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.

Beware of Sea Tomatoes

Arctic lakes are not known for their cute and cuddly organisms. But to be fair, they must endure crazy extremes. During the summer they are blasted with 24 hours a day of ultraviolet radiation, and during the winter they endure months of icy blackness, and low levels of life-sustaining nutrients all around.

And yet, some life seems to thrive in this environment. Take for example, the sea tomato. Sea tomatoes are round, plumn and look adorable. However, they are actually colonies of toxin-producing cyanobacteria. And they are piling up on the bottom of Greenland’s lakes. Although sea tomatoes are not uncommon in general, the sheer size and abundance of these particular pile ups are unusual.

Read about it over at Eos. So strange…

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The controversy over a kingfisher

Over at Huffington Post, Marc Bekoff, recently wrote an article lambasting Christopher Filardi for collecting a Moustached Kingfisher, a rare bird endemic in the Solomon Islands.

Now, there are two sides to this particular controversy, and I am going to do my darnest NOT to pick one.

Side one: How dare you kill that kingfisher!

The HP article criticized killing a rare bird for collection as the opposite of a conservation effort. It is likened to hunting endangered species, and  compassionate conservation. (RadioLab anyone? Don’t mind if I do…)

Side two: You need these kinds of specimen for conservation. And biology. 

An excellent public post was written by my friend Josef Uyeda here.

Additionally, Dr. Filardi himself responded justifying his decision, and why specimens are important over at the Audobon society.

Was it right or was it wrong? You decide.

Holding kingfisher II.jpg.CROP.promovar-mediumlarge

 

 

Find fireflies, help keep the forests alight

Fireflies

Across eastern North America, one of the most magical signs of summertime is the beginning of firefly activity—hundreds or thousands of flying beetles, their abdomens glowing or flashing, filling twilight backyards and woodland clearings with floating lights.

But those displays—which fireflies put on to attract mates—are getting rarer. Or seem to be, anyway—but we don’t have the kind of comprehensive census of firefly activity that could really tell us how they’re doing. A citizen science project out of Clemson University aims to change that by enlisting anyone with a smartphone or a home internet connection:

The objective of the Clemson Vanishing Firefly Project is to promote environmental
sustainability and stewardship through the participation of local communities in environmental science research. The Clemson Vanishing Firefly Project offers a mobile app that everyone – from elementary students to seniors – can use to measure firefly populations in their communities from neighborhoods, to parks and anywhere in the world they may go!

To help, you follow the project site’s instructions for learning how to count fireflies, then use a smartphone app or a webpage form to report what you see, when, and where. Why not collect some data while you admire the lights in the forest?

(Hat tip to Erik Runquist, on Twitter.)

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.

Natural History in the -omics era

This post is a guest contribution by Michael Harvey, graduate student in Robb Brumfield‘s lab at the Museum of Natural Science at Louisiana State University. Mike studies avian evolution, phylogenomics, and Neotropical ornithology. 

Blackwater river…approximate Bayesian computation…dawn song…genomic islands…wing chord…target DNA enrichment…

My life as an evolutionary biologist straddles two worlds. I study the comparative phylogeography of Amazonian birds, and on the one hand my research involves laboratory and computational methods that push the limits of new technologies and analytical techniques, and on the other, expeditions to the tropics that are nearly indistinguishable from the natural history work conducted by Victorian era biologists. I am a PhD student at Louisiana State University, and for most of the year my work is in the lab and at my desk. For several months of the year, however, my work is general ornithological collecting expeditions to the Amazon Basin.

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Friday Coffee Break, St. Patty’s Style

Irish Coffee

Every 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.

First of all, my deepest apologies for the lateness of this post.  As you may know I am a 4th year medical student and today was Match Day and I was deep in the throws of celebrating the completion of 4 years of medical education as well as learning where I will be training for the next three years in Family Medicine.   So, without further adieu, your links for this week.

CJ decided to that there were too many good links and had to share several.  First, as a skater herself she found an article relating to transmission of skin flora between close team mates and those competing in roller derby.  Next she decided to share how the sequester is going to affect science jobs and the next few years could be difficult.  But finally, a cool post on five animals that could possibly take over the world, which makes me look at spiders a little closer now.

Next, Jeremy likes the fact that new evidence from the Mars rover is favorable to the possibility of conditions that could have sustained life on the red planet.

From Sarah, some very cool slow mo predator vs. prey footage.  Gotta say this is pretty awesome!  She also found some up close and personal pics of jumping spiders.

From Noah, a video documenting several scientists as they inventory one of the worlds most biodiverse locations, the Yasuni Biosphere Reserve.

Finally, in the spirit of March Madness, from Devin comes a battle of the Mammals. “Mammal March Madness from the Mammal’s Suck blog. Although the tournament is purely fictional, the facts and natural history information given out during the extended live tweet rounds are amazing. The first rounds are already complete, but tune in for the exciting finals. Live action via twitter: @Mammals_Suck and general info via the website:”