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Monday, December 28, 2015

Ancient genomes from Ireland point to population upheavals in Atlantic Europe during the Neolithic and Bronze Age

Open access at PNAS:

Abstract: 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.

Cassidy et al., Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome, PNAS, Published online before print December 28, 2015, doi: 10.1073/pnas.1518445113

Sunday, December 27, 2015

Next year the Armenian Plateau hypothesis will collapse

It's been a great year for population genetics and paleogenomics, and also for this blog. I churned out a lot of data in 2015 and managed to make a few discoveries that were subsequently confirmed, or at least, backed up by academia. For instance:

- first to show with ancient genomes that the Anglo-Saxons made a significant genetic impact on England. See here. Eventually confirmed here.

- first to show that the southern admixture in the Yamnaya pastoralists of the Early Bronze Age steppe was Georgian-related rather than Armenian-related. See here. Confirmed here.

- first to show that Anatolian Neolithic farmers were very similar to European Neolithic farmers, and lacked Ancient North Eurasian (ANE) ancestry. See here. Confirmed here.

- first to show using ancient DNA and formal statistics that South Asia experienced massive gene flow originating in Late Neolithic/Bronze Age Europe. See here. Backed up with my help here.

The fact that Caucasus hunter-gatherers (CHG) like Kotias are essentially an ideal fit for the southern ancestry in the Yamnaya is a big problem for the Armenian Plateau Indo-European homeland hypothesis. This TreeMix graph shows why.

Basically, it looks like the Kotias-related ancestry in the Yamnaya came from the North Caucasus, rather than any place closer to the Near East than Georgia. Unless, of course, the southern Caucasus was populated by unadmixed CHG right until the 4th Millennium BC, when the hypothetical Proto-Indo-Europeans from the Armenian Plateau set off on their journey to Northern Europe around the Caspian Sea. But let's be honest, that's extremely unlikely.

Indeed, I expect that next year we'll see the first Neolithic and Copper Age samples from Armenia and/or surrounds, and even though they will be in large part CHG, they'll be nowhere near unadmixed. This will essentially kill the Armenian Plateau hypothesis, and thus leave the Kurgan or steppe hypothesis as the only plausible choice.

In any case, 2016 will probably be the year when ancient DNA helps to settle the Indo-European homeland question once and for all. So get ready for more ancient DNA from the steppe, but also, among others, from Mesolithic and Neolithic Iran, Mycenaean Greece and the Maikop Culture of the North Caucasus. I'm also pretty sure that the Varna man with the golden codpiece will make an appearance in a paper about Neolithic and Copper Age Bulgaria. Bring it on!

Thursday, December 24, 2015

Maritime colonization of the Aegean in the early 7th Millennium BC

Open access at the Journal of World Prehistory:

Abstract: The process of Near Eastern neolithization and its westward expansion from the core zone in the Levant and upper Mesopotamia has been broadly discussed in recent decades, and many models have been developed to describe the spread of early farming in terms of its timing, structure, geography and sociocultural impact. Until now, based on recent intensive investigations in northwestern and western Anatolia, the discussion has mainly centred on the importance of Anatolian inland routes for the westward spread of neolithization. This contribution focuses on the potential impact of east Mediterranean and Aegean maritime networks on the spread of the Neolithic lifestyle to the western edge of the Anatolian subcontinent in the earliest phases of sedentism. Employing the longue durée model and the concept of ‘social memory’, we will discuss the arrival of new groups via established maritime routes. The existence of maritime networks prior to the spread of farming is already indicated by the high mobility of Epipalaeolithic/Mesolithic groups exploring the Aegean and east Mediterranean seas, and reaching, for example, the Cyclades and Cyprus. Successful navigation by these early mobile groups across the open sea is attested by the distribution of Melian obsidian. The potential existence of an additional Pre-Pottery Neolithic (PPN) obsidian network that operated between Cappadocia/Cilicia and Cyprus further hints at the importance of maritime coastal trade. Since both the coastal and the high seas networks were apparently already well established in this early period, we may further assume appropriate knowledge of geographic routes, navigational technology and other aspects of successful seafaring. This Mesolithic/PPN maritime know-how package appears to have been used by later groups, in the early 7th millennium calBC, exploring the centre of the Anatolian Aegean coast, and in time establishing some of the first permanent settlements in that region. In the present paper, we link this background of newcomers to the western edge of Anatolia with new excavation results from Çukuriçi Höyük, which we have analysed in terms of subsistence strategies, materiality, technology and symbolism. Additionally, further detailed studies of nutrition and obsidian procurement shed light on the distinct maritime affinity of the early settlers in our case study, something that, in our view, can hardly be attributed to inland farming societies. We propose a maritime colonization in the 7th millennium via routes from the eastern Mediterranean to the eastern Aegean, based on previously developed sea networks. The pronounced maritime affinity of these farming and herding societies allows us to identify traces of earlier PPN concepts still embedded in the social-cultural memories of the newcomers and incorporated in a new local and regional Neolithic identity.

Horejs et al., The Aegean in the Early 7th Millennium BC: Maritime Networks and Colonization, Journal of World Prehistory, December 2015, Volume 28, Issue 4, pp 289-330

Thursday, December 17, 2015

At least three genetically distinct Indo-European migrations into South Asia

First came the Indo-Aryans, probably in a couple of waves. Historical linguistics and archeology tell us that they originated on the Trans-Urals steppe in the Sintashta-Andronovo horizon, and pushed south around 2,000 BC to establish themselves as the ruling elite over Central Asian agriculturalists, who were probably in large part of West Asian origin.

There are multiple lines of genetic evidence suggesting that this is indeed what happened, which I discussed in detail in several earlier blog posts, like here.

But arguably the easiest way to show it is with D-stats of the form D(Indo-Aryan,Southeast_Asian; X,Outgroup), where the Indo-Aryans are the Kalash, a population isolate from the Hindu Kush with a relatively low level of extra-West Eurasian admixture and speaking an archaic form of Indo-Aryan. The Southeast Asians are the Dai from southern China, one of the best proxies for the South and East Asian admixture in the Kalash, while X represents a wide variety of present-day and ancient populations in my dataset. The top five D-stats, each based on well over 500K SNPs, are listed below:

Kalash Dai Kotias Ju_hoan_North 0.0684 22.704
Kalash Dai Sintashta Ju_hoan_North 0.0632 25.036
Kalash Dai Georgian Ju_hoan_North 0.0625 30.991
Kalash Dai Afanasievo Ju_hoan_North 0.0612 24.496
Kalash Dai Yamnaya_Samara Ju_hoan_North 0.0611 27.97

Really cool results. Obviously, Kotias is the recently published Caucasus hunter-gatherer (CHG) genome. The Kalash appear to carry the highest level of Kotias-related ancestry among present-day populations, which they probably acquired from both the Central Asian agriculturists and Indo-Aryan invaders. At the same time, however, Georgians show the highest affinity to Kotias because they harbor less extra-West Eurasian admixture.

After the Indo-Aryans came the Iranians, in all likelihood also from the steppe. They were either an offshoot of Sintashta-Andronovo or the more westerly Srubnaya Culture. I'd say the D-stats below, of the form D(Eastern_Iranian,Southeast_Asian)(X,Outgroup), are inconclusive, because the differences are small, and the outcome possibly affected by the methodology and/or sampling bias.

Tajik_Shugnan Dai Sintashta Ju_hoan_North 0.0716 26.427
Tajik_Shugnan Dai Poltavka Ju_hoan_North 0.0695 25.234
Tajik_Shugnan Dai Afanasievo Ju_hoan_North 0.0691 24.703
Tajik_Shugnan Dai Srubnaya Ju_hoan_North 0.069 28.266
Tajik_Shugnan Dai Corded_Ware_Germany Ju_hoan_North 0.0684 27.328

But again, the top five results make a lot of sense in the context of historical linguistics and archeology. By the way, Tajik Shugnans are a population isolate in the Pamir Mountains, like the Kalash with low level extra-West Eurasian admixture, and thus likely to be among the best available reference groups for early Eastern Iranians.

Interestingly, based on that list the Shugnans look more European than the Kalash. In large part this might be a reflection of the sharp rise in the level of European-specific Western hunter-gatherer (WHG) admixture on the steppe during the Middle Bronze Age, probably caused by population movements originating at the western edge of the steppe and/or in East Central Europe (see here).

As far as I can tell, the fact that the Shugnans and Kalash have around the same level of extra-West Eurasian admixture means that I can try to hone in on the differences between their steppe-derived ancestry with D-stats of the form D(Kalash,Tajik_Shugnan)(Kotias,X). The top result seems to confirm my hunch, because Loschbour is, of course, a Western hunter-gatherer.

Loschbour 0.0149 3.874
Basque_Spanish 0.0113 4.232
Anatolia_Neolithic 0.0112 4.257
Karelia_HG 0.0105 3.005
Poltavka 0.01 3.539
Corded_Ware_Germany 0.0099 3.734
Afanasievo 0.0094 3.213
Srubnaya 0.0094 3.538
Yamnaya_Kalmykia 0.0091 3.362
Albanian 0.0088 3.419
Altai_IA 0.0088 3.087
Sintashta 0.0088 3.146
Greek 0.0076 3.094

Full output available here

More recently, during historic times, large parts of northern South Asia were settled by the Balochi, a Western Iranian people from the South Caspian region, whose ancestors were probably Indo-Europeanized a couple millennia earlier by Proto-Iranians from the steppe moving west across the Iranian Plateau. D-stats comparing the Balochi to the Kalash and Shugnans, respectively, clearly reflect the Near Eastern origins of the Balochi.

BedouinB 0.0104 6.151
Anatolia_Neolithic 0.0094 5.495
Druze 0.0084 5.228
Cypriot 0.0082 4.839
Syrian 0.0079 4.714
Armenian 0.0063 3.935
Satsurblia 0.0059 2.472
Georgian 0.0055 3.443
Iranian 0.0055 3.345
Abkhasian 0.0053 3.279
Greek 0.0052 3.166


Okunevo -0.0081 -3.552
Karelia_HG -0.0104 -4.666

Full output available here

Satsurblia 0.007 2.078
BedouinB 0.0051 2.277

Basque_Spanish -0.0073 -3.156
Mezhovskaya -0.0085 -3.045
Altai_IA -0.0092 -3.677
Scythian_IA -0.0092 -3.108
Yamnaya_Samara -0.0095 -4.092
Karitiana -0.0098 -3.501
Karasuk -0.0099 -4.322
Andronovo -0.01 -4.09
Sintashta -0.01 -3.951
Corded_Ware_Germany -0.0102 -4.34
Srubnaya -0.0106 -4.605
Yamnaya_Kalmykia -0.011 -4.511
MA1 -0.0118 -3.691
Okunevo -0.0122 -3.783
Poltavka -0.0125 -5.043
Afanasievo -0.0136 -5.235
Loschbour -0.0148 -4.201
Karelia_HG -0.0208 -6.537

Full output available here

In this analysis I used ancient samples from the recently published Jones et al. and Mathieson et al. studies, available on request from the authors and at the Reich lab website here, respectively. The present-day samples are from the Human Origins dataset, also available at the Reich lab website.

Saturday, December 12, 2015

The Scythian

Time to have a look at the Scythian steppe warrior from the Mathieson et al. dataset. This is the first Scythian individual to be genotyped.

He comes from the Volga steppes of 380-200 cal BCE and belongs to Y-chromosome haplogroup R1a, which is the dominant Y-haplogroup in Scythian and related remains tested to date.

His genome-wide data puts him closest to Northeast and Northwest Europeans from among present-day populations, rather than West and South Asians, who should, in theory, carry significant Scythian ancestry. We can probably put this down to the complex ancestry of West and South Asians.

Moreover, he can be modeled as a mixture of Middle Bronze Age Potapovka people of the Volga steppes and present-day Nganasans of Siberia. This gels rather nicely with archaeological evidence, which suggests that Scythians were the descendants of Bronze Age Eastern European migrants to South Siberia, who expanded west across the Eurasian steppe during the Iron Age and eventually ended up back in Europe.

Identical-by-State (IBS) similarity

Lithuanian 0.645247
Estonian 0.645233
Latvian 0.645024
Russian_Kostroma 0.644946
Irish 0.644902
Orcadian 0.644792
Norwegian 0.644754
Belorussian 0.644727
Swedish 0.644667
Polish 0.644664
Austrian 0.644639
Danish 0.644587
English_Cornwall 0.644556
Belgian 0.644552
Scottish_Argyll 0.644548

Full output available here

Outgroup f3 shared drift statistics

Estonian 0.313726
Latvian 0.313664
Lithuanian 0.313574
Russian_Orel 0.313346
Finnish_Southwest 0.312997
Orcadian 0.312768
Norwegian 0.312768
Belorussian 0.312676
Russian_Kostroma 0.312669
Swedish 0.312608
Karelian 0.312567
Polish 0.31243
Irish 0.312281
Polish_Estonian 0.312156
Finnish 0.312102

Full output available here

qpAdm mixture model

Potapovka 0.913
Nganasan 0.087
chisq 5.815 tail prob 0.213365

Full output available here

Mathieson et al., Genome-wide patterns of selection in 230 ancient Eurasians, Nature, Published online 23 November, 2015doi:10.1038/nature16152. Genotype dataset available here.

See also...

The Poltavka outlier

Wednesday, December 9, 2015

Mixed marriages on the early Eneolithic steppe

It looks like Sredny Stog was the early vector for the spread of both Anatolian Neolithic and Caucasus hunter-gatherer (CHG) admixture onto the steppe, from the west and east, respectively:

These data testify the assumption about the existence of mixed Tripolye-Sredniy Stog marriages, because Tripolye population represented the Mediterranean anthropological type according to the not numerous Tripolye burials (Потехина 1999, c.154). It is interesting, that the massive Protoeuropoid type was typical for the oldest and the most eastern monuments of Sredniy Stog, while mesomorphic Mediterranean type was typical for the Igren cemetery, which was one of the youngest monuments related to the second and third periods of the Sredniy Stog culture and synchronous to the Tripolye B I and B I-II.


Appearance of pottery with pearls at the settlements of the third period of Sredniy Stog culture and glossy ceramics without ornamentation in the eastern variant sites, as well as the group of vessels with the steppe traces at the Svobodnoe settlement, allow me to assume the existence of mixed marriages between the Sredniy Stog and Northern Caucasus population.

Source: Early Eneolithic in the Pontic Steppes, book by Nadezhda Sergeenva Kotova, available at here.