The Molecular Ecologist: Relentless Evolution

Medium Ground-Finch (Geospiza fortis) Darwin’s finches, like this medium ground finch, are a prime example of what John Thompson calls “relentless evolution.” Photo by David Cook Wildlife Photography.

When I was just starting graduate school, one of the first things I wanted was readings to get me up to speed on the current state of research on the evolution of interactions between species. My dissertation advisor handed me The Geographic Mosaic of Coevolution, by John Thompson (who, it should be said, had been my advisor’s postdoctoral mentor). Thompson turned out to be just the author for the job, wrangling a huge body of research into a clear, straightforward text, and all in support of his argument that metapopulation dynamics—populations linked by migration across a landscape of varied environments—are the engine driving much of evolution.

Now, Thompson’s published a new book, titled Relentless Evolution, which pretty much picks up where The Geographic Mosaic left off. And I’ve reviewed it for The Molecular Ecologist.

Gould’s “paradox of the visibly irrelevent” holds that, if we are to understand the river of evolutionary history, we must look below the spume and spray of year-to-year adaptative change to find the deeper currents that can, over time, carve canyons. In his new book Relentless Evolution (University of Chicago Press, $35.00 in paperback), John N. Thompson makes the opposing argument with gusto: To Thompson, studying the roiling eddies that Gould dimissed as transient and superficial is the only way to understand the deeper currents, and the river’s course ahead of us.

Should you run out and buy a copy? If you’re even slightly on the fence, I suggest you go read my whole review.◼

The Molecular Ecologist: Using R to model the spatial distributions of species

Environmental variation across the range of Joshua tree. Image via The Molecular Ecologist.

This week at The Molecular Ecologist, I’m showing how to use the popular open-source statistical programming language R to estimate species distribution models.

Species distribution models (SDMs) are handy any time you want to extrapolate where a species might be based on where you know it actually is. Maybe you’re trying to figure out where would be fruitful to do more sampling; maybe you want to know where your favorite critters probably lived back during the last ice age; maybe you want to know what regions will be suitable for your favorite critters after another century of global climate change.

Given how widely useful SDMs are, it’s very nice to be able to estimate them using multiple methods implemented within a single open-source framework. To get a taste of the capabilities provided by R and a select set of add-on packages, go read the whole thing.◼

The Molecular Ecologist: If genes aren’t independent “beans,” speciation is easier

Three-spined stickleback profile Threespine sticklebacks are a classic case of speciation caused by natural selection. Photo by wolfpix.

This week at The Molecular Ecologist, my friend and collaborator Chris Smith writes, with two coauthors, about a new study simulating adaptive speciation in the face of gene flow, and the effects of linkage among genes involved in the adaptive divergence:

Models of speciation that involve ongoing gene flow remain controversial because gene flow is expected to homogenize differences between populations. However, genome-level effects may facilitate speciation with gene flow. For example, selection against immigrants may have the effect of reducing realized gene flow, even at loci that are not under divergent selection (Rundle & Nosil 2005). This global reduction in gene flow and increased divergence across the genome due to divergent selection is termed ‘Genome Hitchhiking’ (Feder et al. 2012). Genome hitchhiking may be enhanced by fitness epistasis – multiple loci interacting synergistically to cause reductions in fitness that are greater than selection acting on any one locus.

It turns out that speciation is more probable in models that don’t treat genes like independently evolving beans in a beanbag, bearing out a classic criticism of simple speciation models made most prominently by Ernst Mayr. However, true linkage among the selected genes isn’t necessary, either. All in all, this is an exciting new development for those of us who think natural selection might be important in forming new species, so you should definitely 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.◼

Herd immunity, unfalsifiable hypotheses, and the search for the missing heritability

Image created with Pulp-O-Mizer.

It’s been a busy week at the other blogs with which I’m variously affiliated. So busy that I’m going to run down what’s up at Nothing in Biology Makes Sense! and The Molecular Ecologist in a single omnibus post.

First up, Nothing in Biology Makes Sense!: My younger brother Jon (@Bonovox1984), who’s in his third fourth year of medical school, led off with a post on a new study of “herd immunity”—the effect whereby people who haven’t been vaccinated benefit from reduced risk of disease if they’re living around lots of people who have been vaccinated. Then Prosanta Chakrabarty (@LSU_FISH) continued the NiB tradition of blasphemy by explaing why creationism is not—and can never be—science. And finally, we announced that Nothing in Biology will be hosting the March 2013 Carnival of Evolution—you can see how to submit your evolution-related blog posts and other online content right here.

Then, over at the Molecular Ecologist, Tim Vines posted Molecular Ecology‘s first-ever list of top reviewers to provide some recognition for the volunteer labor that goes into a good peer-review process. And I wrote about a cool new study that goes looking for the “missing” heritability in quantitative trait locus studies—and finds a lot of it, with the help of lots of statistical power. (It turns out that a lot of the missing heritability is hiding in genes of small effect, which is exactly what some folks have long speculated.)◼

Have yourself a scientific Christmas

The love makes beautiful. frosted landscape for christmas xmas and happy new year pour noël et le nouvel an Photo by Thierry.

Have yourself a scientific Christmas,
May your teaching load be light!
Next year maybe funding will not be so tight.
Have yourself a scientific Christmas,
Pipette your last lane …
Don’t stir the reagents with that candy cane!

You’re done with your holiday shopping and ready to read about selective breeding of Christmas trees, right? Well, then the Molecular Ecologist has just the post for you. Or maybe you’d rather check out an old Denim and Tweed post about mistletoe population genetics?

And a happy midwinter celebration of your choice to all!◼

The Molecular Ecologist: The Carnival of knowing what I know now

This advice won’t even cost you five cents. Image via nola.com.

That carnival of advice based on personal experience from previous career stages? Yep, it’s online today at The Molecular Ecologist. Head on over for a heaping helping of introspection, snark, and (mostly) sober reflection from across the science blogosphere.◼

The Molecular Ecologist: Which programming languages should I learn for bioinformatics?

Over at The Molecular Ecologist, Mark Christie runs down the considerations to take into account when you’re thinking about making the effort to learn a programming language — he focuses specifically on bioinformatics, but his points really apply for just about anything you’d do with a script.

Perl and Python programs are (typically) compiled each time before they run and they are often not compiled to the same extent as C and C++ (but see PyPy for Python). This means that C and C++ typically run faster and require less memory after a program has been completed. Like most things in life, however, there is a tradeoff in that C and C++ programs usually require more lines of code because there are more details that have to be specified in each program. Thus there is a tradeoff between time spent developing, writing, and debugging code and the time that the program takes to run through completion.

Planning your first bioinformatics project? You should probably go read the whole thing.◼

Knowing what I know now: Let’s make it a carnival!

County Fair Photo by Justin in SD.

Cross-posted from The Molecular Ecologist.

So, not long after I posted my advice for grad school, and said I hoped that The Molecular Ecologist ultimately collect similar posts from a whole bunch of people, Scicurious e-mailed to point out that there’s a thing we do in the blogosphere when we want to collect a bunch of posts on a particular topic: we hold a carnival!

So the plan is now that The Molecular Ecologist will host a “Knowing What I Know Now” carnival on Monday, December 10, and if you’re working in science at any career stage, you’re invited! All you need to do is write up a few things you wish you’d known in your previous career stage that would’ve helped you prepare for your current career stage. (i.e., grad students, write about undergrad; postdocs, about grad school; and so on.) In my original post I may have over-emphasized the academic career track — we’d love to hear advice about preparing for work in industry, or with a non-academic nonprofit, or in government, too.

If you have a blog, write up your advice as a post and either e-mail the link to me or post it in the comments below. If you don’t have a blog, we’ll be happy to post your contribution at The Molecular Ecologist — again, e-mail me to set that up. Please send all your links and post contributions by Saturday, December 8, and I’ll pull them together for the carnival post on the 10th.

Ready? Set? Start your advice-ing.◼

The Molecular Ecologist: Knowing what I know now (about grad school)

2007 - Day 113 - This England Tea. It’s important. Photo by Jonathan_W.

In what I hope will be the start of a whole series of posts about careers in science, I’ve taken a stab at writing down what I wish I’d known to do (and what I’m glad I did) during graduate school, over at The Molecular Ecologist:

I can’t claim to have any blinding new insights — my own career is very much still under construction. But I’ve been interacting with a number of freshly-arrived graduate students this semester, and I’ve found myself thinking, after conversations with them, about what I might have done differently back when I was looking ahead to five (oops, six) years of grad school — and about what I did that worked out pretty well.

And no, I will not apologize for the choice of videos I’ve used to illustrate the complete post.◼