A Conversation about High Throughput Sequencing and General Biology

In a recent keynote address at the High Throughput Sequencing for Neuroscience meetings, Sean Eddy from the Howard Hughes Medical Institute addresses the need for biologist to do their own sequence analysis. Although this talk was given by a neuroscience rather than an evolutionary biologist, the conversation is generally applicable to the entire biological community.

Favorite quotes:

“But if you’re a biologist pursuing a hypothesis-driven biological problem, and you’re using using a sequencing-based assay to ask part of your question, generically expecting a bioinformatician in your sequencing core to analyze your data is like handing all your gels over to some guy in the basement who uses a ruler and a lightbox really well.”

“If you learned to implement it in Perl — and you could do this in an afternoon, with a few lines of Perl code — I think you would find yourself endowed with a superpower, like Wonder Woman with her golden lasso of truth, and it’s a superpower that a biologist can use with surprising effectiveness on large data sets.”

Find the whole article here.

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Tracing the start of monarch butterflies’ epic journey, in their genes

Monarch butterflies (Danaus plexippus) are among the most widely recognized wild creatures in North America. Their distinctive orange-and-black wings, which warn predators that the butterflies are chock full of toxins from the milkweed they eat, make them easily spotted in backyard flower beds. They’re also known for a massive annual migration, flying thousands of miles between wintering colonies in central Mexico and summer sites across the United States and Canada. More recently, it’s been discovered that female monarchs infected by parasites respond by laying their eggs on food plants that can prevent the parasite from infecting their offspring.

Monarchs are also one of the more visible victims of the massive changes humans have made to the world around us. Increased conversion of farmland to corn production has reduced the supply of milkweed, the butterflies’ only food plant, across much of the Midwest. It’s gotten so bad the number of monarchs making the annual migration back to Mexico hit a record low last year, and while things were better in 2014, a nationwide campaign to encourage planting of milkweed in home gardens is only beginning.

For all our familiarity with monarchs, we’ve known remarkably little about their evolutionary history. That’s changing rapidly now, as evidenced by a paper published last month in the journal Nature, which uses a big new genetic dataset to trace the origins of some of the monarch’s most distinctive features.

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The evolution of human facial diversity

Signalling individual identity is critical in many aspects of human social interaction (click for video!).

We all rely on our ability to recognize other people’s faces to get along in the world. Most people don’t think too hard about this, it’s so fundamental to our existence. But it turns out that in order to stand out in the crowd, you need to be, well different. A recent study shows that human faces are in fact, much more different from one another than other traits, and suggests that this high facial diversity has evolved specifically to signal individual identity. It’s a pretty interesting story, and I look forward to digging into the details.

Check out this NatGeo piece on the work, and the original publication (paywalled).

Literature Cited:
Sheehan, Michael J., and Michael W. Nachman. “Morphological and population genomic evidence that human faces have evolved to signal individual identity.” Nature Communications 5 (2014).

Population geneticists to Nicholas Wade: You know nothing of our work!

Okay, I’m paraphrasing in that headline, but only barely. From Science Insider:

A best-seller by former New York Times science writer Nicholas Wade about recent human evolution and its potential effects on human cultures has drawn critical reviews since its spring publication. Now, nearly 140 senior human population geneticists around the world, many of whose work was cited in the book, have signed a letter to The New York Times Book Review stating that Wade has misinterpreted their work.

The letter is online, and it doesn’t mince words:

Wade juxtaposes an incomplete and inaccurate account of our research on human genetic differences with speculation that recent natural selection has led to worldwide differences in I.Q. test results, political institutions and economic development. We reject Wade’s implication that our findings substantiate his guesswork. They do not.

We are in full agreement that there is no support from the field of population genetics for Wade’s conjectures.

To those of us who’ve been complaining about Wade’s misappropriation of basic population genetics in support of his ideas about what people of different races may or may not be “adapted” to do, this is the equivalent of that scene from Annie Hall, except with more than a hundred Marshall McLuhans. Updated to add: The full list of 139 folks who signed the letter is posted here.

Sometimes, life is kinda like that. Hat tip to Jennifer Ouellette for the Science Insider story.

Updated to add: See also coverage by Nature, with some choice quotes from signatories; and by Jennifer Raff, who writes, “A strong blow has been dealt to scientific racism today.” Also, from Ed Yong:

A guide to the science and pseudoscience of A Troublesome Inheritance, part III: Has natural selection produced significant differences between races?

This is the third in a series of guest posts in which Chris Smith will examine the evolutionary claims made in Nicholas Wade’s book A Troublesome Inheritance. You can read part I here, and part II here. Chris is an Associate Professor of Evolutionary Ecology at Willamette University. He uses population genetic approaches to understand coevolution of plants and insects, and he teaches the interdisciplinary course “Race, Racism, and Human Genetics” with Emily Drew.

A Troublesome Inheritance was published in 2014 by Penguin Books. Cover image via Google Books.

This spring former New York Times science writer, Nicholas Wade, released his latest book on human evolution, A Troublesome Inheritance: Genes, Race, and Human History. In it, Wade argues that genetic studies completed in the eleven years since the Human Genome Project was completed reveal real and important differences between human races. Unsurprisingly, the book’s release has been met with a sharply divided critical reception.Whereas the book has been widely embraced by those on the political right, and by the white identity movement, it has been panned by anthropologists, evolutionary biologists, and population geneticists. For the last two weeks at Nothing in Biology Makes Sense, I’ve been looking in depth at the literature that Wade uses to support his ideas. Last week I considered Wade’s argument that natural selection acting on the MAO-A gene – a neurotransmitter implicated in aggression and impulsivity – has led to behavioral differences between races. This week I will consider Wade’s larger claim that natural selection has produced numerous differences between races.

Throughout the book Wade continually repeats the mantra that natural selection on humans has been “recent, copious, and regional.” It would be hard to find an evolutionary biologist that would disagree with these rather vague pronouncements. Indeed, there are a multitude of studies showing that natural selection has acted on humans, and there is persuasive evidence that selection has caused evolutionary changes in human populations as we have adapted to diverse environments over the course of the last several thousand years (see, for example, Yi et al., 2010).

However, scratching the surface reveals that when he says that natural selection has been “recent, copious, and regional,” what Wade actually means is that natural selection has been “radical, complete, and racial.” By Wade’s account, natural selection has dramatically reshaped the human genome, producing major differences between races. This much more dramatic interpretation is entirely unsupported by the literature, however. In truth, Wade vastly overstates the portion of the human genome that shows evidence for natural selection, and where there has been recent natural selection acting on humans, its effect has primarily been to create genetic differences between members of the same race, and similarities between people of different races.

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Q: What do your friends and your fourth cousins have in common?

you smell

A: Their genetic relatedness to you.

A new study out in PNAS this week suggests that you may have even more in common with your friends than you think.  In particular, you are more likely to share your sense of smell.

“People often talk about how their friends feel like family. Well, there’s some new research out that suggests there’s more to that than just a feeling. People appear to be more like their friends genetically than they are to strangers, the research found.  Some of the genes that friends were most likely to have in common involve smell. “We tend to smell things the same way that our friends do,” Fowler says. The study involved nearly 2,000 adults.”

Read (or listen) to the story at NPR (or check out the original article here for more data and less speculation).

A guide to the science and pseudoscience of A Troublesome Inheritance, part II: Has natural selection favored violent behavior in some human populations?

This is the second in a series of guest posts in which Chris Smith will examine the evolutionary claims made in Nicholas Wade’s book A Troublesome Inheritance. You can read part I here. Chris is an Associate Professor of Evolutionary Ecology at Willamette University. He uses population genetic approaches to understand coevolution of plants and insects, and he teaches the interdisciplinary course “Race, Racism, and Human Genetics” with Emily Drew.

A Troublesome Inheritance was published in 2014 by Penguin Books. Cover image via Google Books.

Last week at Nothing In Biology Makes Sense, I began critiquing Nick Wade’s latest book, A Troublesome Inheritance. The book has produced a firestorm of criticism, largely because it argues that evolution has produced significant cultural and behavior differences between races.

Wade makes many sweeping claims, among them: that natural selection has made the English inherently fiscally prudent and more likely to defer gratification by saving for tomorrow, that events early in the history of Judaism caused the Jews to evolve features predisposing them to careers in banking, and that genetic variation in certain neurochemicals has made Africans inherently more violent.

Wade hangs these seemingly bizarre conclusions on the mantle of modern population genetics, which he claims confirms the existence of ‘three primary races,’ that have evolved real and significant cultural differences between them. By heavily referencing the scientific literature, Wade manages, as Mike Eisen put it, to “give the ideas that he presents… the authority of science… What separates Wade’s theories – in his own mind – from those of a garden variety racist is that they are undergirded by genetics.”

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