March 06, 2015

Craniofacial plasticity in ancient Peru

Anthropologischer Anzeiger doi:10.1127/anthranz/2015/0458

Craniofacial plasticity in ancient Peru

Jessica H. Stone; Kristen Chew; Ann H. Ross; John W. Verano

Numerous studies have utilized craniometric data to explore the roles of genetic diversity and environment in human cranial shape variation. Peru is a particularly interesting region to examine cranial variation due to the wide variety of high and low altitude ecological zones, which in combination with rugged terrain have created isolated populations with vastly different physiological adaptations. This study examines seven samples from throughout Peru in an effort to understand the contributions of environmental adaptation and genetic relatedness to craniofacial variation at a regional scale. Morphological variation was investigated using a canonical discriminant analysis and Mahalanobis D2 analysis. Results indicate that all groups are significantly different from one another with the closest relationship between Yauyos and Jahuay, two sites that are located geographically close in central Peru but in very different ecozones. The relationship between latitude/longitude and face shape was also examined with a spatial autocorrelation analysis (Moran’s I) using ArcMap and show that there is significant spatial patterning for facial measures and geographic location suggesting that there is an association between biological variation and geographic location.


March 03, 2015

Oxhide ingots in Scandinavian rock art

Antiquity / Volume 89 / Issue 343 / February 2015, pp 191-209

Representations of oxhide ingots in Scandinavian rock art: the sketchbook of a Bronze Age traveller?

Johan Ling and Zofia Stos-Gale

Bronze Age trade networks across Europe and the Mediterranean are well documented; Baltic amber and bronze metalwork were particularly valued commodities. Here it is argued that demand for copper and tin led to changes in Scandinavian trade routes around 1600 BC, which can be linked to the appearance of figurative rock art images in southern Scandinavia. Images identified as oxhide ingots have been discovered in Sweden and suggest that people from Scandinavia were familiar with this characteristically Mediterranean trading commodity. Using trace element and lead isotope analysis, the authors argue that some bronze tools excavated in Sweden could have been made of Cypriot copper; these two discoveries suggest that Scandinavians were travelling to the Mediterranean, rather than acting through a middle man.


March 02, 2015

mtDNA from Lengyel culture in Poland

PLoS ONE 10(2): e0118316. doi:10.1371/journal.pone.0118316

Between the Baltic and Danubian Worlds: The Genetic Affinities of a Middle Neolithic Population from Central Poland

Wiesław Lorkiewicz et al.

For a long time, anthropological and genetic research on the Neolithic revolution in Europe was mainly concentrated on the mechanism of agricultural dispersal over different parts of the continent. Recently, attention has shifted towards population processes that occurred after the arrival of the first farmers, transforming the genetically very distinctive early Neolithic Linear Pottery Culture (LBK) and Mesolithic forager populations into present-day Central Europeans. The latest studies indicate that significant changes in this respect took place within the post-Linear Pottery cultures of the Early and Middle Neolithic which were a bridge between the allochthonous LBK and the first indigenous Neolithic culture of north-central Europe—the Funnel Beaker culture (TRB). The paper presents data on mtDNA haplotypes of a Middle Neolithic population dated to 4700/4600–4100/4000 BC belonging to the Brześć Kujawski Group of the Lengyel culture (BKG) from the Kuyavia region in north-central Poland. BKG communities constituted the border of the “Danubian World” in this part of Europe for approx. seven centuries, neighboring foragers of the North European Plain and the southern Baltic basin. MtDNA haplogroups were determined in 11 individuals, and four mtDNA macrohaplogroups were found (H, U5, T, and HV0). The overall haplogroup pattern did not deviate from other post-Linear Pottery populations from central Europe, although a complete lack of N1a and the presence of U5a are noteworthy. Of greatest importance is the observed link between the BKG and the TRB horizon, confirmed by an independent analysis of the craniometric variation of Mesolithic and Neolithic populations inhabiting central Europe. Estimated phylogenetic pattern suggests significant contribution of the post-Linear BKG communities to the origin of the subsequent Middle Neolithic cultures, such as the TRB.


Y chromosome mutation rate: 0.82x10-9

This is in Russian, but seems to be using Anzick-1, Ust-Ishim, K14 to get the mutation rate. Fu et al. who just used Ust Ishim got 0.7-0.9 for this which seems very similar, and also identical to the 0.82x10-9 value of Poznik et al. So, for the time being this seems like the value to use, although tighter confidence intervals would be welcome.

The Russian Journal of Genetic Genealogy (Русская версия), Vol 6, No 2 (2014)/Vol 7, No 1 (2015)

Константа скорости SNP мутаций Y-хромосомы по данным полного секвенирования

Дмитрий Адамов, Владимир Гурьянов, Сергей Каржавин, Владимир Таганкин, Вадим Урасин


Накопление данных тестирования BigY, FGC, с одной стороны, публикация сиквенсов Y-хромосомы древних образцов Anzick-1, Ust-Ishim, K14, с другой, дает возможность оценить среднюю скорость однонуклеотидных (SNP) мутаций. Авторы разработали собственный метод отбора истинных мутаций в современных и древних образцах и несколькими способами определили с высокой точностью константу скорости SNP мутаций - 0.82·10-9 в год на п.н.о. (95% CI: (0.70-0.94) ·10-9).


March 01, 2015

8,000 year old wheat in Britain

Britain received farming later than most of Europe, but perhaps it received one of the products of farming well before any farmers set foot on the island. I've always wondered if news (and at least some products) of the agricultural revolution spread far and wide before the revolution itself did. Did foragers at the northwestern end of Europe hear stories of the strange new people that had already appeared 8,000 years ago on the opposite end of the continent?

Was this an isolated incident or will we be finding wheat elsewhere in pre-farming Europe? 

Science 27 February 2015: Vol. 347 no. 6225 pp. 998-1001

Sedimentary DNA from a submerged site reveals wheat in the British Isles 8000 years ago 

Oliver Smith et al.

The Mesolithic-to-Neolithic transition marked the time when a hunter-gatherer economy gave way to agriculture, coinciding with rising sea levels. Bouldnor Cliff, is a submarine archaeological site off the Isle of Wight in the United Kingdom that has a well-preserved Mesolithic paleosol dated to 8000 years before the present. We analyzed a core obtained from sealed sediments, combining evidence from microgeomorphology and microfossils with sedimentary ancient DNA (sedaDNA) analyses to reconstruct floral and faunal changes during the occupation of this site, before it was submerged. In agreement with palynological analyses, the sedaDNA sequences suggest a mixed habitat of oak forest and herbaceous plants. However, they also provide evidence of wheat 2000 years earlier than mainland Britain and 400 years earlier than proximate European sites. These results suggest that sophisticated social networks linked the Neolithic front in southern Europe to the Mesolithic peoples of northern Europe.


Two observations on the ancestry of Armenians

I was thinking a bit on how to interpret the findings of the new Haber et al. preprint, and especially the idea that "29% of the Armenian ancestry may originate from an ancestral population best represented by Neolithic Europeans." I looked at the globe13 proportions, and strangely enough, I had estimated that the three Armenian samples (Armenian_D, Armenians, and Armenians_15_Y) have 28-29% of the Mediterranean component that is modal in Sardinians. This seems like a curious coincidence which has raised my confidence that Haber et al. is picking something real.

Looking back at my inferences of Armenian ancestry, it seems (according to globe13) to come completely from West_Asian, Mediterranean, and Southwest_Asian. The Mediterranean component seems real enough as it seems to match Sardinians/early European farmers well. I am not so sure about the Southwest Asian component which is modal in Yemen Jews and may represent population-specific drift in relatively recent Arabians. The West_Asian component is bimodal in Caucasus and Gedrosia, so it can't be the result of a very drifted population in either region (unless there is spooky action at a distance). 

Another curious finding is the lack of North_European in a latitudinal "column" of populations from the Yemen, through the Levant to the South Caucasus (Georgians and Armenians). It seems that North_European is the only one of the four major Caucasoid components that Armenians lack to any important degree. There is a rather abrupt change between the South Caucasus (~1%) and the North Caucasus (15-20%). It seems that the Greater Caucasus did act like a barrier to gene flow. The K=4 analysis of the same dataset that produced K=13 (globe13) also shows the same barrier: all three Armenian samples and Georgians have ~0% of "Amerindian" (which is surely correlated to "Ancient North Eurasian" ancestry and via it with North_European), but North Caucasians and Europeans have 4-10%.  It's clear that this influence did not cross the Greater Caucasus, as Armenians and Georgians lack it. 

February 27, 2015

The plight of the Assyrians

ISIS Onslaught Engulfs Assyrian Christians as Militants Destroy Ancient Art
ISTANBUL — The reports are like something out of a distant era of ancient conquests: entire villages emptied, with hundreds taken prisoner, others kept as slaves; the destruction of irreplaceable works of art; a tax on religious minorities, payable in gold.

A rampage reminiscent of Tamerlane or Genghis Khan, perhaps, but in reality, according to reports by residents, activist groups and the assailants themselves, a description of the modus operandi of the Islamic State’s self-declared caliphate this week. The militants have prosecuted a relentless campaign in Iraq and Syria against what have historically been religiously and ethnically diverse areas with traces of civilizations dating to ancient Mesopotamia.

The latest to face the militants’ onslaught are the Assyrian Christians of northeastern Syria, one of the world’s oldest Christian communities, some speaking a modern version of Aramaic, the language of Jesus.
The New York Times reporter need not have gone to so distant a past to find parallels to the plight of the Assyrians, as this is merely a repeat of what happened only a hundred years ago.

February 26, 2015

Estonian biocentre high coverage Y chromosome sequences and Turkic data

Courtesy of the good people of the Estonian biocentre:
The Y chromosome data seems particularly exciting (there is a spreadsheet of populations in the download directory). One of the weaknesses of the 1000 Genomes data was that it didn't have any populations between Tuscany and East/South Asia, and the new dataset seems to rectify that.

The Turkic dataset is probably the one used for the preprint The Genetic Legacy of the Expansion of Turkic-Speaking Nomads Across Eurasia. Since I overlooked this when it came out last summer, I'll post about it when the paper is published in a journal.

February 25, 2015

KNM-LH1: a 23,000 year old human from Kenya

From the paper:
KNM-LH 1 and other Pleistocene African specimens, all of which are potentially sampling candidate populations for dispersals across and out of Africa during the Late Pleistocene (12–15, 50, 59), differ substantially not only from recent Africans but also from individuals drawn from Holocene LSA archaeological sites. KNM-LH 1 and other Pleistocene African specimens (found with MSA and LSA artifacts) are also distinct from most EUP individuals.
Things are looking good for my Afrasian-Palaeoafrican admixture hypothesis which postulates that modern Africans are a mixture of "Afrasians" (a group of humans that also spilled over into Eurasia and/or back-migrated to Africa) and various groups of very divergent "Palaeoafrican" populations. In the context of this hypothesis, greater African genetic diversity is understood not as the result of a bottleneck of epic proportions during Out-of-Africa, but rather as a result of admixture between the two groups.

PNAS doi: 10.1073/pnas.1417909112

Late Pleistocene age and archaeological context for the hominin calvaria from GvJm-22 (Lukenya Hill, Kenya)

Christian A. Tryon et al.

Kenya National Museums Lukenya Hill Hominid 1 (KNM-LH 1) is a Homo sapiens partial calvaria from site GvJm-22 at Lukenya Hill, Kenya, associated with Later Stone Age (LSA) archaeological deposits. KNM-LH 1 is securely dated to the Late Pleistocene, and samples a time and region important for understanding the origins of modern human diversity. A revised chronology based on 26 accelerator mass spectrometry radiocarbon dates on ostrich eggshells indicates an age range of 23,576–22,887 y B.P. for KNM-LH 1, confirming prior attribution to the Last Glacial Maximum. Additional dates extend the maximum age for archaeological deposits at GvJm-22 to >46,000 y B.P. (>46 kya). These dates are consistent with new analyses identifying both Middle Stone Age and LSA lithic technologies at the site, making GvJm-22 a rare eastern African record of major human behavioral shifts during the Late Pleistocene. Comparative morphometric analyses of the KNM-LH 1 cranium document the temporal and spatial complexity of early modern human morphological variability. Features of cranial shape distinguish KNM-LH 1 and other Middle and Late Pleistocene African fossils from crania of recent Africans and samples from Holocene LSA and European Upper Paleolithic sites.


February 24, 2015

Mutation rate again (Lipson et al. 2015)

This estimate is in-between 1.2 and 2.5x10-8, the two most quoted values for this parameter. It seems like such an important number that I'm wondering if it would be possible to brute force estimate it. Maybe people who have whole genomes of parents-offspring should get together and do the mother of all meta-analyses to pin down this number.

From the paper:
For example, a recent method for estimating population split times from coalescent rates placed the median split of African from non-African populations at 60–80 ky and the split of Native Americans from East Asians at ∼ 20 ky, both assuming a per-generation mutation rate of 1.25 × 10−8 and an average generation interval of 30 years [28]. [...] Using our inferred rate also makes the dates more recent, but only by a factor of about 1.3 rather than 2, i.e., ∼ 46–61 and 15 ky (with some associated uncertainty both from the model and from our estimated rate), neither of which contradicts external evidence.
The first of these estimated splits overlaps the dates of estimated Neandertal admixture by the Ust' Ishim and Kostenki papers. For a variety of reasons that I've repeated ad nauseam, I think that the split of Africans from non-Africans first happened about 100ka with Out-of-Africa-into-Arabia. But, if there was back-migration into Africa, maybe this can be brought down. The 15ky value for the East Asian/Native America split seems too young: it's as late as could plausibly maintained for the colonization of the Americas, but the split of the two must have happened some time before that (because the ancestors of Native Americans and East Asians would have split long before a group of them made the crossing into the Americas).


Calibrating the Human Mutation Rate via Ancestral Recombination Density in Diploid Genomes

Mark Lipson et al.

The human mutation rate is an essential parameter for studying the evolution of our species, interpreting present-day genetic variation, and understanding the incidence of genetic disease. Nevertheless, our current estimates of the rate are uncertain. Classical methods based on sequence divergence have yielded significantly larger values than more recent approaches based on counting de novo mutations in family pedigrees. Here, we propose a new method that uses the fine-scale human recombination map to calibrate the rate of accumulation of mutations. By comparing local heterozygosity levels in diploid genomes to the genetic distance scale over which these levels change, we are able to estimate a long-term mutation rate averaged over hundreds or thousands of generations. We infer a rate of 1.65 +/- 0.10 x 10^(-8) mutations per base per generation, which falls in between phylogenetic and pedigree-based estimates, and we suggest possible mechanisms to reconcile our estimate with previous studies. Our results support intermediate-age divergences among human populations and between humans and other great apes.


February 23, 2015

Spread of Leprosy into Medieval Europe

Infection, Genetics and Evolution Volume 31, April 2015, Pages 250–256

A migration-driven model for the historical spread of leprosy in medieval Eastern and Central Europe

Helen D. Donoghue et al.

Leprosy was rare in Europe during the Roman period, yet its prevalence increased dramatically in medieval times. We examined human remains, with paleopathological lesions indicative of leprosy, dated to the 6th–11th century AD, from Central and Eastern Europe and Byzantine Anatolia. Analysis of ancient DNA and bacterial cell wall lipid biomarkers revealed Mycobacterium leprae in skeletal remains from 6th–8th century Northern Italy, 7th–11th century Hungary, 8th–9th century Austria, the Slavic Greater Moravian Empire of the 9th–10th century and 8th–10th century Byzantine samples from Northern Anatolia. These data were analyzed alongside findings published by others. M. leprae is an obligate human pathogen that has undergone an evolutionary bottleneck followed by clonal expansion. Therefore M. leprae genotypes and sub-genotypes give information about the human populations they have infected and their migration. Although data are limited, genotyping demonstrates that historical M. leprae from Byzantine Anatolia, Eastern and Central Europe resembles modern strains in Asia Minor rather than the recently characterized historical strains from North West Europe. The westward migration of peoples from Central Asia in the first millennium may have introduced different M. leprae strains into medieval Europe and certainly would have facilitated the spread of any existing leprosy. The subsequent decline of M. leprae in Europe may be due to increased host resistance. However, molecular evidence of historical leprosy and tuberculosis co-infections suggests that death from tuberculosis in leprosy patients was also a factor.


Scandinavian team looking for Indo-Europeans in Kazakhstan

An article in the Astana Times. If anyone has any additional information via Kazakh or Scandinavian media, or can find the press release referred to in the article, feel free to share.

  Scandinavian Team Searches for Indo-European Homeland through Kazakhstan DNA

A Scandinavian team has come to Kazakhstan in search of the common homeland of all Indo-European peoples, collecting bone fragments for analysis in the Centre for Geogenetics at the University of Copenhagen.

The researchers are looking for a genetic connection to match the linguistic connections that have already been drawn, Norwegian historian Sturla Ellingvag of the Explico Historical Research Foundation told The Astana Times on Feb. 20. “We’re trying to find a connection in science, in our DNA, to prove that there is indeed a connection, between, for example, Norwegians and the people in Kazakhstan. And also we are looking for a homeland, which is somewhere on the Caspian steppe, or in Russia, or some say it’s in Armenia or Ukraine. There are many different theories.”

The researchers collected about 120 Bronze and early Iron Age bone samples in total from Pavlodar, Kostanai and Karaganda during their week-long trip to Kazakhstan, from Feb. 14 – 21. Kazakhstan is fascinating, the researcher says, because it contains human remains that are “so far back on the DNA map.”

The 4,000 year old samples they’ve found have been very well preserved, Ellingvag said. “I can only speak from meeting archaeologists in Astana and here in Karaganda, but I’m very much impressed by the professionalism and also by the exhibitions they have,” he said.

The project to search for the ancestral homeland of the Indo-European peoples falls under the umbrella of a large grant from the Danish government and is being supported by the Kon-Tiki Museum in Oslo, Gotenburg University in Sweden and the University of Copenhagen in Denmark, which has one of the best historical DNA analysis labs in the world and which is where the analysis on the Kazakh remains will actually be done. Universities in Karaganda, Pavlodar and Kostanai are also involved.

The Kurgan hypothesis posits that the speakers of proto-Indo-European, the hypothesized common ancestor of the massive Indo-European language group, originally lived on the Pontiac-Caspian steppe, an area of land stretching from the Black Sea to the Caspian Sea and including parts of Russia, Ukraine and northwest Kazakhstan, beginning around the fifth millenium B.C. The hypothesis describes the spread of the language family from the steppe in every direction. “Kurgan” is a term for a type of burial mound common in the Caucasus, across Kazakhstan and beyond.

“Two thousand years ago, we started having Kurgan graves in Scandinavia,” said Ellingvag. The commonalities between burial mounds in Norway and Scythian/Saka mounds in Kazakhstan are striking, he said. “[The Scythian people] had these ornaments, these animal ornaments, which are very, very important in Scandinavian art … and the ornaments are actually quite similar, which is striking, it’s very special.”

The Kurgan hypothesis has been somewhat substantiated by genetic evidence so far, according to a press release by the Kon-Tiki Museum on the project, and advances in the technology for doing historical DNA research over the past few years means it is now possible to get closer to finding this genetic and linguistic starting point for most of the peoples of Europe.

“During the past 15 years, the Y-DNA R1a haplogroup has been characterised as a genetic signal of the Proto-Indo-Europeans. The theory now looks more plausible than ever, thanks to recent discoveries about its structure and phylogeography. Moreover, the Y-DNA R1a haplogroup has been found in numerous ancient remains supposedly belonging to early Indo-Europeans,” the press release explains.

A separate but related project is looking into the DNA of ancient horses. The Kurgan culture is credited with being the first to domesticate the horse.

The research team includes Ellingvag, Danish DNA-scientist Peter Damgaard and Bettina Heyerdahl, daughter of Norwegian archaeologist and explorer Thor Heyerdahl. They are also working with Kazakh researcher Emma Usmanova.
I could also find this Youtube video from this expedition.

Italic "Eteocretan" Sea peoples?

Stranger things have happened...

TALANTA XL-XLI (2008-2009), 151-172


Luuk de Ligt

The whereabouts of the homeland or homelands of the so-called Sea Peoples have been endlessly debated. This article re-examines this problem by looking at one of the ‘Eteocretan’ inscriptions from the town of Praisos. It is argued that this text is written in an Indo-European language belonging to the OscanUmbrian branch of the Italic language family. Based on this finding it is suggested that this language must have arrived in eastern Crete during the Late Bronze Age, when Mycenaean rulers recruited groups of mercenaries from Sicily, Sardinia and various parts of the Italian peninsula. When the Mycenaean state system collapsed around 1200 BC, some of these groups moved to the northern Aegean, to Cyprus and to the coastal districts of the Levant. It is also suggested that this reconstruction explains the presence of an Etruscan-speaking community in sixth-century-BC Lemnos. An interesting corollary of this theory is that the Sea Peoples were present in the Mycenaean world some considerable time before its collapse in the early twelfth century

Link (pdf)

February 22, 2015

Y chromosomes and Catalan surnames

Some really rich data in the supplements.

European Journal of Human Genetics advance online publication 18 February 2015; doi: 10.1038/ejhg.2015.14

Y-chromosome diversity in Catalan surname samples: insights into surname origin and frequency

Neus Solé-Morata et al.

The biological behavior of the Y chromosome, which is paternally inherited, implies that males sharing the same surname may also share a similar Y chromosome. However, socio-cultural factors, such as polyphyletism, non-paternity, adoption, or matrilineal surname transmission, may prevent the joint transmission of the surname and the Y chromosome. By genotyping 17 Y-STRs and 68 SNPs in ~2500 male samples that each carried one of the 50 selected Catalan surnames, we could determine sets of descendants of a common ancestor, the population of origin of the common ancestor, and the date when such a common ancestor lived. Haplotype diversity was positively correlated with surname frequency, that is, rarer surnames showed the strongest signals of coancestry. Introgression rates of Y chromosomes into a surname by non-paternity, adoption, and transmission of the maternal surname were estimated at 1.5−2.6% per generation, with some local variation. Average ages for the founders of the surnames were estimated at ~500 years, suggesting a delay between the origin of surnames (twelfth and thirteenth centuries) and the systematization of their paternal transmission. We have found that, in general, a foreign etymology for a surname does not often result in a non-indigenous origin of surname founders; however, bearers of some surnames with an Arabic etymology show an excess of North African haplotypes. Finally, we estimate that surname prediction from a Y-chromosome haplotype, which may have interesting forensic applications, has a ~60% sensitivity but a 17% false discovery rate.


Multiple opportunities for Out-of-Africa

Geology doi: 10.1130/G36401.1

Alluvial fan records from southeast Arabia reveal multiple windows for human dispersal

Ash Parton et al.

The dispersal of human populations out of Africa into Arabia was most likely linked to episodes of climatic amelioration, when increased monsoon rainfall led to the activation of drainage systems, improved freshwater availability, and the development of regional vegetation. Here we present the first dated terrestrial record from southeast Arabia that provides evidence for increased rainfall and the expansion of vegetation during both glacial and interglacial periods. Findings from extensive alluvial fan deposits indicate that drainage system activation occurred during Marine Isotope Stage (MIS) 6 (ca. 160–150 ka), MIS 5 (ca. 130–75 ka), and during early MIS 3 (ca. 55 ka). The development of active freshwater systems during these periods corresponds with monsoon intensity increases during insolation maxima, suggesting that humid periods in Arabia were not confined to eccentricity-paced deglaciations, and providing paleoenvironmental support for multiple windows of opportunity for dispersal out of Africa during the late Pleistocene.


February 20, 2015

Bronze Age mixing of multiple populations => Armenians (?)

As far as I can tell, the hypothesis of "several mixtures" comes from looking at many pairs of populations and seeing that different types of pairs seem like they mixed to make Armenians. Possibility (1) is that Armenians have multiple mixtures, and possibility (2) is that none of the sources work very well.

Hellenthal et al. did not find mixture in Armenians, but they worked with a different methodology and smaller sample size. Either, the N=173 sample size enabled detection of this admixture, or differences in methodology account for differences in conclusions. If true, the admixture dates in this paper would be some of the earliest discovered by looking at modern populations (without the help of ancient DNA).

The TreeMix analysis (Figure 4) is inconclusive about admixture from a population best represented by Neolithic Europeans. There is no plot of residuals in this figure, so this model with one migration event may not be adequate. Prior knowledge suggests that it isn't, as Pakistani and European populations have no admixture in Figure 4.

It's great that the authors will share their data!
As of this writing, the data is not "live"; it might appear when the paper is published.

bioRxiv doi:

Genetic evidence for an origin of the Armenians from Bronze Age mixing of multiple populations

Marc Haber et al.

The Armenians are a culturally isolated population who historically inhabited a region in the Near East bounded by the Mediterranean and Black seas and the Caucasus, but remain underrepresented in genetic studies and have a complex history including a major geographic displacement during World War One. Here, we analyse genome-wide variation in 173 Armenians and compare them to 78 other worldwide populations. We find that Armenians form a distinctive cluster linking the Near East, Europe, and the Caucasus. We show that Armenian diversity can be explained by several mixtures of Eurasian populations that occurred between ~3,000 and ~2,000 BCE, a period characterized by major population migrations after the domestication of the horse, appearance of chariots, and the rise of advanced civilizations in the Near East. However, genetic signals of population mixture cease after ~1,200 BCE when Bronze Age civilizations in the Eastern Mediterranean world suddenly and violently collapsed. Armenians have since remained isolated and genetic structure within the population developed ~500 years ago when Armenia was divided between the Ottomans and the Safavid Empire in Iran. Finally, we show that Armenians have higher genetic affinity to Neolithic Europeans than other present-day Near Easterners, and that 29% of the Armenian ancestry may originate from an ancestral population best represented by Neolithic Europeans.