PoBI paper BTFO

We next analyzed UK Biobank population structure in conjunction with ancient DNA samples. Modern European populations are known to have descended from three ancestral populations: Steppe, Mesolithic Europeans and Neolithic farmers 21,22 . We projected ancient samples from these three populations as well as ancient Saxon samples 24 onto the UK Biobank PCs (Figure 3, Supplementary Figure 4, see Online Methods). These populations were primarily differentiated along PC1 and PC3, indicating higher levels of Steppe ancestry in northern UK populations.

Additionally, the lack of any ancient sample correlation with PC2 suggests that Welsh populations are not differentially admixed with any ancient population in our data set, and likely underwent Welsh-specific genetic drift. We confirmed these findings by projecting pan- European POPRES 26 samples onto the UK Biobank PCs (see Online Methods, Supplementary Figure 5) noting that of the continental European populations, Russians (who have the most Steppe ancestry) lie on one side and Spanish and Italians (who have least) 22 lie on the other side along PC1 and PC3, and that none of the continental European populations projected onto the same regions as the Welsh on PC2 and PC5.

In addition to the impact of ancient Eurasian populations, we know that the genetics of the UK has been strongly impacted by Anglo-Saxon migrations since the Iron Age 24 , with the Angles arriving in eastern England and the Saxons in southern England. The Anglo-Saxons interbred with the native Celts, which explains much of the genetic landscape in the UK. We analyzed a variety of samples from Celtic (Scotland and Wales) and Anglo-Saxon (southern and eastern England) populations from modern Britain in conjunction with the PoBI samples 20 and 10 ancient Saxon samples from eastern England 24 in order to assess the relative amounts of Steppe ancestry. [. . .] We consistently obtained significantly positive f4 statistics, implying that both the modern Celtic samples and the ancient Saxon samples have more Steppe ancestry than the modern Anglo-Saxon samples from southern and eastern England. This indicates that southern and eastern England is not exclusively a genetic mix of Celts and Saxons. There are a variety of possible explanations, but one is that the present genetic structure of Britain, while subtle, is quite old, and that southern England in Roman times already had less Steppe ancestry than Wales and Scotland.

Population structure of UK Biobank and ancient Eurasians reveals adaptation at genes influencing blood pressure. Kevin Galinsky, Po-Ru Loh, Swapan Mallick, Nick J Patterson, Alkes L Price doi: http://dx.doi.org/10.1101/055855

Note: I find it unlikely the pattern they observe is a holdover from Roman times. I suspect it will turn out the decrement of Steppe ancestry in England stems from a continual trickle of continental genes into England over the past 1000 years (from which the fringes of the British Isles were comparatively isolated).

Also supports my impression that the Wellcome Trust paper still overestimated the degree of Iron Age British admixture in modern England (given that the authors had assumed a simple two-way admixture, while the authors of the above preprint provide evidence "southern and eastern England is not exclusively a genetic mix of Celts and Saxons").

Related:

• People of the British Isles project paper
• Iron Age and Anglo-Saxon genomes from East England reveal British migration history

Paleolithic European mtDNA

Pleistocene Mitochondrial Genomes Suggest a Single Major Dispersal of Non-Africans and a Late Glacial Population Turnover in Europe (free full text):

How modern humans dispersed into Eurasia and Australasia, including the number of separate expansions and their timings, is highly debated [ 1, 2 ]. Two categories of models are proposed for the dispersal of non-Africans: (1) single dispersal, i.e., a single major diffusion of modern humans across Eurasia and Australasia [ 3–5 ]; and (2) multiple dispersal, i.e., additional earlier population expansions that may have contributed to the genetic diversity of some present-day humans outside of Africa [ 6–9 ]. Many variants of these models focus largely on Asia and Australasia, neglecting human dispersal into Europe, thus explaining only a subset of the entire colonization process outside of Africa [ 3–5, 8, 9 ]. The genetic diversity of the first modern humans who spread into Europe during the Late Pleistocene and the impact of subsequent climatic events on their demography are largely unknown. Here we analyze 55 complete human mitochondrial genomes (mtDNAs) of hunter-gatherers spanning ∼35,000 years of European prehistory. We unexpectedly find mtDNA lineage M in individuals prior to the Last Glacial Maximum (LGM). This lineage is absent in contemporary Europeans, although it is found at high frequency in modern Asians, Australasians, and Native Americans. Dating the most recent common ancestor of each of the modern non-African mtDNA clades reveals their single, late, and rapid dispersal less than 55,000 years ago. Demographic modeling not only indicates an LGM genetic bottleneck, but also provides surprising evidence of a major population turnover in Europe around 14,500 years ago during the Late Glacial, a period of climatic instability at the end of the Pleistocene.

More ancient DNA from Britain supporting significant later Anglo-Saxon genomic impact

Genomic signals of migration and continuity in Britain before the Anglo-Saxons:

The purported migrations that have formed the peoples of Britain have been the focus of generations of scholarly controversy. However, this has not benefited from direct analyses of ancient genomes. Here we report nine ancient genomes (~1 ×) of individuals from northern Britain: seven from a Roman era York cemetery, bookended by earlier Iron-Age and later Anglo-Saxon burials. Six of the Roman genomes show affinity with modern British Celtic populations, particularly Welsh, but significantly diverge from populations from Yorkshire and other eastern English samples. They also show similarity with the earlier Iron-Age genome, suggesting population continuity, but differ from the later Anglo-Saxon genome. This pattern concords with profound impact of migrations in the Anglo-Saxon period. Strikingly, one Roman skeleton shows a clear signal of exogenous origin, with affinities pointing towards the Middle East, confirming the cosmopolitan character of the Empire, even at its northernmost fringes.

The full text is freely accessible. More:

Ancient sample ancestry within Britain

To place our ancient genomes within a detailed British context, we next plotted these in a background PCA using 3,075 published genotypes from British3, Irish23 and southern Netherlands samples24. The modern samples were analysed using SNP genotypes at ~250,000 loci and projected into a single plot using smartpca (Fig. 3a). As in Burton et al.3 the first component of the variation was informative for the structure within Britain. Given the close ancestral relationships between these populations and their well-known history of migrational exchange, a substantial overlap between regional groups was both expected and observed. However, by considering median values, one can see a clear progression from Irish samples at one pole through Scottish, Welsh, English to the Dutch cohort at the other extreme. In this plot the York Romans cluster centrally close to the modern Welsh median value, along with the Iron-Age genome. The local Anglo-Saxon is placed differently, closest to modern East Anglians between the English and Dutch medians.

This first component also offers an opportunity to compare within the English sample. Figure 3b shows a boxplot of PC1 values for each subsample and structure is evident, with higher median values in Eastern regions such as East Anglia, East Midlands, intermediate values in the southern and western parts and lower values in the north and northwest. This pattern is more clearly seen in a geographical plot of interpolated values (Fig. 5a). When the York Romans are compared together with each modern cohort, they are most similar to the Welsh distribution of PC1 values and differ significantly from all other regional groups, apart from those from North and Northwest England (Mann–Whitney test; Fig. 3b, Supplementary Note 2 and Supplementary Table 13). An interesting difference is the marked one between the Driffield Terrace ancient and contemporary Yorkshire samples (P=0.003), implying regional discontinuity. It is also worth noting that the PC1 coordinate of the Anglo-Saxon individual is closer to the median PC1 value of East Anglians, possibly reflecting a more pronounced contribution of Germanic immigrants to eastern British populations. However, we note the inherent uncertainty in drawing inference from a single sample.

Ancient Irish genomes confirm Bronze Age steppe incursion

Press release: First ancient Irish human genomes sequenced.

BBC: Ancient DNA sheds light on Irish origins.

Guardian: Origins of the Irish down to mass migration, ancient DNA confirms.

These settlers were followed by people, initially from the Pontic steppe of southern Russia, who knew how to mine for copper and work with gold, and who carried the genetic variant for a blood disorder called haemochromatosis, a hereditary genetic condition so common in Ireland that it is sometimes called Celtic disease.

These people also brought with them the inherited variation that permits the digestion of milk in maturity – much of the world becomes intolerant to the milk sugar lactose after infancy – and they may even have brought the language that became what is now Irish. Some of them, too, had blue eyes.

“There was a great wave of genome change that swept into Europe from above the Black Sea into Bronze Age Europe and we now know it washed all the way to the shores of its most westerly island,” said Dan Bradley, professor of population genetics at Trinity College Dublin.

“And this degree of genetic change invites the possibility of other associated changes, perhaps even the introduction of language ancestral to western Celtic tongues.”

The Dublin team and colleagues from Queens University Belfast report in the Proceedings of the National Academy of Sciences that the two great changes in European prehistory – the emergence of agriculture and the advance of metallurgy – were not just culture shifts: they came with new blood. An earlier population of hunter gatherers was successively overwhelmed by new arrivals. And in Ireland, these new settlers began to define a nation.

But the latest study throws more light on the birth of a nation. All three dead men from Rathlin Island carried what is now the most common type of Irish Y chromosome, inherited only from male forebears. [. . .]

And Lara Cassidy, a researcher in genetics at Trinity College Dublin and another co-author, said “Genetic affinity is strongest between Bronze Age genomes and modern Irish, Scottish and Welsh, suggesting establishment of central attributes of the insular Celtic genome 4,000 years ago.”

The PNAS paper: Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome

The Neolithic and Bronze Age transitions were profound cultural shifts catalyzed in parts of Europe by migrations, first of early farmers from the Near East and then Bronze Age herders from the Pontic Steppe. However, a decades-long, unresolved controversy is whether population change or cultural adoption occurred at the Atlantic edge, within the British Isles. We address this issue by using the first whole genome data from prehistoric Irish individuals. A Neolithic woman (3343–3020 cal BC) from a megalithic burial (10.3× coverage) possessed a genome of predominantly Near Eastern origin. She had some hunter–gatherer ancestry but belonged to a population of large effective size, suggesting a substantial influx of early farmers to the island. Three Bronze Age individuals from Rathlin Island (2026–1534 cal BC), including one high coverage (10.5×) genome, showed substantial Steppe genetic heritage indicating that the European population upheavals of the third millennium manifested all of the way from southern Siberia to the western ocean. This turnover invites the possibility of accompanying introduction of Indo-European, perhaps early Celtic, language. Irish Bronze Age haplotypic similarity is strongest within modern Irish, Scottish, and Welsh populations, and several important genetic variants that today show maximal or very high frequencies in Ireland appear at this horizon. These include those coding for lactase persistence, blue eye color, Y chromosome R1b haplotypes, and the hemochromatosis C282Y allele; to our knowledge, the first detection of a known Mendelian disease variant in prehistory. These findings together suggest the establishment of central attributes of the Irish genome 4,000 y ago.

Ancient DNA: Late Upper Paleolithic Swiss and Caucasus hunter-gatherers sequenced

Upper Palaeolithic genomes reveal deep roots of modern Eurasians (open access):

We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic–Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers ~45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers ~25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe ~3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.

Press release: 'Fourth strand' of European ancestry originated with hunter-gatherers isolated by Ice Age

Selection against Neanderthal introgression (two biorxiv preprints)

The Strength of Selection Against Neanderthal Introgression

Ivan Juric, Simon Aeschbacher, Graham Coop
doi: http://dx.doi.org/10.1101/030148

Hybridization between humans and Neanderthals has resulted in a low level of Neanderthal ancestry scattered across the genomes of many modern-day humans. After hybridization, on average, selection appears to have removed Neanderthal alleles from the human population. Quantifying the strength and causes of this selection against Neanderthal ancestry is key to understanding our relationship to Neanderthals and, more broadly, how populations remain distinct after secondary contact. Here, we develop a novel method for estimating the genome-wide average strength of selection and the density of selected sites using estimates of Neanderthal allele frequency along the genomes of modern-day humans. We confirm that East Asians had somewhat higher initial levels of Neanderthal ancestry than Europeans even after accounting for selection. We find that there are systematically lower levels of initial introgression on the X chromosome, a finding consistent with a strong sex bias in the initial matings between the populations. We find that the bulk of purifying selection against Neanderthal ancestry is best understood as acting on many weakly deleterious alleles. We propose that the majority of these alleles were effectively neutral-and segregating at high frequency-in Neanderthals, but became selected against after entering human populations of much larger effective size. While individually of small effect, these alleles potentially imposed a heavy genetic load on the early-generation human-Neanderthal hybrids. This work suggests that differences in effective population size may play a far more important role in shaping levels of introgression than previously thought.

The Genetic Cost of Neanderthal Introgression

Kelley Harris, Rasmus Nielsen
doi: http://dx.doi.org/10.1101/030387

Approximately 2-4% of the human genome is in non-Africans comprised of DNA intro- gressed from Neanderthals. Recent studies have shown that there is a paucity of introgressed DNA around functional regions, presumably caused by selection after introgression. This observation has been suggested to be a possible consequence of the accumulation of a large amount of Dobzhansky-Muller incompatibilities, i.e. epistatic effects between human and Neanderthal specific mutations, since the divergence of humans and Neanderthals approx. 400-600 kya. However, using previously published estimates of inbreeding in Neanderthals, and of the distribution of fitness effects from human protein coding genes, we show that the average Neanderthal would have had at least 40% lower fitness than the average human due to higher levels of inbreeding and an increased mutational load, regardless of the dominance coefficients of new mutations. Using simulations, we show that under the assumption of additive dominance effects, early Neanderthal/human hybrids would have experienced strong negative selection, though not so strong that it would prevent Neanderthal DNA from entering the human population. In fact, the increased mutational load in Neanderthals predicts the observed reduction in Neanderthal introgressed segments around protein coding genes, without any need to invoke epistasis. The simulations also predict that there is a residual Neanderthal derived mutational load in non-African humans, leading to an average fitness reduction of at least 0.5%. Although there has been much previous debate about the effects of the out-of-Africa bottleneck on mutational loads in non-Africans, the significant deleterious effects of Neanderthal introgression have hitherto been left out of this discussion, but might be just as important for understanding fitness differences among human populations. We also show that if deleterious mutations are recessive, the Neanderthal admixture fraction would gradually increase over time due to selection for Neanderthal haplotypes that mask human deleterious mutations in the heterozygous state. This effect of dominance heterosis might partially explain why adaptive introgression appears to be widespread in nature.

"Eight thousand years of natural selection in Europe" preprint - updated with Anatolian Neolithic and other data

Eight thousand years of natural selection in Europe

The arrival of farming in Europe around 8,500 years ago necessitated adaptation to new environments, pathogens, diets, and social organizations. While indirect evidence of adaptation can be detected in patterns of genetic variation in present-day people, ancient DNA makes it possible to witness selection directly by analyzing samples from populations before, during and after adaptation events. Here we report the first genome-wide scan for selection using ancient DNA, capitalizing on the largest genome-wide dataset yet assembled: 230 West Eurasians dating to between 6500 and 1000 BCE, including 163 with newly reported data. The new samples include the first genome-wide data from the Anatolian Neolithic culture, who we show were members of the population that was the source of Europe's first farmers, and whose genetic material we extracted by focusing on the DNA-rich petrous bone. We identify genome-wide significant signatures of selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height. [. . .]

Our sample of 26 Anatolian Neolithic individuals represents the first genome-wide ancient DNA data from the eastern Mediterranean. Our success at analyzing such a large number of samples is likely due to the fact that at the Barcin site–the source of 21 of the working samples–we sampled from the cochlea of the petrous bone 9 , which has been shown to increase the amount of DNA obtained by up to two orders of magnitude relative to teeth (the next-most-promising tissue) 3 . Principal component (PCA) and ADMIXTURE 10 analysis, shows that the Anatolian Neolithic samples do not resemble any present-day Near Eastern populations but are shifted towards Europe, clustering with Neolithic European farmers (EEF) from Germany, Hungary, and Spain 7 (Fig. 1b, Extended Data Fig. 2). Further evidence that the Anatolian Neolithic and EEF were related comes from the high frequency (47%; n=15) of Y-chromosome haplogroup G2a typical of ancient EEF samples 7 (Supplementary Data Table 1), and the low F ST (0.005-0.016) between Neolithic Anatolians and EEF (Supplementary Data Table 2). These results support the hypothesis 7 of a common ancestral population of EEF prior to their dispersal along distinct inland/central European and coastal/Mediterranean routes. The EEF are slightly more shifted to Europe in the PCA than are the Anatolian Neolithic (Fig. 1b) and have significantly more admixture from Western hunter-gatherers (WHG), shown by f 4 -statistics (|Z|>6 standard errors from 0) and negative f 3 -statistics (|Z|>4) 11 (Extended Data Table 3). We estimate that the EEF have 7- 11% more WHG admixture than their Anatolian relatives (Extended Data Fig. 2, Supplementary Information section 2).

On the presence of the "East Asian" EDAR variant in Scandinavian hunter-gatherers:

We find a surprise in six Scandinavian hunter-gatherers (SHG) from the Motala site in southern Sweden. In three out of six samples, we observe the haplotype carrying the derived allele of rs3827760 in the EDAR gene (Extended Data Fig. 5), which affects tooth morphology and hair thickness and has been the subject of a selective sweep in East Asia 24 , and today is at high frequency in East Asians and Native Americans. The EDAR derived allele is largely absent in present-day Europe except in Scandinavia, plausibly due to Siberian movements into the region millennia after the date of the Motala samples. The SHG have no evidence of East Asian ancestry 4,7 , suggesting that the EDAR derived allele may not have originated not in East Asians as previously suggested 24 . A second surprise is that, unlike closely related western hunter-gatherers, the Motala samples have predominantly derived pigmentation alleles at SLC45A2 and SLC24A5.

Polygenic selection on height in Europe:

We also tested for selection on complex traits. The best-documented example of this process in humans is height, for which the differences between Northern and Southern Europe have driven by selection 25 . To test for this signal in our data, we used a statistic that tests whether trait-affecting alleles are both highly correlated and more differentiated, compared to randomly sampled alleles 26 . We predicted genetic heights for each population and applied the test to all populations together, as well as to pairs of populations (Fig. 4). Using 180 height-associated SNPs 27 (restricted to 169 where we successfully targeted at least two chromosomes in each population), we detect a significant signal of directional selection on height (p=0.002). Applying this to pairs of populations allows us to detect two independent signals. First, the Iberian Neolithic and Chalcolithic samples show selection for reduced height relative to both the Anatolian Neolithic (p=0.042) and the Central European Early and Middle Neolithic (p=0.003). Second, we detect a signal for increased height in the steppe populations (p=0.030 relative to the Central European Early and Middle Neolithic). These results suggest that the modern South-North gradient in height across Europe is due to both increased steppe ancestry in northern populations, and selection for decreased height in Early Neolithic migrants to southern Europe. We do not observe any other significant signals of polygenetic selection in five other complex traits we tested: body mass index 28 (p=0.20), waist-to-hip ratio 29 (p=0.51), type 2 diabetes 30 (p=0.37), inflammatory bowel disease 21 (p=0.17) and lipid levels 16 (p=0.50).

Linguistics, Archaeology & Genetics conference abstracts

This conference, aimed at "integrating new evidence for the origin and spread of the Indo-European languages", will take place next week. Some abstracts (pdf):

Close genetic relationship of Neolithic Anatolians to early European farmers

Iosif Lazaridis 1,2 , Songül Alpaslan 3 , Daniel Fernandes 4 , Mario Nowak 4 , Kendra Sirak 4 , Nadin Rohland 1,2 , Swapan Mallick 1,2,5 , Kristin Stewardson 1,5 , Fokke Gerritsen 6 , Nick Patterson 2 , Ron Pinhasi 4, *, David Reich 1,2,5, *

We study 1.2 million genome-wide single nucleotide polymorphisms on a sample of 26 Neolithic individuals (~6,300 years BCE) from northwestern Anatolia. Our analysis reveals a homogeneous population that was genetically similar to early farmers from Europe (F ST =0.004±0.0003 and frequency of 60% of Y-chromosome haplogroup G2a). We model Early Neolithic farmers from central Europe and Iberia as a genetic mixture of ~90% Anatolians and ~10% European hunter-gatherers, suggesting little influence by Mesolithic Europeans prior to the dispersal of European farmers into the interior of the continent. Neolithic Anatolians differ from all present-day populations of western Asia, suggesting genetic changes have occurred in parts of this region since the Neolithic period. We suggest that the language spoken by the homogeneous Anatolian-European Neolithic farmers is unlikely to have been the same as that spoken by the Yamnaya steppe pastoralists whose ancestry was derived from eastern Europe and a different population from the Caucasus/Near East [Haak et al. 2015], and discuss implications for alternative models of Indo-European dispersals.

The Genetic History and Structure of Britain

Nick Patterson, Broad Institute, Boston and David Reich, Harvard Medical School and Broad Institute, Boston

The recently published paper on the genetic structure of Britain (Leslie et al. Nature 2015) has shown subtle genetic variation correlating with geography. Here we reexamine the evidence in the light of our understanding of the genetics of Ancient Europe and comment on some implications for how Indo-Europeans spread into Europe.

In search for initial Indo-European gene pool from genome-wide data on IE popula- tions as compared with their non-IE neighbors

Oleg Balanovsky, Vavilow Institue of General Genetics, Russian Academy of Sci- ences, Moscow

From Yamnaya to Bell Beakers: Mechanisms of Transmission in an Interconnected Europe, 3500–2000 BC

Volker Heyd, Universtiy Bristol, Bistol and University of Helsinki, Helsinki

Yamnaya Peoples in the East and Bell Beakers Users in the West are rightly seen as the apogees in a long-term process of individualisation, gender differentiation, warrior display and internationalisation/unification that fundamentally change the face of the European Continent from the mid fourth and throughout the third millennium BC. We can only approach the reasons why prehistoric peoples and cultures from regions across Europe, which were no more than marginally in touch before, join in the same emblematic pottery, new drinking habits, similar burial customs, anthropomorphic stelae, ostentatious display of weapons and other paraphernalia, and thus common values. However rather than seeing this development as an internal European progress I want to point to the importance of the Pontic-Caspian steppes, and a 2000 years lasting interaction scenario of infiltrating Suvorovo-Novodanilovka, Nizhnemikhailovka-Kvityana and Yamnaya peoples and populations with their more sedentary contemporaries in southeast Europe, the Carpathian basin and northeast of the Carpathian bow. A crucial part of this interaction –besides migrations and the exchange of genes and goods as recently highlighted in several publications not only in Nature and Science– is the forwarding of innovations in the sphere of subsistence economy. We see this archaeologically in a further importance of animal husbandry, with larger herds, specialised breeding and new forms of herding management in particular for cattle. This obviously sets in motion a substantial shift in general mobility patterns and of communication networks.

It is easily conceivable that this interaction must also have had a profound impact on the whole settlement organisation and people’s way-of-life, in consequence probably fundamentally affecting the basics of societies and thus challenging the whole system of ideas, imaginations, morale, symbols and terms – a new world-view and ultimately the base for a new language.

Pre-Indo-European speech carrying a Neolithic signature emanating from the Aegean

Guus Kroonen, Institute for Nordic Studies and Linguistics, Copenhagen University, Copenhagen

When different Indo-European speaking groups settled Europe, they did not arrive in terra nullius. Both from the perspective of the Anatolian hypothesis 1,2,3 and the Steppe hypothesis, 4,5,6 the carriers of Indo-European speech likely encountered existing populations that spoke dissimilar, unrelated languages. Relatively little is known about the Pre-Indo-European linguistic landscape of Europe, as the Indo-Europeanization of the continent caused a largely unrecorded, massive linguistic extinction event. However, when the different Indo-European groups entered Europe, they incorporated lexical material from Europe’s original languages into their own vocabularies. 7 By integrating these “natural samples” of Pre-Indo-European speech, the original European linguistic and cultural landscape can partly be reconstructed and matched against the Anatolia and the Steppe hypotheses. My results reveal that Pre-Indo-European speech contains a clear Neolithic signature emanating from the Aegean, 8 and thus patterns with the prehistoric migration of Europe’s first farming populations. 9,10,11 These results also imply that Indo-European speech came to Europe following a later migration wave, and therefore favor the Steppe Hypothesis as a likely scenario for the spread of the Proto-Indo-Europeans. 12

Autosomal DNA from Atapuerca pre- or proto-Neanderthals

DNA from Neandertal relative may shake up human family tree

The Sima people, who lived before Neandertals, were thought to have emerged in Europe. Yet their teeth, jaws, and large nasal cavities were among the traits that closely resembled those of Neandertals, according to a team led by paleontologist Juan-Luis Arsuaga of the Complutense University of Madrid. As a result, his team classified the fossils as members of Homo heidelbergensis, a species that lived about 600,000 to 250,000 years ago in Europe, Africa, and Asia. Many researchers have thought H. heidelbergensis gave rise to Neandertals and perhaps also to our species, H. sapiens, in the past 400,000 years or so. [. . .]

After 2 years of intense effort, paleogeneticist Matthias Meyer of the Max Planck Institute for Evolutionary Anthropology has finally sequenced enough nuclear DNA from fossils of a tooth and a leg bone from the pit to solve the mystery. [. . .] They scanned this DNA for unique markers found only in Neandertals or Denisovans or modern humans, and found that the two Sima fossils shared far more alleles—different nucleotides at the same address in the genome—with Neandertals than Denisovans or modern humans. “Indeed, the Sima de los Huesos specimens are early Neandertals or related to early Neandertals,” suggesting that the split of Denisovans and Neandertals should be moved back in time, Meyer reported at the meeting. [. . .]

“It resolves one controversy—that they’re in the Neandertal clade,” says paleoanthropologist Chris Stringer of the Natural History Museum in London. “But it’s not all good news: From my point of view, it pushes back the origin of H. sapiens from the Neandertals and Denisovans.” The possibility that humans were a distinct group so early shakes up the human family tree, promising to lead to new debate about when and where the branches belong.

Darren Curnoe points out:

What are the broader implications of the research for understanding the evolution of living humans?

First, the finding pushes the age of the shared human-Neanderthal ancestor well beyond 400,000 years ago, suggesting our species, H. sapiens, might also be at least this old.

Also, with the Atapuerca group living in Europe, it’s even possible that our species evolved in this or an adjacent region of Eurasia, and later migrated back into Africa.

And being close to the common ancestor, the Atapuerca fossils give us real insights into what it must have looked like and the ancestral body form of our own species.

The fossils from Europe, Asia and Africa from around this time are physically very diverse, with some researchers thinking they represent multiple species, only one of which could be the ancestor of living humans.

Question is, which one?

This new research suggests the European branch is closest among them all and deserves much more attention in this regard.

In contrast, we don’t know, and will doubtless ever know, whether Homo naledi had anything to do with the evolution of living humans, least of all whether its brain, mind or behaviour were anything like our own.

ASHG 2015: ancient Anatolians similar to European Neolithic farmers and distinct from modern Near Easterners

Genome-wide data on 34 ancient Anatolians identifies the founding population of the European Neolithic.

I. Lazaridis1,2 ; D. Fernandes3 ; N. Rohland1,2 ; S. Mallick1,2,4 ; K. Stewardson1,4 ; S. Alpaslan5 ; N. Patterson2 ; R. Pinhasi*3 ; D. Reich*1,2,4

1) Department of Genetics, Harvard Medical School, Boston, MA USA; 2) Broad Institute of MIT and Harvard, Cambridge, MA USA; 3) Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland; 4) Howard Hughes Medical Institute, Harvard Medical School, Boston, MA USA; 5) Independent physical anthropologist, Netherlands.

It has hitherto been difficult to obtain genome-wide data from the Near East. By targeting the inner ear region of the petrous bone for extraction [Pinhasi et al., PLoS One 2015] and using a genome-wide capture technology [Haak et al., Nature, 2015] we achieved unprecedented success in obtaining genome-wide data on more than 1.2 million single nucleotide polymorphism targets from 34 Neolithic individuals from Northwestern Anatolia (~6,300 years BCE), including 18 at greater than 1× coverage. Our analysis reveals a homogeneous population that is genetically a plausible source for the first farmers of Europe in the sense of (i) having a high frequency of Y-chromosome haplogroup G2a, and (ii) low Fst distances from early farmers of Germany (0.004 ± 0.0004) and Spain (0.014 ± 0.0009). Model-free principal components and model-based admixture analyses confirm a strong genetic relationship between Anatolian and European farmers. We model early European farmers as mixtures of Neolithic Anatolians and Mesolithic European hunter-gatherers, revealing very limited admixture with indigenous hunter-gatherers during the initial spread of Neolithic farmers into Europe. Our results therefore provide an overwhelming support to the migration of Near Eastern/Anatolian farmers into southeast and Central Europe around 7,000-6,500 BCE [Ammerman & Cavalli Sforza, 1984, Pinhasi et al., PLoS Biology, 2005]. Our results also show differences between early Anatolians and all present-day populations from the Near East, Anatolia, and Caucasus, showing that the early Anatolian farmers, just as their European relatives, were later demographically replaced to a substantial degree.

Ancient genomes from Iberia

Both papers are freely accessible.

A common genetic origin for early farmers from Mediterranean Cardial and Central European LBK cultures (pdf; supplementary material)

The spread of farming out of the Balkans and into the rest of Europe followed two distinct routes: an initial expansion represented by the Impressa and Cardial traditions, which followed the Northern Mediterranean coastline; and another expansion represented by the LBK tradition, which followed the Danube River into Central Europe. While genomic data now exist from samples representing the second migration, such data have yet to be successfully generated from the initial Mediterranean migration. To address this, we generated the complete genome of a 7,400 year-old Cardial individual (CB13) from Cova Bonica in Vallirana (Barcelona), as well as partial nuclear data from five others excavated from different sites in Spain and Portugal. CB13 clusters with all previously sequenced early European farmers and modern-day Sardinians. Furthermore, our analyses suggest that both Cardial and LBK peoples derived from a common ancient population located in or around the Balkan Peninsula. The Iberian Cardial genome also carries a discernible hunter-gatherer genetic signature that likely was not acquired by admixture with local Iberian foragers. Our results indicate that retrieving ancient genomes from similarly warm Mediterranean environments such as the Near East is technically feasible.

Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques (pdf; supplementary material)

The consequences of the Neolithic transition in Europe—one of the most important cultural changes in human prehistory—is a subject of great interest. However, its effect on prehistoric and modern-day people in Iberia, the westernmost frontier of the European continent, remains unresolved. We present, to our knowledge, the first genome-wide sequence data from eight human remains, dated to between 5,500 and 3,500 years before present, excavated in the El Portalón cave at Sierra de Atapuerca, Spain. We show that these individuals emerged from the same ancestral gene pool as early farmers in other parts of Europe, suggesting that migration was the dominant mode of transferring farming practices throughout western Eurasia. In contrast to central and northern early European farmers, the Chalcolithic El Portalón individuals additionally mixed with local southwestern hunter–gatherers. The proportion of hunter–gatherer-related admixture into early farmers also increased over the course of two millennia. The Chalcolithic El Portalón individuals showed greatest genetic affinity to modern-day Basques, who have long been considered linguistic and genetic isolates linked to the Mesolithic whereas all other European early farmers show greater genetic similarity to modern-day Sardinians. These genetic links suggest that Basques and their language may be linked with the spread of agriculture during the Neolithic. Furthermore, all modern-day Iberian groups except the Basques display distinct admixture with Caucasus/Central Asian and North African groups, possibly related to historical migration events. The El Portalón genomes uncover important pieces of the demographic history of Iberia and Europe and reveal how prehistoric groups relate to modern-day people.

Iron Age and Anglo-Saxon genomes from East England reveal British migration history

A preprint on some ancient DNA work in England is up. Researchers sequenced samples from seven early and middle Anglo-Saxon period and three late Iron Age (presumably Celtic) skeletons.

We  generated  a  principal  component  plot  of  the  ten  ancient  samples  together with  relevant  European  populations  selected  from  published  data 10,11  (Extended data  Figure  3).  The  ancient  samples  fall  within  the  range  of  modern  English  and Scottish  samples,  with  the  Iron  Age  samples  from  Hinxton  and  Linton  falling closer  to  modern  English  and  French  samples,  while  most  Anglo-­Saxon  era samples  are  closer  to  modern  Scottish  and  Norwegian  samples.  Overall,  though, population  genetic  differences  between  these  samples  at  common  alleles  are very  slight.

While  principal  component  analysis  can  reveal  relatively  old  population structure,  such  as  generated  from  long-­‐term  isolation-­‐by-­‐distance  models 12 , whole  genome  sequences  let  us  study  rare  variants  to  gain  insight  into  more recent  population  structure. [. . .]

There are  striking  differences  in  the  sharing  patterns  of  the  samples,  illustrated  by  the ratio  of  the  number  of  rare  alleles  shared  with  Dutch  individuals  to  the  number shared  with  Spanish  individuals  (Figure  2a).   The  middle  Anglo-­‐Saxon  samples from  Hinxton  (HS1,  HS2,  HS3)  share  relatively  more  rare  variants  with  modern Dutch  than  the  Iron  Age  samples  from  Hinxton  (HI1,  HI2)  and  Linton  (L).  The early  Anglo-­‐Saxon  samples  from  Oakington  are  more  diverse,  with  O1  and  O2 being  closer  to  the  middle  Anglo-­‐Saxon  samples,  O4  exhibiting  the  same  pattern as  the  Iron  Age  samples,  and  O3  showing  an  intermediate  level  of  allele  sharing, suggesting  mixed  ancestry.  The  differences  between  the  samples  are  highest  in low  frequency  alleles  and  decrease  with  increasing  allele  frequency.  This  is consistent  with  mutations  of  lower  frequency  on  average  being  younger, reflecting  more  recent  distinct  ancestry,  compared  with  higher  frequency mutations  reflecting  older  shared  ancestry.  

Comparing the relative number of rare alleles shared with the Dutch and Spanish samples, the researchers estimate 30% Anglo-Saxon admixture in the present-day East English and 20% in the Scottish and Welsh.

We  also  examined  using  the  same  method  30  modern  samples  from  the  UK10K project   16 ,  10  each  with  birthplaces  in  East  England,  Wales  and  Scotland.  Overall, these  samples  are  closer  to  the  Iron  Age  samples  than  to  the  Anglo-­‐Saxon  era samples  (Figure  2a).  There  is  a  small  but  significant  difference  between  the  three modern  British  sample  groups,  with  East  English  samples  sharing  slightly  more alleles  with  the  Dutch,  and  Scottish  samples  looking  more  like  the  Iron  Age samples.  To  quantify  the  ancestry  fractions,  we  fit  the  modern  British  samples with  a  mixture  model  of  ancient  components,  by  placing  all  the  samples  on  a linear  axis  of  relative  Dutch  allele  sharing  that  integrates  data  from  allele  counts one  to  five  (Figure  2b).  By  this  measure  the  East  England  samples  are  consistent with  30%  Anglo-­‐Saxon  ancestry  on  average,  with  a  spread  from  20%  to  40%, and  the  Welsh  and  Scottish  samples  are  consistent  with  20%  Anglo-­‐Saxon ancestry  on  average,  again  with  a  large  spread  (Supplementary  Table  2).  An alternative  and  potentially  more  direct  approach  to  estimate  these  fractions  is  to measure  rare  allele  sharing  directly  between  the  modern  British  and  the  ancient samples.  While  being  much  noisier  than  the  analysis  using  Dutch  and  Spanish outgroups,  this  yields  consistent  results  (Extended  Data  Figure  4  and Supplementary  Table  2).  In  summary,  this  analysis  suggests  that  only  20-­‐30%  of the  ancestry  of  modern  Britons  was  contributed  by  Anglo-­‐Saxon  immigrants, with  the  higher  number  in  East  England  closer  to  the  immigrant  source.  The difference  between  the  three  modern  groups  is  surprisingly  small  compared  to the  large  differences  seen  in  the  ancient  samples,  although  we  note  that  the UK10K  sample  locations  may  not  fully  reflect  historical  geographical  population structure  because  of  recent  population  mixing.

I have not thought about it deeply, but the rare variant comparison method used by the authors seems like it should produce reasonable results, at least for the relatively straightforward admixture estimates (with the understanding that Anglo-Saxons and Iron Age Britons are not the only two possible source populations for the modern British). I will say I was surprised to see Britain sharing a branch with Finland in this plot (even though it's a short one) to the exclusion of Denmark and Netherlands:

I've seen a few people interpret this study's estimates as a vindication of the ridiculous admixture estimates featured in the People of the British Isles project paper. For me, the ancient DNA results confirm my initial impression: the methods the POBI authors used to generate their estimates of ancient admixture were useless for divining what they thought they could divine.

That this 30% estimate informed by ancient DNA falls within the range of estimates suggested by the POBI authors is primarily a testament to the extremely broad range of possible admixture estimates they offered up (spanning 10% to 50%, depending on what one subjectively deemed "likely"). The POBI authors themselves were pushing for ~10% Anglo-Saxon admixture in the 19th-century Central and South English population (and if I recall correctly ~0% in the Welsh). POBI volunteers were primarily middle-aged or older people who could document four grandparents all born in particular locations. The UK10K modern British samples appearing in the ancient DNA paper are not screened in a similar manner, but are simply classified based on the sample donor's birth place. This means at least a couple generations (and probably disproportionately important generations, at that, as concerns mobility) of additional homogenization will have taken place.

So I have little doubt POBI samples from East Anglia (proxies for 19th-century East Anglians) would produce higher estimates of Anglo-Saxon admixture than "East England" UK10K samples (though apparently at present only microarray data, and not the whole genome sequencing data that would be necessary for the rare variant comparisons, is available for POBI samples). Levels up to 40% or higher Anglo-Saxon admixture in 19th-century East Anglians would not surprise me. And whatever the 19th-century number turns out to be, Anglo-Saxon admixture in England likely would have been progressively higher going back in time toward before the Norman conquest.

Gene flow into England over the past millennium (from Wales, Scotland, Ireland, and France) will have tended to make the English look less Anglo-Saxon and more "Iron Age". The Scandinavian component in the Normans and particularly their followers was probably outweighed by the French; and subsequently France probably remained one of the main sources of continental immigrants into England at least down to the Huguenots. It's said around 50,000 Huguenots came to England (against a 17th-century English population of around 5 million). 1% does not sound like an especially large wave (and it's certainly not by the standards of modern mass immigration), but these immigrants were concentrated in south and east England:

Huguenot settlement was concentrated in London and the south, East Anglia and the Fens

Even a relative trickle of continental immigrants over the past 1000 years might have had a noticeable cumulative effect on the English gene pool, and Scottish, Welsh, and Irish gene flow into England over the past millennium is likely even more significant. 24% of British claim Irish ancestry recent enough to be aware of, including 77% of those in London. Around 10% of the UK population is estimated to have an Irish grandparent.

Filtering recent Irish immigration into Scotland might also lead to higher estimates of Anglo-Saxon admixture there, as well (though recent English immigration too would need to be excluded). Recent English immigration into Wales may mean the 20% Anglo-Saxon admixture estimate is significantly inflated (though going off the 20% estimate for modern Welsh I would guess 19th-century Welsh speakers had at least ~10% Anglo-Saxon-like admixture).

According to the authors:

The  genetic  analyses  described  above  add  significantly  to  our  picture  of  Anglo-­Saxon  migration  into  Britain.   In  the  cemetery  at  Oakington  we  see  evidence  even in  the  early  Anglo-­Saxon  period  for  a  genetically  mixed  but  culturally  Anglo-­Saxon  community ^21,22 ,  in  contrast  to  claims  for  strong  segregation  between newcomers  and  indigenous  peoples ⁷ .  The  genomes  of  two  sequenced  individuals are  consistent  with  them  being  of  recent  immigrant  origin,  from  different continental  source  populations,  one  was  genetically  similar  to  native  Iron  Age samples,  and  the  fourth  was  an  admixed  individual,  indicating  intermarriage.   Despite  this,  their  graves  were  conspicuously  similar,  with  all  four  individuals buried  in  flexed  position,  and  with  similar  grave  furnishing.  Interestingly  the wealthiest  grave,  with  a  large  cruciform  brooch,  belonged  to  the  individual  of native  British  ancestry  (O4),  and  the  individual  without  grave  goods  was  one  of the  two  genetically  “foreign”  ones  (O2),  an  observation  consistent  with  isotope analysis  at  West  Heslerton  which  suggests  that  new  immigrants  were  frequently poorer   ^23,24 .  Given  this  mixing  apparent  around  500CE,  and  that  the  modern population  is  no  more  than  30%  of  Anglo-­Saxon  ancestry,  it  is  perhaps  surprising that  the  middle  Anglo-­Saxon  individuals  from  the  more  dispersed  field  cemetery in  Hinxton  all  look  genetically  consistent  with  unmixed  immigrant  ancestry.  One possibility  is  that  this  reflects  continued  immigration  until  at  least  the  Middle Saxon  period.  

In fact, there's nothing really inconsistent with the "Anglo-Saxon apartheid" paper in the mixed earlier samples and unmixed later samples. The Anglo-Saxon period samples tested here are all female. It's easy to imagine intermarriage rates may have been higher among the earliest Anglo-Saxon settlers, when their fraction of the total British population would have been smallest -- especially if females were to any degree underrepresented among the incoming Anglo-Saxons.

From the "Anglo-Saxon apartheid" paper (Evidence for an apartheid-like social structure in early Anglo-Saxon England):

We have only considered the effects of differences in ethnic reproductive advantage and inter-ethnic marriage rate on patterns of genetic variation. If there were no sex bias in the intermarriage rate, then we would expect these effects to be equal for the different genetic systems (mitochondrial DNA, Y-chromosome, X-chromosome, autosomes). However, part of the motivation for this study was to seek an explanation for the discrepancy between archaeological estimates of the size of the Anglo-Saxon migration (Härke 1998, 2002; Hills 2003) and estimates based on Y-chromosome data (Weale et al. 2002; Capelli et al. 2003). There are three further factors that could exacerbate replacement of indigenous Y-chromosomes. The first is that when intermarriage does occur the offspring may be more likely to assume the identity of the father, thus reducing the effective intermarriage rate, as it would affect patterns of Y-chromosome diversity. The second is that forced extra-marital matings are more likely to occur between Anglo-Saxon men and native British women than the reverse since, as the law codes of Ine indicate, the degree of punishment was determined by the social status of the victim. The third is based on the theory that relatively ‘good condition’ males tend to out-reproduce females of a similar condition, whereas relatively ‘poor condition’ females tend to out-reproduce their male counterparts (Trivers & Willard 1973). From this, a strategy of sex-biased parental investment, whereby relatively wealthy parents favour wealth transfer to their sons, should emerge (Hartung 1976). Such a phenomenon is supported by genealogical data (Boone 1986) and should lead to an asymmetric increase in the population frequency of Y-chromosomes carried by wealthy men, when compared to the other genetic systems.

The motivation for this study was to reconcile the discrepancy between, on the one hand, archaeological and historical ideas about the scale of the Anglo-Saxon immigration (Hills 2003), and on the other, estimates of the genetic contribution of the Anglo-Saxon immigrants to the modern English gene pool (Weale et al. 2002; Capelli et al. 2003). We have shown that this discrepancy can be resolved by the assumption of an apartheid-like social structure within a range of plausible values for interethnic marriage and socially driven reproductive advantage following immigration (Woolf 2004). Perhaps most strikingly, our model indicates that, by using plausible parameter values, the genetic contribution of an immigrant population can rise from less than 10% to more than 50% in as little as five generations, and certainly less than fifteen generations. Similar processes are likely to have shaped patterns of genetic variation in other ‘conquest societies’ of the period, and perhaps more recently (Carvajal-Carmona et al. 2000).

The ancestry and affiliations of Kennewick Man

Kennewick Man ancient DNA. The paper is openly accessible. Results pretty much as I expected.

We find that Kennewick Man is closer to modern Native Americans than to any other population worldwide.

The paper is marred by strained, politically-motivated attempts to tie Kennewick Man specifically to "the Confederated Tribes of the Colville Reservation (Colville), one of the five tribes claiming Kennewick Man". So those interested in aboriginal American population structure are probably better off ignoring much of the authors's narrative and looking directly at the data.

A major Indo-European contribution to the spread lactase persistence after all?

Ewen Callaway ("DNA data explosion lights up the Bronze Age: Population-scale studies suggest that migrants spread steppe language and technology."):

Ancient population genomics also offer insights on physical and physiological traits. Allentoft’s team found that the ability to digest milk into adulthood — nearly universal in northern Europeans today — was rare in Bronze Age Europeans, contradicting earlier claims that the trait helped early European farmers to gain calories from milk. Of the 101 sequenced individuals, the Yamnaya were most likely to have the DNA variation responsible for lactose tolerance, hinting that the steppe migrants might have eventually introduced the trait to Europe.

Related: More ancient DNA evidence of Indo-European mass migrations

More ancient DNA evidence of Indo-European mass migrations

Population genomics of Bronze Age Eurasia (figures; supplementary information):

The Bronze Age of Eurasia (around 3000–1000 BC) was a period of major cultural changes. However, there is debate about whether these changes resulted from the circulation of ideas or from human migrations, potentially also facilitating the spread of languages and certain phenotypic traits. We investigated this by using new, improved methods to sequence low-coverage genomes from 101 ancient humans from across Eurasia. We show that the Bronze Age was a highly dynamic period involving large-scale population migrations and replacements, responsible for shaping major parts of present-day demographic structure in both Europe and Asia. Our findings are consistent with the hypothesized spread of Indo-European languages during the Early Bronze Age. We also demonstrate that light skin pigmentation in Europeans was already present at high frequency in the Bronze Age, but not lactose tolerance, indicating a more recent onset of positive selection on lactose tolerance than previously thought.

Dienekes links to the raw data:

Investigation of Bronze Age in Eurasia by sequencing from 101 ancient human remains.

The Bronze Age (BA) of Eurasia (c. 3,000-1,000 years BC, 3-1 ka BC) was a period of major cultural changes. Earlier hunter-gathering and farming cultures in Europe and Asia were replaced by cultures associated with completely new perceptions and technologies inspired by early urban civilization. It remains debated if these cultural shifts simply represented the circulation of ideas or resulted from large-scale human migrations, potentially also facilitating the spread of Indo-European languages and certain phenotypic traits. To investigate this and the role of BA in the formation of Eurasian genetic structure, we used new methodological improvements to sequence low coverage genomes from 101 ancient humans (19 > 1X average depth) covering 3 ka BC to 600 AD from across Eurasia. We show that around 3 ka BC, Central and Northern Europe and Central Asia receive genetic input through people related to the Yamnaya Culture from the Pontic-Caspian Steppe, resulting in the formation of the Corded Ware Culture in Europe and the Afanasievo Culture in Central Asia. A thousand years later, genetic input from North-Central Europe into Central Asia gives rise to the Sintashta and Andronovo Cultures. During the late BA and Iron Age, the European-derived populations in Asia are gradually replaced by multi-ethnic cultures, of which some relate to contemporary Asian groups, while others share recent ancestry with Native Americans. Our findings are consistent with the hypothesised spread of Indo-European languages during early BA and reveal that major parts of the demographic structure of present-day Eurasian populations were shaped during this period. We also demonstrate that light skin pigmentation in Europeans was already present at high frequency during the BA, contrary to lactose tolerance, indicating a more recent onset of positive selection in the latter than previously believed.

DNA Deciphers Roots of Modern Europeans (NYT):

About 4,500 years ago, the final piece of Europe’s genetic puzzle fell into place. A new infusion of DNA arrived — one that is still very common in living Europeans, especially in central and northern Europe.

The closest match to this new DNA, both teams of scientists found, comes from skeletons found in Yamnaya graves in western Russia and Ukraine.

Archaeologists have long been fascinated by the Yamnaya, who left behind artifacts on the steppes of western Russia and Ukraine dating from 5,300 to 4,600 years ago. The Yamnaya used horses to manage huge herds of sheep, and followed their livestock across the steppes with wagons full of food and water.

It was an immensely successful way of life, allowing the Yamnaya to build huge funeral mounds for their dead, which they filled with jewelry, weapons and even entire chariots. [. . .]

The Copenhagen team’s study suggests that the Yamnaya didn’t just expand west into Europe, however. The scientists examined DNA from 4,700-year-old skeletons from a Siberian culture called the Afanasievo. It turns out that they inherited Yamnaya DNA, too.

Related: Massive migration from the steppe is a source for Indo-European languages in Europe; Penny starting to drop for academics

Autosomal DNA from 2,500-year old Etruscans

Dienekes points to a Biology of Genomes poster ("Assessment of Whole-Genome capture methodologies on single- and double-stranded ancient DNA libraries from Caribbean and European archaeological human remains") that includes a PCA with a few Etruscan samples (the poster text mentions two samples, but the PCA includes three).

If you imagine a line running from the American and British samples (CEU and GBR) through the Spanish (IBS) and Tuscan (TSI) samples, I expect Southern Italian samples would be out past Tuscans on this line and Middle Easterners would be beyond Southern Italians.

The Etruscan samples are shifted north and/or west relative to modern Tuscans (exactly the opposite of what we'd expect if Etruscans had predominantly Near Eastern origins). Since, in the absence of other gene flow, Italic, Celtic, and Germanic admixture in Tuscany would be expected to pull Tuscans north/west relative to Etruscans, it's clear Tuscany has been influenced by southern/eastern gene flow within the past 2,500 years (with potential sources including Roman slaves, medieval slaves, Jews, and southern Italians).

Massive migration from the steppe is a source for Indo-European languages in Europe

New preprint confirming what those of us who were paying attention were able to infer years ago:

We generated genome-wide data from 69 Europeans who lived between 8,000-3,000 years ago by enriching ancient DNA libraries for a target set of almost four hundred thousand polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies and to obtain new insights about the past. We show that the populations of western and far eastern Europe followed opposite trajectories between 8,000-5,000 years ago. At the beginning of the Neolithic period in Europe, ~8,000-7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary, and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a ~24,000 year old Siberian6. By ~6,000-5,000 years ago, a resurgence of hunter-gatherer ancestry had occurred throughout much of Europe, but in Russia, the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but from a population of Near Eastern ancestry. Western and Eastern Europe came into contact ~4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced ~3/4 of their ancestry to the Yamnaya, documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least ~3,000 years ago, and is ubiquitous in present-day Europeans. These results provide support for the theory of a steppe origin of at least some of the Indo-European languages of Europe. [. . .]

R1a and R1b are the most common haplogroups in many European populations today 18,19 , and our results suggest that they spread into Europe from the East after 3,000 BCE. Two hunter-gatherers from Russia included in our study belonged to R1a (Karelia) and R1b (Samara), the earliest documented ancient samples of either haplogroup discovered to date. These two hunter-gatherers did not belong to the derived lineages M417 within R1a and M269 within R1b that are predominant in Europeans today 18,19 , but all 7 Yamnaya males did belong to the M269 subclade 18 of haplogroup R1b.

Ust'-Ishim: Ancient DNA offers the first of what I expect in the coming years will be many disappointments to those emotionally invested in a SE Asian origin for K-M526

It's been asserted, on crude phylogeographic grounds, that K-M526 originated in South East Asia. A SE Asian origin for K-M526 is credible if you ignore the rest of the Y phylogeny, starting with K-M9, and all other available information. Sadly for Hector, reality, with this recent publication, has again chosen to side with "Eurocentrists".

I don't expect the Hectors will gracefully accept their beating, but to others the presence of a previously unknown branch of K(xLT) in Siberia 45,000 years ago should be a pretty clear signal that the idea of a 500 year sprint from West or Central Asia to an already-inhabited SE Asia, followed, after an indefinite pause, by a repopulating of the world from Sundaland (if not the islands of Wallacea), all while failing to carry any trace of Denisovan admixture back to the future civilized world is an unnecessary and improbable fantasy.

The cline of Denisovan admixture, from faint, highly-selected remnants in mainland SE Asia to maxima among Melanesians and Australian Aborigines, has always pointed to gene flow into the region after its initial settlement rather than out of it, the K-bearers being one obvious candidate for the major source of this dilution. I'd also say it's more likely than not that they (an M526-carrying population of Central Asian origin) are the ones who brought culture to Hector's ancestors.

Investigating Population History Using Temporal Genetic Differentiation

Investigating Population History Using Temporal Genetic Differentiation

The rapid advance of sequencing technology, coupled with improvements in molecular methods for obtaining genetic data from ancient sources, holds the promise of producing a wealth of genomic data from time-separated individuals. However, the population-genetic properties of time-structured samples have not been extensively explored. Here, we consider the implications of temporal sampling for analyses of genetic differentiation and use a temporal coalescent framework to show that complex historical events such as size reductions, population replacements, and transient genetic barriers between populations leave a footprint of genetic differentiation that can be traced through history using temporal samples. Our results emphasize explicit consideration of the temporal structure when making inferences and indicate that genomic data from ancient individuals will greatly increase our ability to reconstruct population history.

SMBE 2014: Genotyping of 390,000 SNPs in more than forty 3,000-9,000 year old humans from the ancient Russian steppe

Genotyping of 390,000 SNPs in more than forty 3,000-9,000 year old humans from the ancient Russian steppe

David Reich ^{1 ,2}, Nadin Rohland^{1 ,2}, Swapan Mallick^{1 ,2}, Iosif Lazaridis¹, Eadaoin Harney¹, Susanne Nordenfelt¹, Qiaomei Fu³, Matthias Meyer³, Dorcas Brown⁴, David Anthony⁴, Nick Patterson^2
1Harvard Medical School, Boston, MA, USA, ²Broad Institute of Harvard and MIT, Cambridge, MA, USA, ³Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, ⁴Hartwick College, Oneonta, NY, USA

 A central challenge in ancient DNA research is that for many bones that contain genuine DNA, the great majority of molecules in sequencing libraries are microbial. Thus, it has been impractical to carry out whole genome analyses of substantial numbers of ancient individuals.  We report a strategy for in-solution capture of ancient DNA from approximately 390,000 single nucleotide polymorphism (SNP) targets, adapting a method of Fu et al. PNAS 2013 who enriched a 40,000 year old DNA sample for the entire chromosome 21. Of the SNPs targets, the vast majority overlap the Affymetrix Human Origins array, allowing us to compare the ancient samples to a database of more than 2,700 present-day humans from 250 groups.
We applied the SNP capture as well as mitochondrial genome enrichment to a series of 65 bones dating to between 3,000-9,000 years ago from the Samara district of Russia in the far east of Europe, a region that has been suggested to be part of the Proto-Indo-European homeland. We successfully extracted nuclear data from 10-90% of targeted SNPs for more than 40 of the samples, and for all of these samples also obtained complete mitochondrial genomes. We report three key findings:

• Samples from the Samara region possess Ancient North Eurasian (ANE) admixture related to a recently published 24,000 year old Upper Paleolithic Siberian genome. This contrasts with both European agriculturalists and with European hunter-gatherers from Luxembourg and Iberia who had little such ancestry (Lazaridis et al. arXiv.org 2013). This suggests that European steppe groups may have been be implicated in the dispersal of ANE ancestry across Europe where it is currently pervasive.
• The mtDNA composition of the steppe population is primarily West Eurasian, in contrast with northwest Russian samples of this period (Der Sarkissian et al. PLoS Genetics 2013) where an East Eurasian presence is evident.
• Samara experienced major population turnovers over time: early samples (>6000 years) belong primarily to mtDNA haplogroups U4 and U5, typical of European hunter-gatherers but later ones include haplogroups W, H, T, I, K, J.

We report modeling analyses showing how the steppe samples may relate to ancient and present-day DNA samples from the rest of Europe, the Caucasus, and South Asia, thereby clarifying the relationship of steppe groups to the genetic, archaeological and linguistic transformations of the late Neolithic and Bronze ages.

[Via Greg Cochran.]