contains many more independent “gene trees” than most DNA data sets used to estimate phylogenies.

To learn how we tackled all those gene trees, and what we found when we did, go read the whole thing.◼

Sequencing: The Next Generation

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Wasn't expecting this on my evening jog. Sighted in the woods near Northgate Park, Durham. For real. Photo by jby.

I’m spending the next two weeks in Durham, North Carolina, for the NESCent workshop on next-generation sequencing. Which is to say, a workshop about collecting great big genetic datasets, and what you can do with them once you have them. I’ll be stretching my programming skills to the maximum, and hopefully getting a head start on some ideas I’ve had for good old Medicago truncatula.

If time permits, I may take a page from Carl Boettinger’s literally open lab notebook and post some notes and thoughts here as the workshop progresses, but it’s looking likely to be a full two weeks, and time may very well not permit. ◼

What’s in that dissertation, anyway?

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About to take the plunge. Photo by jby.

So, what with getting my sparrows in a row for my dissertation defense on Friday, I haven’t written any new science post for this week. But! As it happens, I have written about most of the component chapters of my dissertation—so in lieu of something new this week, why not check out those posts?

  • The first chapter of my dissertation is a literature review about the phenomenon ecologists call ecological opportunity, and how it may or may not explain big, rapid evolutionary changes. I’ve also written about this topic for the Scientific American guest blog.
  • The second chapter uses phylogenetic methods to reconstruct what yucca moths were like before they were yucca moths.
  • The third chapter presents a mathematical model of coevolution between two species, and determines what kind of interactions—predation, parasitism, mutualism, competition—can cause those species to evolve greater diversity.
  • The fourth chapter is the latest work on my lab’s big study of Joshua trees and their pollinators. The material I’m including in this chapter hasn’t been reviewed and published yet, but you can read the most recent Joshua tree post to learn what we know so far, and what kinds of questions we still want to answer.

Regular posting resumes next week, provided that I pass my defense and the celebrating afterward doesn’t interfere with my blogging capacity.

Coevolutionary constraints may divide Joshua trees

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Scientists love it when the real world validates our more theoretical predictions. It helps, of course, if those predictions are rooted in the real world to begin with. This is more or less what happened in my own research, with results reported in two just-published scientific papers. In the first, which I discussed last week, my coauthor and I showed that some kinds of species interactions can reduce the diversity of the interacting species [PDF]. Today, I’m turning to the second, in which my coauthors and I found exactly this predicted pattern in one such species interaction, the pollination mutualism between Joshua tree and yucca moths.

The new paper, published this month in the Journal of Evolutionary Biology, examines the phenotypic variation of two forms of Joshua tree and the two different moth species that pollinate it. The data show that although the Joshua trees pollinated by different moths are very different from each other, those pollinated by the same moth species are extremely similar [PDF].

Two forms of Joshua tree pollinated by different moth species, seen here side by side, don’t vary much among themselves. (Flickr: jby)

This is a nice confirmation of the theory paper because it strongly suggests that coevolution between mutualists like Joshua tree and its pollinators works the way the theoretical model assumes it does, with natural selection favoring individuals who best match their partners in the other species.

Continue reading →

Not all species interactions are (co)evolved equal

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Biologists have long thought that coevolutionary interactions between species help to generate greater biological diversity. This idea goes all the way back to The Origin of Species, in which Darwin proposed that natural selection generated by competition for resources helped cause species to diverge over time:

Natural selection, also, leads to divergence of character; for more living beings can be supported on the same area the more they diverge in structure, habits, and constitution, of which we see proof by looking at the inhabitants of any small spot or at naturalised productions.
—Darwin (1859), page 128.

In the twentieth century, this idea was extended into suggestions that coevolution between plants and herbivores or flowers and pollinators helped to generate the tremendous diversity of flowering plants we see today. In general, biologists have found that strong coevolutionary interactions are indeed associated with greater diversity.

Yet although there is a well-established association between coevolution and evolutionary diversification, correlation isn’t causation. Furthermore, every species may coevolve with many others, and diversification that seems to be driven by one type of interaction might actually be better explained by another. It has even been suggested that coevolution rarely causes speciation at all.




Species interact in a lot of different ways, as antagonists, competitors, and mutualists. Do all these interactions shape diversity the same way? (Flickr: jby)

One step toward determining how often coevolution promotes diversification would be to identify what kinds of coevolutionary interaction are more likely to generate diversity. This is precisely the goal of a paper I’ve just published with Scott Nuismer in this month’s issue of The American Naturalist. In it, we present a single mathematical model that compares a wide range of species interactions to see how they shape diversification, and that model shows that coevolution doesn’t always promote diversity [PDF].

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Before they were yucca moths

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This post was chosen as an Editor's Selection for ResearchBlogging.orgYuccas and yucca moths have one of the most peculiar pollination relationships known to science. The moths are the only pollinators of yuccas, carrying pollen from flower to flower in specialized mouthparts and actively tamping it into the tip of the pistil. Before she pollinates, though, each moth lays eggs in the flower—the developing yucca seeds will be the only thing her offspring eat. How does such a specialized, co-adapted interaction evolve in the first place? My coauthors and I attempted to answer this question in a paper just published in the Biological Journal of the Linnean Society, by reconstructing the ecology of yucca moths before they were yucca moths [PDF].

Continue reading →

Interview at Coyote Crossing

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Nature writer and photographer Chris Clarke is a great fan of yuccas and yucca moths—he’s working on a book about Joshua trees right now—and so he asked me to answer a few questions about the latest research on the evolutionary history of yucca moths, which was just published in the Biological Journal of the Linnean Society. Check out Clarke’s discussion of the mutualism, and our e-mailed interview, on his blog Coyote Crossing. Look for a post about the paper, with some basic explanation of the methods used in it, right here at D&T next Tuesday.

Ladybird beetle on a Joshua tree leaf. Photo by jby.