The Woolly Mammoth’s Last Stand

Woolly mammoths once flourished from northern Europe to Siberia. As the last ice age drew to a close some 10,000 years ago, the mainland population perished, victims of climate change and human hunters.

However, a remote island population survived for 6000 years after the mainland had died off. And from a tooth of a male mammoth, geneticists have now deciphered the reason the population ultimately went extinct.

Read about it in the New York Times.


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 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.

Preventing Flies from Interbreeding

“Pour some cold cream into a cup of hot, black coffee, and you end up with a drink that’s midway between the two ingredients in color, temperature, and flavor. A similar kind of blending can occur if members of closely related species frequently mate with each other, but many species have mechanisms to prevent such mixing.” -HHMI News

My new favorite analogy about species inbreeding, and one that every academic can relate to.

But seriously, over at Howard Hughes Medical Institute Jay Shendure and Harmit Malik (a researcher I have long admired) has come up with a clever series of experiments to find the gene responsible for keeping two fly species separate.

Read about their new technique here!


23andMe will resume (some) genetic health testing


(Flickr: Nathan Nelson)

Via the New York Times, it looks like the home genotyping company 23andMe is getting the go-ahead from the US Food and Drug Administration to give customers medical information linked to their personal genetics. But not just any medical information:

The new health-related information 23andMe will provide is called carrier status. That relates to whether people have genetic mutations that could lead to a disease in their offspring, presuming the other parent has a mutation in the same gene and the child inherits both mutated genes. There will be information on 36 diseases, including cystic fibrosis, sickle cell anemia and Tay-Sachs.

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When infection is unavoidable, fruit flies ramp up recombination

So, you wanna head back to my place after this and make some recombinant offspring?

Imagine you find yourself in the midst of a large-scale epidemic, similar to the scenarios portrayed in movies like Contagion or Outbreak (or both!). The disease is extremely contagious, and the probability of becoming infected is high. Now imagine that scientists fail to discover a cure. There is no Dustin Hoffman-led team of military virologists available to develop a vaccine and save humanity, and the disease persists, with the potential to infect subsequent generations. In this harsh, disease-ridden environment, how could you ensure that your future offspring would survive?

It turns out, if you were a fruit fly, you might rely on recombination.

Disease is thought to have played a major role in shaping the reproductive strategies of animals. The Red Queen hypothesis predicts that species experiencing parasite-related selection pressures are more likely to evolve sexual reproduction, along with increased rates of outcrossing and recombination. This is because, in the ongoing evolutionary arms race between hosts and parasites, a little bit of genetic variation can make it a lot harder for the parasite to “win.”

But while strategies for increasing genetic variation may improve disease resistance, they often come at a cost. Increased recombination, in particular, can reduce fitness by breaking up locally adaptive combinations of alleles. One potential way to get around this issue is to increase recombination rates only when the risk of infection is high. However, we have yet to observe direct evidence of parasite-induced recombination in animals.

In a study recently published in Science, Singh et al. sought to investigate the capacity of fruit flies to plastically increase recombination in response to infection. To do this, the researchers infected Drosophila melanogaster females with a variety of parasites, and observed the proportion of recombinant offspring the females produced.

In order to track recombination events, researchers took advantage of the known genetic basis of two visible phenotypic traits. The ebony locus and the rough locus occupy nearby positions on the same chromosome in D. melanogaster, and recessive mutations at each of these loci have easily identifiable effects on the phenotype. For this study, the researchers generated females heterozygous at both ebony and rough.

Next, the researchers infected females with one of several different types of parasites. Two distinct (but similarly disturbing-sounding) methods were used to infect flies, depending on the type of parasite involved. In some trials, the researchers stabbed adult flies in the thorax with a needle covered in disease-causing bacteria. In other trials, the researchers housed larval flies with female parasitic wasps, allowing the wasps to inject their eggs directly into the larvae. Seriously, these flies must have been terrified.

A parasitic wasp (Leptopilina heterotoma) probes for fruit fly larvae with her ovipositor.

A parasitic wasp (Leptopilina heterotoma) probes for fruit fly larvae with her ovipositor. (Photo courtesy of Dr. Michael Martin)

Finally, the researchers backcrossed infected females to double-mutant males, and examined the resulting offspring. Sorting through thousands of individual flies, researchers identified recombinant offspring as those that exhibited one mutant trait but not the other.

As predicted by the Red Queen hypothesis, infected females produced significantly more recombinant offspring than non-infected females. The researchers saw this pattern across all types of infection studied, including infection by species that parasitize D. melanogaster in the wild. Furthermore, the effect persisted across host life stages, with females producing more recombinant offspring even when infection occurred during the larval stage of development.

The study also provided some insight on the underlying mechanism for making more recombinant offspring, which – surprisingly – appears not to involve an actual increase in recombination rate. Instead, the culprit looks to be some form of transmission distortion, whereby recombinant gametes are promoted at the expense of non-recombinants.

This study highlights the remarkable ability of individual organisms to rapidly respond to changes in the environment, as well as the central role disease has played in shaping the evolutionary trajectory of animals.

But the reason I’m REALLY excited about these findings is because of their potential to reinvigorate the post-apocalyptic science fiction genre.

Picture this: 50 years after the emergence of an unprecedentedly deadly cross-species pathogen, the majority of the planet’s human population has been wiped out. The only people remaining are the highly recombinant offspring of those infected with (and ultimately killed by) the disease. In a world where survival of the fittest reigns supreme, these exceptionally disease-resistant individuals must attempt to rebuild society as they contend with resource shortages, lawless bands of savages, and the unknown genetic ramifications of the extreme levels of heterozygosity within their population.

It sounds like the beginnings of a pretty solid screenplay to me.

While you’re waiting for my movie to hit theaters, you can read the full text of the Science article here. And check out the video below (courtesy of Dr. Michael Martin), which shows a parasitic wasp female attempting to deposit her eggs in some (probably pretty freaked out) fruit fly larvae.

Did Marine Mammals Merge Molecularly? Maybe.

Morphological convergence is one of the most striking patterns in evolution. Just among mammals there are spectacular and bizarre examples of distantly related species that share surprisingly similar adaptations. I bet you’ve heard of saber-toothed cats. But what about marsupial saber-toothed cats? Raccoons are surely familiar, but have you heard of raccoon dogs? Or the earless, eyeless oddity that is the golden mole, which somehow looks almost exactly like the equally earless and eyeless notoryctid marsupial mole? My favorite, though, might be the lesser hedgehog tenrec from Madagascar, which bears the same tiny coat of spiked armor as the common hedgehog but is more closely related to an elephant.

Skull from the marsupial saber-toothed “cat” Thylacosmilus.

Skull from a placental saber-toothed cat Smilodon.

Until recently, most scientists studying evolutionary convergence have focused on the converged phenotype (external appearance), but with the arrival of ever-cheaper DNA sequencing technologies, scientists can efficiently study patterns of convergent genotypes across thousands of genes in species that appear to have converged at the phenotypic level.

Now, I know dancing sharks are the preferred marine species of the moment, but allow me to reignite your interest in some other denizens of the sea. Last month, a team of researchers published a study in Nature examining how genes in three marine mammal lineages might have converged independently on the same solution to the very hard physiological problem of living in the ocean after millions of years evolving on land (Foote et al. 2015). Their results are hardly conclusive but do illustrate a compelling new way to think about and study convergence now that genomes are getting so cheap to produce.

Katy Perry and her dancing sharks at the 2015 Super Bowl

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Under selection, an endangered species runs low on evolutionary “fuel”

Atlapetes pallidiceps

A pale-headed brushfinch, Atlapetes pallidiceps. (Wikimedia Commons:Aves y Conservación/NBII Image Gallery)

The pale-headed brushfinch, Atlapetes pallidiceps, is a conservation success story, or at least the first chapter of one. The birds were thought to be extinct, until a 1998 survey [PDF] of Ecuador’s Yunguilla Valley found four nesting pairs, and observed them foraging for insects and fruit. Following that rediscovery, the Fundacion Jocotoco secured a reserve encompassing the brush finches’ known territory, and took steps to control brood-parasitic cowbirds that were threatening them. Now, the population is five times bigger, with as many as 200 of the birds living in the reserve.

Have the brush finches’ rebounded enough to secure their population for the future? Populations that decline so precipitously can lose genetic variation, and may not regain it even if their numbers increase again. With reduced genetic variation, species that have undergone such a “population bottleneck” event may be unable to respond to natural selection imposed by disease or changing environments.

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