Coming soon: Crowd-funding a Joshua tree genome

Joshua trees at Tikaboo Valley, Nevada (Flickr: jby)

Joshua trees at Tikaboo Valley, Nevada (Flickr: jby)

I’m very excited to announce a new project, with a new model for doing science: The Joshua Tree Genome Project, in which I’m working with a bunch of smart, accomplished folks to sequence the genome of my favourite spiky desert plant. A sequenced Joshua tree genome will provide the framework to understand how coevolution with highly specialized pollinators has shaped the history of Joshua trees, and to use the landscape genomics skills I’ve developed with the Medicago HapMap Project and AdapTree to understand how the trees cope with extreme desert climates — and how to ensure they have a future in a climate-changed world.

Perhaps most excitingly (terrifyingly?) we’re going to raise some of the funds to do the genome sequencing by crowdfunding, using the Experiment.com platform. So please keep an eye on the project site, follow our Twitter feed, and Like our Facebook page to make sure you don’t miss your chance to help understand Joshua trees’ evolutionary past and ensure their future.

Social Evolution Forum: Evolution in response to ecological conditions changes ecological conditions

Daphnia magna adult and juvenile. (Flickr: NTNU Faculty of Natural Sciences and Technology)

Daphnia magna adult and juvenile. (Flickr: NTNU Faculty of Natural Sciences and Technology)

I am very happy to be among the members of the Evolution Institute’s new community blog, the Social Evolution Forum. The team includes a bunch of terrific geneticists and anthropologists and people with more social-science-y backgrounds … and me, with a publication record that’s easily 90% research on plants, which do not have societies in any meaningful sense, and interactions between plants and other things that are not really very social, either — moths, or bacteria. Still, nothing in biology makes sense except in the light of evolution, and evolution is very much what I study, and I have written about the biology of the most quintessentially social species, Homo sapiens quite a bit in the past.

All the same, for my inaugural post to SEF, I’m leaning into my role as the generalized evolutionary ecologist with a kind of post I haven’t written in some time, it feels like: a brief discussion of a cool new experiment in rapid evolutionary change and its ecological consequences.

Evolution in response to natural selection over a few weeks or months may not seem like it could matter much, but a recent experiment with one tiny evolutionary champion shows that it can, in fact, have measurable effects on a whole community of interacting species. The communities in question are the kinds found in ponds all over the world, in which swarms of small crustaceans compete to graze and prey on algae and other microorganisms, and evade death in the gaping maws of minnows and sticklebacks. One of these crustaceans is Daphnia magna, the common water flea, which has a life cycle that turns out to be quite convenient for scientists who want to watch evolutionary change in real time.

As you’ll find if you read the whole thing, Jelena H. Pantel and her coauthors raised clonally-reproducing Daphnia in artificial environments with communities of competing crustaceans for about three months — ten water-flea generations or so. They then used individuals sampled from those evolved populations to colonize new communities, and compared what happened to those communities to ones started with Daphnia that hadn’t had time to evolve. It’s a nice experiment in ecological consequences of evolutionary change — and how that change can actually feed back to alter the conditions that caused it in the first place.

And, when you’re done with that, check out great opening articles by Arun Sethuraman, Lee Alan Dugatkin, Jennifer Raff, and Anthony Biglan — that should give a pretty good sense of the variety of voices and expertise you can expect at SEF.

Nothing in Biology Makes Sense: Nature’s Nether Regions, by Menno Schilthuizen, reviewed

Jewelwing Love

Jewelwing damselflies (Calopteryx maculata) mating. (Flickr: Lisa Brown)

Over at Nothing in Biology Makes Sense, I’ve posted a long-overdue review of a terrific little book about naughty parts. Genitals. Junk. It’s called Nature’s Nether Regions, by evolutionary biologist and entomologist Menno Schilthuizen, and it puts the weird world of (animal) reproductive anatomy on full display, while avoiding the cliches and pitfalls into which so many popular accounts of sex and evolution fall.

The book’s subtitle What the Sex Lives of Bugs, Birds, and Beasts Tell us About Evolution, Biodiversity, and Ourselves, might be a bit ominous to a reader familiar with the many hazards of evolutionary hypothesizing about human behavior, but Schlithuizen’s chatty tour of animals’ sexual anatomy dodges them all. He does this, in large part, by devoting far more time and attention to the “evolution” and “biodiversity” than to “ourselves,” putting the rather pedestrian reproductive arrangements of Homo sapiens in their place amidst the baroque diversity of appendages, receptacles, secretions, and behaviors other animals employ to multiply their kinds.

Go read the whole review, which includes some sampling of the natural history Schilthuizen covers, and then check out the book itself.

New place, new project

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.

No, E.O. Wilson didn’t invent the term “evolutionary biology”

Screenshot of the OED entry for "evolutionary biology."

Screenshot of the OED entry for “evolutionary biology.”

This View of Life, the evolution-centric online magazine, has a long “conversation” with myrmecologist E.O. Wilson, one of the most prominent evolutionary biologists of the era following the “Modern Synthesis” in the second half of the Twentieth Century, and still one of the leading popularizers of evolution. It’s a long ramble, but worth your reading time, I dare say. Though, to be honest, I only found out about it because of this aside that TVOL highlighted in a tweet:

I can’t say Jim [Watson] and I were friends because I was the only younger professor in what came to be known as evolutionary biology—a term I invented, incidentally—as I started here in Harvard, and it was Jim Watson’s wish that I and other old fashioned biologists not leave the university but find a place elsewhere than the biological laboratories. So we were not on friendly terms. [Emphasis added.]

Wow! No one was using the term evolutionary biology before E.O. Wilson? That would be pretty nifty, but it’s also easy to fact-check. I did it by looking up the phrase in the online Oxford English Dictionary over breakfast. And I found a citation to this, on page 140 of St. George Mivart’s book Contemporary Evolution, an Essay on Some Recent Social Changes, published in 1876:

The second instance is that of the apparent conflict between evolutionary biology and Christian dogma, and indeed, no better test question as to the effect of scientific progress on Christianity could well be devised. [Emphasis added.]

The OED also has a citation from 1920, nine years before Wilson was born, which refers to work by T.H. Huxley, one of the contributors to the Modern Synthesis. [Correction: Whoops, nope, Thomas Henry Huxley isn’t the Modern Synthesis guy; that’s his grandson Julian. I SHOULD HAVE KNOWN THIS.] So, I’d go so far as to say that it looks like evolutionary biology pre-dates Wilson considerably, and was probably even in common use by the time he joined the faculty at Harvard.

Update: Following from Dave Harris’s response on Twitter, I see that evolutionary biology, as a fraction of all mentions of biology in Google’s Ngrams text database, does start climbing upward in the mid-1960s, coincident with Wilson’s early career. Wilson’s work surely contributed to that increase in the use of the term, though I think it’s quite unlikely he’s solely responsible.

Life, um, finds a way

The LA Review of Books has just posted my review of Unnatural Selection: How We Are Changing Life, Gene By Gene—a highly accessible book about how insect pests, weeds, disease organisms, wildlife, and even cancer cells evolve in response to the chemicals and drugs we use to contain them. I particularly focus on the skin-crawling case of bedbugs:

Bedbugs are a particularly intimate example, at least from the human perspective, of the broader trend. Surveys of exterminators report that between 2001 and 2007, the number of bedbug infestations across North America increased 20-fold, concentrated in places like apartment complexes, college dormitories, and homeless shelters in major urban areas. Some of this resurgence is due to international travel. Major ports like New York, San Francisco, and Miami are epicenters of bedbug activity, and genetic surveys show that the bugs are arriving from multiple populations, not spreading from a single geographic source. Still, a large part of the bedbug revival is attributable to the fact that the bugs have developed a resistance to many of the insecticides that kept them down for decades.

Go read the whole thing, and try not to scratch.

The Molecular Ecologist: Fishing for genetic signals of adaptation

Atlantic Salmon

Adult Atlantic salmon. (Flickr: Matt Hintsa)

Over at The Molecular Ecologist, I discuss a new paper that exemplifies how we’re going to be studying the genetics of adaptation in the age of high-throughput DNA sequencing—even if it doesn’t quite live up to that promise. It’s a study of adaptation in Atlantic salmon, whose lifestyle makes them uniquely suitable for a particuar sampling design:

Salmon hatch in freshwater rivers, and spend at least their first year in that environment before swimming downstream to the ocean, where they develop into reproductively mature adults. When they’re ready to mate, they migrate back from the ocean, up the river where they hatched to spawn at the site of their birth. Those major migrations and the transitions between freshwater and salt-water are likely to be major selective events for salmon, and they offer convenient times to catch and study salmon from roughly the same age-cohort: when they migrate downstream to the ocean, and when they return to their birth-river.

By taking genetic samples of juvenile salmon on their way out to sea, and then adults on swimming upstream to breed, you can test for genetic changes—adaptation—that has occurred over the course of the fishes’ life in the ocean. And that’s exactly what the authors of this paper did—go read the whole post to find out how it worked.

Nothing in Biology Makes Sense: The key to a secure global future is evolution

Sunrise from the Fall River Road

A mountain vista in Colorado, with trees killed by pine beetles in the foreground. (Flickr: John B. Kalla)

Over at Nothing in Biology Makes Sense, I discuss a big new review article on all the ways understanding evolutionary biology will be critical for human health and development in the next hundred years:

The long list of authors, led by Scott P. Carroll and including Ford Denison, whose lab is just down the hall from my office at the University of Minnesota, explicitly connect evolutionary principles to global goals for sustainable development. These include the reduction of both “chronic lifestyle” diseases and infectious diseases, establishment of food and water security, clean energy, and maintenance of healthy ecosystems. Carroll and his coauthors divide the applications of evolution to these problems into cases where evolution is the problem, and those where evolution may offer the solution.

I’m going to be citing this paper in every grant application I write for the next decade, I suspect. Go read the whole post, and download the original article from Science Express.

Chris Smith takes on that Troublesome book

Cain and Abel

Cain and Abel, in medieval stained glass. Photo by Fr Lawrence Lew.

Over at Nothing in Biology Makes Sense, Chris Smith has been writing a series of posts digging deep into the evolutionary claims made in Nicholas Wade’s book A Troublesome Inheritance. Last week, Chris debunked the claim that human population genetics naturally sorts into “races”—this week, he’s taking on Wade’s claim that variation at a particular gene has made some human populations more prone to violence than others:

Although some studies have found genetic variants in the MAO-A promoter region that are more common in some ethnic groups than in others (Sabol et al. 1998; Widom & Brzustowicz 2006; Reti et al. 2011) it is likely that these genetic variants are not –on their own– associated with violent or impulsive behavior (Caspi et al. 2002; Widom & Brzustowicz 2006). Instead, genetic variation in the MAO-A promoter seems to make some children less able to recover from abuse and childhood trauma, and therefore more likely to act out later in life (Caspi et al. 2002; Widom & Brzustowicz 2006). Simply carrying the ‘low expression’ allele in the MAO-A promoter does not have any effect at all on impulsivity or aggression.

Chris co-teaches a class on exactly the topics covered in A Troublesome Inheritance, so I highly recommend you read the whole thing, and follow the series to its conclusion.