Just a heads up, I will be tweeting from the 10th Bay Area Population Genomics meeting at Stanford next weekend (Saturday the 24th). Registration is closed, so if you are curious about this sort of thing and live in the Bay Area keep an eye on the Google Group. I should probably provide a blog roundup if I’m going to be tweeting.
In the 1990s there was an enormous controversy over a Native American skeleton which was termed “Kennewick Man”. Most of the dispute was rooted in the fact that the morphological characteristics of the remains did not resemble modern indigenous peoples. In fact, the features may have been more European-like, with reconstructions tending toward uncanny resemblances to the actor Patrick Stewart. A new paper in Science purports resolve this question, Late Pleistocene Human Skeleton and mtDNA Link Paleoamericans and Modern Native Americans. Here’s the key section from the abstract:
…This skeleton dates to between 13,000 and 12,000 calendar years ago and has Paleoamerican craniofacial characteristics and a Beringian-derived mitochondrial DNA (mtDNA) haplogroup (D1). Thus, the differences between Paleoamericans and Native Americans probably resulted from in situ evolution rather than separate ancestry.
When I was in college a Korean American friend confided to me that his roommate had an issue. He had seen a q-tip in the waste-bin, and what was at the end of it was shocking to him. What my friend was describing was wet earwax (Google it yourself if you want to see it). As this was the first time he was living with a non-Korean he had assumed that everyone’s earwax was dry, like his own. The maps above and to the left show you the frequencies of the allele which has an extremely strong correlation with this trait. In Korea the frequency of dry earwax is close to 100%. Since the expression pattern for dry earwax is recessive, you need two copies of the derived allele, so in any population where the ancestral variant exists in appreciate frequencies you’ll have the wet variant of the trait.
This is why in 2006 a Japanese group published research in this area, A SNP in the ABCC11 gene is the determinant of human earwax type. A substantial minority of Japanese happen to have wet earwax. And it turns out that wet earwax has some other associations of interest. Read More
If you haven’t, please watch Frontline’s The United States of Secrets. Also, note that the American government engages is a policy of malicious and false prosecution to induce cooperation and silence dissent when it suits their interests.On the balance I do think America is the “good guys,” but the world is a lot more Song and Ice of Fire than Lord of the Rings. Many Americans are complacent about government abuse of power because they don’t ever think that they’ll be subject to capricious and corrupt prosecution. Out of sight, out of mind. Meanwhile those in the halls of power understand that there’s a different set of rules for them. These are facts, and I hope the reality of these facts makes Americans more conscious of how people in other nations view us.
A quick post to clarify things. When we talk about human variation and history we’re talking about phenomena which we need to decompose into different levels of analysis, because there are major differences in terms of methodology and questions we’re asking. Too often public presentation tends to melt them together and confuse separate strands.
First, there is the level of phylogeny. The question here relates to the history of human genes and populations. With the rise of genomic technologies it is trivially easy to identify human clusters, and not that much harder to infer historical-demographic events. This is important, because due to Richard C. Lewontin’s popularization of the correct point that most human genetic variation is partitioned within, not across, populations, the public is under the impression that population structure is trivial. It’s not. Some extant modern human populations may have diverged from the rest of our species as early as ~100,000 years ago (the Khoisan peoples of southern Africa). Gene flow between even Eurasian populations can be rather attenuated over the over of 50,000 years (e.g., Northeast Asians seem to have had minimal gene flow from other Eurasian populations over the past ~30,000 years).
Probably the most interesting paper that came out in the past week, Large-Scale Psychological Differences Within China Explained by Rice Versus Wheat Agriculture
Of late people have been leaving off-topic comments early on in threads. I don’t understand why this is happening, as I always post (or try to) an “Open Thread” every Sunday. I don’t post enough at this point where this isn’t usually on the front page, or near it. Please make use of it! From now on I’m going to just not publish off-topic comments because it seems a little rude that people don’t post them in “Open Thread”. I see the beginning of all comments as I have to approve them manually right now, so there’s no reason to hijack another thread. It just annoys me, and probably makes me less likely to actually respond.
A lot of these off-topic comments lately have been about Nick Wade’s new book, A Troublesome Inheritance: Genes, Race and Human History. The reason I haven’t reviewed it is that I haven’t read it, and the reason I haven’t read it is that I don’t have the time. It is easy for me to read an article or paper, and then put up a quick response. Or perhaps one of my own analyses of data sets I have lying around. To read a book and then review it takes a lot more time. Second, there have already been a lot of reactions on the book, so I don’t see what I would have to add. Nick actually told me around four years ago that he was thinking about writing this book, so its appearance did not surprise me at all, though the mainstream reaction seems more muted than I would have guessed.
PLoS GENETICS has finally published the paper which reported on the Iron Age Thracian ancient DNA results, Population Genomic Analysis of Ancient and Modern Genomes Yields New Insights into the Genetic Ancestry of the Tyrolean Iceman and the Genetic Structure of Europe. This seems to be a work which is an improvement on the margins, though it is adding solidity to a somewhat muddled picture of migrations and mixing in prehistory. It is important as the authors themselves admit that inferences from ancient DNA are constrained by the fact that we just don’t have that many samples. Basically everyone is attempting construct models predicated on the samples that we have, but that often leads us astray, even if the results themselves are trustworthy.
I should mention that the image above is of Spartacus, who was famously a Thracian. It is in Bulgaria, which covers part of ancient Thrace. But from the genetics that I’ve seen I’m rather sure now that the Slavic migrations had a very strong impact on Southeast Europe, and modern Bulgarians are far more “hunter-gatherer” than the ancient ones were. This points us to the complexity and nuance of historical-cultural memory. Bulgaria derives from the name of the Bulgars, who were Turkic. But modern Bulgarians speak a Slavic language, not ancient Thracian, and I think it is likely that they have at least as much exogenous Slavic ancestry as they do ancient Thracian (and by late antiquity in any case most people in Thrace were speaking Greek or Latin).
As I have stated before one of the strangest things to me is the ‘urban myth’ among many biologists that 10% of children exhibit misattributed paternity. In plain English, one out of ten fathers of any given child are not their biological fathers, though that is the social understanding. So this excludes children who were adopted and such. In general these are explicitly cases where the putative father is unaware that he’s been cuckolded. The 10% figure is a nice round number, and I regularly hear it in the public arena, but it is also surprisingly pervasive among academic scientists. A few years ago I was in a seminar where a behavioral ecologist alluded to the figure in passing, and being who I am I had to raise my hand and object that it just wasn’t the true. The researcher, who did not work with humans, was genuinely surprised at my objection, and didn’t seem to be particularly invested in the figure he gave, and was quite open to updating his beliefs about this issue. I experienced this again on Twitter recently, where a biologist casually referred to the 10% value, and I pointed to my 2010 post which leans heavily a on 2006 meta-analysis, which suggests values closer to 1-3%. Instead of being defensive, he simply acceded to the new information.
More recent work seems to have confirmed this finding: Low historical rates of cuckoldry in a Western European human population traced by Y-chromosome and genealogical data. It seems obvious that a 10% rate of confused paternity is going to show up in a discordance between genetic and genealogical paternal lines. The authors of the above paper use two methods:
…based on an unbiased population-wide sample, the Y chromosomes of presumed patrilineally related males were compared with each other. Subsequently, EPP rates were estimated based on the discrepancy between the legal genealogy and the actual genetic relatedness. Second, the historical EPP rate within Flanders was estimated based on the genetic traces of a substantial past migration event from northern France to Flanders.
Most of the time I’m focusing on population genetic time scales when I think of evolutionary change. That is, allele frequency shifts within a species level lineage, or narrower. Since this is amenable to experimental analysis obviously there are advantages. But sometimes I really wonder if I’m doing a disservice to myself not paying more attention to examinations of evolutionary change on the scale of tens of millions of years and across whole clades which might have thousands of species. A new paper in PLoS BIOLOGY, Rates of Dinosaur Body Mass Evolution Indicate 170 Million Years of Sustained Ecological Innovation on the Avian Stem Lineage
is very interesting. Here’s the author summary:
Animals display huge morphological and ecological diversity. One possible explanation of how this diversity evolved is the “niche filling” model of adaptive radiation—under which evolutionary rates are highest early in the evolution of a group, as lineages diversify to fill disparate ecological niches. We studied patterns of body size evolution in dinosaurs and birds to test this model, and to explore the links between modern day diversity and major extinct radiations. We found rapid evolutionary rates in early dinosaur evolution, beginning more than 200 million years ago, as dinosaur body sizes diversified rapidly to fill new ecological niches, including herbivory. High rates were maintained only on the evolutionary line leading to birds, which continued to produce new ecological diversity not seen in other dinosaurs. Small body size might have been key to maintaining evolutionary potential (evolvability) in birds, which broke the lower body size limit of about 1 kg seen in other dinosaurs. Our results suggest that the maintenance of evolvability in only some lineages explains the unbalanced distribution of morphological and ecological diversity seen among groups of animals, both extinct and extant. Important living groups such as birds might therefore result from sustained, rapid evolutionary rates over timescales of hundreds of millions of years.
As this paper is predicated on nifty statistical analysis one has to be careful at taking the results at face value. Subsequent reanalysis might yield a different conclusion. But it is certainly an intriguing possibility that clade-level selection of some sort might be operating. I’m still very skeptical of what to even think about this, or how to conceptualize the dynamic. But that’s often a good thing.