Category Archives: blogrolling

Nothing in Biology Makes Sense: An evolutionary origin for diabetes?

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550d - Bubblegum Bowl Photo by @Doug88888.

This week at the collaborative blog Nothing in Biology Makes Sense!, Jon Yoder (my brother) takes a look at the possible evolutionary origins of type II diabetes from his perspective as a medical student:

Currently, around 285 million people worldwide are affected and that number could potentially climb to 430 million by the year 2030. Diabetes also accounts for 12% of all health care expenditure. It is also a highly genetically associated disease, at least Type 2 Diabetes. Now, in type 2 diabetes the individual will have high levels of circulating insulin. Insulin is a key regulator of fat storage. It is released following meals in response to glucose from the meal and stimulates the uptake of that glucose into liver, muscle and fat. It also acts to antagonize other hormones that would breakdown and use the stored glucose as energy. So, this is where I got to thinking, if there is a gene that is linked evolutionarily to helping survive famine, is there a potential link between such genes and diabetes.

To find out more, go read the whole thing.◼

The Molecular Ecologist: Genes … in … space!

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(A) Geography, and (B) genetics. Figure 2 from Wang et al. (2012).

I’ve got a new post up over at The Molecular Ecologist, discussing a new paper that tries to take a quantitative approach to a phenomenon that keeps turning up in human population genomic datasets, in which genetic data mirrors the geography of the places it was collected.

It’s something of a classic result in human population genomics: Go out and genotype thousands of people at thousands of genetic markers. (This is getting easier to do every day.) Then summarize the genetic variation at your thousands of markers using Principal Components Analysis, which is a method for transforming that genetic data set into values on several statistically dependent “PC axes.” Plot the transformed summary values for each of your hundreds of samples on the first two such PC axes, and you’ll probably see that the scatterplot looks strikingly like the map of the places where you collected the samples.

Of course “looks strikingly like” is not a very quantitative statement. To see how the new study deals with that problem, go read the whole thing. And yes, I manage to shoehorn in a reference to the Muppets.◼

The Molecular Ecologist: ABC, quick as A-B-C

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If I said you had a nice posterior Reverend Bayes, would you take offense? Photo via WikiMedia Commons.

Over at The Molecular Ecologist, new contributor Peter Fields—a Ph.D. student studying plant-pathogen coevolution at the University of Virginia—writes about approximate Bayesian computation and a new approach to this still-developing method of statistical inference that can make it quite a bit faster.

ABC functions upon the rationale that the likelihood might be approximated through the use of simulation and simulation summary statistics2, and that the evaluation of model fit to a dataset can be identified through a comparison of Ss derived from simulated scenarios and calculation of those same summaries on an observed, empirical dataset. In theory, simulation summaries are selected to provide maximal distinction amongst competing models. In practice, identifying these summaries isn’t always easy, and is the object of continued research3

For an introduction to ABC, and a description of the new approach, go read the whole thing.◼

The Molecular Ecologist: Isolating isolation by distance

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Linanthus parryae population Linanthus parryae. Photo by naomi_bot.

And now I present my first “real” post as a contributor at the Molecular Ecologist, a discussion of a new review article pointing out that population geneticists aren’t doing a great job dealing with one of the best-known patterns in population genetics, isolation by distance, or IBD. You may recall that I discussed IBD in a more historical context way back in the day on this very website. It’s simply a pattern in which populations located close to each other are more genetically similar than populations farther away from each other, which arises because most critters (or their seeds, or larvae, or pollen) are less likely to move longer distances. But IBD can be conflated with a number of other patterns population geneticists often try to detect:

So let’s say you’ve collected genetic data from sites on either side of a line you think might be biologically significant—a pretty standard-issue population genetics study. You run your data through Structure, and find two clusters of collection sites that line up pretty well with that Line of Hypothesized Biological Significance. As a followup, you conduct an AMOVA with the collection sites grouped according to their placement by Structure, and you find that the clusters explain a significant fraction of the total genetic variation in your data set. Therefore, you conclude that the LHBS is, in fact, a significant barrier to dispersal.

Except that as we’ve just discussed, everything you’ve just found could be a consequence of simple IBD plus the fact that you’ve structured your sampling so that your LHBS happens to bisect the landscape you’re studying. And just to add to the frustration, even if you’d started out by testing for IBD before you started with all of the tests for population structure, a significant result in a Mantel test for IBD wouldn’t necessarily mean that population structure wasn’t there.

To find out how the author of the new review article suggests we deal with the complications outlined above, go read the whole thing.◼

Big, bloggy news

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Starting today, I’m officially part of the crew at the Molecular Ecologist, the group blog associated with the journal Molecular Ecology, as both a contributor and a sort of coordinator/administrator.

Molecular Ecology‘s managing editor Tim Vines first approached me about joining the site back at Evolution 2012, and I’m excited to start talking about the many wonderful uses of molecular genetic data with Holly Bik, Mark Christie, Nick Crawford, and Peter Fields. We’re hoping to bring in lots of guest posters as well. (And if you’re interested, send me an e-mail.) Although the Molecular Ecologist is affiliated with Molecular Ecology, the vision of the site is not to promote the journal itself, but to build a space for the community of scientists interested in the journal’s subject matter. As part of that effort, we’ve launched a Molecular Ecologist page on Facebook, and I’m taking over @molecologist on Twitter.

This doesn’t mean I’ll stop posting at Nothing in Biology Makes Sense!, much less here at D&T; the Molecular Ecologist is aimed at a somewhat different audience than either of my other online locales, and while this may spread me a little thinner, I expect I’ll be covering different topics at each site.◼

Nothing in Biology Makes Sense: Why the “paleo diet” doesn’t make sense

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Nuts! Gathering hazelnuts is a nice way to spend an afternoon, but a lousy diet plan. Photo by ParaScubaSailor.

Just up at the collaborative science blog Nothing in Biology Makes Sense!: Sarah Hird takes down the “paleo diet” trend, which is based on eating what we think our ancestors ate before the invention of agriculture. Readers of D&T will recognize some of the points Sarah makes:

… this assumes that no evolution has occurred since the advent of agriculture. This is demonstrably false. One example of post-agricultural evolution is the human lactase gene, which breaks down lactose, the dominant sugar in milk. In ancestral humans this gene was turned off after infancy; those humans would have been “lactose-intolerant”. Most humans of European descent now have a mutation that keeps that gene turned on their entire lives. Not surprisingly, this gene spread throughout Europe at approximately the same time cattle were domesticated. There are other known examples of agricultural dietary adaptation, and doubtless more to be discovered. If we are going to use evolution to justify our dietary choices, why throw out the last 10,000 years of it?

That’s just a taste (heh) of Sarah’s objections; for the full case against trying to eat like a hunter-gatherer, you’ll need to go read the whole thing.◼

Nothing in Biology Makes Sense: The evolution of lizards on islands. No, not those lizards.

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Hemidactylus granti. Photo via Nothing in Biology Makes Sense!

Over at the collaborative science blog Nothing in Biology Makes Sense!, Noah Reid describes a new study dissecting the evolutionary history of island-dwelling lizards—not the field model Caribbean Anolis, but geckoes in the genus Hemidactylus, living on islands in the Indian Ocean.

The Socotra archipelago is a particularly interesting, but poorly studied island system. Socotra consists of four islands in the Indian Ocean. It is extremely isolated (150 miles from the horn of Africa, 240 miles from the Arabian Peninsula) yet it has a continental origin. That means it was once part of the supercontinent Gondwana and suggests that some species may have lived there since it first became an island (~17.6 million years ago). Socotra has a very high level of endemism, with 37% of its plant species and 90% of its reptiles occurring nowhere else.

To find out how some of those endemic reptiles got to Socotra, go read the whole thing.◼

New blog on the block

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Awesome Bitches Dissertating is a blog by two queer University of Minnesota doctoral students (one of whom is a friend of mine) who have achieved the “All but Dissertation” stage of grad school, and wanted an online venue to vent about academic bureaucracy, the exquisite pain of dissertation writing, and, yes, the appropriate use of the word “bitch.”◼

Nothing in Biology Makes Sense: Music, evolved?

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SATB Choral Music Music. Photo by Andy Buscemi.

Over at the collaborative science blog Nothing in Biology Makes Sense!, guest contributor James Gaines writes about the evolutionary context of music-making.

Music is one of the few social constructs that truly permeates human culture, and reasons for this have fascinated scientists and philosophers for centuries. Even Darwin himself wrote on the subject, speculating about whether and how natural selection could explain it. Today, there seem to be three major ideas behind why music evolved.

For a breakdown of those three evolutionary hypotheses, go read the whole thing.◼