Further caution on admixture estimates: at the edges of variation

My recent analysis of the Yunusbayev et al. (2011) revealed an interesting anomaly: the Armenians_Y sample tested much more "European" than the existing Armenians_D and Armenians (from Behar et al. (2010)).

A related "anomaly" was the use of some of my newer Dodecad tools that have been targeted to particular regions (e.g., Europe and West Asia for the newer euro7 calculator) by individuals from outside these regions (e.g., South Asia for euro7). Of course, I have cautioned against such use, but can we say something about why their use is not a very good idea.

Suspecting a systematic effect, I decided to investigate.

My geometric intuition is encapsulated in the following figure:

Suppose that a cline has been inferred from B to A1. Suppose that dist(A1, B) = dist(A2, B). So, A1 and A2 differ from each other in an orthogonal direction relative to their difference from B.

Now, if we project A2 onto the BA1 line, we see that A2 appears "intermediate" between them. The converse would occur if we project A1 onto the BA2 line.

This is reminiscent of my ciriticism of Moorjani et al. (2011) in that shifts away from a linear cline cause spurious admixture to be inferred. But, it is more general:

• A2 may differ from A1 because it has cryptic admixture from an unsampled group, or vice versa
• A2 may differ from A1 because of random genetic drift

We can go one step further and consider a population that is not only "off-cline", but beyond its edges. This can be seen in the following figure:

As you can see, now A2 (which is beyond the edge of the horizontal cline) cannot be projected between B and A1.

In order to examine this intuition, I carried out a few simple tests.

I set B to be HGDP North_Italians, A1 to be Behar et al. (2010) Armenians (with 3 outliers excluded), and A2 to be Yunusbayev et al. (2011) Armenians_Y.

1) Unsupervised analysis

North_Italian 100.0 0.0

Armenians_Y 1.3 98.7

Armenians 2.8 97.2

2) Supervised analysis: Armenians_Y as test population; North_Italian, Armenians fixed

North_Italian 100.0 0.0

Armenians_Y 0.6 99.4

Armenians 0.0 100.0

3) Supervised analysis: Armenians as test population; North_Italian, Armenians_Y fixed

North_Italian 100.0 0.0

Armenians_Y 0.0 100.0

Armenians 2.7 97.3

These results seem to confirm the geometric intuition.

Populations beyond the cline

Now, I will add Assyrians_D, a population that seems closely related to Armenians, but appear to be a little more "eastern" in most analyses. So, it is "beyond" the North_Italian-Armenian cline.

1) Unsupervised analysis

North_Italian 100.0 0.0

Armenians_Y 3.6 96.4

Armenians 5.3 94.7

Assyrians 0.6 99.4

2) Supervised analysis: Assyrians, Armenians as test populations; North_Italian, Armenians_Y fixed

North_Italian 100.0 0.0

Armenians_Y 0.0 100.0

Armenians 3.8 96.2

Assyrians 0.5 99.5

Again, the intuition is confirmed. A reasonable recommendation is to avoid mapping populations that are geographically outside the convex hull of the fixed populations.

Long clines

The effect described in this post is expected to abate in "long clines". For example, the amount of drift between Miaozu and She populations from east Asia is expected to be miniscule relative to the distance of either population to North Italians:

1) Unsupervised analysis

North_Italian 100 0

Miaozu 0 100

She 0 100

2) Supervised analysis: She as test population; North_Italian, Miaozu fixed

(identical)

3) Supervised analysis: Miaozu as test population; North_Italian, She fixed

(identical)

Conclusion

In determining the relative position of individuals along clines it is useful to remember:

• The position is most accurately determined when the edges of the cline are most securely "fastened". Use as many populations and individuals from the perimeter of the region under study as possible.
• The position is most accurately determined when the cline is long; small deviations due to drift or incomplete sampling at the edges are miniscule compared to the length of the cline. Components marking continent-wide distances (e.g., Europeans vs. East Asians) are estimated more accurately than those marking shorter distances (e.g., Southern Europeans vs. West Asians)

The way forward

There is no simple solution to the problem identified in this post. For short clines (e.g., within Europe) that are not securely fastened (few individuals from outlying groups), we can expect relatively large systematic errors.

As an analogy, imagine trying to measure the height of a 5-year old on the wall with measuring tape and a book. If you don't keep the book steady, one of the endpoints of your measurement will be "wobbly". If you don't keep your measuring tape vertical, your measurement will be off.

What can we do to solve this problem? Sample, sample, sample. There is no shortcut. The gross details of the genetic landscape (such as the relationship between major continental groups) are easy to infer, but the details will always have room for improvement.

Affluent hunter-gatherers revisited

I think we need to get rid of the "affluent hunter-gatherer" paradigm altogether. There is no doubt that humans were well-adapted to the hunter-gatherer lifestyle for a very long time. Species that aren't well-adapted tend to die out.

It is also true that the onset of the Neolithic was associated with negative health trends, exhibited e.g., in skeletal pathologies, and probably the result of a greater disease load due to higher population densities and a shift in diet.

Nonetheless, we should keep in mind that ten thousand years have passed since the onset of agriculture. People have had time to adapt, both in terms of their genetic endowment, and their culture, which mitigates the potential negative effects of the new mode of living. Primitivism in the sense of either fads like the "Paleolithic diet", or in glorifying living hunter-gatherers as some sort of ideal is a rejection of the progress our species has made.

Anthropol Anz. 2011;68(4):349-66.

!Kung nutritional status and the original "affluent society"--a new analysis.
Bogin B.

Abstract
The theme of the 2011 meetings of the German Anthropological Society, "Biological and Cultural Markers of Environmental Pressure", provides the entree to revisit one of Anthropology's most enduring canons - hunters and gathers are well-nourished and healthy. The Dobe !Kung foragers of the Kalahari Desert often serve as a model of hunter-gatherer adaptation for both extant and Paleolithic humans. A re-analysis of food intake, energy expenditure, and demographic data collected in the 1960s for the Dobe !Kung finds that their biocultural indicators of nutritional status and health were, at best, precarious and, at worst, indicative of a society in danger of extinction. Hunting and gathering is the lifestyle to which the human species was most persistently adapted, in terms of the biological, cultural, and emotional meanings of the word 'adapted.' However, the few remaining foraging groups studied in the 20th Century are unlikely to serve as the ideal models of that ancient way of life.

Link

Secular trends in some Russian populations

Anthropol Anz. 2011;68(4):367-77.

Secular trends in some Russian populations.

Godina EZ

Abstract
Secular changes of body measurements in children have been the subject of studies in many different countries. In recent years, there has been an increase in BMI associated with a significant trend towards obesity in both Europe and the US. The aim of the present study was to analyze trends in body measurements and BMI in Russia from the 1960's to the beginning of the 21st century. This was done at three locations of the Russian Federation: the city of Moscow, the cities of Saratov and Naberezhnye Chelny in the Volga-river area. In addition, data on secular changes of Abkhazian children were analyzed. A large number of anthropometric measurements were taken on each individual including height, weight, arm, leg and trunk lengths (estimated), body diameters and circumferences, skinfold thickness, head and face dimensions. Stages of secondary sex characteristics also were evaluated; data on menarcheal age were collected by status-quo and retrospective methods. Changes in hand grip strength have been evaluated in some of the samples. While stature was increasing during these years, weight, chest circumference and BMI were characterized by negative changes, which became more obvious in elder girls. Changes in handgrip strength also showed negative trends. There were noticeable changes in head and face measurements, which were expressed in more elongated head and face forms, i.e. the head became longer and narrower with narrower and higher faces. Secular changes in head and facial morphology may be considered part of the general trend.

Link

"Comparing Ancient and Modern DNA Variability in Human Populations" abstracts

Excerpts from the conference site.

Temporal differentiation across a West-European Y-chromosomal cline - genealogy as a tool in human population genetics
Maarten H.D. Larmuseau et al.

The pattern of population genetic variation and allele frequencies within a species are unstable and are changing in time according to different evolutionary factors. For humans, it is possible to combine detailed patrilineal genealogical records with deep Y-chromosome genotyping to disentangle signals of historical population genetic structures due to the exponential increase of genetic genealogical data. To test this approach we studied the temporal pattern of the 'autochthonous' micro-geographical genetic structure in the region of Brabant in Belgium and The Netherlands (Northwest-Europe). Genealogical data of 881 individuals from Northwest-Europe were collected from which 634 family trees showed a residence within Brabant for at least one generation. The Y-chromosome genetic variation of the 634 participants was investigated using 110 Y-SNPs and 38 Y-STRs and linked to particular locations within Brabant on specific time periods based on genealogical records. Significant temporal variation in the Y-chromosome distribution was detected through a north-south gradient in the frequencies distribution of subhaplogroup R1b1b2a1 (R-U106), next to an opposite trend for R1b1b2a2g (R-152). The gradient on R-U106 faded in time and became even totally invisible during the Industrial revolution in the first half of the 19th century. Therefore, genealogical data for at least 200 year are required to study small-scale 'autochthonous' population structure in Western-Europe.

The Dutch medieval and post-medieval genetic landscapes
Eveline Altena et al.

Since 2005 many archeological human skeletons have been sampled for DNA research under forensic conditions in The Netherlands. This enables us to perform a large scale genetic survey on reliable genetic data from the prehistory until the present. The majority of the available archaeological DNA samples, though, originate from medieval and post-medieval sites. Here we present preliminary autosomal and Y-chromosomal data from more then 500 archaeological human skeletons, excavated at several medieval and post-medieval sites. We also compare these historical genetic data with data from more then 2000 modern Dutch males.

Comparing ancient and modern DNA variability in North Eastern Iberia: the Neolithic impact of first farmers
Cristina Gamba et al.

Archaeological, anthropological and demographic hypotheses can be tested by comparing ancient and modern DNA from human samples in a diachronical context. In this case, it was possible to evaluate genetic continuity or discontinuity between different periods, and/or to infer ancient human migrations in a set of Iberian samples. We evaluated the demographic impact associated to the spread of the Neolithic in North Eastern Iberia. We recovered mitochondrial DNA from 13 Early Neolithic specimens from three archaeological sites: Can Sadurní, Chaves and Sant Pau. A bayesian simulation approach was performed to compare the obtained results with Middle Neolithic and modern samples from the same region. We tested different scenarios to determine which among them better explained the analyzed data. By comparing simulated and observed FST values, we observed genetic differentiation between Early Neolithic and Middle Neolithic populations, which suggests that at the beginning of the Neolithic, genetic drift played an important role.
Genetic differentiation was also observed between Early Neolithic and modern- day populations. These data are compatible with the arrival of small genetically-distinctive groups at the beginning of the Neolithic, suggesting a pioneer colonization of North Eastern Iberia by first farmers.

The following abstract is interesting as it suggests we should not view the "Neolithic" as a singular event. X2 was also discovered in Megalithic France, as well as a likely immigrant population from the Near East and the Caucasus in the Tarim Basin, and Bronze Age Eulau. From a paper on the Reidla et al. (2003): Overall, it appears that the populations of the Near East, the Caucasus, and Mediterranean Europe harbor subhaplogroup X2 at higher frequencies than those of northern and northeastern Europe (P less than .05) and that X2 is rare in Eastern European as well as Central Asian, Siberian, and Indian populations and is virtually absent in the Finno-Ugric and Turkic-speaking people of the Volga-Ural region.

Where are all the "WIX"? Rare European maternal lineages W, I, and X2 in the past and present
Esther J. Lee et al.

Studies utilizing ancient DNA to examine past populations in Europe have increased dramatically in recent years. Specifically, mitochondrial DNA (mtDNA) sequences for over 100 individuals in prehistoric Europe have been sequenced and published. Scholars have intensively focused on the so-called Neolithic transition in Europe, the transformation from hunter-gatherer lifestyle to agro-pastoralism, and continue to debate whether the process was a result of population movement or cultural dispersion. Both hypotheses continue to be tested and genetics analyses from past and present populations have suggested a complex movement of people and cultures across Eurasia. This work focuses on the mtDNA haplogroups identified in past European populations that are rare in the present, haplogroups W, I, and X2. New data will be presented from Neolithic Funnel Beaker collective burials sites, a late Neolithic Bell Beaker site, and an Iron Age Halstatt site in Germany, in which the three maternal lineages are identified. Among the published European Neolithic data, haplogroup X2 appears in late Neolithic sites in Germany and France but not in the earlier LBK culture. Haplogroup X2 shows an intriguing phylogenetic landscape with a wide geographical distribution at an overall low frequency, but on the other hand, pockets of high diversity and frequency among certain modern western Eurasian populations have been described. The discussion focuses on whether the presence of the three haplogroups in the past is a result of ascertainment bias or some viable population movement.

The following seems to suggest Denisova admixture in the East Asian mainland, and not just the island groups, identified in the recent Reich et al. (2011) paper. The sentence about biased Neandertal similarity with increasing distance to Africa is also interesting; the data that is available so far shows non significant differences in Neandertal similarity among Eurasians, although the published values do seem to show higher (and perplexing) averages in China vs. Europe.

Archaic human ancestry in East Asia
Pontus Skoglund & Mattias Jakobsson

Recent studies of ancient genomes have suggested that gene flow from archaic hominin groups to the ancestors of modern humans occurred on two separate occasions during the modern human expansion out of Africa. At the same time, decreasing levels of human genetic diversity have been found at increasing distance from Africa as a consequence of human expansion out of Africa. We re-analyzed the signal of archaic ancestry in modern human populations and we investigated how serial founder models of human expansion affect the signal of archaic ancestry using simulations. We show that genetic drift coupled with an ascertainment bias for common alleles can cause artificial, but largely predictable, differences in affinity to archaic genomes between descendants of an admixture event. In genotype data from non-African humans, this effect results in a biased genetic similarity to Neandertal with increasing distance from Africa. In addition to the two previously reported connections between non-Africans and Neandertals as well as between Oceanians and a Denisovan archaic human genome from Siberia, we found a significant affinity between East Asians (in particular Southeast Asians) and the Denisovan genome, a pattern that is not expected under a model of solely Neandertal-related admixture in the ancestry of East Asians. This observation could be explained either by substantial migration from Oceania into East Asia, or more common history between anatomically modern- and archaic populations than previously proposed.

Diet of Byzantine Greeks

AJPA DOI: 10.1002/ajpa.21601

Reconstructing the diets of Greek Byzantine populations (6th–15th centuries AD) using carbon and nitrogen stable isotope ratios

Chryssi Bourbou et al.

Documentary evidence and artistic representations have traditionally served as the primary sources of information about Byzantine diet. According to these sources, Byzantine diet was based on grain (primarily wheat and barley), oil, and wine, supplemented with legumes, dairy products, meat, and marine resources. Here, we synthesize and compare the results of stable isotope ratio analyses of eight Greek Byzantine populations (6th–15th centuries AD) from throughout Greece. The δ13C and δ15N values are tightly clustered, suggesting that all of these populations likely consumed a broadly similar diet. Both inland and coastal Byzantine populations consumed an essentially land-based C3 diet, significant amounts of animal protein, and possibly some C4 plants, while no evidence of a general dependence on low-δ15N legumes was observed. One interesting result observed in the isotopic data is the evidence for the consumption of marine protein at both coastal sites (a reasonable expectation given their location) and for some individuals from inland sites. This pattern contrasts with previous isotopic studies mainly on prehistoric Greek populations, which have suggested that marine species contributed little, or not at all, to the diet. The possibility that fasting practices contributed to marine protein consumption in the period is discussed, as are possible parallels with published isotope data from western European medieval sites.

Link

No higher borrowing in hunter gatherer languages

PLoS ONE 6(9): e25195. doi:10.1371/journal.pone.0025195

Does Lateral Transmission Obscure Inheritance in Hunter-Gatherer Languages?

Claire Bowern et al.

In recent years, linguists have begun to increasingly rely on quantitative phylogenetic approaches to examine language evolution. Some linguists have questioned the suitability of phylogenetic approaches on the grounds that linguistic evolution is largely reticulate due to extensive lateral transmission, or borrowing, among languages. The problem may be particularly pronounced in hunter-gatherer languages, where the conventional wisdom among many linguists is that lexical borrowing rates are so high that tree building approaches cannot provide meaningful insights into evolutionary processes. However, this claim has never been systematically evaluated, in large part because suitable data were unavailable. In addition, little is known about the subsistence, demographic, ecological, and social factors that might mediate variation in rates of borrowing among languages. Here, we evaluate these claims with a large sample of hunter-gatherer languages from three regions around the world. In this study, a list of 204 basic vocabulary items was collected for 122 hunter-gatherer and small-scale cultivator languages from three ecologically diverse case study areas: northern Australia, northwest Amazonia, and California and the Great Basin. Words were rigorously coded for etymological (inheritance) status, and loan rates were calculated. Loan rate variability was examined with respect to language area, subsistence mode, and population size, density, and mobility; these results were then compared to the sample of 41 primarily agriculturalist languages in [1]. Though loan levels varied both within and among regions, they were generally low in all regions (mean 5.06%, median 2.49%, and SD 7.56), despite substantial demographic, ecological, and social variation. Amazonian levels were uniformly very low, with no language exhibiting more than 4%. Rates were low but more variable in the other two study regions, in part because of several outlier languages where rates of borrowing were especially high. High mobility, prestige asymmetries, and language shift may contribute to the high rates in these outliers. No support was found for claims that hunter-gatherer languages borrow more than agriculturalist languages. These results debunk the myth of high borrowing in hunter-gatherer languages and suggest that the evolution of these languages is governed by the same type of rules as those operating in large-scale agriculturalist speech communities. The results also show that local factors are likely to be more critical than general processes in determining high (or low) loan rates.

Link

Aboriginal genome analysis and ethics

Ewen Callaway discusses ethical issues surrounding the publication of an Australian Aborigine full genome sequence from a hair sample collected about a hundred years ago by a British scientist.

From the article:

"To be sequencing DNA from the hair of a deceased indigenous person is uncharted ethical territory," says Emma Kowal, a cultural anthropologist at the University of Melbourne.

Sequencing DNA from the hair of a deceased indigenous person is nothing new. Scientists have done it, for example, on Napoleon's hair. But, of course, "indigenous", is a code word for pre-European. Everyone's genome is a composite of bits that have arrived at different times from different places. There is nothing "indigenous" about any of our DNA, unless we believe in fables like that of Erichthonius. What is the use of the concept of "indigeneity"? To make cultural anthropologists feel good about their role as protectors of "indigenous people".

Of course, I believe that anthropologists should not just go ahead and get DNA from the dead. But, as far as I can tell, Haddon did not go around the world with a pair of scissors chasing after people for hair samples. Nor are there, as far as I can tell, any close relatives of the deceased that might object to his full genomic sequence (and by implication half, or a quarter of their sequence) being published. So, where is the ethical problem?

More from the article:

But some scientists are jittery about how others in the Aboriginal community might receive the project, and worry that it could set back efforts to engage Aboriginals in genetic research. "In a sense, every Aboriginal Australian has had something about themselves revealed to the world without their consent," says Hank Greely, who directs the Center for Law and the Biosciences at Stanford University in California.

In other words: let's not do genetic research because it might prevent us from doing genetic research. Of course something has been revealed about Aboriginal Australians by the use of this sample. Something has been revealed about me whenever there are Greek DNA samples published. There have been tons of genetic studies on Jews, Finns, African Americans, etc., should we seek the "consent" of every group one belongs to before doing a study? I'm human, and I object to studies comparing humans with chimpanzees, because it might reveal something about me without my consent...

More:

Aboriginal Australians endured centuries of repression by European colonists, but their wariness of genetic research owes much to the Human Genome Diversity Project (HGDP). This 1990s international collaboration aimed to catalogue the genetic diversity of populations worldwide, but sparked concerns that indigenous peoples were being subjected to neocolonial 'bioprospecting'. "Probably the strongest opposition we ran into anywhere in the world" was in Australia, says Greely, who was an ethical adviser to the project. Plans to include Aboriginal Australian DNA were eventually scrapped, and the furore's impact continues to reverberate, says Kowal. "The damage that the HGDP has done for the prospect of doing genetic research with Aboriginal people has been significant." Researchers who work with Aboriginal Australians are now expected to obtain consent not only from the individuals concerned, but also from local and sometimes state-wide groups representing Aboriginal communities across Australia.

I believe in empirical evidence. There are dozens of human populations represented in the Human Genome Diversity Panel that have been used and re-used by scientists and amateurs like myself alike. Can any of the professional kind souls point to a single bad thing that has happened to any of these populations because of it?

What about the rights of individual Aboriginal Australians? Suppose that you are an Aboriginal Australian who wants to learn about his ancestry and origins, the same with all those Europeans, Africans, Asians, etc. who buy genetic ancestry tests or visit genealogy, archaeology, and history forums. Why should your natural desire to learn about your own past, and the natural desire of anthropologists and geneticists to learn about human history have to go through the bureaucracy of community- and state-level "representatives"?

More:

A Danish bioethical review board did not believe it was necessary to review the project because it viewed the hair as an archaeological specimen and not a biological one, Willerslev says. However, after his team sequenced the genome, an Australian colleague put Willerslev in touch with the Goldfields Land and Sea Council, a body based in Kalgoorlie, Western Australia, that represents the 5,000 or so Aboriginal Australians living in the region where Haddon collected the hair sample. In June, Willerslev flew to the region to describe his project to the organization's board and to seek its approval. He says that if the board had rejected his proposal, he would have ended the project and left the genome unpublished.

I am glad that the "Land and Sea Council" gave Willerslev its consent. But, seriously, who are they to decide whether the hair sample should be used or not?

It could be argued that Haddon's unknown hair donor did not authorize a particular use of his hair sample. But, it is ludicrous to expect people from the past to anticipate all the potential uses that their tissues may have in the future. Nor is there any evidence that the anonymous donor authorized some council representing 5,000 future Aboriginal Australians, including a few of his distant relatives to prevent it from being used.

More:

Despite Willerslev's efforts, "I would suggest there would be a certain amount of unrest in the indigenous communities", says van Holst Pellekaan. Greely agrees that Willerslev's team should have reached out to other Aboriginal groups.

So, it is not only sufficient for the future local council to get in on the consent action, but it is proposed that the one from the next town, or halfway around Australia should be involved too.

Scientists should not victimize DNA donors or their communities, but neither should they acquiesce to a never-ending political game of "consent", whereby they must appease every busybody elected or unelected "representative" before doing their work.

Mark Stoneking has it about right:

"I think they did everything anyone could reasonably expect them to," counters Mark Stoneking, a molecular anthropologist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. He published a complementary analysis of Aboriginal genomes last week, using DNA samples obtained by other scientists with the consent of the Aboriginal Australian individuals involved.

But, I would argue that they did more than anyone could reasonably expect them to. Since there is no evidence that the sample was collected illegally and unethically, and since the Danish review board approved the study, there would have been no reason not to publish the study if the "Goldfields Land and Sea Council" had objected. I would be pissed if I was a member of the research group that did all this work without intending or actually causing harm to anybody, and I was told not to publish because some council said so.

Moreover, the issue is one of basic scientific integrity: scientists should seek to understand the world as it is, including patterns of human diversity and history.

Suppose that Willerslev had reached a different conclusion, e.g., that Australian Aborigines arrived 5,000 years ago, and this was rejected by local interest groups because it clashed with their oral histories. Are scientists only to publish results that are acceptable to studied populations' traditions and mythologies, and be prevented from publishing those that falsify them?

More:

Having a set of widely accepted guidelines for studying such samples would help to guide researchers, journals and funding agencies, says Stoneking. "Hopefully some sort of standards can be developed so everyone feels comfortable going ahead with this research," he says.

I agree. A set of guidelines would have twofold utility:

1. To prevent researchers from engaging in unethical behavior. We don't want scientists to get people's DNA and then use it against them in a demeaning manner, or profiting from its potential commercial uses.
2. To prevent professional complainers from stopping scientific research when it might or does clash with local lore or ill-defined interests
   

Uzbeks as the nexus, Altai as the source of Turkic expansions

I have often used Uzbeks as a convenient population to assess the extent of Central Asian Turkic admixture in West Eurasia. The recent Yunusbayev et al. (2011) paper has provided some interesting supporting evidence for that use:


I have extended lines from Uzbeks through the four different western Eurasians Turkic populations: Turks, Turkmen, Nogais, and Chuvashs. It is interesting that these lines intersect West Eurasians at different points:

• The line of Turks (Anatolia) with Armenians and Georgians
• The line of Turkmen (Iran) with Iranians
• The line of Nogais (North Caucasus) with Chechens
• The line of Chuvashs (far eastern Europe) beyond Russians

These are what we expect if ancestral Turkic speakers en route from their ultimate eastern homeland were roughly like modern-day Uzbeks at some stage before their settlement in west Eurasia. The linearity of the Uzbek-Turkic population-Native population triples is striking

The only case where the fit is not almost perfect is that of the Chuvashs, who are the most northern population. It is easy enough to discover the cause of this. Chuvash have ~1.1% South Asian, as opposed to ~8.2% in the Uzbeks. There is a north-south latitudinal cline of the "South Asian" component in middle Eurasia, and the ancestors of the Chuvash moved at the northern end of that cline; of the Uzbeks at the middle.

If we add a line linking Russians with Chuvashs, we can reconstruct the hypothetical Proto-Chuvashs as a population that differed from Uzbeks in being less "South Asian", which confirms the Dodecad admixture data:

The mystery is further resolved once we look at the following PCA plot from my article On the northern/southern Caucasoid contributions to Asia


Notice that Turks, Uzbeks and the pair of Altai and Dolgan fall along one line, while Chuvashs, Russians, and the pair of Altai/Dolgan along another.

So, the data seems consistent with the idea that the primary source of the westward Turkic expansions was something like the Altai (pics) and Dolgan, undergoing transformations and successive admixtures all the way to the Mediterranean and eastern Europe.

mtDNA of Oceanians (Ballantyne et al. 2011)

Forensic Sci Int Genet. 2011 Sep 20. [Epub ahead of print]

MtDNA SNP multiplexes for efficient inference of matrilineal genetic ancestry within Oceania.

Ballantyne KN, van Oven M, Ralf A, Stoneking M, Mitchell RJ, van Oorschot RA, Kayser M.

Abstract

Human mitochondrial DNA (mtDNA) is a convenient marker for tracing matrilineal bio-geographic ancestry and is widely applied in forensic, genealogical and anthropological studies. In forensic applications, DNA-based ancestry inference can be useful for finding unknown suspects by concentrating police investigations in cases where autosomal STR profiling was unable to provide a match, or can help provide clues in missing person identification. Although multiplexed mtDNA single nucleotide polymorphism (SNP) assays to infer matrilineal ancestry at a (near) continental level are already available, such tools are lacking for the Oceania region. Here, we have developed a hierarchical system of three SNaPshot multiplexes for genotyping 26 SNPs defining all major mtDNA haplogroups for Oceania (including Australia, Near Oceania and Remote Oceania). With this system, it was possible to conclusively assign 74% of Oceanian individuals to their Oceanian matrilineal ancestry in an established literature database (after correcting for obvious external admixture). Furthermore, in a set of 161 genotyped individuals collected in Australia, Papua New Guinea and Fiji, 87.6% were conclusively assigned an Oceanian matrilineal origin. For the remaining 12.4% of the genotyped samples either a Eurasian origin was detected indicating likely European admixture (1.9%), the identified haplogroups are shared between Oceania and S/SE-Asia (5%), or the SNPs applied did not allow a geographic inference to be assigned (5.6%). Sub-regional assignment within Oceania was possible for 32.9% of the individuals genotyped: 49.5% of Australians were assigned an Australian origin and 13.7% of the Papua New Guineans were assigned a Near Oceanian origin, although none of the Fijians could be assigned a specific Remote Oceanian origin. The low assignment rates of Near and Remote Oceania are explained by recent migrations from Asia via Near Oceania into Remote Oceania. Combining the mtDNA multiplexes for Oceania introduced here with those we developed earlier for all other continental regions, global matrilineal bio-geographic ancestry assignment from DNA is now achievable in a highly efficient way that is also suitable for applications with limited material such as forensic case work.

Link

Bronze age Y-chromosomes and mtDNA from Liao River (northern China)

From the paper:

The dominant haplogroup in the Dadianzi people was D4 shared by
five individuals who were associated with four different haplotypes.
The other haplotype belonging to haplogroup D in the Dadianzi population
was designated as D5 by the mutation at site 16 189 (T to C).
The haplogroup M7c included two haplotypes, which were shared by two
individuals in ancient Dadianzi people. The other haplogroups, including
A4, F1b, G1a, M9a, M10 and M8z, were each present in one individual.

Seven male samples were chosen for Y chromosome SNPs among
the 14 individuals. Three samples (S1, S2 and S13) exhibited the
mutations M89C-T, M9C-G, M214T-C and M231G-A, which
were attributed to haplogroup N ( N1C). Two samples (S8 and S12)
exhibited the mutations: M89C-T, M9C-G, M175-5 bp del and
M122T-C, belonging to haplogroup O3 (M122). We failed to obtain
any product from two samples (S5 and S14) (Table 3).

Journal of Human Genetics advance online publication 22 September 2011; doi: 10.1038/jhg.2011.102

Genetic characteristics and migration history of a bronze culture population in the West Liao-River valley revealed by ancient DNA

Hongjie Li et al.

In order to study the genetic characteristics of the Lower Xiajiadian culture (LXC) population, a main bronze culture branch in northern China dated 4500–3500 years ago, two uniparentally inherited markers, mitochondrial DNA and Y-chromosome single-nucleotide polymorphisms (Y-SNPs), were analyzed on 14 human remains excavated from the Dadianzi site. The 14 sequences, which contained 13 haplotypes, were assigned to 9 haplogroups, and Y-SNP typing of 5 male individuals assigned them to haplogroups N (M231) and O3 (M122). The results indicate that the LXC population mainly included people carrying haplogroups from northern Asia who had lived in this region since the Neolithic period, as well as genetic evidence of immigration from the Central Plain. Later in the Bronze Age, part of the population migrated to the south away from a cooler climate, which ultimately influenced the gene pool in the Central Plain. Thus, climate change is an important factor, which drove the population migration during the Bronze Age in northern China. Based on these results, the local genetic continuity did not seem to be affected by outward migration, although more data are needed especially from other ancient populations to determine the influence of return migration on genetic continuity.

Link

Unexpected ancient mtDNA from Neolithic Hungary

This seems like a tie-in to another recent post on Neolithic and Bronze Age Ukraine. I don't think even a science fiction writer could have predicted the kinds of ancient DNA results we are getting from Europe. We have genetic discontinuity between Paleolithic and Neolithic, and between Neolithic and present, and, apparently, discontinuity between Neolithic cultures themselves, and wholly unexpected links to East Asia all the way to Central Europe.

When faced with data such as this, one can only say: what the hell happened during European prehistory?

UPDATE (8 Jun 2012): The age of these remains has been questioned.

Journal of Human Genetics advance online publication 15 September 2011; doi: 10.1038/jhg.2011.103

HVS-I polymorphism screening of ancient human mitochondrial DNA provides evidence for N9a discontinuity and East Asian haplogroups in the Neolithic Hungary

Zsuzsanna Guba et al.

Analysis of mitochondrial mutations in the HVS-I region is an effective method for ancient human populational studies. Discontinuous haplotype data between the first farmers and contemporary Europeans has been described before. Our contribution is based on a survey initiated on the Neolithic skeletons from Hungarian archaeological sites in the Alföld. This Lowland, the Hungarian Plain, is well excavated as an important region for spread of Neolithic culture from Near East and Balkans toward Central and Western Europe, started circa 8000 years ago. HVS-I sequences from nt15977 to nt16430 of 11 such specimens with sufficient mitochondrial DNA preservation among an extended Neolithic collection were analysed for polymorphisms, identifying 23 different ones. After assigning all single-nucleotide polymorphisms, a novel, N9a, N1a, C5, D1/G1a, M/R24 haplogroups were determined. On mitochondrial control mutations at nt16257 and nt16261, polymorphic PCRs were carried out to assess their distribution in remains. Neolithic data set was compared with contemporary Vác samples and references, resulting in higher frequency of N9a in Alföld as a remarkable genetic discontinuity. Our investigation is the first to study mutations form Neolithic of Hungary, resulting in an outcome of Far Eastern haplogroups in the Carpathian Basin. It is worth further investigation as a non-descendant theory, instead of a continuous population history, supporting genetic gaps between ancient and recent human populations.

Link

First aboriginal Australian genome published

Aboriginal Australians (AA) have been somewhat of a black hole in population genetics research. So, it's great news that after today's Reich et al. paper on Denisova admixture, there is another new paper that presents the first full genome sequence of an aboriginal Australian.

I don't know why it has been so difficult to study AAs so far; my guess is that some type of politics has prevented it, similar to those that have hindered population genetics research in some Amerindian groups. Unfortunately, the current publication does not seem to represent the beginning of a new era in AA research, as the genome does not belong to a living AA, but rather to a 100-year old hair sample.

On one hand this makes sense: old DNA is preferable to fresh one when one deals with populations that have undergone admixture in recent times. I don't know how many AA have European admixture, but my guess is that, surely, pure-blooded living AA still exist, so, one could in principle obtain DNA from them.

Nonetheless, we should be thankful for the new data which provide a much needed new data point of mankind's diversity. Also, given recent developments, even a single genome may prove to be invaluable.

The supplementary material (pdf) has, as usual, most of the interesting details of the paper.

Coverage in the Australian.

(to be continued)

UPDATE: I will take the age estimates in the paper with a grain of salt, because they are not independent estimates, but rely on a calibration of the European-East Asian split (fixed at 2,000 generations), and the Out-of-Africa event (fixed at 3,500 generations). Hence, from the supplement:

Based on how our model was set up, the European-Aboriginal Australian and African-Aboriginal Australian split times that we presented above could be no less than 2,000 and 3,500 generations ago, respectively.

So, at most the data shows that Europeans are closer related to East Asians than either of them is to Australian aboriginals. The actual ages in years are conditioned on the timing of the aforementioned events, which, in turn, have been estimated in the past using various assumptions (see my recent post on Gronau et al. 2011).

Science DOI: 10.1126/science.1211177

An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia

Morten Rasmussen et al.

ABSTRACT

We present an Aboriginal Australian genomic sequence obtained from a 100-year-old lock of hair donated by an Aboriginal man from southern Western Australia in the early 20th century. We detect no evidence of European admixture and estimate contamination levels to be below 0.5%. We show that Aboriginal Australians are descendants of an early human dispersal into eastern Asia, possibly 62,000 to 75,000 years ago. This dispersal is separate from the one that gave rise to modern Asians 25,000 to 38,000 years ago. We also find evidence of gene flow between populations of the two dispersal waves prior to the divergence of Native Americans from modern Asian ancestors. Our findings support the hypothesis that present-day Aboriginal Australians descend from the earliest humans to occupy Australia, likely representing one of the oldest continuous populations outside Africa.

Link

Widespread Denisovan admixture (Reich et al. 2011)

Table S2 from the paper (pdf) gives the Denisova admixture as a fraction of the Papuan New Guinea highlander Denisova admixture. It seemed almost certain to me that Australian aboriginals would register such admixture, as they have often been described, on physical anthropological grounds, as closer to Papuans than to any other human population. But, it is nice to see the evidence (or lack thereof) for Denisova admixture quantified in various groups described as "Negrito" or "Australoid" by traditional physical anthropology.

The inference, by the authors, that Denisova admixture took place in Southeast Asia itself makes sense to me. This admixture may have been variable to begin with, but it was reduced in Southeast Asia itself as the number of modern humans in it grew, absorbing the Denisova-admixed early inhabitants, with the latest episode taking the form of the arrival of East Eurasian populations (traditional Mongoloids) that seem to lack this admixture altogether.

The interesting question now seems to be: with Denisovans spread from the Altai to Southeast Asia, how did the ancestors of East Asians avoid having any?

UPDATE: Figure 1 from the paper shows Denisovan admixture as a fraction of that in New Guineans:

One of the most interesting findings of the paper is that the extent of Denisova admixture is strongly correlated with the extent of Near Oceanian (Australian-Papuan) admixture.

An interesting question is to what extent does Denisova admixture contribute to the differentiation between Australasians and other modern humans? The following admixture graph gives an idea:

You can see that 7% Denisova introgression into the ancestors of Australians/New Guineans is inferred to have been "diluted" by roughly 50-50 admixture with Denisova-deficient modern humans, leading to the ~4% figure of Denisova admixture in extant Australians/New Guineans. This was further diluted in populations like Mamanwa, by admixture with East Asians.

It seems likely that inter-population differentiation within the species H. sapiens may be driven, at least in part, by admixture with archaic humans, and is not only the result of isolation post-Out of Africa. If Franz Weidenreich were alive, he would probably be smiling.

UPDATE II: A possible reason why East Asians lack Denisovan admixture is given by Mark Stoneking, as quoted in Nature:

Stoneking says that this pattern hints at at least two waves of human migration into Asia: an early trek that included the ancestors of contemporary Aboriginal Australians, New Guineans and some other Oceanians, followed by a second wave that gave rise to the present residents of mainland Asia. Some members of the first wave (though not all of them) interbred with Denisovans. However, the Denisovans may have vanished by the time the second Asian migrants arrived. This also suggests that the Denisovan's range, so far linked only to a cave in southern Siberia, once extended to Southeast Asia and perhaps Oceania.

Given that the Denisova hominin is about 41ka old, that would imply that East Asian ancestors moved through their territory after that date, when the Denisovans were already extinct, partially absorbed by first-wave "Australasian-like" people.

We must also consider the possibility that the Denisovans themselves may have been intrusive to Siberia; could the Altai Denisovans be remnants of a Southeast Asian population that fled out of the way of the modern humans that migrated to Australasia? If that is the case, then East Asian ancestors may lack Denisovan admixture because they had already reached the far east when Denisovans started moving north.

I, for one, can't wait until we start getting ancient DNA from Upper Paleolithic H. sapiens, who knows what new surprises are in store for us?

The American Journal of Human Genetics, 22 September 2011
doi:10.1016/j.ajhg.2011.09.005

Denisova Admixture and the First Modern Human Dispersals into Southeast Asia and Oceania

David Reich et al.

It has recently been shown that ancestors of New Guineans and Bougainville Islanders have inherited a proportion of their ancestry from Denisovans, an archaic hominin group from Siberia. However, only a sparse sampling of populations from Southeast Asia and Oceania were analyzed. Here, we quantify Denisova admixture in 33 additional populations from Asia and Oceania. Aboriginal Australians, Near Oceanians, Polynesians, Fijians, east Indonesians, and Mamanwa (a “Negrito” group from the Philippines) have all inherited genetic material from Denisovans, but mainland East Asians, western Indonesians, Jehai (a Negrito group from Malaysia), and Onge (a Negrito group from the Andaman Islands) have not. These results indicate that Denisova gene flow occurred into the common ancestors of New Guineans, Australians, and Mamanwa but not into the ancestors of the Jehai and Onge and suggest that relatives of present-day East Asians were not in Southeast Asia when the Denisova gene flow occurred. Our finding that descendants of the earliest inhabitants of Southeast Asia do not all harbor Denisova admixture is inconsistent with a history in which the Denisova interbreeding occurred in mainland Asia and then spread over Southeast Asia, leading to all its earliest modern human inhabitants. Instead, the data can be most parsimoniously explained if the Denisova gene flow occurred in Southeast Asia itself. Thus, archaic Denisovans must have lived over an extraordinarily broad geographic and ecological range, from Siberia to tropical Asia.

Link

Inference of ancient human demography from individual genomes (Gronau et al. 2011)

This new paper is reminiscent of Li & Durbin (2011), in that it also fits a model of ancient human demography based on individual genome sequences. Unlike that paper, it also considers a San individual, and is hence a good realization of the project I proposed in response to the Li & Durbin paper.

As is so often the case, the absolute age estimates are based on a calibration, which is spelled out quite nicely in the supplementary material (pdf; p. 55). In particular, the age estimates are based on:

• Human-chimp divergence of 6.5Mya
• Generation length of 25 years

As the authors note, their calibration results in:

an adjusted estimate of the per generation mutation rate would be slightly more than 2 × 10−8 mutations per site. This adjusted estimate agrees well with independent estimates of 1.8–2.5 ×10−8 (Nachman and Crowell, 2000; Kondrashov, 2003). It is slightly higher than recently reported estimates of 1.0–1.3 ×10−8 (The 1000 Genomes Project Consortium, 2010; Lynch, 2010; Roach et al., 2010), but, considering the many sources of uncertainty in these studies, we do not regard this difference as a serious concern. It is difficult to reconcile per-generation mutation rate estimates as low as 1×10−8 with the observed levels of human/chimpanzee genomic divergence.

However, Nachman & Crowell do not provide a mutation rate estimate independent of demography. As can be seen from Table 3 of their paper, their mutation rate estimate depends on human-chimp speciation as well as assumptions on ancestral effective population size. First, they assume a generation length of 20 years, hence their calibrations need to be scaled: 6.5My in 25y generations is equivalent to 5.2My in 20y generations. Nachman and Crowell estimate the mutation rate at 2.5x10-8 and 1.4x10-8 with an effective size of 10,000 individuals and speciation at 5 or 5.5Mya.

Hence, their mutation rate estimate for 5.2My would be between 1.4x10-8 and 2.5x10-8, i.e., close to the value of Gronau et al. (2011), assuming that the effective population size was 10,000 individuals. Gronau et al. estimate the effective population size at 9,000 individuals. So, there is nothing independent about N&C's age estimate: it is dependent on the effective population size, and the Gronau et al.'s mutation rate/effective size estimate of 2.0x10-8/9,000 individuals may be consistent with the data, but so is a lower mutation rate and higher effective size.

Note that, unlike Li & Durbin, Gronau et al. do not consider a model with a structured African population, or the presence of archaic admixture. These would have produced observed divergence times by a combination of a younger divergence between modern human groups, coupled with admixture with a more distantly diverged (archaic or "Palaeoafrican") population, for which there is now genetic and palaeoanthropological evidence.

I do not have a strong opinion how the 2-fold mutation rate difference between different papers will be resolved. If the slower empirical estimates are accepted, then this would result in deeper divergences between human populations, as well as an earlier human-chimp split, but the difference is not necessarily linear.

As I have noted before, there is no reason I can think of why parent-offspring rates should be slower than evolutionary ones. Two potential processes might actually make them appear faster: phantom mutations based on current whole genome sequencing technology, or loss of mutations due to drift across geological time scales. So, unless there is a technical reason for the low 1000Genomes rate, I'm more inclined to trust it rather than circular calibrations of demography/mutation rate/effective population size. In any case, we will have more full genome sequences from family members in the coming years, so the mutation rate will be calibrated directly, without recourse to human-chimp speciation or ancestral population sizes.

A slower mutation rate would make sense to me on palaeoanthropological grounds:

• The authors estimate European/East Asian divergence at 30-45kya. But, the presence of clearly derived Caucasoid morphology in the Upper Paleolithic population of Europe, suggests to me that divergence may have begun some time before.
• Table S2 of adjusted Mahalanobis distances from Harvati et al. (2011) leaves little doubt that the Eurasian anatomically modern humans (EAM) from the Levant (Skhul/Qafzeh) are related to subsequent Eurasians. EAM has a distance of -0.25 to later Upper Cave from China (UC); 6.42 to recent Oceanians (OCE); 7.19 to Upper Paleolithic Eurasians. All of the above are well-within the maximum divergence observed between any two modern human groups. Ancestral Eurasians likely lived before 100ky, and did not split from Africans only 50ky.
• If there was a long isolation between Khoe-San and the rest of mankind, then where did it happen? It is no longer plausible to postulate multiple fully modern groups in Africa that are absolutely absent from the palaeoanthropological record in the timeframe in question, in reproductive isolation to the multiple archaic or archaic-like ones that keep turning up.
• How did the ur-humans in Africa manage reproductive isolation for tens of thousands of years between themselves (Khoe-San vs. rest or moderns vs. archaics), but apparently mixed a-plenty right after they left Africa with Neandertals/Denisovans? Were Neandertal women really that sexy?
• Actually, the fragmentary record, as it stands, has not revealed any traces of a Proto-San population, and the Hofmeyr skull from South Africa stands as an outlier in the African paleoanthropological record with its strong affinities to Upper Paleolithic Eurasians.

We are only now beginning to harness the power of full human genomes for evolutionary inferences, but it is inevitable that a new theory of human origins will appear that will reconcile the different and conflicting lines of evidence. That theory must take into account latent admixture as a cause of African genetic diversity, and it must also harmonize with the paleoanthropological record.

Related:

• Archaic admixture in Africa confirmed
• Early divergence of Khoesan ancestors (Veeramah et al. 2011)
• A good idea for a new project
• Human population history from single human genomes (Li & Durbin 2011)
• John Hawks: What is the human mutation rate?

Nature Genetics (2011) doi:10.1038/ng.937

Bayesian inference of ancient human demography from individual genome sequences

Ilan Gronau et al.

Whole-genome sequences provide a rich source of information about human evolution. Here we describe an effort to estimate key evolutionary parameters based on the whole-genome sequences of six individuals from diverse human populations. We used a Bayesian, coalescent-based approach to obtain information about ancestral population sizes, divergence times and migration rates from inferred genealogies at many neutrally evolving loci across the genome. We introduce new methods for accommodating gene flow between populations and integrating over possible phasings of diploid genotypes. We also describe a custom pipeline for genotype inference to mitigate biases from heterogeneous sequencing technologies and coverage levels. Our analysis indicates that the San population of southern Africa diverged from other human populations approximately 108–157 thousand years ago, that Eurasians diverged from an ancestral African population 38–64 thousand years ago, and that the effective population size of the ancestors of all modern humans was ~9,000.

Link

Latent admixture causes spurious serial founder effect

There is a series of interesting papers on Amerindian populations in the early view section of the American Journal of Physical Anthropology. One of them struck my interest, because it deals with an issue that has been a familiar topos of this blog, and has, in my opinion, much greater potential applicability than the settlement of the Americas.

The basic idea of the paper is the following: the serial founder effect (SFE) is a model, whereby populations expand by successive splits, with daughter populations expanding and colonizing new territories. It is a tree model, with the nodes furthest from the root representing late founder populations, and the ones closest to the root representing early splits close (geographically and temporally) to the initial colonization impetus.

Gene identity is the probability that two random alleles from either two individuals in a population, or from two individuals from different populations will be identical. This has been used to argue for a SFE in the Americas, because it apparently matches expectations: the most basal populations are in north America, and gene identity increases toward south America.

However, the authors of the current paper show that the observed pattern is due to European admixture in native American populations; this makes the north American populations (that are more European-admixed and hence more different than the rest) appear both more basal and more diverse.

From the paper:

Many aspects of the pattern of neutral genetic variation in the Americas are consistent with the predictions of the serial founder effects process. The NJ tree is rooted in northern North America, it shows a northsouth pattern of internal branching, and gene identity within populations increases steadily with increasing geographic distance from Beringia. However, admixture with Europeans could account for all of these features. The tree is rooted in northern North America because the gene identities between the three northern North America populations and the other Native American populations are particularly low (Fig. 2). European admixture has contributed to this low identity, and, in principle, it could account for the position of the root. The Admixture tree (Fig. 5A) topology indicates that the north-south pattern of branching in the NJ tree might be the result of relatively high admixture in northern North America, intermediate levels in Central America and northern South America, and low levels in eastern South America. The partial correlation analyses show that the north-south increase in gene identity within populations can also be explained by geographically patterned admixture (Table 2). We conclude that geographically patterned admixture between Native Americans and Europeans has obscured our ability to reconstruct precontact evolutionary processes in the Americas.

Of course, this is an extremely important piece of work that future studies of Amerindian populations must take into account. It is no longer feasible to interpret the observed gene identity pattern in the Americas as a remnant of the migration and spread of Amerindian ancestors thousands of years ago. It is more likely a result of much more recent events, namely the different intensity of European admixture in post-1492 times.

Hunley and Healy is important not only for the Americas, however. The serial founder effect has been evoked to explain both the spread of modern humans from east Africa, as well as more recent Neolithic expansions in different parts of the world. We must now be vigilant that these patterns may, in part, be the result of latent admixture.

In the Americas, we know (from historical documents) that this admixture took place, and we have relatively unadmixed populations still in existence. But, there may very well have been admixture events before the birth of history, and many ancestral populations may no longer exist in unadmixed form. So, we may be interpreting patterns of modern human variation as the result of ancient colonization processes, oblivious to the presence of latent admixture.

For example, there is an increase in gene identity from eastern Africa through Arabia, and India, all the way to Siberia, and southward across the Americas. Hunley and Healy deal with the latter part of this cline, but the whole of it has been interpreted as evidence of an orderly Out of Africa colonization as a series of founder effects.

However, the Eurasian portion of the pattern may also be spurious: current east Africans, for example, are partially admixed, both with West Eurasians and with people from other parts of the continent. Likewise, Arabians often have African admixture, whereas South Asians have been convincingly shown to be largely 2-way mixes of West Eurasians and "Ancestral South Indians". To top it all off, we now have convincing evidence that archaic admixture may have played a role in the evolution of some living Africans: this would furthermore increase their gene diversity and contribute to a perceived Eurasian cline.

Tree models are orderly and well-behaved. It would be great if people behaved that way, because the math would be easier. But, people aren't laboratory mice that follow predefined paths in a maze: they mix with their neighbors, they split and move forward, but sometimes, they split and move backward. Hopefully, H&H's paper will lead to an increased appreciation of admixture in the human story, beyond the case of the Americas.

AJPA DOI: 10.1002/ajpa.21506

The Impact of Founder Effects, Gene Flow, and European Admixture on Native American Genetic Diversity

Keith Hunley and Meghan Healy

Abstract
Recent studies have concluded that the global pattern of neutral genetic diversity in humans reflects a series of founder effects and population movements associated with our recent expansion out of Africa. In contrast, regional studies tend to emphasize the significance of more complex patterns of colonization, gene flow, and secondary population movements in shaping patterns of diversity. Our objective in this study is to examine how founder effects, gene flow, and European admixture have molded patterns of neutral genetic diversity in the Americas. Our strategy is to test the fit of a serial founder effects process to the pattern of neutral autosomal genetic variation and to examine the contribution of gene flow and European admixture to departures from fit. The genetic data consist of 678 autosomal microsatellite loci assayed by Wang and colleagues in 530 individuals in 29 widely distributed Native American populations. We find that previous evidence for serial founder effects in the Americas may be driven in part by high levels of European admixture in northern North America, intermediate levels in Central America, and low levels in eastern South America. Geographically patterned admixture may also account for previously reported genetic differences between Andean and Amazonian groups. Though admixture has obscured the precise details of precontact evolutionary processes, we find that genetic diversity is still largely hierarchically structured and that gene flow between neighboring groups has had surprisingly little impact on macrogeographic patterns of genetic diversity in the Americas.

Link

Chris Stringer video on BBC on Iwo Eleru skulls

Skull points to a more complex human evolution in Africa

"[The skull] has got a much more primitive appearance, even though it is only 13,000 years old," said Chris Stringer, from London's Natural History Museum, who was part of the team of researchers.

"This suggests that human evolution in Africa was more complex... the transition to modern humans was not a straight transition and then a cut off."

Prof Stringer thinks that ancient humans did not die away once they had given rise to modern humans.

They may have continued to live alongside their descendants in Africa, perhaps exchanging genes with them, until more recently than had been thought.

The researchers say their findings also underscore a real lack of knowledge of human evolution in the region.

My previous blog post on the published article here.

A thing that has troubled me in reading a few recent palaeoanthropological comparative analyses is the fact that the Omo I, the "modern" of the ~195ka Omo skulls, as well as Herto do not seem to be included. Is this a case of anthropologists guarding their data, a problem that seems to have particularly plagued paleoanthropology? This is not an idle question: how would these ~200ka and ~150ka finds, widely touted as our ancestors fare when placed in the same analysis as the skulls of Harvati et al. (2011) or Mounier et al. (2011)?

Omo II, the most "archaic" of the Omo skulls was included in Mounier et al. (2011) and seemed to be related to Skhul 5 and Jebel Irhoud 1, which would probably place it in the intermediate (archaic/modern) category. How about Omo I?

I don't know, and I'd like to see some hard numbers on exactly how modern it is compared to extant humanity. It has often been repeated, for example, that the Skhul/Qafzeh hominins from the Levant represent an early Out-of-Africa movement, but they appear, at least in the latest Harvati et al. analysis to be well within the range of modern human variation, and certainly more so than all the included African samples of similar, or even younger age.

This seems counterintuitive: if, as the current orthodox theory holds, modern humans -in the strict sense of being like living people- originated in Africa ~200ka and spread to the rest of the world ~60ka, why are the Mt. Carmel hominins apparently more modern than their African counterparts of similar age? Remember, that it has been hypothesized that Skhul/Qafzeh represent a population that may be mixing with Eurasian Neandertals, which would make them less like modern people, not more.

Moreover, if modern humans did originate in Africa ~200ka, then why did they admix with archaic Africans only ~35ka (per Hammer et al. 2011) and had not replaced archaic Africans even ~13ka? Apparently, the current narrative proposes, they replaced all archaic hominins in Eurasia in practically a few thousands of years, but they could not achieve the same in nearly 0.2My in Africa? Or, they admixed with archaic Eurasians before they admixed with their next-door neighbors, the archaic Africans? Something does not seem right.

How would Omo I and Herto fare if they had been included? Ancestral H. s. sapiens, where art thou? Let's find out.