Tag: Genetic History

The Age of Heroes

By Razib Khan | August 15, 2012 6:42 pm

Sometimes when you read reviews or papers you need to look very closely at what people say in a tentative speculative fashion. That’s because though the prose may be as such when read plainly and without context, you often have more prior information as to the background of the authors. In other words, assertions which literally seem cautious are actually foreshadowing likely probabilities down the pipeline, because the authors are not distant third-party observers, but active participants in the production of new insights. I think that’s what’s going on in a new paper in Trends in Genetics, The genetic history of Europeans:

Future research should also reveal the effects of post-Neolithic demographic processes, including migration events, which preliminary data suggest had a major impact upon the distribution of genetic variation. These include events associated with Bronze Age civilizations, Iron Age cultures, and later migrations, including those triggered by the rise and fall of Empires. Challenges remain in being able to sequence aDNA routinely from serial samples in the range of megabases, and in the development of software that allows spatially-explicit simulation of genome-scale data, but advances in these areas are now a weekly occurrence and the stage is set for a rapid increase in our knowledge on the evolutionary history of AMH in Europe.

I’d have said this was crazy a few years ago. No longer.


South Asians too are sons of the farmers?

By Razib Khan | December 17, 2010 2:58 pm

I mentioned a few days ago that a friend was trying to get together some data to analyze the genetic variation of South Asians. By a strange coincidence Dienekes just published a more detailed analysis of South Asians…and uncovered something very interesting, though not that surprising. Some technical preliminaries:

A note of caution: The reduced marker set (~30k) means that a lot of noise is added in the admixture estimates. In particular, many individuals are likely to get low-level admixture from population sources that can be attributed to noise. But, as we will see, the small marker set does not really affect either the power of the GALORE approach, or of ADMIXTURE to infer meaningful clusters.

In addition to the various online sources of public data Dienekes got about a dozen South Asians. I was one of those South Asians, DOD075. In many ways I’m a rather standard issue South Asian, similar to Gujaratis, except that I have a substantial ‘East Asian’ component. More concretely, between 1/6 and 1/7 of my ancestry seems to be of eastern origin, far higher than the norm among South Asians. The rest of my ancestry was mostly South Asian specific, with a minor, but significant ‘West Asian’ component common across northern India.

Rerunning with more data with different samples Dienekes came out with a different set of ancestral components. Of particular interest to me he broke down the East Asian between East Asian proper and Southeast Asian. Below are a selection of populations with ancestral components + me. I’ve also renamed a few components. North Kannadi = Dravidian and Irula = Indian tribal. Indian = Generic Indian. Looking at the Fst it seems that Indian endogamy and population bottlenecks has had an effect…look at the North Kannadi distance from everyone else.

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CATEGORIZED UNDER: Genetics, Genomics

The flux of genes on the South Seas

By Razib Khan | November 22, 2010 12:29 am

Huli Wigman from the Southern Highlands, Painting of Tahitian Women on the Beach by Paul Gauguin

ResearchBlogging.orgMany demographic models utilized in genetics are rather simple. Yet the expansion and retreat of various demes in post-Ice Age Europe seems to be far more complex than had previously been assumed, though I suspect part of the rationale for the original simplicity was a preference for theoretical parsimony in the face of a paucity of data. The landscapes traversed by our species are rich and topographically convoluted. Not only does the land vary, from plains, to deserts, to mountains, but the climate shifts radically over time and space. In the pre-modern age when humans were more dependent on environmental exigencies these fluxes in ecological and climatic parameters were essential in sharping the arc of human demographic expansion and contraction.

Oceanias_RegionsThis is why a closer examination of the prehistory of Oceania is so appealing: here you have a physical geography which is radically constrained and so reduces the degrees of freedom of human movement and habitation. Unlike Europe, South Asia, or much of Africa, the time depth of the residence of the current indigenous inhabitants of Australia is on the order of 40 – 50,000 years. It seems likely that the indigenous people of the island of New Guinea to the north are from the same original settlement of Sahul, the ancient super-continent which consisted of New Guinea, Australia, and Tasmania. After the initial sweep out to the farthest reaches of what became Tasmania, there was a later push to the east of New Guinea, to the Solomon Islands,~30,000 years before the present. Then nothing for tens of thousands of years. The march of humanity seemed to stand still on the shores of the Solomons, just as the hominin lineage had once been cordoned off from Sahul by the forbidding seas between it and Sundaland, the Ice Age peninsula of Southeast Asia which was later submerged and became the western portion of Indonesia and Malaysia. The stasis was shocked by the Austronesians, a seafaring peoples who seem to have exploded out from somewhere between Borneo and Taiwan within the last 10,000 years, likely just on the margins of written history. The most famous of th Austronesian peoples are the Polynesians, who pushed across the Pacific, and likely even had some tentative contact with the New World. A less well known case is Madagascar, whose inhabitants speak an Austronesian language with clear affinities to a dialect of Borneo. The map below shows rough distribution of Austronesian peoples:

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CATEGORIZED UNDER: Genetics, Genomics

What intra- & inter- population genetic variance tells us

By Razib Khan | November 8, 2010 2:30 pm

uyafrThe figure to the left is a composite merged from two different papers. One analyzes the patterns of genetic variation within African Americans, and the other the patterns within the East Turkic ethnic group, the Uyghurs. The bar plots show the ancestral element which is similar to two parent populations which resemble Europeans and Africans or East Asians. Looking at total aggregate ancestral quanta we infer that African Americans are on the order of 15-25% European in ancestry, and 75-85% African. Uyghurs seem to be a composite in even measure of a European-like group, and an East Asian-like group. This makes total sense phenotypically; most African Americans look more African, while Uyghurs seem to exhibit a phenotype on average which spans the middle-range between West and East Eurasians.

Central_Asian_Buddhist_MonkBut we’re clearly missing something when we focus purely on a population level statistic. Each “slice” of the bar plot actually represents an individual. Note the contrast between African Americans and Uyghurs. There is relatively little intra-individual variation among Uyghurs, while there is a great deal of such variation among African Americans. Why? Population geneticists have looked at linkage disequilibrium in both African Americans and Uyghurs, and inferred that the former went through an admixture phase much more recently than the latter. Though you don’t really have to be a population geneticist to have known that about African Americans. The ethnogenesis of the group African Americans as a cultural entity occurred in the period between 1650 and 1850. Genetically they are a compound of African, European, to some extent Native American, ancestry. For the Uyghurs we have thinner textual evidence, but the visual and genetic data point to a “western” Indo-European speaking population in the Tarim basin before the arrival of the Turks sometime in the second half of the first millenium A.D. The assumption is that after the initial admixture event and the absorption of the pre-Turkic substrate there was no population substructure. Over time the two components distributed themselves evenly across the population over a period of 1,000-1,500 years.

From this we can infer that patterns of individual variation within populations, as well as between closely related populations, can tell us a great deal. Today the Dodecad Ancestry Project posted a file with the population ancestries broken down by individuals. Looking at this sort of fine-grained data patterns can jump out based on what you already know. Below is a slide show I created which highlights some patterns of interest.

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CATEGORIZED UNDER: Genetics, Genomics, History

Assyrians & Finns in a worldwide genetic context

By Razib Khan | November 4, 2010 5:45 pm

Dienekes is now allowing people to “out” themselves in terms of their ancestry on a comment thread over at the Dodecad Ancestry Project. One of the major purposes of the project has been to survey variation in under-sampled groups which could give us insights into human genetic history. Yesterday I pointed to an analysis of Europeans from the British Isles to Russia. Basically Northern Europeans. There wasn’t anything too revolutionary about the nature of the results; rather, it confirmed some patterns we’d seen. Additionally it obviously didn’t resolve issues of timing, though it clarified hypotheses on the margin.

The main benefit of the ADMIXTURE bar plots is that it gives you a gestalt sense of relationships in a quantitative fashion. This is especially important for groups in the Eurasian Heartland, who are in some ways at the center of both genetic and cultural exchange. In the comments above some information was divulged as the provenance of two clusters of samples, Finns and Assyrians. The Assyrians here presumably represents the remnants of Mesopotamia’s Christian majority at the time of the Arab conquests in the 7th century. Prior to the Arab conquests Mesopotamia had been under the rule of the Sassanid Persian dynasty for nearly four centuries, but by early 7th century the Syriac speaking majority by and large adhered to a range of Christian sects (the balance seem to have been heterodox non-Christian Gnostics and Jews), with the ancient Church of the East dominant. Because of the social constraints which Christians were placed under within the Muslim Middle East prior to the modern era these communities may be particular informative as to the demographic impact of the Arab conquests, and the cosmopolitan and international nature of the Muslim polities and how they reshaped the genetics of the Middle East. A good approximation is that the Christian minorities are the dominant parent population of the Muslim majority, but that because of their tendency to withdraw into more isolated regions and their enforced economic marginality they would have not intermixed so much with the influx of slaves, both northern (Turk and Slav), Indian, and African, which characterized much of Mesopotamia over the past 1,400 years.

Below the fold is a slide show. I’ve reedited just a touch (removed a few populations, put the labels in larger fonts, etc.). First the total population set. Then I’ve dropped the Finns and Assyrians, respectively, into the global population set (obscure some which are less relevant).

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CATEGORIZED UNDER: Genetics, Genomics, History

The blood of kings

By Razib Khan | October 14, 2010 2:33 pm

429px-Ludvig_XVI_av_Frankrike_porträtterad_av_AF_CalletOne of the more fertile grounds of modern genetics with all its various tools is that it makes for some interesting possibilities of inquiry in relation to the genealogy of aristocratic elites. The vast majority of us have very shallow roots in terms of genealogy. Some of this ignorance can be compensated if you have a clear and distinct group identity. If you are a Cohen or a Levite you have some notional conception of your line of ancestry. If you are a member of a Chinese patrilineage your genealogy likely can be traced at least hundreds of years, and possibly nearly one thousand years. Many European nations, in particular in the Nordic nations, have excellent church records which go back centuries.

High aristocratic elites are different in the scope of what we know. For most of history marriage for them was a matter of politics, not war, and the details of their lives were often recorded punctiliously. The births of royal children may have been attended by most of the court at some point to certify legitimacy. Some European lines have deep histories indeed. There are two direct male line descendants of Hugh Capet who reign today, Juan Carlos of Spain and Henri of Luxembourg. Hugh was a Robertian, a descendant of Robert of Hesbaye, who was a ruler of a region in modern Belgium. Robert of Hesbaye was derived from the Frankish elite, but the details seem to be unclear. But it seems then that Juan Carlos of Spain and Henri of Luxembourg should be of Robert of Hesbaye’s lineage, and so have a paternal line going back 1,200 years.

I began to think of this when a friend with a strong interest in genealogy pointed me to this short article, Genetic analysis of the presumptive blood from Louis XVI, king of France:

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Where writing is silent

By Razib Khan | August 16, 2010 11:35 am

In my post on Empires of the Word I observed that quite often the written record is silent on many matters which only language or genes tell us must have occurred. The Indo-Aryan character of the dominant language on the island of Sri Lanka seems to be a geographical anomaly in the least, but perhaps most strange of all is the existence of a language and ethnic group of clear Southeast Asian provenance on the island of Madagascar. To my knowledge Arab, Persian and South Asian sources do not record the existence of a prominent Southeast Asian maritime diaspora which spanned the Indian ocean in the years before 1000 A.D., but we know that it did exist. A new paper on the genetics of the island of Comoros fleshes out another piece of the puzzle, Genetic diversity on the Comoros Islands shows early seafaring as major determinant of human biocultural evolution in the Western Indian Ocean:

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CATEGORIZED UNDER: Genetics, History

Men & ideas on the move: settled lands & colonized minds

By Razib Khan | April 30, 2010 9:15 am

I am currently reading Peter Heather’s Empires and Barbarians: The Fall of Rome and the Birth of Europe. This is a substantially more hefty volume in terms of density than The Fall of the Roman Empire: A New History of Rome and the Barbarians . It is also somewhat of a page turner. One aspect of Heather’s argument so far is his attempt to navigate a path between the historically tinged fantasy of what its critics label the “Grand Narrative” of mass migration of barbarian tribes such as the Goths, Vandals and Saxons during the 4th to 6th centuries, dominant before World War II, and its post-World World II counterpoint. As a reaction against this idea archaeologists have taken to a model of pots-not-people, whereby cultural forms flow between populations, and identities are fluid and often created de novo. This model would suggest that only a tiny core cadre of “German” “barbarians” (and yes, often in this area of scholarship the most banal terms are problematized and placed in quotations!) entered the Roman Empire, and the development of a Frankish ruling class in the former Gaul, for example, was a process whereby Romans assimilated to the Germanic identity (with the shift from togas to trousers being the most widespread obvious illustration of Germanization of norms). I believe that liberally applied this model is fantasy as well. Being a weblog where genetics is important, my skepticism of both extreme scenarios is rooted in new scientific data.

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The science of human history as written by Herodotus

By Razib Khan | March 28, 2010 2:15 am

The following passage is from the epilogue of The Real Eve: Modern Man’s Journey Out of Africa by Stephen Oppenheimer:

In this book I have offered a synthesis of genetic and other evidence. Everything points to a single southern exodus from Eritrea to the Yemen, and to all the non-African male and female gene lines having arisen from their respective single out-of-Africa founder lines in South Asian (or at least near the southern exit). I regard the genetic logic for this synthesis as a solid foundation, and I have based the rest of my reconstruction of the human diaspora upon it. Obviously, the ‘choice’ of starting point (mine or theirs) determined all the subsequent routes our ancestors and cousins took. Tracing the onward trails is only possible as a result of marked specificity in regional distribution of the genetic branches The geographic clarity of both male and female gene trees is a big departure from the fuzzy inter-regional picture shown by older genetic studies. The degree of segregation of lines into different countries and continents is in itself good evidence that once they got to their chosen new homes, the pioneers generally stayed put, at least until the Last Glacial maximum forced some of them to move. This conservative aspect of our genetic prehistory also provides a partial explanation for the fact that when we look at a person, we can usually tell, to the continent, where their immediate ancestors came from, and underlies differences that some of us still call ‘race.’

Oppenheimer wrote the above in the early aughts, as his book was published in 2003. Much of this is generally in line with the ‘orthodoxy’ of the day. I believe that Oppenheimer’s assertion that there was one southern migration out of Africa by anatomically modern humans has gained some advantage over the alternative model of two routes, northern and southern, over the past ten years (Spencer Wells’ The Journey of Man sketches out the two wave model). Other assertions and assumptions have not stood the test of time. In particular, I would contend that generally the ‘conservative aspect of our genetic prehistory’ can no longer be taken for granted. Specifically, it seems likely now that much occurred after the Ice Age and during the Neolithic.

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