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Textbooks are often very expensive. For example the most recent edition of Principles of Population Genetics will run you $50-$100. But it has come to my attention that the third edition of this textbook is potentially much cheaper, with some copies in the <$10 range! Population genetics isn’t quite like math, where 19th century works are still interesting to the non-specialist (population genetics was ‘invented’ in the first decades of the 20th century!). But a lot of the older material is totally relevant and on point, so these previous editions are not just simply historical curiosities. Much of the third and fourth editions of this particular work overlap anyhow, the big difference obviously being genomic techniques and such. But for that you should probably read papers, many of which are thankfully being put out as preprints now.

While I’m at it, I notice there are some affordable copies ($10-$20) of Genetics of Human Populations. This is a very old work from decades ago. But it is an encyclopedic treatment of the post-World War II human genetic literature, much of which has been forgotten or faded, but perhaps should not be discarded so lightly….

Update: I realize on second thought that it was remiss of me to not point out that Graham Coop and Joe Felsenstein both have free population genetics resources which readers might find highly useful. Also see these notes from U Conn.

Modern evolutionary genetics owes its origins to a series of intellectual debates around the turn of the 20th century. Much of this is outlined in Will Provines’ The Origins of Theoretical Population Genetics, though a biography of Francis Galton will do just as well. In short what happened is that during this period there were conflicts between the heirs of Charles Darwin as to the nature of inheritance (an issue Darwin left muddled from what I can tell). On the one side you had a young coterie around William Bateson, the champion of Gregor Mendel’s ideas about discrete and particulate inheritance via the abstraction of genes. Arrayed against them were the acolytes of Charles Darwin’s cousin Francis Galton, led by the mathematician Karl Pearson, and the biologist Walter Weldon. This school of “biometricians” focused on continuous characteristics and Darwinian gradualism, and are arguably the forerunners of quantitative genetics. There is some irony in their espousal of a “Galtonian” view, because Galton was himself not without sympathy for a discrete model of inheritance!

In the end science and truth won out. Young scholars trained in the biometric tradition repeatedly defected to the Mendelian camp (e.g. Charles Davenport). Eventually, R. A. Fisher, one of the founders of modern statistics and evolutionary biology, merged both traditions in his seminal paper The Correlation between Relatives on the Supposition of Mendelian Inheritance. The intuition for why Mendelism does not undermine classical Darwinian theory is simple (granted, some of the original Mendelians did seem to believe that it was a violation!). Many discrete genes of moderate to small effect upon a trait can produce a continuous distribution via the central limit theorem. In fact classical genetic methods often had difficulty perceiving traits with more than half dozen significant loci as anything but quantitative and continuous (consider pigmentation, which we know through genomic methods to vary across populations mostly due to half a dozen segregating genes or so).

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Outreach is a buzz term in academic science right now. Scientists have to publish. And they have to teach. Then there is service (e.g. committees and such). Outreach is now part of the service element. It doesn’t need to be hard or sophisticated. Not only that, outreach can be general (to the public) and specific (to your peers). As an example of what I’m talking about Michael Eisen’s blog is more aimed toward a broad audience, though on occasion he delves specifically into the science which is the bread and butter of his research. Haldane’s Sieve is more tightly focused on researchers working at the intersection of evolution, genomics, and population genetics. But even it expands further out toward biologists who take an interest in specific evolutionary or genomic questions in their own research (e.g., I have known several molecular biologists who had no idea who was behind Haldane’s Sieve, but had read the site because of an interest in a specific preprint).

This isn’t rocket science, so to speak. Information dissemination is pretty easy right now, and that is theoretically one of the major things which drives science. This should be a great time for scientific progress! Is it? In genomics, yes, though that’s not because of more efficient flow of information, as opposed to technology. With that prefatory comment, I think John Hawks’ recent jeremiad is worth reading, Speak up and matter:

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For replication here are the variables:

Row: EATGM POLINFGM BIZINFGM MEDAGRGM MEDINFGM GMMED GMPOL GMBIZ POLINFNK

Column: POLVIEWS(r:1-3″Liberal”;4″Moderate”;5-7″Conservative”)

There results are presented below (rows add up to 100% for each question).

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Anyone who reads the genomic posts with any interest on his weblog must read Daniel Lawson’s fine review of the topic which he has posted on arXiv, Populations in statistical genetic modelling and inference (via Haldane’s Sieve). Even if you don’t have a population genetic and genomic background the gist is entirely accessible. If you do have a population genetic and genomic background and haven’t used various packages such as STRUCTURE or EIGENSOFT yourself, I would recommend reading Lawson’s characterizations, as they are all spot on.

Also, if you have not, I recommend Lawson’s website for ChromoPainter and fineSTRUCTURE. The utility of these methods is outlined in the paper Inference of Population Structure using Dense Haplotype Data.

I am going to get back to the eugenics debate at some point, but it is hard to motivate myself. This is due to a combination of complacency and sanguinity. Many of those who use eugenics as a “scare word” or are “very concerned about it” don’t really seem to get past generalities when it comes to the present situation (i.e., there is detailed exploration of past atrocities, and some exploration of rather unrealistic scenarios, such as occurred with the “Chinese eugenic” story, but little concrete engagement with realities such as the high abortion rates for positive tests for Down syndrome). In more crass and intellectually vapid discussions liberals and conservatives tend to use eugenics as a term of selectively useful instrumental rhetoric, a bludgeoning instrument only in the mindless screaming discourse.

Meanwhile, we have advances like the whole genome sequencing of second trimester fetuses. This is still basic science, but in genomics basic science is translated really fast to the consumer market. I’m ~90 percent sure my daughter will have a 10 x whole genome sequence by the end of 2014 (I might even get her parents in on the game for a trio). So, submitted for your interest are two papers on first trimester noninvasive screens for Down syndrome due to aneuploidies (and other syndromes). Non-Invasive First Trimester Blood Test Reliably Detects Down’s Syndrome and Other Genetic Fetal Abnormalities:

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A few year ago there was a minor controversy when some evolutionary genomicists reported that they had reconstructed the genome of the extinct Taino people of Puerto Rico by reassembling fragments preserved in contemporary populations long since admixed. The controversy had to do with the fact that some individuals today claim to be Taino, and therefore, they were not an extinct population. Though that controversy eventually blew over, the methods lived on, and continue to be used. Now some of the same people who brought you that have come out with work which reconstructs the recent demographic history of the Caribbean, both maritime and mainland, using genomics.  Even better, it’s totally open access because it’s up on arXiv, Reconstructing the Population Genetic History of the Caribbean (please see the comments at Haldane’s Sieve as well, kicked off by little old me). Though the authors pooled a variety of data sets (e.g., HapMap, POPRES, HGDP) the focus is on the populations highlighted in the map above.

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It was >100 degrees where I live today.

It’s an exciting time for those interested in the evolutionary genomics of the dog. In 2010 a big SNP-array paper came out, Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Today we’re going whole genome, which is important because many of the SNP-arrays are ascertained on domestic dogs (i.e., they are designed to pick up dog variation, and so may distort our perception of the variation in wolves). Recently I talked about an analysis of the evolutionary genomics of the dog, The genomics of selection in dogs and the parallel evolution between dogs and humans. The main interesting result of that group was to push the divergence of the dog and wolf lineages further back in time, ~30,000 years, in line with some archaeological and mtDNA finds. I did not find their arguments for the origin of the dog in East Asian convincing. Now a new preprint on arXiv, Genome Sequencing Highlights Genes Under Selection and the Dynamic Early History of Dogs, pushes this even further.

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