ALDER signal of admixture in Ashkenazi Jews

(You can skip the first part if you want, and head straight to the RESULTS section)

Previous studies on uniparental markers have indicated that Ashkenazi Jews (AJ) were formed by admixture between a Near Eastern population and European host populations; the evidence for the former element seems pretty clear on the basis of Y-chromosomes where Jews possess a relatively high frequency of Y-haplogroup J1 (and a few others) that are quite rare in non-Jewish north/east Europeans. As for the latter, it seems probable on the basis of the location of Ashkenazi Jews on PCA plots where they tend to occupy an intermediate position between extant populations of the Levant (including Near Eastern Jews) and non-Jewish Europeans.

Anyone who has played around with genetic data will know that while AJ may be positioned in the aforementioned "intermediate" location within the "West Eurasian continuum" between Europe and Near East, they tend to form their own cluster at higher dimensions. And, indeed, this is why it's fairly easy for a clustering algorithm, such as my "Clusters Galore" (MCLUST/MDS) approach to pick out a very specific AJ cluster (e.g., here, or here, using a fastIBD approach). An Ashkenazi Jewish-specific cluster also pops out at higher K in ADMIXTURE analyses. This cluster may reflect endogamy within the AJ community until quite recent times.

One way of detecting admixture in a group is through the use of f3-statistics. The statistic f3(AJ; European, Near_East) could be negative --which would indicate admixture-- but it is usually not -at least in the combinations of (European, Near_East) I've tried, and this is consistent with either the presence admixture or absence of admixture.

A simple and intuitive way to see why post-admixture drift might mask the presence of admixture can be seen by means of a simple calculation. Remember that the f3-statistic's +/- sign depends on the +/- sign of quantities (c-a)*(c-b) where c is an allele frequency in the admixed (?) population we are investigating, and a, b in the two reference populations. We can pick a to be less than b with no loss of generality.

In the absence of strong drift (e.g., if all populations have a very large number of individuals), then the allele frequency c=xa+(1-x)b where x is the amount of admixture --between 0 and 1-- from group A and (1-x) from group B, and this c will be maintained little changed in the post-admixture phase. With the aid of a little algebra, we get that:

(c-a)*(c-b) = (xa+(1-x)b-a)*(xa+(1-x)b-b)
= (xa+b-xb-a)*(xa+b-xb-b) =
= x(x-1)(a-b)^2

and this is of course negative because we assumed that x was less than 1.

In a large population, this c will remain near-constant, because of the lack of strong drift. As long as it remains within the interval (a,b), then (c-a)*(c-b) will also remain negative, and so will the f3 statistic.

But, what if strong drift affects the admixed population? Allele frequencies fluctuate more wildly in larger populations, so c might go outside the (a,b) interval. Without loss of generality, assume that c becomes greater than b in which case (c-a)*(c-b) will become positive.

The f3-statistic averages over many SNPs, so, depending on (i) the initial differentiation of the admixed populations, which could be seen as b-a, and (ii) the amount of drift, which causes c to jump outside the (a, b) interval as discussed above, it is possible that the evidence for admixture may disappear.

So, relying on allele frequency differences may help obliterate the signal of admixture. But, there is a different signal of admixture that uses the decay of admixture linkage-disequilibrium, most recently discussed in the ALDER paper. The admixture LD signal's evidence may also disappear in time, but only because the signal occurs at increasingly lower genetic distances over time due to recombination. Thankfully, it tends to occur at large enough --for the last few thousand years-- distances, for which the SNP density of existing genotyping platforms that measure a few hundred thousand SNPs per individual is sufficient.

METHODS

Naturally I was curious to see whether the admixture LD mechanism would produce the evidence of admixture that the f3-statistics did not. I combined three datasets in my possession (HGDP by Li et al. Behar et al. and Yunusbayev et al. ) and identified sets of European and Semitic populations. (Remember that these sets are non-exhaustive, but presumably usable surrogates for the true mixing populations exist within them):

Abhkasians_Y, Adygei, Belorussian, Bulgarians_Y, Chechens_Y, Chuvashs, French, French_Basque, Georgians, Hungarians, Lezgins, Lithuanians, Mordovians_Y, North_Italian, North_Ossetians_Y, Orcadian, Romanians, Russian, Sardinian, Spaniards, Tuscan, Ukranians_Y

and:

Bedouin, Druze, Egyptans, Ethiopian_Jews, Ethiopians, Iraq_Jews, Jordanians, Lebanese, Morocco_Jews, Palestinian, Saudis, Sephardic_Jews, Syrians, Yemenese, Yemen_Jews

I used my Dodecad Project sample of AJ which numbers 36 individuals and is larger than any other usable public sample available to me.

(ALDER was run with default parameters, using the Rutgets recombination map for Illumina chips, and with the merged dataset prepared with a --geno 0.03 flag. Note that the Ashkenazi_D sample consists of individuals typed on different Illumina platforms from 23andMe and FamilyTreeDNA. The total number of SNPs considered was 527,165.)

RESULTS

I report below the tests for which ALDER reported "success" for the test with no warnings:

The median of all these estimates is 36.78 generations or 1070 years which corresponds to a calendar date of 910CE, assuming the sample's birthday was 1980, and a generation length of 29 years.

Palamara et al. placed the beginning of demographic expansion of AJ in a similar timeframe (33 generations), following a severe founder effect reducing the population to ~270 individuals. Such a founder effect may have indeed served to produce positive f3-statistics, masking the presence of admixture, the occurrence of which appears to be substantiated on the basis of the ALDER test of admixture.

As for the levels of admixture, using a 1-ref analysis with the European populations, I get the following lower bounds:

I'd be interested in hearing people's opinions on the plausibility of these dates/proportions, as well as their potential historical associations; a lot of factors might affect these results, so perhaps this analysis could be improved in the future.

Who inhabited the Jubbah lake in the Nefud Desert during the Middle Paleolithic?

Many readers may have heard of the Nefud Desert while watching Lawrence of Arabia (was that filmed on location?). It is hard to imagine that desolate landscape as being instrumental in the tale of human origins, but it may very well have been. A new paper describes Middle Paleolithic settlement evidence from the Jubbah Palaeolake, especially during MIS stages 7 and 5.

Arabia is a very interesting case for a variety of reasons: It has to be implicated one way or another in the tale of human origins and dispersals: it lies in the natural route Out-of-Africa, and in the intermediate space between the early modern human remains from Ethiopia, the later modern humans from the Levant, as well as the disputed late Neandertals of West Asia.

Unfortunately, current climatic conditions, as well as past episodes desiccation have resulted in substantial population; if anyone wanted to find out what the people who lived there during the Middle Paleolithic were like, he will find little continuity between them and the current inhabitants. The lack of genetic evidence is, unfortunately also accompanied by a general lack of anthropological evidence. Industries with links to Africa or the Levant are devoid of associated remains. But, the paper produces a hopeful note:

Yet, recent support for an MIS 5 expansion of Homo sapiens comes from archaeological finds of characteristic Middle Palaeolithic technologies in Arabia in MIS 5e–c [19]–[20] and nuclear genomic estimates which indicate that the split between Africans and non-Africans occurred as early as 130 to 90 ka [41], consistent with fossil finds of Homo sapiens in the Levant [52], [53] and at the time of possible interbreeding of Homo sapiens and Neanderthals [54]. These controversies indicate the need to recover hominin fossils in Arabia, which is feasible given the identification of Pleistocene mammalian fauna in a nearby lake basin of the Nefud [24], [55].

In the absence of genes or bones, we can only make inferences based on stones, which may not have a direct correspondence with populations. While Figure 17 from the paper (left) shows a clear differentiation of India vis a vis. the west, relationships in the Near East and Africa are not as clear cut; Skhul resembles North Africa (Haua Fteah and Aterian) and it would be tempting to associate them with Homo sapiens. But, Horn of Africa MSA  -where the earliest anatomically modern humans were found- is linked to El Wad, Tabun C, and Jebel Qattar/Katefeh, the latter two sites being the ones from the Nefud.

Tabun is associated with Neandertals, although that attribution, like most everything in palaeoanthropology is controversial.So, it might be possible that the Jubbah was occupied by Neandertals too, and this might make this population a prime candidate for the signal of Neandertal admixture carried by non-Africans.

At present, there seem to be two candidates for the modern human Out-of-Africa: Skhul (Levant; linked to Northwest Africa here) and the Nubian technocomplex of (south Arabia; linked to Northeast Africa). I don't have a clear picture of how it may have all played out; it would certainly be wonderful if it were possible to extract DNA from, say, Skhul/Qafzeh modern humans or the Levantine Neandertals, because that would definitely show how (i) the former may either be related to later Eurasians, or may be a failed experiment as hitherto supposed, and (ii) the latter might be a source of Neandertal DNA in non-Africans, or indeed something much closer to modern humans as their morphological intermediacy might suggest.

PLoS ONE 7(11): e49840. doi:10.1371/journal.pone.0049840

Hominin Dispersal into the Nefud Desert and Middle Palaeolithic Settlement along the Jubbah Palaeolake, Northern Arabia

Michael D. Petraglia et al.

The Arabian Peninsula is a key region for understanding hominin dispersals and the effect of climate change on prehistoric demography, although little information on these topics is presently available owing to the poor preservation of archaeological sites in this desert environment. Here, we describe the discovery of three stratified and buried archaeological sites in the Nefud Desert, which includes the oldest dated occupation for the region. The stone tool assemblages are identified as a Middle Palaeolithic industry that includes Levallois manufacturing methods and the production of tools on flakes. Hominin occupations correspond with humid periods, particularly Marine Isotope Stages 7 and 5 of the Late Pleistocene. The Middle Palaeolithic occupations were situated along the Jubbah palaeolake-shores, in a grassland setting with some trees. Populations procured different raw materials across the lake region to manufacture stone tools, using the implements to process plants and animals. To reach the Jubbah palaeolake, Middle Palaeolithic populations travelled into the ameliorated Nefud Desert interior, possibly gaining access from multiple directions, either using routes from the north and west (the Levant and the Sinai), the north (the Mesopotamian plains and the Euphrates basin), or the east (the Persian Gulf). The Jubbah stone tool assemblages have their own suite of technological characters, but have types reminiscent of both African Middle Stone Age and Levantine Middle Palaeolithic industries. Comparative inter-regional analysis of core technology indicates morphological similarities with the Levantine Tabun C assemblage, associated with human fossils controversially identified as either Neanderthals or Homo sapiens.

Link

U7 in Rostov Scythians

I found it quite interesting that in terms of mtDNA, the Rostov Scythians studied by der Sarkissian resembled closely the Shugnans of Tajikistan, who speak an eastern Iranian language. The author finds links between the Scythians and the "Central Asian Corridor", in particular with respect to mtDNA haplogroup U7.

This "Central Asian Corridor" sensu der Sarkissian (Iraq, Iran, Pakistan, India) seems to touch Frachetti's Inner Asian Mountain Corridor (shown below) in the region of the Pamirs.

Interestingly, the Sughnans belong, anthropologically to the Pamir-Ferghana type, which was also called Central Asian interfluvial type, the rivers in question being the Oxus and Jaxartes (Amu Darya and Syr Darya). And, of course, between these two rivers was the heartland of the Bactria Margiana Archaeological Complex, which I have previously linked with the Indo-Iranians.

Wells et al. studied Y-chromosomes of Sughnans, Yagnobis and other Iranic survivals of Tajikistan more than 10 years ago, and it will be very well worth revisiting them with newer methods. The area east of the Caspian and west of the IAMC intersects so much history, that any data from from it (new or ancient) would be extremely useful.

In my own experiments there has been an unambiguous "South Asian" genetic component in almost all Iranic peoples, even the westernmost Kurds. While the interpretation of this component is not easy, it does point to a genetic relationship between its possessors and Central/South Asia, with notable contrasts between Kurds/Iranians and their non-Iranic Armenian/Anatolian/Caucasian neighbors.

The occurrence of mtDNA haplogroup U7 in the Rostov Scythians is also consistent with a link between the Iranian nomads who penetrated into Europe with the area east of the Caspian, and it is also, of course, consistent with the narrative of Herodotus who recorded the migration of the Scythians into Europe.

There is a widely held theory that the origin of the Indo-Iranians are to be sought in eastern Europe. That theory appears inconsistent both with the "South Asian" autosomal signal in Iranic groups, and with the mtDNA evidence. Consider, again, the evidence of der Sarkissian:

Now, if Rostov Scythians were primarily descended from Mesolithic West Eurasians or even Bronze Age ones, then we would expect them to cluster at the "top", approaching the northern Europeoid extrema of PWC and Bronze Age Altai (ALT-BA). On the contrary, their position is well to the "south" of all European Bronze Age groups, and intermediate between Europeans and Iron Age Asian groups from south Siberia and Kazakhstan (KUR-IA, KAZ-IA). Again, this is compatible with an east-west migration during the Iron Age.

It might be worth speculating on the possible autosomal history of the steppe, for which the mtDNA evidence complements others: I offer that the long-term trend will be one of diminishing "North European", increasing "West Asian" and "East Eurasian" influences across the Neolithic-Bronze-Iron Age boundaries. At the western end of the steppe, there may also be "Mediterranean"/Sardinian-like infusions from the Balkans and Central Europe, although these clearly did not influence Inner/South Asia (where Mediterranean components shrink to non-existence), and Europe proper was mostly the recipient rather than the emitter of populations to Asia. Hopefully, autosomal data to test this conjecture will be made available in the coming years.

Mitochondrial DNA in Ancient Human Populations of Europe (der Sarkissian 2011)

Going over the 322 pages of thesis may take a while, but feel free to comment on it if you discover any interesting nuggets in the text. The following view of West/East Eurasian mtDNA surrounding the beginning of the Iron Age may be useful, and seems to parallel the results of a recent paper on Pazyryk mtDNA:

Of course, since the thesis was published we have new data from West Siberia/Ukraine that suggest that the penetration of east Eurasian lineages covered a great area to the west of the indicated region even prior to the Iron Age.

We can be fairly sure that "non-East Eurasian admixed" populations existed during the Bronze Age in three portions of the Eurasian landmass, separated by the Black and Caspian Seas: west of the Black Sea (Balkans/Central Europe); between Black and Caspian Seas (Caucasus) and east of the Caspian Sea (Kazakhstan and Turkmenistan). But how did these three regions contribute to the West Eurasian elements found on a west-east axis across Eurasia today? And, to what extent did the early east Eurasian elements that penetrated well into eastern Europe in the Neolithic-to-Bronze Age contribute to latter populations of the area vs. more recent expansions from the Altai and Central Asia during the Iron Age?

Here is a PCA of the pre-Iron Age individuals, compared with modern populations:

Both "Tarim" (TAR) and "Neolithic Lake Baikal" (LOK) appear well within east Eurasian variation. But, of the West Eurasian groups, Pitted Ware Complex (PWC), i.e., Neolithic hunter-gatherers from NE Europe and Bronze Age Altai (ALT-BA) appear clearly "northern Europeoid" across the 2nd PC, as do, to a lesser extent, C/N European Hunter-Gatherers (HG) and Kurgan burials from south Siberia (KUR-BA), but Bronze Age Kazakhstan (KAZ-BA) appear to be southern Europeoid, and, also, noticeably more "West Eurasian" than the others. Clearly, the West Eurasian elements were not homogeneous, with some of them (such as KAZ-BA) apparently derived from the southern Caucasoid zone -which largely did not experience east Eurasian admixture- and others from the northern Caucasoid zone that did.

The Rostov Scythian sample (in red) appears to belong to the southern Caucasoid zone (across PC2), but East Eurasian-shifted relative to modern Europeans and Bronze Age Kazakhstan.

Now, let's look at the Iron and post-Iron Age samples:

Egyin Gol (EG) from Mongolia and Sargat Siberians appear clearly as East Eurasians; Pazyryk Altai (ALT-IA), Iron Age Kazakhstan (KAZ-IA) and South Siberia Kurgan (KUR-IA) show decreasing East Eurasian influence; also notice the decidedly "southern" shift of the West Eurasian element among them.

This seems broadly consistent with the ideas of Molodin et al. about the gradual appearance (in their Siberian sample) of Caucasoid mtDNA types from the Neolithic to the Iron Age, with the early Neolithic U-dominated population finally receiving a full set of diverse West Eurasian lineages only during the Iron Age from the south.

It will certainly be very exciting when samples such as these can be tested for autosomal or Y-chromosome DNA, and I'm looking forward to the day when this can be done on a large scale.

Type: Thesis
Title: Mitochondrial DNA in ancient human populations of Europe.
Author: Dersarkissian, Clio Simone Irmgard
Issue Date: 2011
School/Discipline: School of Earth and Environmental Sciences

Abstract: The distribution of human genetic variability is the result of thousand years of human evolutionary and population history. Geographical variation in the nonrecombining maternally inherited mitochondrial DNA has been studied in a wide array of modern populations in order to reconstruct the migrations that have participated in the spread of our ancestors on the planet. However, population genetic processes (e.g., replacement, genetic drift) can significantly bias the reconstruction and timing of past migratory and demographic events inferred from the analysis of modern-day marker distributions. This can lead to erroneous interpretations of ancient human population history, a problem that potentially could be circumvented by the direct assessment of genetic diversity in ancient humans. Despite important methodological problems associated with contamination and post-mortem degradation of ancient DNA, mitochondrial data have been previously obtained for a few spatially and temporally diverse European populations. Mitochondrial data revealed additional levels of complexity in the population history of Europeans that had remained unknown from the study of modern populations. This justifies the relevance of broadening the sampling of ancient mitochondrial DNA in both time and space. This study aims at filling gaps in the knowledge of the genetic history of eastern Europeans and of European genetic outliers, the Saami and the Sardinians. This study presents a significant extension to the knowledge of past human mitochondrial diversity. Ancient remains temporally-sampled from three groups of European populations have been examined: north east Europeans (200 – 8,000 years before present; N = 76), Iron Age Scythians of the Rostov area, Russia (2,300 – 2,600 years before present; N = 16), Bronze Age individuals of central Sardinia, Italy (3,200 – 3,400 years before present; N = 16). The genetic characterisation of these populations principally relied on sequencing of the mitochondrial control region and typing of single nucleotide polymorphisms in the coding region. Changes in mitochondrial DNA structure were tracked through time by comparing ancient and modern populations of Eurasia. Analysis of haplogroup data included principal component analysis, multidimensional scaling, fixation index computation and genetic distance mapping. Haplotypic data were compared by haplotype sharing analysis, phylogenetic networks, Analysis of the Molecular Variance and coalescent simulations. The sequencing of a whole mitochondrial genome in a north east European Mesolithic individual lead to defining a new branch within the human mitochondrial tree. This work presents direct evidence that Mesolithic eastern Europeans belonged to the same Palaeolithic/Mesolithic genetic background as central and northern Europeans. It was also shown that prehistoric eastern Europeans were the recipients of multiple migrations from the East in prehistory that had not been previously detected and/or timed on the basis of modern mtDNA data. Ancient DNA also provided insights in the genetic history of European genetic outliers; the Saami, whose ancestral population still remain unidentified, and the Sardinians, whose genetic differentiation is proposed to be the result of mating isolation since at least the Bronze Age. This study demonstrates the power of aDNA to reveal previously unknown population processes in the genetic history of modern Eurasians.

Link

Populations histories with a diffusion process formulation

On the left you can see the best topology on a diffusion time scale. It might be interesting that CEU (YRI) appear closer to Africans (Eurasians) than JPT (BIA; Biaka Pygmies).

Mol Biol Evol (2012) doi: 10.1093/molbev/mss257

Inferring population histories using genome-wide allele frequency data

Mathieu Gautier and Renaud Vitalis

The recent development of high throughput genotyping technologies has revolutionized the collection of data in a wide range of both model and non-model species. These data generally contain huge amounts of information about the past demographic history of populations.

 In this study we introduce a new method to estimate divergence times on a diffusion time-scale from large SNP datasets, conditionally on a population history which is represented as a tree. We further assume that all the observed polymorphisms originate from the most ancestral (root) population, i.e. we neglect mutations that occur after the split of the most ancestral population. This method relies on a hierarchical-Bayesian model, based on Kimura's time-dependent diffusion approximation of genetic drift. We implemented a Metropolis–Hastings within Gibbs sampler to estimate the posterior distribution of the parameters of interest in this model, which we refer to as the Kimura model. Evaluating the Kimura model on simulated population histories, we found that it provides accurate estimates of divergence time. Assessing model fit using the deviance information criterion (DIC) proved efficient for retrieving the correct tree topology among a set of competing histories. We show that this procedure is robust to low-to-moderate gene flow, as well as to ascertainment bias, providing that the most distantly related populations are represented in the discovery panel. As an illustrative example, we finally analyzed published human data consisting in genotypes for 452,198 SNPs from individuals belonging to four populations worldwide.

Our results suggest that the Kimura model may be helpful to characterize the demographic history of dierentiated populations, using genome-wide allele frequency data.
Link

f3-statistics on craniometric data?

It occurred to me that the concept of f3-statistics, originally developed to detect admixture by exploiting allele frequency difference anti-correlations could very well be applied to craniometric data as well.

The basic idea is quite simple: suppose that for a metric trait, two populations A and B have mean value a and b and that a third population C is formed by mixture between A and B. Unlike allele frequencies where the admixed population's frequency will be between a and b immediately post-admixture, anthropometric traits may respond in unexpected ways to admixture (e.g., heterosis might cause first-generation offspring to exceed both their parents in height, rather than exhibit an intermediate value). I will leave the justification of the hypothesis that "mixed-origin offspring will possess intermediate metric traits" to the physical anthropologists, who may have gathered data on such things, and, for the present, I will take it for granted.

So, assuming that c, the mean trait in the mixed population, is between a and b, we can easily see that (c-a)(c-b) will be negative, and hence so will be the correlation coefficient (over many traits) between C-A and C-B, where by C-A I denote the k-long vector difference of mean trait values between populations C and A.

Going back to my analysis of Howells' dataset, I calculated population means for 57 traits over the NORMALIZED_DATA array of modern populations (in which sexual dimorphism has been removed and traits of different scale have been normalized in standard deviation units), and calculated 30*choose(29,2) correlations for each of 30 populations, expressed as a mixture of any pair of the remaining 29.

I list below, the top 20 anti-correlations, and highlight a few in bold (third population as mixture of first two):


BURIAT ANDAMAN PHILLIPI -0.54005191575771
EGYPT BURIAT NORSE -0.490018084440697
ANDAMAN ANYANG HAINAN -0.48323680182295
BURIAT ANDAMAN HAINAN -0.480939028739347
EGYPT BURIAT ZALAVAR -0.476445836100052
ANDAMAN ANYANG PHILLIPI -0.457902384166767
DOGON BURIAT PHILLIPI -0.416551851781419
BERG EASTER_I ZALAVAR -0.378996437433417
AUSTRALI BURIAT ARIKARA -0.375898166338775
BURIAT EASTER_I MOKAPU -0.37169703838378
ESKIMO ANDAMAN S_JAPAN -0.366611599944932
ESKIMO PERU N_JAPAN -0.354535077363928
TOLAI BURIAT ARIKARA -0.348110323746154
BERG EGYPT ZALAVAR -0.344843098962355
DOGON ESKIMO GUAM -0.344577928128792
TOLAI BURIAT GUAM -0.338804214799388
ESKIMO PHILLIPI GUAM -0.336537918547276
DOGON BURIAT HAINAN -0.332635954428392
TASMANIA BURIAT ARIKARA -0.331301837598433
ESKIMO PERU S_JAPAN -0.330302035072489

Some interesting ones:

• Philippines as Buriat+Andaman; this makes sense if Philippines is the result of admixture between an "East Asian" and a "Negrito" population
• Norse as Egypt+Buriat; the Howells "Egypt" sample is "Mediterranean" in the classical sense. Perhaps this involves the same "East Eurasian"-like signal of admixture detected by genetic methods? Similar signal also occurs for Zalavar (from Hungary)
• Hainan as Andaman+Anyang; south Chinese as Neolithic Chinese+"Negrito"-like old south Chinese?
• Arikara as Buriat+Australian; admixture between "Australoid" Paleo-Indians and "Mongoloid" ones? or between 1st wave Indians and later ones (sensu Reich et al. 2012)?
• Guam as Tolai+Buriat; admixture between "Papuan"-like and East Asian-like people in Polynesia?

As with "normal" f3-statistics, absence of a negative correlation does not reject admixture; this may be especially the case here, because phenotypes may be affected by strong natural selection during the post-admixture period.

And, there are some difficult-to-interpret cases (e.g., Philippines as Buriat+Dogon) which may point to limitations of the method; for example, the Dogon may act as a stand-in for the "equatorial"-like physique of the true "Andaman"-like mixing element. Presumably such limitations can be overcome by limiting the analysis to "selectively neutral" traits, rather than the whole suite of 57 Howells variables used here.

I certainly think that the idea ought to be investigated further: it might be redundant when genetic data are available, but may prove useful in the analysis of admixture when such data do not exist, e.g., in anthropological data of prehistoric specimens from hot climates where archaeogenetic evidence may never materialize. 

Pre-Neolithic Mediterranean Island settlement

PhysOrg coverage of a Science perspective:

Modern science has held that islands such as Cyprus and Crete were first inhabited by seafaring humans approximately 9,000 years ago by agriculturists from the late Neolithic period. Simmons writes that research over the past 20 years has cast doubt on that assumption however and suggests that it might be time to rewrite the history books. He cites evidence such as pieces of obsidian found in a cave in mainland Greece that were found to have come from Melos, an island in the Aegean Sea and were dated at 11,000 years ago as well as artifacts from recent digs on Cyprus that are believed to be from approximately 12,000 years ago. He adds that some researchers have also found evidence that something, or someone caused the extinction of pygmy hippos on Cyprus around the same time.  

Simmons also suggests that the first inhabitants of many of the Mediterranean islands may not have been modern humans at all. Instead, he says evidence has been found that shows that they might have been Neanderthals, or Homo Erectus. Recent excavations on Crete have turned up artifacts that are thought to be 110,000 years old, for example, and a stone axe was found that is believed to have been made on the same island as far back as 170,000 years ago. Since modern humans are believed to have come into being roughly 100,000 to 200,000 years ago, the possibility exists that such artifacts were left behind by an early ancestor or cousin.

Science 16 November 2012: Vol. 338 no. 6109 pp. 895-897 DOI: 10.1126/science.1228880

Mediterranean Island Voyages

Alan Simmons

Some of the classical world's most innovative cultures developed on Mediterranean islands, but their earlier human use is poorly known. The islands, particularly those further from the mainland such as Crete and Cyprus, were thought to have been first colonized about 9000 years ago by late Neolithic agriculturalists with domesticated resources. Until about 20 years ago, claims of earlier, pre-Neolithic occupations on any of the islands did not stand up to critical scrutiny (1), but current investigations are challenging these perceptions. Discoveries on Cyprus, Crete, and some Ionian islands suggest seafaring abilities by pre-Neolithic peoples, perhaps extending back to Neanderthals or even earlier hominins. In Cyprus, Neolithic sites have been documented that are nearly as early as those on the mainland.

Link

Effect of genomic inversions on population genetic parameters

Genetics doi: 10.1534/genetics.112.145599

The Effect of Genomic Inversions on Estimation of Population Genetic Parameters from SNP Data

Nafisa-Katrin Seich al Basatena et al.

In recent years it has emerged that structural variants have a substantial impact on genomic variation. Inversion polymorphisms represent a significant class of structural variant, and despite the challenges in their detection, data on inversions in the human genome are increasing rapidly. Statistical methods for inferring parameters such as the recombination rate and selection coefficient have generally been developed without accounting for the presence of inversions. Here we exploit new software for simulating inversions in population genetic data, invertFREGENE, to assess the potential impact of inversions on such methods. Using data simulated by invertFREGENE, as well as real data from several sources, we test whether large inversions have a disruptive effect on widely applied population genetics methods for inferring recombination rates, for detecting selection, and for controlling for population structure in genome-wide association studies (GWAS). We find that recombination rates estimated by LDhat are biased downward at inversion loci relative to the true contemporary recombination rates at the loci but that recombination hotspots are not falsely inferred at inversion breakpoints as may have been expected. We find that the iHS method for detecting selection appears robust to the presence of inversions. Finally, we observe a strong bias on the genome-wide results of principle components analysis (PCA), used to control for population structure in GWAS, in the presence of even a single large inversion, confirming the necessity to thin SNPs by LD at large physical distances in order to obtain unbiased results.

Link

First Polynesian settlement: 2838±8 BP

PLoS ONE 7(11): e48769. doi:10.1371/journal.pone.0048769

High Precision U/Th Dating of First Polynesian Settlement

David Burley et al.

Previous studies document Nukuleka in the Kingdom of Tonga as a founder colony for first settlement of Polynesia by Lapita peoples. A limited number of radiocarbon dates are one line of evidence supporting this claim, but they cannot precisely establish when this event occurred, nor can they afford a detailed chronology for sequent occupation. High precision U/Th dates of Acropora coral files (abraders) from Nukuleka give unprecedented resolution, identifying the founder event by 2838±8 BP and documenting site development over the ensuing 250 years. The potential for dating error due to post depositional diagenetic alteration of ancient corals at Nukuleka also is addressed through sample preparation protocols and paired dates on spatially separated samples for individual specimens. Acropora coral files are widely distributed in Lapita sites across Oceania. U/Th dating of these artifacts provides unparalleled opportunities for greater precision and insight into the speed and timing of this final chapter in human settlement of the globe.

Link

TreeMix paper "officially" published

~8 months after the paper was pre-published in Nature Precedings, it is also "officially" published in PLoS Genetics. In the meantime, I count 18 uses of the label TreeMix in my blog, which includes both uses of the treemix software itself and its auxiliary threepop and fourpop programs; I also wrote a small script that converts ADMIXTURE output into TreeMix format, and generally had a lot of fun using it. I'm glad I didn't have to wait 8 months to learn that something like TreeMix existed.

In the grand scheme of things, an 8-month head start may not be much, but consider that perhaps someone else might either have a use for TreeMix or the desire to build on it, and if they decide to make their research available prior to official publication, then, perhaps an additional few months might be gained. And, if someone else still decides to follow up on them then...

There are many arguments for immediate publication of research results, but I think that the potential for speeding up scientific progress is one of the best ones.

In the old days, it was really necessary to impose a delay between the time when a scientist placed a final full stop to his paper and the time it appeared on another scientist's desk: publication involved significant expenses of paper, ink, and labor, so the frivolous or erroneous had to be weeded out; dissemination involved expensive transport by carriage or boat; storage involved a building, and bookshelves, and additional cost.

All these costs have shrunk to insignificance; imposing delays to research dissemination now accounts to little more than placing a sleep() call in the unending loop of scientific advancement. And, the one remaining argument for post-review publication ("weeding out the frivolous or erroneous") carries little weight: pre-review publication is a better guarantor of quality by exposing research to many more eyes and minds that may scrutinize it more carefully, having rid themselves of the idea that "if it's published it must be good".

PLoS Genet 8(11): e1002967. doi:10.1371/journal.pgen.1002967

Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

Joseph K. Pickrell1, Jonathan K. Pritchard

Many aspects of the historical relationships between populations in a species are reflected in genetic data. Inferring these relationships from genetic data, however, remains a challenging task. In this paper, we present a statistical model for inferring the patterns of population splits and mixtures in multiple populations. In our model, the sampled populations in a species are related to their common ancestor through a graph of ancestral populations. Using genome-wide allele frequency data and a Gaussian approximation to genetic drift, we infer the structure of this graph. We applied this method to a set of 55 human populations and a set of 82 dog breeds and wild canids. In both species, we show that a simple bifurcating tree does not fully describe the data; in contrast, we infer many migration events. While some of the migration events that we find have been detected previously, many have not. For example, in the human data, we infer that Cambodians trace approximately 16% of their ancestry to a population ancestral to other extant East Asian populations. In the dog data, we infer that both the boxer and basenji trace a considerable fraction of their ancestry (9% and 25%, respectively) to wolves subsequent to domestication and that East Asian toy breeds (the Shih Tzu and the Pekingese) result from admixture between modern toy breeds and “ancient” Asian breeds. Software implementing the model described here, called TreeMix, is available at http://treemix.googlecode.com.

Link

500 thousand year old spear tips

I'll add the abstract when I see it on the Science website.

Archaeologists identify spear tips used in hunting a half-million years ago

TORONTO, ON – A University of Toronto-led team of anthropologists has found evidence that human ancestors used stone-tipped weapons for hunting 500,000 years ago – 200,000 years earlier than previously thought. 

"This changes the way we think about early human adaptations and capacities before the origin of our own species," says Jayne Wilkins, a PhD candidate in the Department of Anthropology at the University of Toronto and lead author of a new study in Science. "Although both Neandertals and humans used stone-tipped spears, this is the first evidence that the technology originated prior to or near the divergence of these two species," says Wilkins. 

... 

Wilkins and colleagues from Arizona State University and the University of Cape Town examined 500,000-year-old stone points from the South African archaeological site of Kathu Pan 1 and determined that they had functioned as spear tips.

Science 16 November 2012: Vol. 338 no. 6109 pp. 942-946 DOI: 10.1126/science.1227608

Evidence for Early Hafted Hunting Technology

Jayne Wilkins1 et al.

ABSTRACT

Hafting stone points to spears was an important advance in weaponry for early humans. Multiple lines of evidence indicate that ~500,000-year-old stone points from the archaeological site of Kathu Pan 1 (KP1), South Africa, functioned as spear tips. KP1 points exhibit fracture types diagnostic of impact. Modification near the base of some points is consistent with hafting. Experimental and metric data indicate that the points could function well as spear tips. Shape analysis demonstrates that the smaller retouched points are as symmetrical as larger retouched points, which fits expectations for spear tips. The distribution of edge damage is similar to that in an experimental sample of spear tips and is inconsistent with expectations for cutting or scraping tools. Thus, early humans were manufacturing hafted multicomponent tools ~200,000 years earlier than previously thought.

Link

Swat valley cemetery

A lost civilisation: 3,000-year-old cemetery discovered in Swat

The Italian Archaeological Mission on Wednesday discovered an ancient cemetery dating back thousands of years at Odigram, Swat — a site experts believe was built between 1500 BC to 500 BC.

...

A total of 23 graves have been excavated at the site that seems to be an ancient cemetery, indicating that they belonged to the pre-Buddhist era.

...

“It clearly indicates that Swat Valley was thickly populated at that time. Most probably they were the Dards (a group of people defined by linguistic similarities and not a common ethnic origin, predominantly found in Eastern Afghanistan) and in my view these Dards were somehow linked culturally to the people presently living in Kohistan and Kalash valleys,” revealed Massimo Vidale, a professor of Archaeology at University of Padua. “They probably spoke the Indo-European languages. We can say that the present culture of Kalash and Kohistan in Chitral valley can be linked with the ancient culture of Swat,” Vidale explained.

Pig genome + admixture into European wild boars

Of interest: 

The domestic pig (Sus scrofa) is a eutherian mammal and a member of the Cetartiodactyla order, a clade distinct from rodent and primates, that last shared a common ancestor with humans between 79 and 97 million years (Myr) ago1,2 (http://www.timetree.net). Molecular genetic evidence indicates that Sus scrofa emerged in South East Asia during the climatic fluctuations of the early Pliocene 5.3–3.5 Myr ago. Then, beginning ~10,000 years ago, pigs were domesticated in multiple locations across Eurasia3 (Frantz, L. A. F. et al., manuscript submitted).

also:

We found a clear signal for admixture between North Chinese and European populations of wild boars that we interpret as migrations across Eurasia during the later stage of the Pleistocene (Supplementary Table 24). Moreover, this hypothesis is further supported by the high value of concordance factor on the X chromosomes (Supplementary Table 20). The demographic analysis shows that the last glacial maximum (LGM)-induced bottleneck had similar magnitude in Europe and North China (Figure 2, main text). Together, these evidences suggest the existence of another (besides Asian + European) biogeographic zone for pigs, extending across North Eurasia. 

... 

There was a strong signal for admixture from Asian into European breeds. We found that European domestic breeds such as Landrace and Large White have a significant amount of Asian genetic material (Supplementary Table 24). This admixture is likely to be due to importation of Chinese breeds into Europe (especially UK) at the onset of the 'agricultural' revolution in the late 18th and 19th century.

Nature 491, 393–398 (15 November 2012) doi:10.1038/nature11622

Analyses of pig genomes provide insight into porcine demography and evolution

Martien A. M. Groenen et al.

For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ~1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.

Link

High altitude adaptation in Ethiopia

The anthropometric characteristics on pp. 49-50 may also be of interest. It seems Amhara highlanders are shorter, thinner, and  lighter than their co-ethnic lowlanders. Oromo highlanders, on the other hand, appear to be heavier and less thin. (for males).

arXiv:1211.3053 [q-bio.PE]

The genetic architecture of adaptations to high altitude in Ethiopia

Gorka Alkorta-Aranburu, Cynthia M. Beall, David B. Witonsky, Amha Gebremedhin, Jonathan K. Pritchard, Anna Di Rienzo

Although hypoxia is a major stress on physiological processes, several human populations have survived for millennia at high altitudes, suggesting that they have adapted to hypoxic conditions. This hypothesis was recently corroborated by studies of Tibetan highlanders, which showed that polymorphisms in candidate genes show signatures of natural selection as well as well-replicated association signals for variation in hemoglobin levels. We extended genomic analysis to two Ethiopian ethnic groups: Amhara and Oromo. For each ethnic group, we sampled low and high altitude residents, thus allowing genetic and phenotypic comparisons across altitudes and across ethnic groups. Genome-wide SNP genotype data were collected in these samples by using Illumina arrays. We find that variants associated with hemoglobin variation among Tibetans or other variants at the same loci do not influence the trait in Ethiopians. However, in the Amhara, SNP rs10803083 is associated with hemoglobin levels at genome-wide levels of significance. No significant genotype association was observed for oxygen saturation levels in either ethnic group. Approaches based on allele frequency divergence did not detect outliers in candidate hypoxia genes, but the most differentiated variants between high- and lowlanders have a clear role in pathogen defense. Interestingly, a significant excess of allele frequency divergence was consistently detected for genes involved in cell cycle control, DNA damage and repair, thus pointing to new pathways for high altitude adaptations. Finally, a comparison of CpG methylation levels between high- and lowlanders found several significant signals at individual genes in the Oromo.

Link

Hawaiian origins (Kim et al. 2012)

PLoS ONE 7(11): e47881. doi:10.1371/journal.pone.0047881

Population Genetic Structure and Origins of Native Hawaiians in the Multiethnic Cohort Study

Sung K. Kim et al.

The population genetic structure of Native Hawaiians has yet to be comprehensively studied, and the ancestral origins of Polynesians remain in question. In this study, we utilized high-resolution genome-wide SNP data and mitochondrial genomes of 148 and 160 Native Hawaiians, respectively, to characterize their population structure of the nuclear and mitochondrial genomes, ancestral origins, and population expansion. Native Hawaiians, who self-reported full Native Hawaiian heritage, demonstrated 78% Native Hawaiian, 11.5% European, and 7.8% Asian ancestry with 99% belonging to the B4 mitochondrial haplogroup. The estimated proportions of Native Hawaiian ancestry for those who reported mixed ancestry (i.e. 75% and 50% Native Hawaiian heritage) were found to be consistent with their self-reported heritage. A significant proportion of Melanesian ancestry (mean = 32%) was estimated in 100% self-reported Native Hawaiians in an ADMIXTURE analysis of Asian, Melanesian, and Native Hawaiian populations of K = 2, where K denotes the number of ancestral populations. This notable proportion of Melanesian admixture supports the “Slow-Boat” model of migration of ancestral Polynesian populations from East Asia to the Pacific Islands. In addition, approximately 1,300 years ago a single, strong expansion of the Native Hawaiian population was estimated. By providing important insight into the underlying population structure of Native Hawaiians, this study lays the foundation for future genetic association studies of this U.S. minority population.

Link

Dynamics of genetic and morphological variability within Neandertals (Hawks 2012)

A useful quote:

A problematic aspect of the idea of Levantine  Neandertals is that the very features that distinguish them from European Neandertals tend to  align them with modern humans. For example,  the Amud skeleton has stature and limb proportions that set it apart from European Neandertals,  but that fall within the range of variability of the  Skhul and Qafzeh skeletal remains. Trinkaus  (1995) considered the Near East, including  Shanidar and the Levantine samples, to include  two forms of hominins: “late archaic” and “modern” forms. He argued that the late archaic forms  in the Near East have no close connection to  European Neandertals, and that similar features  reflect mosaicism or generalized archaic morphology in both evolving populations 

Journal of Anthropological Sciences Vol. 90 (2012), pp. 1-17

Dynamics of genetic and morphological variability within Neandertals

John Hawks

Summary - Paleogenomics may suggest changes to the way anthropologists have discussed the dynamics and morphological diversity among Neandertals. Genetic comparisons show that later Neandertals had relatively low autosomal genetic variation compared to recent humans. The known mitochondrial sample from Neandertals covers a broader geographic and temporal range, and shows greater diversity. This review addresses how genetic data compare to morphological and archaeological evidence about Neandertal variation and dynamics. Traditional views emphasized the morphological differences between western and eastern Neandertal populations, and between early and later Neandertals. Genomes broadly support these groupings, without resolving the outstanding question of the affinities of specimens from southwest Asia. However, the pattern of genetic variation appears to reject a long, in situ transformation of Neandertal groups over time, suggesting instead a more rapid process of regional dispersal and partial population replacement. Archaeological indicators sample dynamics on a much finer timescale than morphological or genetic evidence, and point to dispersal and turnover among Neandertals on a regional scale. In this way, genetic evidence may provide a bridge between the timescales relevant to morphological and archaeological comparisons. New ways of looking at the morphology of Neandertals may yield a better picture of their interactions and movements.

Link (pdf)