Crowd-funding a Joshua tree reference genome

(Flickr: jbyoder)

(Flickr: jbyoder)

Remember Joshua trees? If you read this blog, you probably do. They’re an ecological keystone species — and a cultural icon — in the Mojave desert, and they have a fascinating, co-evolving relationship with yucca moths. Some contributors to this very blog, have been studying that pollination relationship and its evolutionary consequences for a decade, building on natural history research that goes back to the time of Charles Darwin.

Up to now, though, modern genetic tools have been of limited use for Joshua trees, because no one has assembled the complete DNA sequence of a Joshua tree. Having a “reference genome” would let those of us who study the trees identify specific genes involved in coevolution with yucca moths, compare the evolutionary effects of that pollination mutualism to natural selection exerted by the harsh environments in which the trees grow, and even use genome-scale data to inform Joshua tree conservation planning.

Well, we’ve decided it’s time to do all of that, and we’re asking for help. A team of folks with expertise in Joshua trees’ natural history, Mojave Desert ecology, and genomic data analysis launched the Joshua Tree Genome Project a couple weeks ago, with a crowd-funding campaign on Experiment.com to pay for part of the DNA sequencing we’d need to assemble a reference genome.

We’re approaching 50% of our funding goal, and leading a competition among projects based at undergraduate universities to recruit the most donors, which could win us $2,000 in matching funds — so even if you give as little as $1, you’re providing a big boost to the project. Go check out the Joshua Tree Genome Project website, and then head on over and pledge your support.

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Scientists at work among the Joshua trees

When he’s not dismantling racist pseudoscience, Chris Smith studies the evolutionary ecology of species interactions. Willamette University sent along a videographer on Chris’s last field trip to study Joshua trees and the moths that pollinate them in central Nevada, and the result is now posted on Vimeo. It’s mainly geared toward showcasing how Willamette undergraduate students participate in the fieldwork, but I’d say it makes the desert look mighty good, too.

Research and teaching postdoc in the population genomics of mutualism

2010.04.05 - Samson out and about

One of your future colleagues in the Smith Lab, hard at work in the field.

Friend of the blog—and longtime collaborator of mine—Chris Smith recently landed an NSF CAREER grant for new research on the causes of evolutionary divergence within the Joshua tree-yucca moth mutualism—and he’s looking for a postdoc to help with it!

The proposed work will take advantage of new genomic resources for the genus Yucca—Joshua tree population genetics is about to get a lot more powerful than the 10 microsatellite loci I used for my dissertation research. And it will involve fieldwork in the Mojave Desert, which is objectively one of the most beautiful empty spaces on the map of North America. Chris is on the faculty of Willamette University, which is an undergraduate institution, so the postdoc position is also a unique opportunity to do basic research in close coordination with an undergraduate teaching program.

Moreover, I can personally recommend Chris as a mentor and collaborator—to the extent that I’ve turned out to be a pretty decent scientist, he’s one of the principal reasons why. (And to the extent that I haven’t, well, that’s a reflection on me, not him.)

The complete job description, and instructions on how to apply, are after the jump.

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

A Joshua tree flower, up close.

A Joshua tree flower, up close.

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 to 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.

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Friday Coffee Break: snail coauthors, rejection letters, Swiss cheese plants, and more

coffee_at_origin_roasting_IMG_0172-784070Every Friday at Nothing in Biology Makes Sense! our contributors pass around links to new scientific results, or science-y news, or videos of adorable wildlife, that they’re most likely to bring up while waiting in line for a latte.

Which Coauthor are you? Sadly during the winter due to snowboarding constraints CJ thinks she is the snail.

Are you looking for an academic job like Jeremy (@JBYoder) and Devin (@devindrown)? Be sure to check out the rejection letters here when you are feeling glum.

More mammal news from Sarah (@sarahmhird) this week: The news on NIH research Chimps being retired and moved to sanctuaries made her pretty happy.

Via Amy: Cornell Launches Archive of 150,000 Bird Calls and Animal Sounds, with recordings going back to 1929.

The Swiss Cheese plant, one of CJ’s favorite tropical plants, is in the news. Can you have only one favorite tropical plant…laughable? Why not check what Christopher Muir has to say over at the American Naturalist or the BBC.

Mutts digest carbs?!?! Oh yeah, that makes perfect sense to Sarah (@sarahmhird). Why not check out what researchers propose as a pathway from wild wolf ancestors to domesticated dogs.

Did your office succumb to the seasonal flu this year? CDC reports had some scary outlooks this winter. Fear not, researchers have ended the moratorium on influenza H5N1 research have resumed work on these important strains.

Friend of the blog Chris Smith is recruiting “citizen scientists” for Joshua tree work. Hear what he has to say over at KNPR.

Notes from the field: What’s Chris doing to that Joshua tree?


ResearchBlogging.orgMy postdoctoral research is shaping up more and more to be hardcore bioinformatics; apart from some time spent trying to get a dozen species of peanut plants to grow in the greenhouse as part of a somewhat long-shot project I’m working on with an undergraduate research associate, I mostly spend my workday staring at my laptop, writing code. It’s work I enjoy, but it doesn’t often give me an excuse to interact directly with the study organism, much less get outdoors. So, when Chris Smith dropped the hint that he could use an extra pair of hands for fieldwork in the Nevada desert this spring, I didn’t need a lot of persuasion.

Chris is continuing a program of research he started back when he was a postdoc at the University of Idaho, and which I contributed to as part of my doctoral dissertation work. The central question of that research is, can interactions between two species help to create new biological diversity? And the specific species we’ve been looking at all these years are Joshua trees and the moths that pollinate them.

Joshua trees, the spiky icon of the Mojave desert, are exclusively pollinated by yucca moths, which lay their eggs in Joshua tree flowers, and whose larvae eat developing Joshua tree seeds. It’s a very simple, interdependent interaction—the trees only reproduce with the assistance of the moths, and the moths can’t raise larvae without Joshua tree flowers. So it’s particularly interesting that there are two species of these highly specialized moths, and they are found on Joshua trees that look … different. Some Joshua trees are tall and tree-ish, and some Joshua trees are shorter and bushy. Maybe more importantly for the moths, their flowers look different, too.

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New papers from NiB contributors

White sands, New Mexico

White gypsum sands: officially an ecological opportunity

Evidently they’re not willing to toot their own horns, so I’ll do it on their behalf: Two of our contributors, Simone Des Roches and Chris Smith, have brand-new publications in print, and both papers are open access, available to anyone who wants to take a look.

Simone’s paper makes the case that the gypsum sands of White Sands, New Mexico, create an “ecological release” for lizards living there, since reduced predator density and diversity on the white dunes lets the lizards use a wider range of habitat types, and achieve higher population density.

First, we provide evidence for ecological opportunity by demonstrating reduced species richness and abundance of potential competitors and predators at White Sands relative to nearby dark soils habitats. Second, we characterize ecological release at White Sands by demonstrating density compensation in the three White Sands lizard species and expanded resource use in White Sands Sceloporus undulatus.

Chris’s paper tests the hypothesis that Joshua trees have expanded their range northward since the last glacial maximum, drawing together many different data sets to find the same signal of population expansion.

Using a database of >5000 GPS records for Joshua trees, and multi-locus DNA sequence data from the Joshua tree and four species of yucca moth, we combined paleaodistribution modeling with coalescent-based analyses of demographic and phylgeographic history. We extensively evaluated the power of our methods to infer past population size and distributional changes by evaluating the effect of different inference procedures on our results, comparing our palaeodistribution models to Pleistocene-aged packrat midden records, and simulating DNA sequence data under a variety of alternative demographic histories.