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Gene Expression Blog

I was aware that Colleen McCullough was ill, so sadly it is no surprise that she has died.

To many McCullough is known for her Masters of Rome series. I particularly think that the first two books in the series, The First Man in Rome and Grass Crown were exceptional. The later novels cover the career of Julius Caesar and his heirs (both Augustus and Antony), which are rather well known to us. In contrast the life and times of Gaius Marius and Lucius Cornelius Sulla are not familiar to many modern people. In fact it is likely that their names would not ring a bell with the vast majority of people due to the decline of the classical education (which was the province of a narrow elite in any case when it was in vogue). But these were significant figures in their time whose influence echoes down the generations. For example, the Marian reforms depicted in The First Man in Rome arguably laid the foundations for the professional Roman legions which were to serve as the basis for the empire of the first few centuries A.D. Caesar nailed the republic’s coffin, but Marius built up much of its superstructure, making the armies loyal to their generals by opening up recruitment to those without other means of support. And Julius Caesar is a less surprising character if you are aware of the precedent of Sulla, whose vicious dictatorship he managed to evade.

Finally, of the peculiar things I recall about Colleen McCullough is that she wrote her massive novels in longhand (or at least her first few ones).

• Category: History • Tags: Colleen McCollough, First Man in Rome 

9780226520438 Evolutionary process can be modeled in both genes and culture. The former is defined by vertical transmission, while the latter can be vertical and/or horizontal. Unlike heritable biological traits, cultural phenotypes have no discernible units of inheritance in a straightforward fashion which can be easily mapped. But some of the formal models common in evolutionary genetics are also utilized in social evolution and behavioral ecology.

One of the easiest aspects of culture to gain a comprehension of is language. Unlike other cultural phenomena, such as religion, language is clear and distinct. Many believe that in some way it is a deep biological competency, and in fact would put it outside of the domain culture altogether because of its unique role at the center of the propagation of cultural “memes.” A new paper in PNAS explores the correlations of language and genes and geography, A comparison of worldwide phonemic and genetic variation in human populations (open access!). In short, the authors find that the differences in transmission of genes and language result in differences in their patterns of distribution. The correlation between genes and geography scales over the whole world. The more distant a population is from a focal group of interest, the more genetically different it is. In contrast the signal of linguistic affinity (or lack thereof) exhibits spatial limits, beyond which the linear relation decays. Beyond 10,000 kilometers more distant languages are no more dissimilar.

bravo There are a few issues to unpack here. First, they used a database of phonemes. I have no idea how one would categorize differences using syntactic features, but it strikes me that someone without more familiarity with this field might argue that looking at variation in phonemes is a bit like looking for the key under the lamp. Interestingly the authors found that phoneme similarities transcend language family. In other words, nearness breeds familiarity through horizontal transmission even if the linguistic groups are dissimilar rather than being part of a dialect continuum.

Second, they suggest that one aspect of phonemes and how they differ from genes is that isolated populations exhibit more richness and diversity, rather than less. This illustrates that there are differences between genetic and cultural process. Not only is there a great deal of horizontal transmission, but cultural processes are subject to a greater “mutation” rate, and selection can be much more efficacious. The latter is why group level selection is more mathematically plausible for culture than genes; competing demes can be much more distinct in culture than genes because minimal gene flow can equilibrate biological differences, while biased transmission of culture can result in insulation of different groups from homogenization (e.g., inheriting your cultural traits from your father, rather than your mother, who may have been kidnapped from an enemy tribe).

Finally, in line with the high mutation rate of language the authors reject earlier findings that it follows the same serial founder model detected in a 2005 paper from some of the same authors. I have to jump in here to suggest that we need be careful about assuming that this paper is a robust result upon which we should build up our model. See Towards a new history and geography of human genes informed by ancient DNA for a slight revision. In any case, the results from the language patterns suggest that Europe is the source of human language, using the same framework as genes where there is a decay of diversity from the ancestral homeland. The authors point out that this is a artifact of the fact that phoneme richness is very low in Oceania and South America, and Europe is equally distant from both regions. In other words language is too protean to gain a signal of the “Out of Africa” movement. I do agree with this. It strikes me that those who attempt to reconstruct language as it was 50,000 years ago are grasping for straws. For example, I do not think that we can presume that clicks are ancestral just because the Khoisan have clicks in their language.

The relationship of patterns of genetic variation and cultural variation are essential to elucidate. That is because I believe that we can’t understand patterns of genetic variation without a clear grasp of the common cultural processes by which human genes propagated over time and space. Language is probably the cultural trait that’s lowest down on the tree, so hopefully researchers will keeping picking at it until the big questions get resolved.

• Category: Science • Tags: Genes, Language 
Citation: Whole-genome sequencing of quartet families with autism spectrum disorder

Citation: Whole-genome sequencing of quartet families with autism spectrum disorder

The above is from the supplements of Whole-genome sequencing of quartet families with autism spectrum disorder. You can read about the research in The New York Times. I just wanted to highlight the above scatterplot, especially panel A, in the interests of pro-natalist alarmism about older fathers.

• Category: Science • Tags: Mutation 

Citation: Convergent evolution of the genomes of marine mammals

Citation: Convergent evolution of the genomes of marine mammals

440px-Ichthyosaurios5 Most of you have heard of convergent evolution. To some extent it’s often most clear and visible in morphological characteristics which are shaped by the basic physical parameters of the universe around us. Physics is nicely predictable. Bats and birds are subtlety different, but a rough congruence is body plan is evident. More striking are the parallels between dolphins, tuna, and the long extinct Ichthyosaurs. There are a finite manner of ways you can be optimally shaped as a vertebrate if you wish to be fast in the viscous waters of our planet. Living torpedoes need to emulate the sleek lineaments of the torpedo. This is probably where you are wondering what’s so interesting about this, as you read this in the illustrated evolution books you perused as a child. Well, Nature Genetics has a neat new comparative genomic paper out, Convergent evolution of the genomes of marine mammals, which explores on the genomic level what is visible to our naked eyes in terms of macroevolution made flesh in morphological similarities.

It’s an open access paper, and quite short and succinct, so I invite readers to check it out. The methods are straightforward, they sequenced the marine mammal lineages highlighted in red above, and compared them to their sister lineages which had not taken to the oceans, as well as with each other. After comparing regions of the genome they found five genes with evidence of selection across all the parallel lineages, which evolved from very distinct clades of mammals. Some of these genes made sense in terms of their functional relevance for marine organisms. In some cases the substitutions within the gene were distinct. This is to be somewhat expected, as genes are big, and there may be several ways to skin the cat. In contrast in other genes it was the exact same substitution, indicating strong constraint. All good. But then near the end they add this coda:

Our comparison of the genomes of marine mammals has highlighted parallel molecular changes in genes evolving under positive selection and putatively associated with independently evolved, adaptive phenotypic convergence. It has been hypothesized that adaptive evolution may favor a biased subset of the available substitutions, to maximize phenotypic change…and this hypothesis may explain some of our findings of convergent molecular evolution among the marine mammals. However, we also found widespread molecular convergence among the terrestrial sister taxa, suggesting that parallel substitutions might not commonly result in phenotypic convergence. The pleiotropic and often deleterious nature of most mutations may result in the long-term survival of substitutions at a limited number of sites, leaving a signature of molecular convergence within some coding genes. The parallel substitutions in 15 positively selected genes identified in this study likely represent a small proportion of the molecular changes underlying adaptive and convergent phenotypic evolution in marine mammals. Our data therefore indicate that, although convergent phenotypic evolution can result from convergent molecular evolution, these cases are rare, and evolution more frequently makes use of different molecular pathways to reach the same phenotypic outcome.

Basically the expectation here is that obvious convergent evolution is going to drive some similarities on the genomic level. This isn’t too strange an assumption when you note that groups of genes like the Hox show up over and over across many taxa. But the authors also found lots of genomic convergence between terrestrial lineages. This surprised them, because to our naked eye there isn’t any parallelism of form equivalent to what you see among the marine organisms. I think perhaps one aspect we need to consider is that some convergent evolution is in the eye of the beholder. The authors seem to be cryptically pointing to the genotype space being constrained by the genetic correlation matrix, the inability of substitutions to occur because of pleiotropic effects. But what about the possibility that there are similarities between lineages which are not salient in the form of gross morphology? For example, social structure and population density vary between lineages with no particular rhyme and reason (I exaggerate some, but you get the picture when you think of the eusocial mole rat and the eusocial hymenoptera).

Ultimately I think this paper is less important in and of itself than the fact that it sheds light on the possibility that in the near future we’ll get a good sense of the genomic shape of the tree of life, and we’ll have recourse to many high quality genomes all across the tips of the phylogenetic tree. The sorts of comparative methods utilized in this paper also have the good feature of being rather transparent and less abstruse that you often find in population genomic papers.

• Category: Science • Tags: Comparative genomics 

51u-xXl9qUL._SY344_BO1,204,203,200_The Atlantic has a long piece up which basically consists of a list of the usual objections to DNA testing from some Native American groups and individuals (which can be generalized to any indigenous group), Genetic Testing and Tribal Identity: Why many Native Americans have concerns about DNA kits like 23andme. There’s the standard stuff about how Native Americans believe archaeological remains are sacred, etc., and how that conflicts with scientific enterprises. The necessary mention of NAGPRA and such. But this quote was rather “interesting”:

“We know who we are as a people, as an indigenous people, why would we be so interested in where scientists think our genetic ancestors came from?” asks Kim Tallbear, a researcher at the University of Texas at Austin, the author of Native American DNA: Tribal Belonging and the False Promise of Genetic Science, and a member of the Sisseton-Wahpeton Oyate tribe.

Tallbear says that from her perspective, researchers offering to tell tribes where they’re from doesn’t look any different than the Christians who came in to tell them what their religion should be. “Those look like very similarly invasive projects to us,” she said. Tribes haven’t forgotten the history of scientists who gathered native skulls to prove that native people were less intelligent, and thus less entitled to the land they lived on than the white settlers. To them, these genetic questions of origin look pretty similar.

Tallbear explains that to be able to do ethical genetic research on native people in the United States, you need to understand their history. “You have to know something about the history, and about 20th century Native American policy, and how the U.S. as a colonial power dispersed native people from their historic homelands into urban areas and into reservations, how different groups have put tribes together on reservations who never lived together before. You have to know about about relocation and post-World War II politics. If you don’t understand that you can’t begin to ask informed questions about the genetics of Native Americans.”

Kim Tallbear has an academic page. Here’s a sample:

Indigenous, feminist, and queer theory approaches to critical “animal studies” and new materialisms

I have also recently begun to theorize in the area of indigenous, feminist, and queer theory approaches to animal studies and new materialisms. Last year, I co-organized with the Science, Technology, and Society Center at UC Berkeley a symposium on indigenous and other new approaches to animal studies. I was also part of another UC Berkeley symposium last year on New Materialisms where I did a talk on the role of indigenous thought. Both symposia helped mark a space for the role of indigenous thought in these related and burgeoning areas of contemporary social theory and new ethnographic practices.The recent move to “multi-species ethnography” applies anthropological approaches to studying humans and their relations with nonhumans–beings such as dogs, bears, cattle, monkeys, bees, mushrooms, and microorganisms. Such work is both methodologically and ethically innovative in that it highlights how organisms’ livelihoods are co-constituted with cultural, political, and economic forces.

Let’s not beat around the bush here, Native Americans and the government and culture of the United States have a fraught relationship. That is true. But today genetics has pretty much zero relevance to the various political debates and arguments. Issues like tribal membership are determined by the cut & thrust of politics, not genomics. Frankly, these issues are too important to leave to genetics. The possible consequences of genetics are always vague future possibilities. For people who don’t care about abstract genetic questions though even a vanishingly small probability that genetics might impact their concerns is too much of a risk, so naturally they wish to squelch it. And contrary to the implication that Tallbear makes, most scientists who work on Native American genomics don’t do so because of a deep interest in overturning the religious traditions of Native Americans, but because they are interested in the human story, of which Native Americans are an essential part. Rather than ethnic particularism the motives of scientists on the whole are those of universalist humanism.

So one can understand why political activists might balk at the inquiries of geneticists, as universalist humanism often causes problems for those engaged in the great game of ethnic particularism. But what about the academics who lend their voice in support of the latter? As far as Kim Tallbear’s “scholarship” (I hope I’m using quotations appropriately here) it resembles what I saw in Genetics and the Unsettled Past: The Collision of DNA, Race, and History. Basically an exercise in lexical obfuscation in the service of nebulous political aims, but clearly with direct consequences for the careers of a small set of academics who operate in an area where politics and activism blend seamlessly into their professional lives and their reputation among their peer groups.

Many of the assertions that Tallbear and company make about science are not totally unreasonable on the face of it. Science is a human enterprise, and scientists bring their own biases, ideologies, and interests into the execution of their endeavours. To some extent science is subjective, insofar as humans are making the judgements. But when you see where these practitioners of science studies take their project, you understand that they’re basically crazy. That is why people like Steve Fuller end up making apologia for Intelligent Design. And that is why Kim Tallbear can boldly analogize scientists to Christian missionaries. There’s simply no acknowledgement of something I like to call objective reality, so they go straight for the most provocative rhetorical tacks to hammer home their polemic.

Higher_SuperstitionHere is an indisputable fact: science is not religion, and the two are very different enterprises. If you don’t accede to this distinction, you have just lost all touch with the empirical world. It is no surprise that Phillip E. Johnson, the doyen of the Intelligent Design movement, has acknowledged a debt to critical theory. The flight from empiricism is exactly what has occurred to many scholars within science studies, probably because that’s where the career incentives are. Instead of actually pursuing a sociology of science*, they just slot science into the theoretical framework of critical theory, postcolonial studies, Marxist analysis, etc. etc., and generate out their truths deduced from a priori in a stream of prolix papers and prose whose primary purpose is to be read by a few other fellow travellers.

Kim Tallbear is really no different form Steve Fuller insofar as she’s acting as an apologist for Creationism, though a different sort from the Christian one. If Christians made the same arguments as Native American spokespersons in relation to these topics there’s no doubt that scientists would react caustically. But Native Americans are a disadvantaged group, and so the skeptical acid which scientists normally reserve for pre-scientific beliefs is withheld in this case (among social justic types this would be “punching down,” though in this case I think some punching is justified). That’s an empirical sociological fact. But, that doesn’t negate the reality that the scientists are right, and indigenous religious traditions which contradict the idea of migration via Beringia are wrong (as are some of the naive ideas about Native Americans being of the lost tribes of Israel, which was a common belief in 19th century America, and has come down in an evolved form within the Mormon religion). And I don’t mean “right” and “wrong.” I mean right and wrong. Like 0 and 1. Black and white. That’s because positivist science illustrates that social and linguistic ideological construction of the world around us runs up against the boundaries of the fact that the world has patterned and structured order which runs in contravention of human intuitions and biases. Most academics who are skeptical of the “objective” “truth” “claims” of “science” also agree with this fact when they have to put their choices where they mouth is. If they’re diagnosed with “cancer” they won’t put chemotherapy in quotations or demand the services of a tribal shaman. It’s going to be the best science for them and their family. That’s not just a theory, that’s a fact.

* Some scholars do do this, but it’s hard.

Addendum: An interesting sidenote is that the solicitation of many American scientists toward indigenous people in North America is itself an ideological orientation. As an example, many Asian Indians are not very happy with the latest results coming out of human genetics because it conflicts with their religious-social beliefs, but generally this is not much on the radar of researchers who are opining about the genetic history of these billion or so people.

• Category: Ideology, Science • Tags: DNA, Genomics, Native Americans 


parsi2 In the comments below I made the comment that the Parsi people of India, who reputedly arrived in India ~1000 years ago from Iran, are about 25 percent South Asian. By this, I mean that their ancestry is about 75 percent Iranian (presumably Persian), with 25 percent admixture from South Asian populations amongst whom they lived. But my feeling about this was vague, and I decided to check the scientific literature. Unfortunately there hasn’t been a lot of work done in this area with cutting edge genomics. But a cursory examination shows that there’s been substantial migration of Indian women into the Parsi lineage via the mtDNA. In the figure to the right you see that “PA”, the Parsis, have a lot of “South Asian” mtDNA lineages compared to the Iranian groups. This mostly consists of South Asian branches of haplogroup M. It jumps out to you immediately when looking at the haplotypes that the Parsis carry on their mtDNA. I found less on the Y chromosomes, which are less informative in differentiated South Asians from Iranians in any case (the mtDNA difference is much greater between these two regions), but what I did find is that Parsis can be modeled as 100% Iranian on their paternal lineages. This is probably an exaggeration, but as a stylized fact I think it gets to the heart of the matter.

But what would really be useful are autosomal results. Those were hard to find. Noah Rosenberg’s 2006 paper on Indian genetic differentiation using microsatellites did have a Parsi sample. If you look at the results the Parsi do seem South Asian, roughly equivalent to Pathans, an Iranian speaking group in Pakistan which has strong South Asian affinities. But the sample set does not include any Iranian groups from Iran proper, but rather Middle Eastern groups from the Arab world or the Caucasus. Without such a reference population it is hard to gauge Parsi relatedness.

There was one last hope. Harappa DNA has been collecting results for many years now, and I was hoping that there was a Parsi in the sample. There was, just one. I took the Parsi and compared this individual to various Iranian and a few select Indian groups. Here are the admixture results (edited to show only the relevant ancestral clusters):

9780307823069_p0_v1_s260x420 My intention was to read Ian MorrisWar! What Is It Good For?, but I’ve decided on Jonathan Spence’s Emperor of China: Self-Portrait of K’ang-Hsi. I’ve had this book for about seven years, and haven’t gotten to it, but now is a good time since I’ll be tackling Marcus Aurelius: A Life, and Meditations. The relationship between these two topics should be obvious to most readers with some familiarity with history.51NPyQMF0jL Simultaneous to this I’m reading The Northern Crusades on the Kindle. I got about 25% of the way through this book at some point, but had to set it aside. But the history of the Baltic has always been fascinating to me, and I think it’s an interesting topic. Most people seem unaware that the Crusades occurred in northeast Europe as well as the Levant, and that they lasted in active form longer in the north than in the Middle East.

I’ve been considering the role of specialization in science recently. Obviously I’m interested in genetics, and that has sharply constrained by knowledge of the literature. Even within genetics I’m fixated on the topics of evolutionary genomics, with a focus on humans and other mammals. When I was younger my interests were far more catholic, though I don’t know what I can do about this evolution in my focus at this point. We all go through phases, and perhaps in the future can I branch out again.

Finally, can readers people stop leaving comments with the handle “anon” or “anonymous.” I don’t mind if you have these terms in the name, but it gets very difficult to follow people if there are six or seven different individuals who go by “anon.”

• Category: Miscellaneous • Tags: Open Thread 

The New York Times has a piece within the title Experts See Signs of Moderation Despite Houthis’ Harsh Slogans. It mulls over the fact that the Houthi rebels, who are rapidly becoming the establishment, brandish anti-American and anti-Israeli slogans, and are clearly getting Iranian money. The piece mentions that the Houthi rebels are Zaydi, which is a branch of Shia Islam. But to me the article tip-toes around a somewhat important point about Zaydi Shia Islam: it is usually considered the most “Sunni-like” of all the Shia sects. One of the aspects of John Walker Lindh’s biography was that when he was in Yemen he was offended that Sunni and Shia prayed in the same mosques on occasion. This reflects the fact that Zaydi are not as deviated in practice from Sunni Muslims as other Shia. In the article there is the question of an analogy to Hezbollah:

“The Houthis are not Hezbollah,” said Charles Schmitz, an expert on the group and a professor at Towson University, referring to the Iranian-supported group that dominates Lebanon and is actively fighting on behalf of President Bashar al-Assad in Syria. “They are domestic, homegrown, and have very deep roots in Yemen, going back thousands of years.”

All true. But I think it needs to be emphasized that Hezbollah espouses the same Twelve Shia religion as Iran, and the connections between these two groups is historically very deep. The conversion of Iran to Twelver Shia Islam occurred in the 16th century under the direction of ulema imported from southern Lebanon, basically the same group which has supported the rise of Hezbollah. The reciporcal exchange of ulema between this region and Iran has continued down to the present day (see The Shia Revival by Vali Nasr). Any attempt to connect the Houthi to Iran has to be careful, emphasizing the situational aspect of this relationship when compared to Hezbollah. Because of Hezbollah’s ideological and historical identity with the Iranian religious order it is hard to ever imagine a scenario where it acts counter to Iranian interests. This is not the case with other groups which are allied with Iran, such as the Assad regime, whose Alawite sect is only nominally Twelver (due to some political machinations in the 1970s), or the Houthi, whose Zaydi sect was the dominant one within Shia Islam for many hundreds of years before the conversion of Iran to the Twelver set.

• Category: History, Ideology • Tags: Houthi, Yemen, Zaydi 

41DV5KYNJAL A friend passed me this ScienceDaily press release, American liberals and conservatives think as if from different cultures. I suspected that Jon Haidt was on the paper, and I was right, Liberals Think More Analytically (More “WEIRD”) Than Conservatives. Reading the paper the major finding seems to be that Western social liberals, and especially libertarians, exhibit the tendencies which have been defined as “WEIRD”: Western, educated, industrialized, rich, and democratic. In contrast, social conservatives in the West are less WEIRD, and tend to resemble non-Western cultures in cognitive style.

The way that this paper dichotomizes the classes is that the WEIRD tends to be more “analytic” and non-WEIRD more “holistic.” The terminology here is often freighted, and I’be cautious about overemphasizing that aspect. Rather, the key here is that in terms of traits you see a pattern where Western liberals are to a great extent the tail of a particular distribution of mental styles. To illustrate the analytic style of reasoning Joshua Greene, the author of Moral Tribes: Emotion, Reason, and the Gap Between Us and Them, has argued that incest taboos are based on disgust and reflex, rather than reason (or, the reasons are rationalizations). And, that this is clearly from his perspective not a good thing. That is the classic WEIRD tendency; to decompose the broader issue into its parts, and reach logical conclusions, even if they seem absurd or repulsive, and embrace them. Brian Williams is also WEIRD. Very WEIRD.

1361104223 In the above paper they use samples of college students at University of Virginia, those who participated in the moral foundations survey, and a few thousand Chinese students, to test their model. Though the correlations in most cases were modest (e.g., on the order of 0.2 to 0.4), it seems clear from their data that a left-right social orientation can map mapped onto differences in analytic vs. holistic thinking across cultures, and also reflect differences between cultures. Chinese college students raised in urban areas were more analytic if socially liberal. Western college students were more holistic if socially conservative.

I don’t think any of this is going to shock or surprise anyone. Rather, the interesting part to me is how easily it maps onto pattern discerned by the psychological Richard Nisbett, and reported in his book The Geographic of Thought: How Asians and Westerners Think Differently…and Why. Nisbett reported a pattern which in today’s language would have a continuum of WEIRDness like so: Anglosphere & Norden > Continental Europe > rest of the world. These data in that framework suggests that even within the Anglosphere, which is dominated by WEIRD thought, there are a large reservoir of people who reject that paradigm in their daily life. In addition, the correlation with length of time post-industrial, as well as the fact that the tendencies toward WEIRDness are now cropping up in East Asia as well, suggest that in some ways a Whiggish model is broadly correct. Nisbett and Haidt’s group both report that it isn’t particularly difficult to prime individuals to switch from one mode of cognitive style to another.

Finally, many social liberals look at social conservatives as being backward, and in need of being “educated” and “ignorant.” There’s some descriptive truth in this, insofar as there’s a fair amount of evidence that social conservatism is negatively correlated with intelligence and education. But, one can also look at social conservatives as a different culture, as simply not WEIRD. This puts modern social liberals in somewhat of a bind if they are multicultural, because perhaps they are now enjoined to extend their tolerance of other cultures to social conservatives? OK, forget about that.

• Category: History, Science • Tags: Ideology 

horsewheellanguage David Reich and Nick Patterson come down in favor of the steppe as the ur-heimat of the Indo-Europeans, at least those who migrated into Europe, in a recent abstract:

We generated genome-wide data from 65 Europeans who lived between 8,000-3,000 years ago by enriching ancient DNA libraries for a target set of about 390,000 single nucleotide polymorphisms. This strategy decreases the sequencing required to obtain genome-wide data from ancient DNA samples by around 1000-fold, allowing us to study an order of magnitude more individuals than previous studies and to obtain new insights about the past. We show that in western Europe, the farmers of both Germany and Spain >7,000 years ago were descended from a common ancestral stock. These farmers did not replace the earlier hunter-gatherers, but continued to mix with them, leading to a resurgence of hunter-gatherer ancestry in both Germany and Spain ~1,000-2,000 years later. In eastern Europe, the hunter-gatherers of Russia >7,000 years ago were distinct from those of the west, having an increased affinity to a ~24,000 year old individual from Siberia, but this affinity was reduced by ~5,000 years ago in the Yamnaya steppe pastoralists because of admixture with a population of Near Eastern ancestry. Western and Eastern Europe collided ~4,500 years ago with the appearance of the Corded Ware people in Central Europe, who derived at least two thirds of their ancestry from an eastern population closely related to the Yamnaya. The evidence for mass migration into Europe thousands of years after the arrival of agriculture, in combination with linguistic and archaeological data, makes a compelling case for the steppe as a proximate source for the spread of Indo-European languages into Europe.

This is broadly the same data which Iosif Lazaridis presented at ASHG 2014. So this itself is not new. But what I would like to draw your attention to are two posts over at Eurogenes, Ancient DNA points to the Eurasian steppe as a proximate source for Indo-European migrations into Europe, and Yamnaya genomes are a 50/50 mix of eastern Euro foragers and something else ANE-rich. Nick Patterson actually weighed in over in the comment thread for the first post. A comment in the second post was especially amusing:

Over 400 comments on an abstract? You may need to start a forum when the actual paper is released, David.

insearchof Yes, there were over 400 comments on the first post. It shows you how passionate people get about this issue. Some of the associations within this field are of a racialist nature. The Journal of Indo-European Studies was founded by Roger Pearson, though today it is edited by the respectable J. P. Mallory. This is not to say that all of those enthusiastic about this topic are quite so “out there,” but it’s quite emotional.

Until the paper itself comes out I suggest readers bone up on the archaeology, because there’s a wealth of that out there already. From what I recall the Samara samples were form David Anthony, and his The Horse, the Wheel, and Language: How Bronze-Age Riders from the Eurasian Steppes Shaped the Modern World is basically required reading in my opinion if you are interested in this issue. Also, Mallory’s older In Search of Indo-Europeans is probably worth reading as well. We live in interesting times indeed!

• Category: History, Science • Tags: Indo-Europeans 

Citation: Common genetic variants influence human subcortical brain structures, <code>Nature</code> (2015) doi:10.1038/nature14101

Citation: Common genetic variants influence human subcortical brain structures, Nature (2015) doi:10.1038/nature14101

Here’s what we know. Intelligence, as defined by a general factor which explains variation across a range of cognitive tasks, is substantially heritable, with a narrow sense heritability on the order of 0.25 to 0.75 depending on who you talk to and what context.* Intelligence itself exhibits correlations with other traits, from those of social importance, such as education, as well as biological parameters, such as brain size. Additionally, the effect size of genetic variants associated with general intelligence are likely to be very small. This means that you should be immediately skeptical of claims that a common variant segregating in the population explains a large proportion of the variation in intelligence within the population. The history of this area of research, which goes back to linkage studies, is one of non-reproducibility. Large effect quantitative trait loci should already have been picked up by linkage studies decades ago, so I am usually rather skeptical when this old wine is presented again in a genomic guise. In short, the genetic architecture of general intelligence is likely to resemble height, with many loci of small effect.**

This is what Rietveld et al. found last fall in Common genetic variants associated with cognitive performance identified using the proxy-phenotype method. The same sizes were on the order of 10,000 to 100,000 within this study. The top associations within this study explain less than 1% of the variation within the data. It seems likely that the largest effect alleles which influence intelligence variation are about an order of magnitude smaller in impact than those for height. A new paper in Nature, Common genetic variants influence human subcortical brain structures, looks at the morphology of the brain, synthesizing imaging, cognitive neuroscience, and genomics. Here’s the abstract:

…To investigate how common genetic variants affect the structure of these brain regions, here we conduct genome-wide association studies of the volumes of seven subcortical regions and the intracranial volume derived from magnetic resonance images of 30,717 individuals from 50 cohorts. We identify five novel genetic variants influencing the volumes of the putamen and caudate nucleus. We also find stronger evidence for three loci with previously established influences on hippocampal volume and intracranial volume. These variants show specific volumetric effects on brain structures rather than global effects across structures. The strongest effects were found for the putamen, where a novel intergenic locus with replicable influence on volume (rs945270; P = 1.08 × 10−33; 0.52% variance explained) showed evidence of altering the expression of the KTN1 gene in both brain and blood tissue. Variants influencing putamen volume clustered near developmental genes that regulate apoptosis, axon guidance and vesicle transport. Identification of these genetic variants provides insight into the causes of variability in human brain development, and may help to determine mechanisms of neuropsychiatric dysfunction.

Paul Thompson was involved in the research, so I am confident that it was be done thoroughly (and the author list is long enough that I hope they checked for obvious problems!). To correct for population stratification within this European sample they looked at the top for dimensions of variation, and used a regression model to capture other variables which might be confounded with the SNPs in question. The small proportion of variation explained actually increases my confidence, in that it seems to be in the same order of magnitude as the type of studies looking at endophenotypes.

Because of their sheer number I doubt that there’s a great short term likelihood of annotating all the genes responsible for variation in intelligence. Rather, I wonder if the ultimate goal is something similar to what occurred with statins. Find a small effect locus, and target a drug at that locus to help cure cognitive illnesses such as schizophrenia. It stands to reason that the same loci which impact general intelligence would also shape cognitive phenotypes which we term pathological.

* So if heritability in the narrow sense is 0.50 that means half the variation in intelligence in the population can be explained by variation of genes in the population. By way of comparison, height is 0.80 to 0.90 heritable in the narrow sense in the developed world. This does not mean that the correlation between parents and offspring is 0.80 or 0.90 for height. In fact the correlation is closer to 0.50 for height between parents and offspring and also between siblings.

** An alternative minority viewpoint is many rare alleles of somewhat larger effect.

• Category: Science • Tags: Genomics, GWAS, IQ 

A few weeks ago I wrote on something on the data on abortion views for The New York Times. The main reason is because of the sort of commentary which is now percolating through the media in response to some abortion related legislation. In particular, the implicitly liberal media.* As an example of what I mean, Donald Graham in The Atlantic has a piece titled The Republican Party’s Abortion Bind: Female GOP lawmakers withdrew their support for a late-term ban, demonstrating that the leadership is more than just old, white men. Notice the subhead here, the reference to “old, white men” is the trope which is regularly trotted out. But as I showed in my piece above there’s no sex difference on the whole when it comes to abortion, though conservative women are more likely to be pro-life than conservative men. Graham suggests that “female Republican lawmakers…worried that the rape-reporting restriction was too strict, and that the bill would alienate young voters and women from the party.” From other reporting this is the perception of the lawmakers. Graham also makes an allusion to the fact “everyone knows the GOP faces a demographic time bomb, since its voters are older and whiter and more pro-life than the general population, so it’s risky to do anything that might make it harder to win them over.” Yet despite relaying that some Republican lawmakers think the abortion issue alienates younger voters, he acknowledges that that’s not the case, stating that “It’s a surprising and little-known fact that opinions about abortion have barely budged in the American public in the 42 years since Roe.” If there was a major secular age effect then attitudes toward abortion would change over time as older cohorts died.

There has been trend in recent years for liberal commentators to decry the fact that the media relays the opinions of politicians without scrutinizing their factual content. But that’s somewhat selective. Here is a case where a group of Republican lawmakers are expressing opinions based on facts which are simply not true. Either they know they are not true, or they are not aware of the facts. The media should perhaps enlighten them. But they’re not, because as it happens the reality is most of the media is not sympathetic to the pro-life position.

Here are the facts, as told by Gallup (found with something called Google) and the General Social Survey. From Gallup a few years back, Generational Differences on Abortion Narrow: Support for making abortion broadly illegal growing fastest among young adults. The results show a small trend toward millenials being less supportive of abortion rights than previous generations. I wouldn’t make too big of a deal about this, because the differences are often not that great. But, the trend is real. Rather than being monotonic, there is a pro-choice “peak” among late boomers and gen-Xers, with the oldest cohorts being the most pro-life, but the youngest ones being next in line.

CatusWildAutoCluster_htm_m2d838ae4I repeated the analysis using the “ABANY” variable in the GSS, comparing to age cohorts from 1931 onward. What you can see is that the most pro-choice voters were born between 1951 and 1970. There has been a shift back toward more pro-life positions on the part of gen-Xers, and even more among millenials.

So the young do not support abortion rights to a greater extent than the older cohorts, unless you are talking about senior citizens, though soon enough the most pro-choice generations will actually fall into that category. The more interesting question is why some Republicans often bring up these sorts of talking points whenever push comes to shove on social issues which they purportedly support. Even granting the sincerity of the pro-life views of many Republicans, I think the issue is that it’s really not something they want to get into a war over, because it’s not a primary concern for most of the party. They rely on social conservatives, and so faithfully and stridently pay lip service to their concerns, but generally balk at toughing it out when it comes to legislation.

In the end I think Jon Chait is right in his polemic The Big Con. Economic conservatives call the final shots, and get results. Republicans oppose tax increases on “job creators” passionately. When it comes to legislation around abortion a large portion of the party heads for the hills. What set of issues do you think the Republican party would shut the government down over?

* Here I’m not talking about Mother Jones, but more mainstream journals. Though most of their writers do not take strident liberal positions, they are personally social liberals, and this usually shows. What set of issues do you think the Republican party would shut the government down over?

• Category: Ideology • Tags: Abortion 
Citation: Estimates of <code>Continental Ancestry Vary Widely</code> among <code>Individuals</code> with the <code>Same</code> mtDNA Haplogroup

Citation: Estimates of Continental Ancestry Vary Widely among Individuals with the Same mtDNA Haplogroup

A new paper in The American Journal of Human Genetics, Estimates of Continental Ancestry Vary Widely among Individuals with the Same mtDNA Haplogroup, tells you something which should be obvious:one marker tells you only so much about individual ancestry. In other words, the history of one gene can only tell you so much about the whole genome. Because mtDNA and Y chromosome* does not recombine you can treat it as one long genetic marker. On the coarse grain they can tell us a great deal. Both mtDNA and Y confirmed that it seems the modern human populations seem to be diverged from a group with an African origin. Genomics, even using the whole genome, has confirmed this. Additionally, non-recombining regions of the genome are more tractable for a coalescent framework. They are actually trees.

But Richard Lewontin’s insight that a great deal of human genetic variation is not partitioned across populations, but within them, applies to mtDNA and the Y chromosomes as well. Where Lewontin’s insight misleads is that using just a few more markers one can obtain relatively robust phylogenetic trees which reflect well the population structure and history of a given species. One can see this when one considers mtDNA and Y chromosomal lineages jointly. If someone tells you that their Y chromosomal lineage is R1a1a you can infer that their ancestry is anywhere from Central Europe all the way to South Asia. But if they add that their mtDNA is U2b you can be confident that they are South Asian. U2b spans South Asia, as well as parts of the Middle East. But in the latter zones R1a1a is very rare.

Though the phylogeographic import of mtDNA for a given individual is often questionable, that’s true of any marker. Because mtDNA is amenable to phylogenetic modelling it is still quite useful, especially when making very geographically coarse inferences. But the paper’s argument that the geographic inferences of DTC tests is questionable based on the fact autosomal SNP-chips are the same framework used within the paper to test the informativeness of mtDNA.**

* The NRY

** Disclosure, I have done consulting for Family Tree DNA on their autosomal tests.

• Category: Science • Tags: Personal Genomics 

51Jb17R6p6L._SY344_BO1,204,203,200_ Adrian Goldsworthy’s The Fall of Carthage: The Punic Wars 265-146BC is illustrated on its cover with a photograph of a bust of Hannibal Barca. As you may know Hannibal was the general who led the armies of Carthage in the Italian peninsula during the Second Punic War, to great effect. In fact, until the battle of Zama in North Africa, during the last phases of the war, Hannibal did not lose to a Roman army. And yet despite his record of victory in tactical engagements, he was strategically bested by the Romans and lost the war. Unsurprisingly if there is one figure who looms large in the narrative of The Fall of Carthage it is Hannibal. This is striking because almost all of what we know about these wars comes down to us thanks to the Romans, so our perceptions are coloured by their biases, and he was their great antagonist. And yet it is undeniable that Hannibal’s raw tactical genius won grudging admiration and respect from the Romans. He was a singular figure, with no equivalent among the Romans of his era, with all due apologies to Scipio Africanus. And yet Rome won, and Carthage lost.

9780300137194 Goldsworthy is a military historian, so I was aware that he would focus on the minutiae of military logistics as well as outlining numerous set piece battles. Much of his How Rome Fell dealt with the slow decay of the Roman military system of the early empire over the course of the 3rd century, and the reorganization of the 4th century, which temporarily halted the decline, while ultimately undermining it in the long term through a reliance on allies who exhibited less attachment to Romanitas. One could argue in many ways the late antique Roman military complex resembled that of Carthage more than that of Rome during the late republic and early empire. Though the author gives much space to battles and campaigns, aside from the incredible retelling of the battle of Cannae, one can gloss over the details without loss of the general thrust of the narrative. Battles are won and lost, but the lessons from the war can not be reduced down to the battles.

historyofrome It was simply improbable that Carthage could win a military conflict with Rome over the long run because the Roman system conferred upon the Roman state material and ideological advantages which could not be overcome by military victories, even by a general as creative and competent as Hannibal. The Hellenistic king Pyrrhus learned this, and gave us the term “pyrrhic victory”. In ideological terms Goldsworthy argues that the Roman mindset was one where conflicts were viewed as wars of attrition, where only the victors were left standing. In contrast Carthage, like the Hellenistic states, operated in a more classical Westphalian framework where victory and defeat were never final, but simply instances of a continuous game between elites of distinct polities. But, if it was not for the material advantages of the Roman system its ideological orientation would have been suicidal, because wars of attrition can only be maintained when there are resources to feed them. The Romans relied upon conscript armies of free peasantry, committed to the idea of their republic as an expression of collective will, as well as Italian allies of long standing. Goldsworthy notes that no individual of the Roman elite betrayed their city, nor did any of the Latin allies (the cities who went over to Hannibal during his years in Italy tended to be culturally distant from Rome, whether non-Latin Italian or Greek). And, the citizen base of Rome was notoriously broad, because the Roman system was expansive, assimilating allies and elites of foreign polities over time. This is an ancient feature of Roman society, as at least half of the major patrician lineages are not Latin, but Sabine. This is in contrast to organization of Hellenistic or Carthaginian polities, which were not assimilative, but multicultural and cosmopolitan in a manner more resembling the later Roman system of the imperial period, or empires more generally.* The armies of Carthage and the Hellenistic kingdoms were not manned by citizens, but professionals, whether a standing army, or mercenaries and subject peoples. The army deployed by Hannibal consisted of Libyans, Spaniards, and assorted Italian peoples inimical to the Romans (e.g., the Gauls of the Po valley). Until the last of the conflicts between Rome and Carthage, which took place in the immediate environs of Carthage, Roman amateur soldiers lined up against armies in the service of Carthage, not armies of Carthaginians.

warinhumancivilization The robustness of the Roman system to defeat can be put down to the fact that like the armies of the French Revolution Rome threw its citizenry against its enemies to complete a broad mission, while its contemporaries purchased smaller professional armies to achieve specific tasks. In many circumstances these professionals could obtain victory, but the gains did not have the depth to force the concession of the Roman state, because the state was an expression of the populace, which remained defiant. In Azar Gat’s expansive War in Human Civilization the author reports that numbers available to the military are the major predictor of victory in battle and war. In other words, the side that can throw more resources into the conflict can win if it so chooses. Sometimes those resources are not so obvious to contemporaries. For example, Britain’s rise to power in the 18th century has often been attributed to its ability to borrow money to finance its wars (in contrast, many continental polities were not as creditworthy, and so lacked as many financial resources). There are cases where individuals of particular genius and charisma can change the calculus; Gat for example states that Napoleon Bonaparte’s armies were as successful as forces which were nearly 30% bigger. In other words, Napoleon’s particular genius was worth a third again as many soldiers as he actually had at his disposal. And yet ultimately Napoleon lost his wars . The French innovation of the early modern period of conscripting the whole nation for war could only gain them advantages for so long as other Europeans nations did not imitate them. When they did so they ultimately surpassed them in raw quantity, and emerged victorious.

warandpeaceandwar The particular story in The Fall of Carthage dovetails perfectly with the general model in Peter Turchin’s War and Peace and War: The Rise and Fall of Empires. The Romans of the republic had asabiyah, social cohesion. Against their enemies they exhibited a stance where they accepted that the only alternatives were collective victory or collective extinction. One can speculate why this was so, but clearly that is the key variable in the rise of Rome in the world after the death of Alexander. And it explains the fall of Carthage, which in many ways was a Hellenistic polity, rather than an heir to the ancient traditions of the Levant. In the sense of microeconomics the Carthaginians were homo economicus in comparison to the Romans. The years before the Third Punic War were ones of incredible prosperity for the city of Carthage, as documented in the Roman literary sources as well as archaeology. Rome fought Carthage not because it was weak and poor, but because it was strong and rich. And Rome won because its citizens loved their city more than could be accounted for by any rational calculation. Rome rose as an idea, and it fell as an idea.

* Because history is written by the winners we have little direct documentation from Carthage, but it is noteworthy that the city seems to have resembled Rome’s mixed system of governance, down to having a senate.

• Category: History • Tags: History, Punic Wars, Rome 

James C. Chatters 2002 book

James C. Chatters 2002 book

By now you may have read the breaking news in The Seattle Times that Eske Willerslev’s group is going to publish genetic results on Kennewick Man. This “scoop” was obtained through the freedom of information act, which makes sense since Kennewick Man has been embroiled in political controversy since the beginning of its discovery by James Chatters in the 1990s. The issue is that morphologically the remains were not typical of contemporary Native Americans, which might cause some doubt as to the legitimacy of the social-political rights of the indigenous people of the region today. The social-political aspects have been beaten to death, and I am not particularly interested in that area. Rather, the science is more fascinating, if, somewhat less surprising in light of the results that are going to come out in the near future.

2019387254The most famous reconstruction of Kennewick Man is strange because it resembles British actor Patrick Stewart. Humans use phenotypes, morphology, to ascertain genetic relatedness when DNA is not available. In the 1990s DNA was not available. The inference by many researchers who had access to the remains was that Kennewick Man was different because his morphology may have resembled a person of European heritage. The controversy turned into such a circus that somehow Steve McNallen, arguably America’s foremost Northern European neo-pagan expositor, made claims on the remains on the same grounds as Native American people! Later scholars suggest that perhaps Kennewick Man was not so much European, as not typical of contemporary Native Americans (e.g., perhaps he was part of an early migration of basal East Eurasians related to the Jomon of Japan).

41VAznr2aiL._SX258_BO1,204,203,200_ If the Seattle Times report is correct, and I believe it is, Kennewick Man is part of the ancestral population to modern Native Americans. This should put to bed most of the political debate, since the results are likely to mollify many Native activists. But, there are still details to be fleshed out. A 2012 publication suggests that there was a secondary migration out of Eurasia, which resulted in the Na-Dene group which is common in the northern and western portions of North America. In contrast, Kennewick Man is likely to belong to the first ur-North Americans, who arrived as a relatively small population from Berengia ~15,000 years ago. This is the overwhelming majority of indigenous ancestry, and south of the Rio Grande basically the totality.*

Due for an update!

Due for an update!

The context here is important. One insight of modern ancient DNA is that there has been a great deal of population turnover over the past ~10,000 years, as well as admixture between disparate lineages. When Kennewick Man died ~9,000 years ago Europeans as we understand them did not exist genetically. All across Eurasia, Africa, and Oceania, the Holocene brought radical demographic turnover (with some exceptions such as the Andaman Islands and the deserts of southwest Africa). The New World was somewhat different, as I implied above. There were some demographic disruptions, but south of the Rio Grande, and across the eastern half of North America, the populations descend from a relatively homogeneous founder stock which arrived at the end of the Pleistocene. The fact that many remains seem “atypical” for the morphology of Native Americans is strong evidence of in situ evolution.**

Years ago a physical anthropologist told me that when you look at Amazonian natives they “looked” like Siberians. Yes, they had changed and adapted, but only somewhat. It illustrated to me the powerful constraint of limited genetic variation upon populations. Similarly, though there is variation in pigmentation among native populations in the New World, it is far less than you see in the Old World. Why? Perhaps it is a function of different (or lack thereof) of selective pressures. Or, perhaps the variation wasn’t there for selection in the first place? The history of the Old World has jumbled all our easy narratives. The New World may actually be a godsend because of the simple elegance of its demographic history.

* From my Twitter exchanges with Pontus Skoglund I believe there is some population structure in the founding “First American” group, though not a great deal.

** Admixture is an issue, but that can be obviated by genetic testing, as well as looking at early modern remains.

It looks like a combination of the top and low ends of the socioeconomic distribution, Geographic clusters of underimmunization identified in Northern California:

Underimmunization ranged from 18 percent to 23 percent within clusters, compared with 11 percent outside clusters. Between 2010 and 2012, geographic clusters of underimmunization were found in:

  • the East Bay (Richmond to San Leandro);
  • Sonoma and Napa counties;
  • a small area of east Sacramento;
  • northern San Francisco and southern Marin counties; and
  • a small area of Vallejo.

“Shot limiting,” in which parents limit the number of injections or antigens that children receive during a pediatric visit to two or fewer, was found to cluster in similar areas.

Vaccine refusal ranged from 5.5 percent to 13.5 percent within clusters, compared with 2.6 percent outside clusters. Between 2010 and 2012, geographic clusters of vaccine refusal were found in:

  • the East Bay (El Cerrito to Alameda);
  • Marin and southwest Sonoma counties;
  • northeastern San Francisco;
  • northeastern Sacramento County and Roseville; and
  • a small area south of Sacramento

The paper is not live, but it will be here at some point. In Southern California most of the resistance has been in affluent areas, and in some of these areas the fraction immunized is definitely below the herd immunity threshold. Though this trend looks like it may finally have levelled off in California.

• Category: Science • Tags: Anti-Vaccination, Vaccination 

recomb2 I’m someone who until a few years ago thought of recombination as a pretty boring and static evolutionary genetic parameter. Then I went to a talk by John Novembre which reported on variation between human populations in patterns of recombination (in particular, differences in “hotspots”). For a quick review, recombination is important for two primary reasons. One is molecular genetic, insofar as it seems to have structural value for meiotic process and DNA repair. No recombination is generally not good. Second, recombination maintains the law of independent assortment of traits even on the same chromosome, because over time even nearby genes will be uncoupled in their inheritance due to crossing over. From an evolutionary perspective this is important because in this way “good” and “bad” alleles can be decoupled from other other. Recombination is basically a way to enhance the ability of sex to mix and match variation.

Graham Coop revealed patterns of variation among individuals years ago. For example, it is from Graham’s work that I came to understand to recombination is less common in sperm than in eggs, ergo, you’ll have more variance in genomic contributions from paternal than maternal grandparents. Recently at BAPG XI Laurie Stevison presented work reveal patterns of recombination variation, and the role of PRDM9, across great ape lineages. I tweeted some of the results out, but there were a lot of them. I found the talk interesting, but difficult to take in because there was so much. Now Stevison has put out a preprint, The Time-Scale of Recombination Rate Evolution in Great Apes, and I feel somewhat the same about it. There’s lots of good stuff, but unless you are steeped in this domain it is somewhat difficult to parse it and tease out distinct threads coherently. But, as you can tell from the figure at the top of this post changes in patterns of recombination vary as a linear function of genetic divergence. Some of this stands to reason as the karyotypes of great apes differ. And yet even taking this into account it seems there are differences in patterns such as skew of recombination across the genome (e.g., ~75% of the recombination in human genomes occurs on ~20% of the sequence, with enrichment around telomeres, and very little around centromeres). Looking over Stevison’s preprint I have to wonder as to the role of quality of data in some of the results. Genetic maps are hard to get in some populations, and the ones floating around are not always good. The big takeaway of note for me is that though there is lots of variation in fine scale recombination patterns, there are some broad constraints. That makes sense when you note that there are structural/mechanistic reasons for recombination rooted in the nature of meiosis. It’s not a totally neutral parameter which can explore the full space of possibilities. But, in this context obviously the variation in hotspots shows that there are different ways to skin this cat.

Finally, there’s one issue that jumped out at me, and that is they found that “European human population presents the strongest hotspot usage across the genome.” This aligns with earlier work. But I wonder how much of this tendency to find uniqueness in Europeans is due to the enormous amount of genomic resources available for this population. It’s also intriguing in light of the evidence that the European mutation spectrum is different.

In any case, I think everyone should read this preprint several times. I know I’m going to.

• Category: Science • Tags: Population genomics, Recombination 



SLC24A5 alleles

Many years ago I was perplexed by particular patterns in some genes which have been subject to very strong selection. In particular, the locus SLC24A5 has been subject to a powerful sweep over the last 10,000 years across Western Eurasia, to near total fixation in Europe, but still at high frequencies as far south as India. Yet the derived variant is relatively uncommon in East Asia. Groups which carry the West Eurasian variant, such as the Uyghurs, almost certainly obtained it through admixture processes over the last 10,000 years (in the case of the Uyghurs and various northeast Eurasian ethnicities such as the Mongols, this admixture from West Eurasians is mostly in historical time over the past 2,000 years).

The common sense explanation is that vast regions of interior Eurasia were not highly populated for tens of thousands of years. Even after the Ice Age retreated the Eurasian interior would have been particular inhospitable. Though maps of human migration show where humans have lived at some frequency all across the world, they do not usually show any sign of the density. If densities were low enough in the inter-montane zones of Inner Asia, then for all practical purposes the idea of isolation-by-distance gene flow may not have held for the two antipodes of Eurasia for much of the Pleistocene and early Holocene. So have things changed? I believe so. And it comes down to agriculture, which enabled much higher population densities in areas which were previously simply not feasible areas for hunter-gatherers.

A new paper in Science outlines this for Tibet, Agriculture facilitated permanent human occupation of the Tibetan Plateau after 3600 B.P.. I’ll quote the relevant sections of the paper:

On the basis of the above evidence, the prehistoric human occupation of the NETP can be subdivided into three phases. During the first phase (pre–5200 cal yr B.P.), hunter-gatherers made occasional forays to altitudes reaching above 4300 masl, presumably tracking game. During the second phase (5200 to 3600 cal yr B.P.), a longstanding tradition of millet farming that had become widely established along the middle and lower reaches of the Yellow River extended upstream into the NETP. Millet farming had spread across the Loess Plateau after 5900 cal yr B.P. (17) and subsequently spread across these lower reaches of the NETP from 5200 cal yr B.P. Toward the end of the second phase (4000 and 3600 cal yr B.P.), two significant additions are observed in the crop repertoire (text S4 and fig. S6). The North Chinese crops of broomcorn and foxtail millet were joined or displaced on some sites by the principal cereals of the Fertile Crescent, barley and wheat. There has been much interest in the chronology and consequences of the meeting of east and west staple crops in prehistory (1820). Here, its notable consequence was to facilitate the sustained settlement of the Tibetan Plateau’s higher altitudes. The importation of wheat and barley enabled human communities to adapt to the harsher conditions of higher altitudes in the Tibetan Plateau, a possibility raised in previous studies (15, 21).

The key addition was barley. During phase three, from around 3600 cal yr B.P., sites can be divided into those that lie above or below 2500 masl. In the lower-altitude group, the longstanding crops, broomcorn and foxtail millet, are joined by barley as a third component in an otherwise traditional dietary repertoire. In the higher-altitude group, however, the frost-sensitive millet is absent, and the cold-tolerant barley has moved to a primary position (Fig. 2D). Alongside the presence of wheat (also relatively cold-tolerant) and sheep, the diet at these high altitudes has clearly been transformed, but in a manner that enabled sustained settlement at unprecedented altitudes.

There’s been a lot of interesting work on the genetics of Tibetans recently, from altitude adaptation from archaics, to the inference that a great deal of Tibetan ancestry is actually shared with the Han and other lowland groups in the past three to four thousand years. These results make more sense if you realize that the arrival of more advanced agricultural techniques reshaped the possibilities of habitation for humans at higher densities. In fact, it is almost certainly no coincidence that it is during the period of agriculture that the great fusions between the disparate “branches” of the human family tree came back together; higher population densities across huge areas mean that de facto gene flow no go zones disappeared.

• Category: Science • Tags: Genetics, Tibet 

51Jb17R6p6L._SY344_BO1,204,203,200_ Currently reading Adrian Goldsworthy’s The Fall of Carthage: The Punic Wars 265-146BC. I read his How Rome Fell: Death of a Superpower years ago, so no surprises. He’s a military historian, so battles, down to the alignment of maniples and details of logistics, operate in the foreground. Not normally my cup of tea, but a nice change up from the focus on social history which seems to be more common today in these sorts of treatments. I also have some Anthony Evrett biographies on deck, but I think I’ll probably hit Ian MorrisWar! What Is It Good For?: Conflict and the Progress of Civilization from Primates to Robots first. It’s the sort of “big history” which is a better complement to the sort of narrative history that Goldsworthy seems adept at writing.

One thing about The Fall of Carthage (and to some extent the author’s works more generally) that I like is that it dispels some of the preconceptions we have about pre-modern hand to hand conflict. In particular, a lot of our mental image is what Goldsworthy would term “cinematic.” The reality is that a lot of the pitched battles were very tentative, and full action probably occurred for less than 15 minutes, even if extended hostilities could go on for as long as hours.

Update: I don’t link to other blogs much, partly because I don’t have much time to read them with my other obligations, but Pseudoerasmus runs a shop with very high intellectual quality. Recommended. In a similar vein, Scholars Gate.

• Category: Miscellaneous • Tags: Open Thread 

hartle A friend of mine is beginning grad school and has settled upon a lab. The core research within the laboratory is population genomics, and they now need to get up to speed in the area. Taking a class is certainly the start. You can read Haldane’s Sieve to keep up on the literature, which is a necessity if you are doing genomics work, as texts get out of date quickly. Additionally, Graham Coop, Joe Felsenstein and Kent Holsinger have excellent online notes. The upside to this is that they are free. The downside is sometimes you are away from a computer screen. Often a soft intro recommended by many is John Gillespie’s Population Genetics: A Concise Guide, which nicely has a Kindle edition. But if you are going to do graduate level work, I think it is best to just go whole hog. The Gillespie book is appropriate for a quick course or for the undergraduate level, but you really need something as a reference at some point. And for that nothing beats Daniel Hartl and Andrew Clark’s Principles of Population Genetics. There are other texts out there in this area. For example, I have Philip Hedrick’s Genetics of Populations, and Alan Templeton’s Population Genetics and Microevolutionary Theory. For various reasons I would still pick Hartl & Clark if I had to pick.

falconer I also think it’s important to know quantitative genetics, and for that Trudy MacKay and Douglas Falconer’s Introduction to Quantitative Genetics is the best bet in the business that I know of. It’s an excellent complement to Principles of Population Genetics because it starts with pop gen foundations. Derek Roff’s Evolutionary Quantitative Genetics and Michael Lynch and Bruce Walsh’s Genetics and Analysis of Quantitative Traits are probably too specialized for the beginner, and frankly even many steeped in the field haven’t read those books.

slatkinnielsen There are plenty of other books out there which might suffice in some fashion. In my previous post I mentioned Elements of Evolutionary Genetics. The old John Maynard Smith classic Evolutionary Genetics is also excellent. But if you are working in genomics and want a book less focused on classical methods and geared toward contemporary best practices, then Rasmus Nielsen and Monty Slatkin’s An Introduction to Population Genetics: Theory and Applications is pretty good. It’s a short book, and because it’s in its first edition there are many errors in it. From what I recall it was developed out of notes from a course taught at Berkeley, and it outlines the sort of methods you see in the papers which being published today, utilizing coalescent theory and site frequency spectra. It might be a reasonable quickstart, though I’m not sure it is developed well enough to be a reference (for what it’s worth, I have a copy of it too, and it is being used in graduate level courses here at UC Davis).

• Category: Science • Tags: Population Genetics, Population genomics 
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