The Molecular Ecologist: Scanning the genome for local adaptation

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].◼

Postdoc in genetics of complex traits

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.◼

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

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.◼

Fire ants, foolish flies, and phylogenomics

DSC_9777.jpg Fire ants. Photo by hankplank.

I’m out of town at a conference this week (more on that at a later date), but it’s been a busy one for both blogging and academics. At the Molecular Ecologist, I’ve got a Q&A with Yannick Wurm, the lead author on a cool study that uses high-throughput sequencing data to demonstrate that one species of fire ants has a “social chromosome” which determines how many queens a single colony can support.

In particular this has been extensively studied in the red Solenopsis invicta fire ant: some colonies have up to hundreds of wingless queens, but other colonies contain strictly one single wingless queen. And this is stable: any additional queen you try to add to a single-queen colony is executed by the workers.

Then, at Nothing in Biology Makes Sense! I discuss a new study of local adaptation by a South African daisy, which fools bee flies into mating with its petals, the better to pick up and transport pollen.

What makes G. diffusa more interesting, to an evolutionary biologist, is that not all populations of the daisy practice this deception. The pattern of G. diffusa‘s petals varies across its range—and not all petal patterns prompt the pollinators to hump the flower.

And finally, the first paper from my postdoctoral work in the Tiffin lab is officially online at Systematic Biology. It’s a project in using a very large genetic dataset—tens of thousands of markers—to reconstruct the evolutionary history of the genus Medicago, which includes my current favorite plant. It’s attached to my very first Dryad data package, which provides all the original data underlying the paper. I’ll be writing about this work in more detail in the near future.◼

Notes on a model species

2012.09.20 - Seeds

Seeds. (Flickr: jby)

There are a couple of neat racks on my desk containing rows of plastic tubes, each tube with a drift of tiny, kidney-bean-shaped seeds at the bottom. These are seeds of Medicago truncatula, barrel medick. When I tell people about this plant I’m currently studying, I usually describe it as an unremarkable wildflower native to the Mediterranean. Or I note that it’s a close-ish relative of alfalfa (Medicago sativa).

Medicago truncatula does not have an especially grand heritage. It grows in dry, sunny places throughout the dry, sunny Mediterranean region, forming low tangles of trifoliate leaves and small yellow flowers that eventually ripen into tough, spiky, vaguely barrel-shaped fruits full of those tiny seeds. Some of the seeds on my desk are descended from plants that grew in places like the Temple of Apollo at Curium, Cyprus; but most are from less distinguished locales. In his 2011 monograph on the genus Medicago, Ernest Small quotes a description of M. truncatula‘s habitat as “sandy fields, wet grasslands, wet meadows, strongly overgrazed and degraded garrique, coniferous forests, grasslands, fallow fields, olive groves, and as a weed in cereal and crops and waste places.”

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