“What it begins to suggest is that we’re looking at a ‘Lord of the Rings’-type world – that there were many hominid populations,” says Mark Thomas, an evolutionary geneticist at University College London who was at the meeting but was not involved in the work.
This is in reference to the ancient DNA meeting where David Reich reported that the Denisovans, an exotic archaic population which contributed ~5-10 percent of the ancestry of Papuans, was itself a synthesis of Neandertals and a mysterious group currently unknown. This is not surprising, as the broad outlines of these results were presented at ASHG 2012, though no doubt they’re moving closer to publication. But for this post I want to shift the focus to a different time and place, after the ancient admixture with archaic lineages, and to the reticulation present within our own.
One of the secondary issues which cropped up with Nina Davuluri winning Miss America is that it seems implausible that someone with her complexion would be able to win any Indian beauty contest. A quick skim of Google images “Miss India” will make clear the reality that I’m alluding to. The Indian beauty ideal, especially for females, is skewed to the lighter end of the complexion distribution of native South Asians. Nina Davuluri herself is not particularly dark skinned if you compared her to the average South Asian; in fact she is likely at the median. But it would be surprising to see a woman who looks like her held up as conventionally beautiful in the mainstream Indian media. When I’ve pointed this peculiar aspect out to Indians* some of them of will submit that there are dark skinned female celebrities, but when I look up the actresses in question they are invariably not very dark skinned, though perhaps by comparison to what is the norm in that industry they may be. But whatever the cultural reality is, the fraught relationship of color variation to aesthetic variation prompts us to ask, why are South Asians so diverse in their complexions in the first place? A new paper in PLoS Genetics, The Light Skin Allele of SLC24A5 in South Asians and Europeans Shares Identity by Descent, explores this genetic question in depth.
Much of the low hanging fruit in this area was picked years ago. A few large effect genetic variants which are known to be polymorphic across many populations in Western Eurasia segregate within South Asian populations. What this means in plainer language is that a few genes which cause major changes in phenotype are floating around in alternative flavors even within families among people of Indian subcontinental origin. Ergo, you can see huge differences between full siblings in complexion (African Americans, as an admixed population, are analogous). While loss of pigmentation in eastern and western Eurasia seems to be a case of convergent evolution (different mutations in overlapping sets of genes), the H. sapiens sapiens ancestral condition of darker skin is well conserved from Melanesia to Africa.
I should be careful about being flip on this issue. As recently as the mid aughts (see Mutants) the details of this trait were not entirely understood. Today the nature of inheritance in various populations is well understood, and a substantial proportion of the evolutionary history is also known to a reasonable clarity as far as these things go. The 50,000 foot perspective is this: we lost our fur millions of years ago, and developed dark skin, and many of us lost our pigmentation after we left Africa ~50,000 years ago (in fact, it seems likely that hominins in the northern latitudes were always diverse in their pigmentation)
“There were giants in the earth in those days…when the sons of God came in unto the daughters of men, and they bare children to them, the same became mighty men which were of old, men of renown.” -Genesis 6:4
Seven years ago I wrote a short post, Why patriarchy?, which attempted to present a concise explanation for the ubiquity of what we might term patriarchy in complex societies (i.e., not “small-scale societies”). Broadly speaking my conjecture is that social and political dominance of small groups of males (proportionally) over the past several thousand years is an example of “evoked culture”. The higher population densities in agricultural societies produced a relative surfeit of accessible marginal surplus, which could be given over to supporting non-peasant classes who specialized in trade, religion, and war, all of which were connected. This new economic and cultural context served to trigger a reorganization the typical distribution of power relations of human societies because of the responses of the basic cognitive architecture of our species inherited from Paleolithic humans. Agon, or intra-specific competition, has always been part of the game on human socialization. The scaling up and channeling of this instinct in bands of males totally transformed human societies (another dynamic is elaboration of cooperative structures, though this often manifests as agonistic competition between coalitions of humans).
- Genesis 16:12
By now you may have seen or read two important papers which just came out in Science, 2000 Years of Parallel Societies in Stone Age Central Europe, and Ancient DNA Reveals Key Stages in the Formation of Central European Mitochondrial Genetic Diversity. The details have been extensively explored elsewhere. If you don’t have academic access I highly recommend the supplement of the second paper. It’s also very illuminating if you don’t have a good grasp of the nuts and bolts of archaeology (I do not). I can’t, for example, confirm whether the merging strategies of different archaeological cultures were appropriate or not, because I’m not totally clear in my own head about the nature of these distinct archaeological ‘cultures’ (quotations due to the fact that archaeologists infer culture from material remains, and so they may not be cultures in the sense we understand culture). But the overall finding is clear, in ancient Europe thousands of years ago there were multiple demographic replacements and amalgamations. The post-World War II thesis in archaeology that one could not infer changes in the demographic character from material remains (because the latter can diffuse purely through memetic means) seems to be false. The correspondence is surprisingly tight.
Update: Just watch this movie.
No time to write about it now, but check Science Magazine this afternoon (in a few hours from this posting) for a major paper on ancient mtDNA, and the striking correlation between changes in lineage frequencies and cultures that they discovered. Turns out that when you peel back the palimpsest it is much more complicated and surprising than we’d have thought. National Geographic, which funded the project, already has a post out on it:
What they found was that the shift in the frequency of DNA lineages closely matched the changes and appearances of new Central European cultures across time. In other words, the people who lived in Central Europe 7,000 years ago had different DNA lineages than those that lived there 5,000 years ago, and again different to those that lived 3,500 years ago. Central Europe was dynamic place during the Bronze age, and the genetic composition of the people that lived there demonstrates that there was nothing static about European prehistory.
Genographic Project Director and National Geographic Explorer-in-Residence, Spencer Wells expounds: “spanning a period from the dawn of farming during the Neolithic period through to the Bronze Age, the [genetic] data from the archaeological remains reveals successive waves of migration and population replacement- genetic ‘revolutions’ that combined to create the genetic patterns we see today.”
I hope this doesn’t lead to a new simplicity to replace the old one of no migration.
Sports Illustrated writer David Epstein has a new book out, The Sports Gene: Inside the Science of Extraordinary Athletic Performance. The title strikes me as coarse and reductive, but I am aware that authors do not always have control over such things. I’ve corresponded with Epstein a bit over the past year, and he’s sent me some passages relating to human evolutionary genetics and paleoanthropology to me to make sure they don’t sound crazy. I haven’t had time to read the book, but judging from the interview I listened to on NPR it’s data rich and theory subtle. Though the title seems to imply that athleticism is a single gene trait where most of the variation in the population is due to genetic variation, Epstein denies this and instead presents the reality that athleticism is a complex trait which many dimensions, subject to numerous genetic and environment variables, and, interactions across those variables. That would make for a less sexy subtitle, but it would have had the attribute of being correct.
Before there was Structure there was just structure. By this, I mean that population substructure has always been. The question is how we as humans shall characterize and visualize it in a manner which imparts some measure of wisdom and enlightenment. A simple fashion in which we can assess population substructure is to visualize the genetic distances across individuals or populations on a two dimensional plot. Another way which is quite popular is to represent the distance on a neighbor joining tree, as on the left. As you can see this is not always satisfying: dense trees with too many tips are often almost impossible to interpret beyond the most trivial inferences (though there is an aesthetic beauty in their feathery topology!). And where graphical representations such as neighbor-joining trees and MDS plots remove too much relevant information, cluttered FSTmatrices have the opposite problem. All the distance data is there in its glorious specific detail, but there’s very little Gestalt comprehension.
My friend Zack Ajmal has been running the Harappa Ancestry Project for several years now. This is a non-institutional complement to the genomic research which occurs in the academy. His motivation was in large part to fill in the gaps of population coverage within South Asia which one sees in the academic literature. Much of this is due to politics, as the government of India has traditionally been reluctant to allow sample collection (ergo, the HGDP data uses Pakistanis as their South Asian reference, while the HapMap collected DNA from Indian Americans in Houston). Of course this sort of project is not without its own blind spots. Zack must rely on public data sets to get a better picture of groups like tribal populations and Dalits, because they are so underrepresented in the Diaspora from which he draws many of the project participants.
Once Zack has the genotype one of the primary things he does is add it to his broader data set (which includes many public samples) and analyze it with the Admixture model-based clustering package. What Admixture does is take a specific number of populations (e.g. K = 12) and generate quantity assignments to individuals. So, for example individual A might be assigned 40% population 1 and 60% population 2 for K = 2. Individual B might be 45% population 1 and 55% population 2. These are not necessarily ‘real’ populations. Rather, the populations and their proportions are there to allow you to discern patterns of relationships across individuals.
Since Zack has put his results online, I thought it would be useful to review what patterns have emerged over the past two years, as his sample sizes for some regions are now moderately significant. Though he has K=16 populations, not all of them will concern us, because South Asians do not tend to exhibit many of the components. I will focus on seven: S Indian, Baloch, Caucasian, NE Euro, SE Asian, Siberian and NE Asian. These are not real populations, but the labels tell you which region these components are modal. So, for example, the “S Indian” component peaks in southern India. The “Baloch” in among the Baloch people of southeastern Iran and southwest Pakistan. The “NE Euro” among the eastern Baltic peoples. The last three are Asian components, running the latitude from south to north to center. They only concern the first population of interest, Bengalis. I will combine these last three together as “Asian.”
Below is a table, mostly individuals from Zack’s results (though there are some aggregate results from public data sets). Comments below.
It is well known that Alexander the Great invaded the Indus river valley. Coincidentally in the mountains shadowing this region are isolated groups of tribal populations whose physical appearance is at at variance with South Asians. In particular, they are much lighter skinned, and often blonde or blue eyed. Naturally this led to 19th and early 20th century speculation that they were lost white races, perhaps descended from some of the Macedonian soldiers of Alexander. This was partly the basis of the Rudyard Kipling novel The Man Who Would Be King. Naturally over time some of these people themselves have forwarded this idea. In the case of a group such as the Kalash of Pakistan this conjecture is supported by the exotic nature of their religion, which seems to be Indo-European, and similar to Vedic Hinduism, with minimal influence from Islam.
Like many people I’ve been following the tales of the Hobbits of Flores, H. floresiensis, with some interest since 2004. And, like most people I have no personal expertise or skill which is relevant to evaluating whether this putative hominin species actually is a new species (as opposed to a pathological modern human). So how are we to evaluate a new PLOS ONE article which comes down on the side that it is a new species? First, my very vague impression is that over the past ~10 years the new-species camp has been gaining ground on the pathological-modern-human set. But setting all that aside perhaps the critical issue for me is that the likely reality of archaic human admixture into our own lineage means that the world is far stranger than we had thought in 2004. For various anatomical and paleoanthropological reasons H. floresiensiswas implausible. But as implausible as the idea that the genome of a Siberian hominin would yield admixture in modern Papuans?
Addendum: New York Times on the paper in PLOS ONE.
Last year a paper came out in AJHG which reported that Ethiopian populations seem to be a compound of West Eurasians and Sub-Saharan Africans. This is result itself is not too surprising for a host of reasons. First, Ethiopians and other populations of the Horn of Africa are physically equidistant between West Eurasians and Sub-Saharan Africans. 20th century physical anthropologists sometimes placed them in the “Caucasoid” racial classification for this reason. Second, the languages of the Horn of Africa have Afro-Asiatic affinities. The Cushitic languages (e.g. Somali) have deep connections with more familiar tongues such as Arabic, but Semitic Ethiopian languages (e.g. Amharic) are much closer in historical distance. Third, there has been a fair amount of previous genetic analysis of these populations, and their synthetic character was obvious from those (e.g. mtDNA and Y results suggest a diverse array of haplogroups). What the AJHG paper reported was that the Eurasian ancestors of the Ethiopians admixed with the presumably Sub-Saharan indigenes ~3,000 years ago in a single pulse event, and, their closest modern relations in West Asia today are Levantines. To put a mild gloss on it the dating is controversial (using patterns of decayed genetic correlations of markers across the length of the genome). This is not just clinal variation.
Right before I was to sleep a reader sent me an email which pointed to a Nick Wade piece in The New York Times, Gene Sleuths Find How Some Naturally Resist Cholera. It’s about new research in ScienceTranslational Medicine, Natural Selection in a Bangladeshi Population from the Cholera-Endemic Ganges River Delta. The authors use the “composite of multiple signals” (CMS) test to ascertain regions of the genome subject to natural selection (look for long haplotypes, high frequency derived alleles, and alleles with high cross population frequency differences). The results aren’t too surprising, I was born in Bangladesh, and I can attest to the fact that it’s a germaphobe’s nightmare. Rather, it is a secondary and very minor aspect of the paper which frankly draws my ire. First let’s quote Wade’s treatment:
As a necessary preliminary to testing for natural selection, the researchers looked at the racial composition of the Bengali population and found that they are an Indian population with a 9 percent admixture of East Asian genes, probably Chinese. The admixture occurred almost exactly 52 generations ago, according to statistical calculation, or around A.D. 500, assuming 29 years per generation. The Gupta empire in India was in decline at this time, but it is unclear whether the intermarriage with East Asians took place through trade or conquest. “We can now go back to the historians and see what happened then,” Dr. Karlsson said.
But sometimes science gets garbled in transmission. What do they say in the paper? Again, the relevant section:
Several years ago I reviewed Christopher Beckwith’s magisterial Empires of the Silk Road: A History of Central Eurasia from the Bronze Age to the Present. In many ways Beckwith’s narrative is a refreshing inversion of the traditional form of macrohistory, whereby charter societies along the Eurasian littoral issue civilizing tendrils toward the heartland, and are met with periodic barbaric eruptions which they then have to assimilate. From what I can gather Beckwith is not a subjectivist. Rather, the inversion of perspective serves to flesh out neglected dynamics at work across history and near prehistory. For example he highlights the reality that core polities of the Eurasian littoral often crystallized on the barbaric marches of established civilization via process of synthesis between the two cultures. Zoroastrian religion emerged on the northern frontier in Khorasan rather than the southwestern Iranian heartland of Fars. Han China’s predecessor in the form of the Chin dynasty arose from a marcher state in the northwest, and the same was true of the previous ruling house, that of the Zhou. In India classical Hindu civilization first congealed in an elaborated form in Magadha, on the eastern frontiers of Aryavarta. In the West Rome was fundamentally a barbaric and peculiar fringe polity, with only tenuous connections to Magna Graecia, and arguably more influenced by the enigmatic Etruscans.
The vigor of frontiers is such an established historical cliche that I have no great enthusiasm to revisit it in detail. Rather, following Beckwith I believe we need to seriously revisit the proposition that the vast expanses of the Eurasian heartland beyond the civilized frontiers have served as more than just a source of militarized barbarians bent on exploitation. Yes, all that is true, but it seems likely that the cultural and racial melange at the intersection of internal Eurasian trade networks have fundamentally reshaped the contemporary landscapes in ways we are only now beginning to understand. But first, our worldview has to acknowledge that not all peoples and lands have made contributions of equal weight to the shape of the world.
A concern about the breach of privacy emerged almost immediately. Though I have serious reservations about the sensationalism which BritainsDNA has engaged in, I think it is totally legitimate of them to infer William’s ancestry in the fashion they did. First, Prince William is a public person, and in direct line to the throne of the United Kingdom. Though some of the spin may be distasteful, remember that this is a person who is where he is because of his ancestry. Second, anyone who performs genealogical research is exposing the information of family members, often without their consent. If William’s mtDNA haplogroup was known to be pathogenic than the case for withholding the information from the public seems straightforward. As it is all that was uncovered was relatively banal, that William may have a South Asian ancestress. There’s a lot of information about me that I’d rather not others know first, but that’s not how the world works. In the grand scheme of things this just isn’t a big deal, and we should focus on the more concrete problem of public understanding of science, and long term issues in regards to genetic privacy more generally.
Addendum: I am aware of concerns in regards to paternity. On the whole I generally think in most situations this is probably information that is going to come out in any case, and so it wouldn’t hurt for it to emerge earlier. Additionally, in the cases of historical figures such as Thomas Jefferson’s presumed line of descent there were widely diverging views among the white descendants as to whether they should cooperate because of the possible moral implications. I suspect most would agree it is better to know this information, even though it implied that line of putative black Jefferson descendants may have paternity misassignment in their lineage. Finally, obviously these issues are far diminished in the case of mtDNA, since maternity is guaranteed. Though one never knows if someone who was adopted was never told of his reality.
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.
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.