April 17, 2014

mtDNA history of Oceania (Duggan et al. 2014)

AJHG doi:10.1016/j.ajhg.2014.03.014

Maternal History of Oceania from Complete mtDNA Genomes: Contrasting Ancient Diversity with Recent Homogenization Due to the Austronesian Expansion

Ana T. Duggan et al.

Archaeology, linguistics, and existing genetic studies indicate that Oceania was settled by two major waves of migration. The first migration took place approximately 40 thousand years ago and these migrants, Papuans, colonized much of Near Oceania. Approximately 3.5 thousand years ago, a second expansion of Austronesian-speakers arrived in Near Oceania and the descendants of these people spread to the far corners of the Pacific, colonizing Remote Oceania. To assess the female contribution of these two human expansions to modern populations and to investigate the potential impact of other migrations, we obtained 1,331 whole mitochondrial genome sequences from 34 populations spanning both Near and Remote Oceania. Our results quantify the magnitude of the Austronesian expansion and demonstrate the homogenizing effect of this expansion on almost all studied populations. With regards to Papuan influence, autochthonous haplogroups support the hypothesis of a long history in Near Oceania, with some lineages suggesting a time depth of 60 thousand years, and offer insight into historical interpopulation dynamics. Santa Cruz, a population located in Remote Oceania, is an anomaly with extreme frequencies of autochthonous haplogroups of Near Oceanian origin; simulations to investigate whether this might reflect a pre-Austronesian versus Austronesian settlement of the island failed to provide unequivocal support for either scenario.


April 14, 2014

Chronology of the earliest Upper Paleolithic in northern Iberia (Wood et al. 2014)

From a press release:
The main conclusion -"the scene of the meeting between a Neanderthal and a Cro-magnon does not seem to have taken place on the Iberian Peninsula"- is the same as the one that has been gradually reached over the last three years by different research groups when studying key settlements in Great Britain, Italy, Germany and France. "For 25 years we had been saying that Neanderthals and early humans lived together for 8,000-10,000 years. Today, we think that in Europe there was a gap between one species and the other and, therefore, there was no hybridation, which did in fact take place in areas of the Middle East," explained Arrizabalaga. The UPV/EHU professor is also the co-author of a piece of research published in 2012 that puts back the datings of the Neanderthals. "We did the dating again in accordance with the ultrafiltration treatment that eliminates rejuvenating contamination, remains of the Mousterian, the material culture belonging to the Neanderthals from sites in the south of the Peninsula. Very recent dates had been obtained in them -up to 29,000 years- but the new datings go back to 44,000 years older than the first dates that can be attributed to the Cro-Magnons," explained the UPV/EHU professor.

Journal of Human Evolution Volume 69, April 2014, Pages 91–109

The chronology of the earliest Upper Palaeolithic in northern Iberia: New insights from L'Arbreda, Labeko Koba and La Viña

R.E. Wood et al.

Since the late 1980s, northern Iberia has yielded some of the earliest radiocarbon dated Aurignacian assemblages in Western Europe, probably produced by anatomically modern humans (AMHs). This is at odds with its location furthest from the likely eastern entry point of AMHs, and has also suggested to some that the Châtelperronian resulted from cultural transfer from AMHs to Neanderthals. However, the accuracy of the early chronology has been extensively disputed, primarily because of the poor association between the dated samples and human activity. Here, we test the chronology of three sites in northern Iberia, L'Arbreda, Labeko Koba and La Viña, by radiocarbon dating ultrafiltered collagen from anthropogenically modified bones. The published dates from Labeko Koba are shown to be significant underestimates due to the insufficient removal of young contaminants. The early (c.44 ka cal BP [thousands of calibrated years before present]) Aurignacian chronology at L'Arbreda cannot be reproduced, but the reason for this is difficult to ascertain. The existing chronology of La Viña is found to be approximately correct. Together, the evidence suggests that major changes in technocomplexes occurred contemporaneously between the Mediterranean and Atlantic regions of northern Iberia, with the Aurignacian appearing around 42 ka cal BP, a date broadly consistent with the appearance of this industry elsewhere in Western Europe.


Neandertal admixture not African population structure

Genetics doi: 10.1534/genetics.114.162396

Neandertal Admixture in Eurasia Confirmed by Maximum-Likelihood Analysis of Three Genomes

Konrad Lohse and Laurent A. F. Frantz

Although there has been much interest in estimating histories of divergence and admixture from genomic data, it has proved difficult to distinguish recent admixture from long-term structure in the ancestral population. Thus, recent genome-wide analyses based on summary statistics have sparked controversy about the possibility of interbreeding between Neandertals and modern humans in Eurasia. Here we derive the probability of full mutational configurations in nonrecombining sequence blocks under both admixture and ancestral structure scenarios. Dividing the genome into short blocks gives an efficient way to compute maximum-likelihood estimates of parameters. We apply this likelihood scheme to triplets of human and Neandertal genomes and compare the relative support for a model of admixture from Neandertals into Eurasian populations after their expansion out of Africa against a history of persistent structure in their common ancestral population in Africa. Our analysis allows us to conclusively reject a model of ancestral structure in Africa and instead reveals strong support for Neandertal admixture in Eurasia at a higher rate (3.4−7.3%) than suggested previously. Using analysis and simulations we show that our inference is more powerful than previous summary statistics and robust to realistic levels of recombination.


IBD sharing between modern humans, Denisovans and Neandertals

bioRxiv doi:doi: 10.1101/003988

Sharing of Very Short IBD Segments between Humans, Neandertals, and Denisovans

Gundula Povysil, Sepp Hochreiter

We analyze the sharing of very short identity by descent (IBD) segments between humans, Neandertals, and Denisovans to gain new insights into their demographic history. Short IBD segments convey information about events far back in time because the shorter IBD segments are, the older they are assumed to be. The identification of short IBD segments becomes possible through next generation sequencing (NGS), which offers high variant density and reports variants of all frequencies. However, only recently HapFABIA has been proposed as the first method for detecting very short IBD segments in NGS data. HapFABIA utilizes rare variants to identify IBD segments with a low false discovery rate. We applied HapFABIA to the 1000 Genomes Project whole genome sequencing data to identify IBD segments which are shared within and between populations. Some IBD segments are shared with the reconstructed ancestral genome of humans and other primates. These segments are tagged by rare variants, consequently some rare variants have to be very old. Other IBD segments are also old since they are shared with Neandertals or Denisovans, which explains their shorter lengths compared to segments that are not shared with these ancient genomes. The Denisova genome most prominently matched IBD segments that are shared by Asians. Many of these segments were found exclusively in Asians and they are longer than segments shared between other continental populations and the Denisova genome. Therefore, we could confirm an introgression from Deniosvans into ancestors of Asians after their migration out of Africa. While Neandertal-matching IBD segments are most often shared by Asians, Europeans share a considerably higher percentage of IBD segments with Neandertals compared to other populations, too. Again, many of these Neandertal-matching IBD segments are found exclusively in Asians, whereas Neandertal-matching IBD segments that are shared by Europeans are often found in other populations, too. Neandertal-matching IBD segments that are shared by Asians or Europeans are longer than those observed in Africans. This hints at a gene flow from Neandertals into ancestors of Asians and Europeans after they left Africa. Interestingly, many Neandertal- or Denisova-matching IBD segments are predominantly observed in Africans - some of them even exclusively. IBD segments shared between Africans and Neandertals or Denisovans are strikingly short, therefore we assume that they are very old. This may indicate that these segments stem from ancestors of humans, Neandertals, and Denisovans and have survived in Africans.


April 09, 2014

Svante Paabo talk at NIH

A very interesting bit is from 18:30 and forward, in which he discusses the 45,000y BP modern human from Ust-Ishim. Here is a screenshot from this part of the talk (20:32):

According to Dr. Paabo, Ust-Ishim has longer Neandertal chunks than modern humans and this can be used to estimate that the admixture with Neandertals happened 331+/-99 generations before its time of 45,000y BP, or around 50-60,000y BP.

The coalescence of mtDNA haplogroups M and N has been estimated as ~50 and ~59ky BP respectively using modern human variation, so this seems quite compatible with that. This pretty much proves that there were modern humans in Eurasia before the Upper Paleolithic revolution and disproves Richard Klein's theory that modern humans together with UP technologies spread Out-of-Africa only after 50,000 years ago.

April 03, 2014

Where pastoralist met farmer and East met West (Spengler et al. 2014)

The paper's conclusion:
Archaeobotanical data from Central Eurasian pastoralist campsites have major implications for our understanding of late prehistoric agriculture across Asia. Sites like Tasbas and Begash illustrate the earliest acquisition of domesticated crops by mobile pastoralists and illustrate their capacity to participate in exchanges that bridged East Asian and Central Asian farming cultures by the early third millennium BC. Mobile pastoralists living in (southern) Central Asian alluvial fans and along the mountainous spine of Central Eurasia also integrated farming into their own domestic strategies (at least) by the mid second millenniumBC. Their pastoral mobility and the formation of extensive networks throughout the IAMC helped spread particular grain morphotypes and a mixed plant cohort of wheat, barley, millet and green peas through the mountains between Xinjiang, China and southwest Asia in the second millennium BC. The seasonal campsites of Begash, Tasbas, Ojakly and Site 1211/1219 are the earliest sites thus far reported to break down the strict polarization between nomads and farmers in prehistoric Central Eurasia. They also transform our comprehension of the vast arena of interaction that defines this region in ancient times. 

Proc. R. Soc. B doi:10.1098/rspb.2013.3382

Early agriculture and crop transmission among Bronze Age mobile pastoralists of Central Eurasia

Robert Spengler et al.

Archaeological research in Central Eurasia is exposing unprecedented scales of trans-regional interaction and technology transfer between East Asia and southwest Asia deep into the prehistoric past. This article presents a new archaeobotanical analysis from pastoralist campsites in the mountain and desert regions of Central Eurasia that documents the oldest known evidence for domesticated grains and farming among seasonally mobile herders. Carbonized grains from the sites of Tasbas and Begash illustrate the first transmission of southwest Asian and East Asian domesticated grains into the mountains of Inner Asia in the early third millennium BC. By the middle second millennium BC, seasonal camps in the mountains and deserts illustrate that Eurasian herders incorporated the cultivation of millet, wheat, barley and legumes into their subsistence strategy. These findings push back the chronology for domesticated plant use among Central Eurasian pastoralists by approximately 2000 years. Given the geography, chronology and seed morphology of these data, we argue that mobile pastoralists were key agents in the spread of crop repertoires and the transformation of agricultural economies across Asia from the third to the second millennium BC.


April 02, 2014

Neandertals gave Europeans lipid catabolism genes

Ann Gibbons explains in Did Europeans Get Fat From Neandertals?:
In the latest study, published online today in Nature Communications, Khaitovich and his international team analyzed the distribution of Neandertal gene variants in the genomes of 11 populations from Africa, Asia, and Europe.  
They found that Europeans inherited three times as many genes involved in lipid catabolism, the breakdown of fats to release energy, from Neandertals as did Asians. (As expected, Africans did not carry any of these Neandertal variants.) The difference in the number of Neandertal genes involved with lipid processing was “huge,” Khaitovich says. The study also offers another example of the lingering genetic legacy left in some people today by the extinct Neandertals. 
The team found that Europeans had differences in the concentration of various fatty acids in the brain that were not found in Asians or chimpanzees, which suggests they had evolved recently. The Europeans also showed differences in the function of enzymes that are known to be involved with the metabolism of fat in the brain.
Now the team is trying to figure out what the fatty acids do in the brain and how differences in their concentration might affect function. “We think it’s a very strong effect with very profound physiological changes,” Khaitovich says. “Otherwise, we wouldn’t see it in the brain tissue.” 
The article itself is open access.

Nature Communications 5, Article number: 3584 doi:10.1038/ncomms4584

Neanderthal ancestry drives evolution of lipid catabolism in contemporary Europeans

Ekaterina E. Khrameeva et al.

Although Neanderthals are extinct, fragments of their genomes persist in contemporary humans. Here we show that while the genome-wide frequency of Neanderthal-like sites is approximately constant across all contemporary out-of-Africa populations, genes involved in lipid catabolism contain more than threefold excess of such sites in contemporary humans of European descent. Evolutionally, these genes show significant association with signatures of recent positive selection in the contemporary European, but not Asian or African populations. Functionally, the excess of Neanderthal-like sites in lipid catabolism genes can be linked with a greater divergence of lipid concentrations and enzyme expression levels within this pathway, seen in contemporary Europeans, but not in the other populations. We conclude that sequence variants that evolved in Neanderthals may have given a selective advantage to anatomically modern humans that settled in the same geographical areas.


March 28, 2014

Oldest modern human genome from Siberia ~45 thousand years ago

Just a teaser from Ann Gibbons in Science:
In 2008, Siberian ivory carver Nikolay Peristov was searching for ancient mammoth tusks eroding from the banks of the Irtysh River in western Siberia, when he found fossilized bones instead. Back in his workshop in Omsk, he showed the bones to local paleontologist Aleksey Bondarev, who recognized a human thighbone. Bondarev in turn showed it to an anthropologist friend, and it was passed on up the chain to some of the world's top experts in human evolution. They dated it to 45,000 years ago, making it one of the oldest known modern humans in northern Asia and Europe.

Now, the bone has opened a window on the genetics of our species at a crucial moment: soon after their arrival in northern Eurasia. At a meeting* here last week, paleogeneticist Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, announced that his team has sequenced the thighbone's entire nuclear genome to high accuracy—an astonishing 42x coverage. "This is by far the oldest sequenced genome of a modern human," he said.

Because all living people in Europe and Asia carry roughly the same amount of Neandertal DNA, Pääbo's team thought that the interbreeding probably took place in the Middle East, as moderns first made their way out of Africa. Middle Eastern Neandertal sites are close to Skhul and Qafzeh, so some researchers suspected that those populations were the ones that mingled. But the team's analysis favors a more recent rendezvous. The femur belonged to an H. sapiens man who had slightly more Neandertal DNA, distributed in different parts of his genome, than do living Europeans and Asians. His Neandertal DNA is also concentrated into longer chunks than in living people, Pääbo reported. That indicates that the sequences were recently introduced: With each passing generation, any new segment of DNA gets broken up into shorter chunks as chromosomes from each parent cross over and exchange DNA. Both features of the Neandertal DNA in the femur suggest that the Ust-Ishim man lived soon after the interbreeding, which Pääbo estimated at 50,000 to 60,000 years ago.
The higher Neandertal DNA in the Ust-Ishim sample might be explainable by the negative selection against Neandertal material recently documented.  At 45kya, this sample is right around the time of the Early Upper Paleolithic at Kara-Bom in Siberia (and indeed anywhere), so this will be a hugely interesting sample when it is finally published.

Here is the program of the symposium on which this was apparently discussed (pdf). There seem to be quite a few interesting titles (but no abstracts).

March 27, 2014

Major new article on the deep origins of Y-haplogroup R1a (Underhill et al. 2014)

Five years ago, Underhill et al. (2009) presented a major advance in the study of haplogroup R1a. Much new knowledge was added in the interim by genetic genealogists and some scientists,  and now a major new paper by Peter Underhill comes to update our knowledge of this important and widely spread human lineage.

The shallow coalescence time within R1a will not surprise many genetic genealogists while its diversification in the vicinity of present-day Iran might. A ~5-7kyBP coalescence would make the expansion of R1a lineages presumably visible to future ancient DNA studies which will probably be the final arbiter of the veracity of the date estimate in this paper and its postulated place of origin.

I'll try to digest what the new information has to say about Eurasian prehistory, but in the meantime...

... I will, however, take some time to highlight the passing of the guard from Y-STRs to Y-SNPs which I had long ago anticipated. There is some lingering controversy about the substitution rate on the Y chromosome is, but it is hopeful that this will be resolved before not too long as the price of whole genome sequencing is always dropping and the samples sequenced in this study are probably the first of many to come.

In any case:
Our phylogeographic data lead us to conclude that the initial episodes of R1a-M420 diversification occurred in the vicinity of Iran and Eastern Turkey, and we estimate that diversification downstream of M417/Page7 occurred ~5800 years ago. This suggests the possibility that R1a lineages accompanied demic expansions initiated during the Copper, Bronze, and Iron ages, partially replacing previous Y-chromosome strata, an interpretation consistent with albeit limited ancient DNA evidence.54, 60 However, our data do not enable us to directly ascribe the patterns of R1a geographic spread to specific prehistoric cultures or more recent demographic events. High-throughput sequencing studies of more R1a lineages will lead to further insight into the structure of the underlying tree, and ancient DNA specimens will help adjudicate the molecular clock calibration. Together these advancements will yield more refined inferences about pre-historic dispersals of peoples, their material cultures, and languages.
It would of course be great to get some ancient DNA data from Iran and Eastern Turkey:
Among the 120 populations with sample sizes of at least 50 individuals and with at least 10% occurrence of R1a, just 6 met these criteria, and 5 of these 6 populations reside in modern-day Iran. Haplogroup diversities among the six populations ranged from 0.78 to 0.86 (Supplementary Table 4). Of the 24 R1a-M420*(xSRY10831.2) chromosomes in our data set, 18 were sampled in Iran and 3 were from eastern Turkey. Similarly, five of the six observed R1a1-SRY10831.2*(xM417/Page7) chromosomes were also from Iran, with the sixth occurring in a Kabardin individual from the Caucasus. Owing to the prevalence of basal lineages and the high levels of haplogroup diversities in the region, we find a compelling case for the Middle East, possibly near present-day Iran, as the geographic origin of hg R1a.
Also, the finding that...
The four subhaplogroups of Z93 (branches 9-M582, 10-M560, 12-Z2125, and 17-M780, L657) constitute a multifurcation unresolved by 10 Mb of sequencing; it is likely that no further resolution of this part of the tree will be possible with current technology. Similarly, the shared European branch has just three SNPs.
... seems to imply some Copper-to-Bronze Age guys did more than their fair share of fathering.

European Journal of Human Genetics , (26 March 2014) | doi:10.1038/ejhg.2014.50

The phylogenetic and geographic structure of Y-chromosome haplogroup R1a

Peter A Underhill et al.

R1a-M420 is one of the most widely spread Y-chromosome haplogroups; however, its substructure within Europe and Asia has remained poorly characterized. Using a panel of 16 244 male subjects from 126 populations sampled across Eurasia, we identified 2923 R1a-M420 Y-chromosomes and analyzed them to a highly granular phylogeographic resolution. Whole Y-chromosome sequence analysis of eight R1a and five R1b individuals suggests a divergence time of ~25 000 (95% CI: 21 300–29 000) years ago and a coalescence time within R1a-M417 of ~5800 (95% CI: 4800–6800) years. The spatial frequency distributions of R1a sub-haplogroups conclusively indicate two major groups, one found primarily in Europe and the other confined to Central and South Asia. Beyond the major European versus Asian dichotomy, we describe several younger sub-haplogroups. Based on spatial distributions and diversity patterns within the R1a-M420 clade, particularly rare basal branches detected primarily within Iran and eastern Turkey, we conclude that the initial episodes of haplogroup R1a diversification likely occurred in the vicinity of present-day Iran.


Haplogroup E and Afroasiatic

This is an open access article.

European Journal of Human Genetics advance online publication 26 March 2014; doi: 10.1038/ejhg.2014.41

Y-chromosome E haplogroups: their distribution and implication to the origin of Afro-Asiatic languages and pastoralism

Eyoab I Gebremeskel and Muntaser E Ibrahim

Archeological and paleontological evidences point to East Africa as the likely area of early evolution of modern humans. Genetic studies also indicate that populations from the region often contain, but not exclusively, representatives of the more basal clades of mitochondrial and Y-chromosome phylogenies. Most Y-chromosome haplogroup diversity in Africa, however, is present within macrohaplogroup E that seem to have appeared 21 000–32 000 YBP somewhere between the Red Sea and Lake Chad. The combined analysis of 17 bi-allelic markers in 1214 Y chromosomes together with cultural background of 49 populations displayed in various metrics: network, multidimensional scaling, principal component analysis and neighbor-joining plots, indicate a major contribution of East African populations to the foundation of the macrohaplogroup, suggesting a diversification that predates the appearance of some cultural traits and the subsequent expansion that is more associated with the cultural and linguistic diversity witnessed today. The proto-Afro-Asiatic group carrying the E-P2 mutation may have appeared at this point in time and subsequently gave rise to the different major population groups including current speakers of the Afro-Asiatic languages and pastoralist populations.


Origins of the Tharu

European Journal of Human Genetics advance online publication 26 March 2014; doi: 10.1038/ejhg.2014.36

Unravelling the distinct strains of Tharu ancestry

Gyaneshwer Chaubey et al.

The northern region of the Indian subcontinent is a vast landscape interlaced by diverse ecologies, for example, the Gangetic Plain and the Himalayas. A great number of ethnic groups are found there, displaying a multitude of languages and cultures. The Tharu is one of the largest and most linguistically diverse of such groups, scattered across the Tarai region of Nepal and bordering Indian states. Their origins are uncertain. Hypotheses have been advanced postulating shared ancestry with Austroasiatic, or Tibeto-Burman-speaking populations as well as aboriginal roots in the Tarai. Several Tharu groups speak a variety of Indo-Aryan languages, but have traditionally been described by ethnographers as representing East Asian phenotype. Their ancestry and intra-population diversity has previously been tested only for haploid (mitochondrial DNA and Y-chromosome) markers in a small portion of the population. This study presents the first systematic genetic survey of the Tharu from both Nepal and two Indian states of Uttarakhand and Uttar Pradesh, using genome-wide SNPs and haploid markers. We show that the Tharu have dual genetic ancestry as up to one-half of their gene pool is of East Asian origin. Within the South Asian proportion of the Tharu genetic ancestry, we see vestiges of their common origin in the north of the South Asian Subcontinent manifested by mitochondrial DNA haplogroup M43.


March 16, 2014

Lactase persistence and pastoralism in Africa

AJHG doi:10.1016/j.ajhg.2014.02.009

Genetic Origins of Lactase Persistence and the Spread of Pastoralism in Africa

Alessia Ranciaro et al.

In humans, the ability to digest lactose, the sugar in milk, declines after weaning because of decreasing levels of the enzyme lactase-phlorizin hydrolase, encoded by LCT. However, some individuals maintain high enzyme amounts and are able to digest lactose into adulthood (i.e., they have the lactase-persistence [LP] trait). It is thought that selection has played a major role in maintaining this genetically determined phenotypic trait in different human populations that practice pastoralism. To identify variants associated with the LP trait and to study its evolutionary history in Africa, we sequenced MCM6 introns 9 and 13 and ∼2 kb of the LCT promoter region in 819 individuals from 63 African populations and in 154 non-Africans from nine populations. We also genotyped four microsatellites in an ∼198 kb region in a subset of 252 individuals to reconstruct the origin and spread of LP-associated variants in Africa. Additionally, we examined the association between LP and genetic variability at candidate regulatory regions in 513 individuals from eastern Africa. Our analyses confirmed the association between the LP trait and three common variants in intron 13 (C-14010, G-13907, and G-13915). Furthermore, we identified two additional LP-associated SNPs in intron 13 and the promoter region (G-12962 and T-956, respectively). Using neutrality tests based on the allele frequency spectrum and long-range linkage disequilibrium, we detected strong signatures of recent positive selection in eastern African populations and the Fulani from central Africa. In addition, haplotype analysis supported an eastern African origin of the C-14010 LP-associated mutation in southern Africa.


Back-migration of Yeniseian into Asia from Beringia

PLOS One DOI: 10.1371/journal.pone.0091722

Linguistic Phylogenies Support Back-Migration from Beringia to Asia

Mark A. Sicoli, Gary Holton

Recent arguments connecting Na-Dene languages of North America with Yeniseian languages of Siberia have been used to assert proof for the origin of Native Americans in central or western Asia. We apply phylogenetic methods to test support for this hypothesis against an alternative hypothesis that Yeniseian represents a back-migration to Asia from a Beringian ancestral population. We coded a linguistic dataset of typological features and used neighbor-joining network algorithms and Bayesian model comparison based on Bayes factors to test the fit between the data and the linguistic phylogenies modeling two dispersal hypotheses. Our results support that a Dene-Yeniseian connection more likely represents radiation out of Beringia with back-migration into central Asia than a migration from central or western Asia to North America.


March 10, 2014

Dark pigmentation of Eneolithic and Bronze Age kurgan groups from eastern Europe

This is a very exciting new study that seems to parallel some results from early west Europeans. The authors invoke selection as a possible cause for the massive change in frequency between the Bronze Age and present-day Ukrainians.

An invocation of selection as an explanation requires evidence population continuity, otherwise changes in allele frequency may involve migration of a new frequency-differentiated new population; for example, the massive change in pigmentation in North America over the last 500 years is not due to selection but to migration of Europeans. The authors cannot reject population continuity on the basis of mtDNA haplogroup frequencies, although autosomal data may be more informative for that purpose.

In any case, the fact that the limited sample from western Europe and the much more extensive sample from eastern Europe both show a darker pigmentation than modern Europeans does suggest that interesting changes happened in Europe over the last few thousand years and samples from more recent time periods may better determine the pace of this change.

From the paper:
In sum, a combination of selective pressures associated with living in northern latitudes, the adoption of an agriculturalist diet, and assortative mating may sufficiently explain the observed change from a darker phenotype during the Eneolithic/Early Bronze age to a generally lighter one in modern Eastern Europeans, although other selective factors cannot be discounted. The selection coefficients inferred directly from serially sampled data at these pigmentation loci range from 2 to 10% and are among the strongest signals of recent selection in humans.

The classical Greeks did of course notice that the inhabitants of the north Pontic hinterland, collectively known as Scythians, were extraordinarily light-pigmented. This would imply that major pigmentation change occurred in the steppe over a time span of Bronze Age-Classical Antiquity rather than Bronze Age-present; this would imply even higher selection coefficients (if selection over a population exhibiting continuity is at play).

The Scythians were also thought to be recent arrivals from the east so it is not clear if they were descended from the Bronze Age population of eastern Europe; the crazy selection coefficients that would need to be assumed if there was indeed population continuity might imply that Herodotus got it right again, and the Scythians did in fact arrive from elsewhere. That would of course also imply that people from Central Asia and Siberia (where the Scythians may have come from) were originally lighter than Europeans which does find support from an older study on southern Siberian remains. Ironically, if that is the case, it would mean that the famous light-pigmented mummies of different parts of Inner Asia may not be long-lost European descendants -- as it has sometimes been presumed on the basis of modern-day clines of pigmentation. As usual, ancient DNA continues to surprise.

PNAS doi: 10.1073/pnas.1316513111

Direct evidence for positive selection of skin, hair, and eye pigmentation in Europeans during the last 5,000 y

Sandra Wilde et al.

Eye, hair, and skin pigmentation are highly variable in humans, particularly in western Eurasian populations. This diversity may be explained by population history, the relaxation of selection pressures, or positive selection. To investigate whether positive natural selection is responsible for depigmentation within Europe, we estimated the strength of selection acting on three genes known to have significant effects on human pigmentation. In a direct approach, these estimates were made using ancient DNA from prehistoric Europeans and computer simulations. This allowed us to determine selection coefficients for a precisely bounded period in the deep past. Our results indicate that strong selection has been operating on pigmentation-related genes within western Eurasia for the past 5,000 y.