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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.

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

Scythian_IA
Potapovka 0.913
Nganasan 0.087
chisq 5.815 tail prob 0.213365

Full output available here
Citation...

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...

Genetic origins and legacy of the Scythians and Sarmatians

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 Academia.edu here.

See also...

R1a-M417 from Eneolithic Ukraine!!!11

Thursday, November 26, 2015

The Khvalynsk men


This is where the three Samara Eneolithic or Khvalynsk samples from the recent Mathieson et al. paper plot on my Principal Component Analysis (PCA) of ancient West Eurasia. They're labeled as Steppe_CA (steppe Copper Age). I've also marked them with their Y-chromosome haplogroups.


Individual 10433, belonging to Y-chromosome haplogroup R1a, is almost a pure Eastern European Hunter-Gatherer, which is perhaps surprising, considering he was buried with copper artifacts. On the other hand, sample 10434, the one belonging to haplogroup Q1a, and positioned further east than the other two, appears to have been whacked over the head a few times and simply thrown into a ditch.

The PCA also has most of the other samples featured in Mathieson et al., including Neolithic Anatolians (labeled Anatolia_N), as well as extra samples from Allentoft et al. and Jones et al.

See also...

The Khvalynsk men #2

First Neolithic genomes from Greece


Just in at bioRxiv: Hofmanová et al., Early farmers from across Europe directly descended from Neolithic Aegeans

The main focus of the preprint are five Neolithic genomes from north-central Greece and northwestern Turkey. They're very similar to previously published Neolithic European and Anatolian samples, and strikingly different from present-day Greeks and Turks, pointing to major genetic turnovers in the Aegean region since the Neolithic.

The manuscript also reveals that, somewhat unexpectedly, two Mesolithic individuals from Thessaly, central Greece, belong to mtDNA haplogroup K1c. This is not a marker typical of other Mesolithic Europeans. It's a pity their genome-wide structure wasn't analyzed.

By the way, the key to Figure 2 lists Lithuanians and Mordovians as "Slavic", which is an oversight and needs to be corrected.

A bigger problem, however, is the mixture analysis presented in Figure 3. Loschbour-related ancestry is obviously inflated by East Asian admixture, hence it peaks among such groups as the Nogais of the North Caspian steppe, even though in reality they have very little Western European hunter-gatherer ancestry, if any.

Also, it seems to me that Ashkenazi Jews are used to represent Poles in the mixture analysis, because there's a slither of Yourba admixture in the pie-chart sitting over Poland. If so, that's a bit silly.

Monday, November 16, 2015

Caucasus hunter-gatherers (CHG) and the Indo-European question


The recent Jones et al. palaeogenomics paper focusing on Caucasus hunter-gatherers (CHG) has this to say about the Indo-European and Indo-Aryan expansions:

CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.

...

It has been proposed that modern Indians are a mixture of two ancestral components, an Ancestral North Indian component related to modern West Eurasians and an Ancestral South Indian component related more distantly to the Onge [25]; here Kotias proves the majority best surrogate for the former [28,29] (Supplementary Table 10). It is estimated that this admixture in the ancestors of Indian populations occurred relatively recently, 1,900–4,200 years BP, and is possibly linked with migrations introducing Indo-European languages and Vedic religion to the region (28).

...

Finally, we found that CHG ancestry was also carried east to become a major contributor to the Ancestral North Indian component found in the Indian subcontinent. Exactly when the eastwards movement occurred is unknown, but it likely included migration around the same time as their contribution to the western European gene pool and may be linked with the spread of Indo-European languages. However, earlier movements associated with other developments such as that of cereal farming and herding are also plausible.

To their credit, in that last quote the authors leave open the possibility that CHG arrived in South Asia in multiple waves and with a variety of groups, including Neolithic farmers. Nevertheless, I'd say their comments are still confusing and perhaps also incredibly naive, because essentially they appear to be hoping that in CHG they've identified the Proto-Indo-European and Proto-Indo-Aryan genetic component.

Indeed, a lot of people actually believe that the overwhelming part of the West Eurasian admixture in South Asia should be attributed to the Indo-Aryans. But that's just stupid.

After all, many Dravidian groups that in all likelihood never spoke Indo-Aryan languages carry significant ratios of West Eurasian ancestry. Some of this influence can be explained by admixture with Indo-Aryans, but uniparental markers suggest that much of it was brought from West Asia by the Proto-Dravidians (see here).

Below is the aforementioned Supplementary Table 10. Note that two of the Indian populations that are best modeled with D-stats as mixtures of Kotias (one of the two CHG genomes) and Onge are Dravidian speakers (Mala and Vishwabrahmin or Viskwakarma, a Malayali community). Another three are Indo-Aryans (GujaratiC, GujaratiD and Lodhi), but with high levels of Ancestral South Indian (ASI) admixture, which suggests their ancestors might have been language shifters.

On the other hand, the three populations that are best modeled as Afanasievo (a pastoralist group from the Early Bronze Age steppe) and Onge are all Indo-Aryans (GujaratiA, GujaratiB and Tiwari).




But like I say, South Asia is a complex melting pot of Indo-Aryans, Dravidians, and several other linguistic groups, so a more comprehensive analysis than a comparison of a few D-stats is needed to unravel the origins of its people in a meaningful way.

By the way, Jones et al. also argue that CHG is basically an offshoot of the so called Basal Eurasian clade, which was first described in Lazaridis et al. 2014. I'm highly skeptical of this claim, and I might check it out after I get my hands on the CHG genomes.

Citation...

Jones, E. R. et al. Upper palaeolithic genomes reveal deep roots of modern eurasians. Nat. Commun. 6:8912 doi: 10.1038/ncomms9912 (2015).

See also...

'Fourth strand' of European ancestry originated with (Caucasus) hunter-gatherers isolated by Ice Age

'Fourth strand' of European ancestry originated with (Caucasus) hunter-gatherers isolated by Ice Age


From a news feature about a forthcoming palaeogenomics paper:

"The question of where the Yamnaya come from has been something of a mystery up to now," said one of the lead senior authors Dr Andrea Manica, from Cambridge's Department of Zoology.

"We can now answer that as we've found that their genetic make-up is a mix of Eastern European hunter-gatherers and a population from this pocket of Caucasus hunter-gatherers who weathered much of the last Ice Age in apparent isolation. This Caucasus pocket is the fourth major strand of ancient European ancestry, one that we were unaware of until now," he said

Read more at: 'Fourth strand' of European ancestry originated with hunter-gatherers isolated by Ice Age

Update: the paper is now out and open access at Nature Communications.

The two ancient Georgian genomes belong to Y-chromosome haplogroup J. So it looks like I was right when I said that this type of ancestry mostly entered the European steppe from the Caucasus via female mediated gene flow during the Bronze Age (see here and here).

However, one of the Eastern European Hunter-Gatherers (EHG) from Mathieson et al. 2015 also belonged to haplogroup J. This suggests that there was intermittent gene flow, including some paternal gene flow, between the Caucasus and the steppe well before the Bronze Age.

Nevertheless, it's now even more difficult to accept that Y-haplogroup R1 and the Proto-Indo-Europeans might have originated south of the steppe. Clearly, R1 appears to be a steppe marker from way back, and I seriously doubt that Indo-European languages were introduced into highly patriarchal steppe societies by female migrants from the Caucasus.


Image credit: Nature Communications, dx.doi.org/10.1038/ncomms9912

The Aryan Trail (3500 - 1500 BC)


Cool little website here titled The Aryan Trail (3500 - 1500 BC). A lot of the stuff will look very familiar to those who've been following this blog and the latest ancient DNA results, which, among other things, include the discovery of Y-chromosome haplogroup R1a-Z94 in a sample from a Kurgan burial at Potapovka, near the Volga River, Russia, dated to 2925-2536 cal BCE (see Poltavka_outlier, ID I0432, Mathieson et al. 2015). Of course, R1a-Z94 is one of the most common Y-chromosome haplogroups amongst present-day Indo-Aryans.

Excavations conducted from 1985-1988 in Potapovka exposed four burial mounds, or kurgans, dated between 2200-2000 BC. Beneath kurgan 3 the central grave pit had remains of a man buried with at least two horse heads and the head of a sheep, in addition to pottery vessels and weapons. After the grave pit was filled, a human male was decapitated, his head was replaced with the head of a horse, and he was laid down over the filled grave shaft. This unique ritual provides a convincing antecedent for the Rig Vedic myth of Dadhyac Atharvan who knows the secret of making Soma juice, the nectar of immortality. The Asvins insists that Dadhyac tell them the secret. He refuses. They cut off his head and replaces it with the head of a horse, through which he becomes an oracle and tells them the secret.



Source: The Aryan Trail (3500 - 1500 BC)

Wednesday, November 11, 2015

Genetic substructures in Italy


The main text is behind a pay wall, but the images and supp info freely available here and here. Abstract:

Recent scientific literature has highlighted the relevance of population genetic studies both for disease association mapping in admixed populations and for understanding the history of human migrations. Deeper insight into the history of the Italian population is critical for understanding the peopling of Europe. Because of its crucial position at the centre of the Mediterranean basin, the Italian peninsula has experienced a complex history of colonization and migration whose genetic signatures are still present in contemporary Italians. In this study, we investigated genomic variation in the Italian population using 2.5 million single-nucleotide polymorphisms in a sample of more than 300 unrelated Italian subjects with well-defined geographical origins. We combined several analytical approaches to interpret genome-wide data on 1272 individuals from European, Middle Eastern, and North African populations. We detected three major ancestral components contributing different proportions across the Italian peninsula, and signatures of continuous gene flow within Italy, which have produced remarkable genetic variability among contemporary Italians. In addition, we have extracted novel details about the Italian population’s ancestry, identifying the genetic signatures of major historical events in Europe and the Mediterranean basin from the Neolithic (e.g., peopling of Sardinia) to recent times (e.g., ‘barbarian invasion’ of Northern and Central Italy). These results are valuable for further genetic, epidemiological and forensic studies in Italy and in Europe.

Citation...

Fiorito et al., The Italian genome reflects the history of Europe and the Mediterranean basin, European Journal of Human Genetics advance online publication 11 November 2015; doi: 10.1038/ejhg.2015.233

Saturday, October 31, 2015

Aboriginal Australian Y-chromosomes


Based on a survey of 657 self-declared Aboriginal individuals:

C-M130*(xM8,M38,M217,M347) 1%
C-M347 19%
K-M526*(xM147,P308,P79,P261,P256,M231,M175,M45,P202) 12%
S-P308 12%
M-M186 0.9%
Non-indigenous 56%

Unlike an earlier paper using genome-wide DNA, this study found no signals of gene flow from India to Australia during the Holocene.

Source...

Nagle, N., Ballantyne, K. N., van Oven, M., Tyler-Smith, C., Xue, Y., Taylor, D., Wilcox, S., Wilcox, L., Turkalov, R., van Oorschot, R. A.H., McAllister, P., Williams, L., Kayser, M., Mitchell, R. J. and The Genographic Consortium (2015), Antiquity and diversity of aboriginal Australian Y-chromosomes. Am. J. Phys. Anthropol.. doi: 10.1002/ajpa.22886

Friday, October 30, 2015

European-specific mtDNA U5a2a in ancient remains from Xinjiang, northwest China


I'm skeptical that a 700-year-old mito genome can be used as evidence of prehistoric population movements. Obviously, for that sort of thing we'd need a sequence from before recorded history. Nevertheless, the discovery of mtDNA haplogroup U5a2a in the Eastern Pamirs is still very interesting.

The complete mitochondrial genome of one 700-year-old individual found in Tashkurgan, Xinjiang was target enriched and sequenced in order to shed light on the population history of Tashkurgan and determine the phylogenetic relationship of haplogroup U5a. The ancient sample was assigned to a subclade of haplogroup U5a2a1, which is defined by two rare and stable transversions at 16114A and 13928C. Phylogenetic analysis shows a distribution pattern for U5a2a that is indicative of an origin in the Volga–Ural region and exhibits a clear eastward geographical expansion that correlates with the pastoral culture also entering the Eurasian steppe. The haplogroup U5a2a present in the ancient Tashkurgan individual reveals prehistoric migration in the East Pamir by pastoralists. This study shows that studying an ancient mitochondrial genome is a useful approach for studying the evolutionary process and population history of Eastern Pamir.

Ning et al., Ancient mitochondrial genome reveals trace of prehistoric migration in the east Pamir by pastoralists, Journal of Human Genetics advance online publication 29 October 2015; doi: 10.1038/jhg.2015.128

Thursday, October 29, 2015

Mitochondrial DNA from Maykop + Wolfgang Haak on Near Eastern-related ancestry in Yamnaya


From page 166 of a report posted recently at Academia.edu:

Majkop verfügen sowohl über eine «paläolithische» Haplogruppe (U8) als auch über «neolithische» Haplogruppen: V (Недолужко u. a. 2014), T2, N1. Bei einem Objekt aus einem Grab bei der Staniza Novosvobodnaja fanden wir auch die Haplogruppe М52. Die gewonnenen Daten sprechen für eine (auf dem Niveau der mitochondrialen DNA) mögliche genetische Gemeinschaft der archäologischen Kulturen von Majkop und Novosvobodnaja.

The presence of Indian-specific mtDNA haplogroup M52 is surprising. Maykop territory was located just south of the steppe, but M52 isn't found in any of the Bronze and Iron Age samples from the steppe tested to date.

Here's the comment from Haak, from an abstract titled The role of the Caucasus in the formation of the Eurasia's genetic makeup: Insights and questions from ancient DNA research.

Recent genetic research on autosomal and uniparentally-inherited markers has shown a remarkable genetic uniformity of Caucasian populations despite the region’s notable linguistic and cultural diversity. When compared to neighbouring regions, the smooth genetic transition from the Near/Middle East to the Caucasus is in stark contrast to the marked differences to populations from the East European steppes. Flanked by the Black and the Caspian Seas, it remains unclear to what extent the Caucasus served as a corridor and whether and if so when ancient migrations had affected and shaped the region’s genetic profile. Ancient DNA research on Mesolithic, Neolithic and Bronze Age individuals from Western Eurasia have recently thrown fresh light on the Caucasus as region, which appears to have played a critical role in the formation of the genetic ancestry of the Yamnaya people, Bronze Age pastoralist of the east European steppes. The Yamnaya carry strong signals of eastern hunter-gatherer (EHG) ancestry and ancient Near Eastern ancestry that is different from the one that giving rise to early European farmers. While modern-day Armenians are the best proxy for the putative source population of the EHG dilution in the steppes, it is highly likely that prehistoric cultural groups from the Caucasus will provide a much better temporal and contextual fit.

Actually, I'd say western Georgians are the best proxy for the putative source population of the EHG dilution in the steppes. See here...

Yamnaya's exotic ancestry: The Kartvelian connection

Wednesday, October 28, 2015

Prehistoric African admixture in Iberia


Open access at PLoS ONE:

Determining the timing, identity and direction of migrations in the Mediterranean Basin, the role of “migratory routes” in and among regions of Africa, Europe and Asia, and the effects of sex-specific behaviors of population movements have important implications for our understanding of the present human genetic diversity. A crucial component of the Mediterranean world is its westernmost region. Clear features of transcontinental ancient contacts between North African and Iberian populations surrounding the maritime region of Gibraltar Strait have been identified from archeological data. The attempt to discern origin and dates of migration between close geographically related regions has been a challenge in the field of uniparental-based population genetics. Mitochondrial DNA (mtDNA) studies have been focused on surveying the H1, H3 and V lineages when trying to ascertain north-south migrations, and U6 and L in the opposite direction, assuming that those lineages are good proxies for the ancestry of each side of the Mediterranean. To this end, in the present work we have screened entire mtDNA sequences belonging to U6, M1 and L haplogroups in Andalusians—from Huelva and Granada provinces—and Moroccan Berbers. We present here pioneer data and interpretations on the role of NW Africa and the Iberian Peninsula regarding the time of origin, number of founders and expansion directions of these specific markers. The estimated entrance of the North African U6 lineages into Iberia at 10 ky correlates well with other L African clades, indicating that U6 and some L lineages moved together from Africa to Iberia in the Early Holocene. Still, founder analysis highlights that the high sharing of lineages between North Africa and Iberia results from a complex process continued through time, impairing simplistic interpretations. In particular, our work supports the existence of an ancient, frequently denied, bridge connecting the Maghreb and Andalusia.

Hernández CL, Soares P, Dugoujon JM, Novelletto A, Rodríguez JN, Rito T, et al. (2015) Early Holocenic and Historic mtDNA African Signatures in the Iberian Peninsula: The Andalusian Region as a Paradigm. PLoS ONE 10(10): e0139784. doi:10.1371/journal.pone.0139784

Sardinians: relatively short by design


Behind a pay wall at Nature Genetics:

We report sequencing-based whole-genome association analyses to evaluate the impact of rare and founder variants on stature in 6,307 individuals on the island of Sardinia. We identify two variants with large effects. One variant, which introduces a stop codon in the GHR gene, is relatively frequent in Sardinia (0.87% versus <0.01% elsewhere) and in the homozygous state causes Laron syndrome involving short stature. We find that this variant reduces height in heterozygotes by an average of 4.2 cm (−0.64 s.d.). The other variant, in the imprinted KCNQ1 gene (minor allele frequency (MAF) = 7.7% in Sardinia versus <1% elsewhere) reduces height by an average of 1.83 cm (−0.31 s.d.) when maternally inherited. Additionally, polygenic scores indicate that known height-decreasing alleles are at systematically higher frequencies in Sardinians than would be expected by genetic drift. The findings are consistent with selection for shorter stature in Sardinia and a suggestive human example of the proposed 'island effect' reducing the size of large mammals.

Zoledziewska et al., Height-reducing variants and selection for short stature in Sardinia, Nature Genetics 47, 1352–1356 (2015) doi:10.1038/ng.3403

Also at Nature Genetics...

We report ~17.6 million genetic variants from whole-genome sequencing of 2,120 Sardinians; 22% are absent from previous sequencing-based compilations and are enriched for predicted functional consequences. Furthermore, ~76,000 variants common in our sample (frequency >5%) are rare elsewhere (<0.5% in the 1000 Genomes Project). We assessed the impact of these variants on circulating lipid levels and five inflammatory biomarkers. We observe 14 signals, including 2 major new loci, for lipid levels and 19 signals, including 2 new loci, for inflammatory markers. The new associations would have been missed in analyses based on 1000 Genomes Project data, underlining the advantages of large-scale sequencing in this founder population.

Sidore et al., Genome sequencing elucidates Sardinian genetic architecture and augments association analyses for lipid and blood inflammatory markers, Nature Genetics 47, 1272–1281 (2015) doi:10.1038/ng.3368

Monday, October 26, 2015

Two papers on Ainu genetic structure and origins


Open access at the Journal of Human Genetics:

Various genetic data (classic markers, mitochondrial DNAs, Y chromosomes and genome-wide single-nucleotide polymorphisms (SNPs)) have confirmed the coexistence of three major human populations on the Japanese Archipelago: Ainu in Hokkaido, Ryukyuans in the Southern Islands and Mainland Japanese. We compared genome-wide SNP data of the Ainu, Ryukyuans and Mainland Japanese, and found the following results: (1) the Ainu are genetically different from Mainland Japanese living in Tohoku, the northern part of Honshu Island; (2) using Ainu as descendants of the Jomon people and continental Asians (Han Chinese, Koreans) as descendants of Yayoi people, the proportion of Jomon genetic component in Mainland Japanese was ~18% and ~28% in Ryukyuans; (3) the time since admixture for Mainland Japanese ranged from 55 to 58 generations ago, and 43 to 44 generations ago for the Ryukyuans, depending on the number of Ainu individuals with varying rates of recent admixture with Mainland Japanese; (4) estimated haplotypes of some Ainu individuals suggested relatively long-term admixture with Mainland Japanese; and (5) highly differentiated genomic regions between Ainu and Mainland Japanese included EDAR and COL7A1 gene regions, which were shown to influence macroscopic phenotypes. These results clearly demonstrate the unique status of the Ainu and Ryukyuan people within East Asia.

Jinam et al., Unique characteristics of the Ainu population in Northern Japan, Journal of Human Genetics (2015) 60, 565–571; doi:10.1038/jhg.2015.79; published online 16 July 2015

Open access at Genetics:

Despite recent advances in population genomics, much remains to be elucidated with regard to East Asian population history. The Ainu, a hunter-gatherer population of northern Japan and Sakhalin island of Russia, are thought to be key to elucidating the prehistory of Japan and the peopling of East Asia. Here, we study the genetic relationship of the Ainu with other East Asian and Siberian populations outside the Japanese archipelago using genome-wide genotyping data. We find that the Ainu represent a deep branch of East Asian diversity more basal than all present-day East Asian farmers. However, we did not find a genetic connection between the Ainu and populations of the Tibetan plateau, rejecting their long-held hypothetical connection based on Y chromosome data. Unlike all other East Asian populations investigated, the Ainu have a closer genetic relationship with northeast Siberians than with central Siberians, suggesting ancient connections among populations around the sea of Okhotsk. We also detect a recent genetic contribution of the Ainu to nearby populations, but no evidence for reciprocal recent gene flow is observed. Whole genome sequencing of contemporary and ancient Ainu individuals will be helpful to understand the details of the deep history of East Asians.

Jeong et al., Deep History of East Asian Populations Revealed Through Genetic Analysis of the Ainu, Genetics, Early Online October 23, 2015, doi: 10.1534/genetics.115.178673

Significant local aurochs admixture in modern British and Irish cattle


Open access at Genome Biology:

Background: Domestication of the now-extinct wild aurochs, Bos primigenius, gave rise to the two major domestic extant cattle taxa, B. taurus and B. indicus. While previous genetic studies have shed some light on the evolutionary relationships between European aurochs and modern cattle, important questions remain unanswered, including the phylogenetic status of aurochs, whether gene flow from aurochs into early domestic populations occurred, and which genomic regions were subject to selection processes during and after domestication. Here, we address these questions using whole-genome sequencing data generated from an approximately 6,750-year-old British aurochs bone and genome sequence data from 81 additional cattle plus genome-wide single nucleotide polymorphism data from a diverse panel of 1,225 modern animals.

Results: Phylogenomic analyses place the aurochs as a distinct outgroup to the domestic B. taurus lineage, supporting the predominant Near Eastern origin of European cattle. Conversely, traditional British and Irish breeds share more genetic variants with this aurochs specimen than other European populations, supporting localized gene flow from aurochs into the ancestors of modern British and Irish cattle, perhaps through purposeful restocking by early herders in Britain. Finally, the functions of genes showing evidence for positive selection in B. taurus are enriched for neurobiology, growth, metabolism and immunobiology, suggesting that these biological processes have been important in the domestication of cattle.

Conclusions: This work provides important new information regarding the origins and functional evolution of modern cattle, revealing that the interface between early European domestic populations and wild aurochs was significantly more complex than previously thought.

Park et al., Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle, Genome Biology 2015, 16:234 doi:10.1186/s13059-015-0790-2

Thursday, October 22, 2015

Plague germs may have facilitated Bronze Age expansions from the steppe


Open access at Cell:

Summary: The bacteria Yersinia pestis is the etiological agent of plague and has caused human pandemics with millions of deaths in historic times. How and when it originated remains contentious. Here, we report the oldest direct evidence of Yersinia pestis identified by ancient DNA in human teeth from Asia and Europe dating from 2,800 to 5,000 years ago. By sequencing the genomes, we find that these ancient plague strains are basal to all known Yersinia pestis. We find the origins of the Yersinia pestis lineage to be at least two times older than previous estimates. We also identify a temporal sequence of genetic changes that lead to increased virulence and the emergence of the bubonic plague. Our results show that plague infection was endemic in the human populations of Eurasia at least 3,000 years before any historical recordings of pandemics.


Rasmussen et al., Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago, Cell, Volume 163, Issue 3, p571–582, 22 October 2015, DOI: http://dx.doi.org/10.1016/j.cell.2015.10.009

Also, some juicy quotes at ScienceDaily:

Study co-author Dr Marta Mirazón-Lahr, from Cambridge's Leverhulme Centre for Human Evolutionary Studies (LCHES), points out that a study earlier this year from Willerslev's Copenhagen group showed the Bronze Age to be a highly active migratory period, which could have led to the spread of pneumonic plague.

"The Bronze Age was a period of major metal weapon production, and it is thought increased warfare, which is compatible with emerging evidence of large population movements at the time. If pneumonic plague was carried as part of these migrations, it would have had devastating effects on small groups they encountered," she said.

"Well-documented cases have shown the pneumonic plague's chain of infection can go from a single hunter or herder to ravaging an entire community in two to three days."

University of Cambridge. "Plague in humans 'twice as old' but didn't begin as flea-borne, ancient DNA reveals." ScienceDaily, 22 October 2015. www.sciencedaily.com/releases/2015/10/151022124532.htm.

Monday, October 19, 2015

Reconstructing the genetic history of Siberia and Northeastern Europe


A new preprint on the genetic history of North Eurasia has just appeared at bioRxiv. Here's the abstract:

Siberia and Western Russia are home to over 40 culturally and linguistically diverse indigenous ethnic groups. Yet, genetic variation of peoples from this region is largely uncharacterized. We present whole-genome sequencing data from 28 individuals belonging to 14 distinct indigenous populations from that region. We combine these datasets with additional 32 modern-day and 15 ancient human genomes to build and compare autosomal, Y-DNA and mtDNA trees. Our results provide new links between modern and ancient inhabitants of Eurasia. Siberians share 38% of ancestry with descendants of the 45,000-year-old Ust-Ishim people, who were previously believed to have no modern-day descendants. Western Siberians trace 57% of their ancestry to the Ancient North Eurasians, represented by the 24,000-year-old Siberian Malta boy. In addition, Siberians admixtures are present in lineages represented by Eastern European hunter-gatherers from Samara, Karelia, Hungary and Sweden (from 8,000-6,600 years ago), as well as Yamnaya culture people (5,300-4,700 years ago) and modern-day northeastern Europeans. These results provide new evidence of ancient gene flow from Siberia into Europe.

My initial thought was that the MA1 or Mal'ta boy-related admixture estimate of 57% for Western Siberians (in fact, Mansis) was way too high. However, I checked it using qpAdm and the Mansis from the Human Origins dataset, and apparently it does make sense as a three-way model including MA1, Han Chinese and Georgians. The full qpAdm output is available here.

Mansi
Han 0.367
MA1 0.561
Georgian 0.073

chisq 0.278, tail prob 0.870155

Curiously, I get a very similar result with Eastern European hunter-gatherers (EHG) in place of MA1, and the fit is almost as good. The full output is here.

Mansi
Han 0.402
EHG 0.537
Georgian 0.061

chisq 0.916, tail prob 0.632459

In any case, we can safely assume that Mansis harbor a lot of MA1/EHG-related ancestry. Perhaps as much as ~60%. However, I have to say that this quote from the paper makes no sense whatsoever:

Our findings also point to Western Siberians Mansi as a likely source of the ANE [aka MA1-related] ancestry among northeastern Europeans.

Really? Mansis? Not even proto-Mansis, or some sort of Mansi-related population?

Also, as far as I can see, the authors consider Y-haplogroup N1c1 as an EHG paternal marker, simply because they dated its main expansion to 7,100-4,900 BP based on present-day samples. Please note that Karelia_HG and Samara_HG are classified as EHG.

The Western Siberian admixture into the Eastern Europeans likely began before the Yamnaya culture period (5.3-4.7 kya), since the admixtures with Mansi are also very strong among hunter gatherers from Northeastern Europe from 6.6-8 kya (Karelia HG, Samara HG and to lesser degree Motala HG and Hungary Gamba HG; Fig. S21f-q) that predated the Yamnaya people. Therefore Western Siberian admixtures into northeastern Europe likely began prior to 6,600 years ago, coinciding with the expansion of Y-DNA haplogroup N1c1 among Siberians and northeastern Europeans (7,100-4,900 years ago). Since haplogroup N likely originates in Asia or Siberia, its presence among eastern Europeans likely reflects ancient gene flows from Siberia into Eastern Europe.

The problem is that this isn't yet supported by any direct evidence from ancient DNA. Thus far, we know that EHG carried Y-haplogroups J, R1a and R1b, but no N1c1. Later populations, with significant EHG ancestry, such as Corded Ware, Khvalynsk and Yamnaya, carried mostly R1a and R1b, as well as I2a and Q1a, but again, no N1c1.

That's not to say that N1c1 won't ever turn up in EHG remains. But in my opinion the major subclades of N1c1 can't be associated with EHG, but rather with later populations of more complex origin, such as early Uralic-speakers with significant levels of East Eurasian admixture.

By the way, the claims about Ust-Ishim in the paper are interesting, but in my opinion not very parsimonious based on the data we have at the moment. I could be wrong though. Let's wait and see.

Citation...

Valouev et al., Reconstructing Genetic History of Siberian and Northeastern European Populations, bioRxiv preprint, Posted October 18, 2015, doi: http://dx.doi.org/10.1101/029421

Sunday, October 18, 2015

Lactase persistence and ancient DNA


Iain Mathieson, a Harvard scientist and the lead author of a recent peprint on the history of natural selection in Europe, has a website where he occasionally posts articles. He recently posted a review on the origins and spread of lactase persistence (LP) in Europe. He ends the review with the following comment:

This is actually rather consistent with the Itan et al. result, and it seems plausible to me that the [European LP] allele first appeared in Central Europe, was spread around Europe by the LBK, before being introduced to the steppe later by migration from Europe.

I can imagine that this conclusion won't be everyone's cup of tea, but I'd say it's a reasonable one for the time being.

Also, it's interesting to see the presence of the European LP allele in the Srubnaya Culture remains from the Middle Bronze Age Caspian steppe.

We didn’t find any evidence for LP in early farming populations like the LBK, or in early Bronze age steppe populations like the Yamnaya. In as-yet unreported data, we find a few copies of the allele in the Srubnaya - a later steppe population who seem to have some European Farmer-like ancestry.

The same Srubnaya sample also shows a high ratio of Y-haplogroup R1a-Z93 (4/6), which is today one of the most common Y-haplogroups in South Asia.

Now, the LP allele in South Asia is the same one as in Europe. So what this suggests is that at some point, probably during the later stages of the Bronze Age, steppe nomads closely related to the Srubnaya people moved into South Asia, bringing with them both R1a-Z93 and the European LP allele.

I'm pretty sure we'll be hearing more on that soon from the good people at Broad MIT/Harvard.

Friday, October 16, 2015

Basques are not simply a fusion of Iberian hunter-gatherers and early farmers


I thought I'd revisit the issue of Basque origins with my new Principal Component Analysis (PCA) of West Eurasia. The useful thing about this PCA is that it gets around two problems that routinely affect PCA featuring ancient samples: projection bias, otherwise known as shrinkage, and exaggerated outcomes for individuals with high counts of homozygous genotypes.


A couple of recent papers argued that Basques were the direct descendants of local hunter-gatherers and early Neolithic farmers who arrived in Iberia from the eastern Mediterranean. This is probably correct for the most part, but it doesn't tell the whole story.

On the PCA above, Basques are quite distinct from Early Neolithic, Middle Neolithic and Copper Age Iberians (marked Iberia_EN, Iberia_MN and Iberia_CA, respectively), because they are significantly more eastern. In fact, they cluster with the only Bronze Age Iberian on the plot (Iberia_BA), which is the same individual that I found to harbor steppe-related ancestry (see here).

Thus, the story told by the PCA is that Basques are the progeny of Bronze Age Iberians, who, unlike their Copper Age predecessors, experienced a pulse of steppe-related admixture from the east.

Formal statistics back this up. For instance, here's a quote from the recently revised Mathieson et al. preprint:

However, the statistic f4(Basque, Iberia_Chalcolithic; Yamnaya_Samara,Chimp)=0.00168 is significantly positive (Z=8.1), as is the statistic f4(Spanish, Iberia_Chalcolithic; Yamnaya_Samara, Chimp)= 0.00092 (Z=4.6). This indicates that steppe ancestry occurs in present-day southwestern European populations, and that even the Basques cannot be considered as mixtures of early farmers and hunter-gatherers without it (4).

The key question now is who brought the steppe-related ancestry to Basque country. Were they Indo-Europeans or speakers of Proto-Basque? Also, did they actually come from the steppe, or somewhere nearby, like the Carpathian Basin?

The reason I mention the Carpathian Basin is because, as per the PCA, Basques more or less cluster between Copper Age Iberians and some of the Bronze Age Hungarians (marked Hungary_BA). But this is just one possibility, and I'm not sure at this stage how plausible it looks with, say, formal statistics.

In this analysis I used samples from the Allentoft et al., Gunther et al., Haak et al. and Lazaridis et al. datasets, all of which are publicly available. The latter two are found at the Reich Lab site here. If you're confused by some of the acronyms in the PCA key, see here.

Tuesday, October 13, 2015

New PCA format


From now on, every time a new dataset of ancient West Eurasian samples is made available online, I'll run it like this.


Please note that the plots above include the majority of recently published ancient samples, and yet they are not affected by projection bias, otherwise known as shrinkage. If you're confused by some of the acronyms in the PCA key, see here.

See also...

Basques are not simply a fusion of Iberian hunter-gatherers and early farmers

Saturday, October 10, 2015

Eight thousand years of natural selection in Europe - take 2


Open access at bioRxiv. Lots of new samples in this one. The Principal Component Analysis (PCA) below from the paper appears to be affected by projection bias or shrinkage, but it's more or less correct. Can't wait to get my hands on the genotype data.

Abstract: 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.



Mathieson et al., Eight thousand years of natural selection in Europe, bioRxiv revised preprint, posted October 10, 2015, doi: http://dx.doi.org/10.1101/016477

See also...

Lactase persistence and ancient DNA

ASHG 2015 tweets


Tweets from ASHG 2015 can be found here. By the way, I know that today at 5.15pm, Baltimore time, Razib will be at Iosif Lazaridis' ASHG talk on the genetic affinities of Neolithic Anatolians. If his tweets don't appear there, you'll find them here.

Update: Here are some of those tweets from Razib...

@iosif_lazaridis revision of paper @mathiesoniain with more ancestry stuff on biorxiv soon [in fact, see here]

@iosif_lazaridis [Neolithic Anatolian] mtDNA look familiar to EEF. Y mostly G2a2. also J2 H and I at low frequency. C1 too

@iosif_lazaridis anatolian neolithic close to EEF on pca. but EEF shifted toward WHG #ASHG15

@iosif_lazaridis anatolian neolithic different from modern anatolian and se europe populations.

@iosif_lazaridis eurasian steppe, population transect done. 5,500 to 1,200 BC. author told me some R1a1a possibile stuff here yesterday

@iosif_lazaridis indo-european steppe = EHG + near eastern. new data eneolithic samara. 75% EHG ancestry. 25% "armenian" 5,200 to 4,000 BCE

@iosif_lazaridis poltavka people 3000 to 2200 BC basically like yamnaya. 50% EHG and 50% armenian-like. then srubnaya different.

@iosif_lazaridis srubnaya 2/3 yamnaya 1/3 middle neolithic european

@iosif_lazaridis yamnaya/poltavka went from R1b to R1a in the srubnaya period. z93 group found on bronze age steppe samara (s asian R1a)

@iosif_lazaridis there was back migration of EEF to the steppe after the initial yamnaya migration.

Thursday, October 8, 2015

Ancient Ethiopian genome reveals most Africans have recent Eurasian ancestry (or not)


By recent I mean post-Neolithic, because this genome is only dated to ~4,500 BP. Admittedly though, I am skeptical that all of the Eurasian admixture arrived so late, and await more data points from prehistoric Africa. By the way, this individual belongs to Y-haplogroup E1b1 and mtDNA haplogroup L3. The main text is behind a pay wall, but the supp info is free:

Characterizing genetic diversity in Africa is a crucial step for most analyses reconstructing the evolutionary history of anatomically modern humans. However, historic migrations from Eurasia into Africa have affected many contemporary populations, confounding inferences. Here, we present a 12.5x coverage ancient genome of an Ethiopian male (‘Mota’) who lived approximately 4,500 years ago. We use this genome to demonstrate that the Eurasian backflow into Africa came from a population closely related to Early Neolithic farmers, who had colonized Europe 4,000 years earlier. The extent of this backflow was much greater than previously reported, reaching all the way to Central, West and Southern Africa, affecting even populations such as Yoruba and Mbuti, previously thought to be relatively unadmixed, who harbor 6-7% Eurasian ancestry.

Llorente et al., Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent, Science, Published Online October 8 2015, DOI: 10.1126/science.aad2879

Update 26/01/2016:

Erratum to Gallego Llorente et al. 2015

The results presented in the Report “Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent“ were affected by a bioinformatics error. A script necessary to convert the input produced by samtools v0.1.19 to be compatible with PLINK was not run when merging the ancient genome, Mota, with the contemporary populations SNP panel, leading to homozygote positions to the human reference genome being dropped as missing data (the analysis of admixture with Neanderthals and Denisovans was not affected). When those positions were included, 255,922 SNP out of 256,540 from the contemporary reference panel could be called in Mota. The conclusion of a large migration into East Africa from Western Eurasia, and more precisely from a source genetically close to the early Neolithic farmers, is not affected. However, the geographic extent of the genetic impact of this migration was overestimated: the Western Eurasian backflow mostly affected East Africa and only a few Sub-Saharan populations; the Yoruba and Mbuti do not show higher levels of Western Eurasian ancestry compared to Mota. We thank Pontus Skoglund and David Reich for letting us know about this problem.

Sunday, October 4, 2015

Yamnaya's exotic ancestry: The Kartvelian connection


I've made a discovery. The Near Eastern-related ancestors of the Yamnaya steppe pastoralists were also the ancestors of present-day Georgian Mingrelians, or their very close relatives, and in all likelihood speakers of Kartvelian, which has a long history in the Caucasus. Here's a nice map from Wikipedia and a pic of some Mingrelians. Check out the impressive headware.



TreeMix is very specific and precise about this. In my analyses, based on a couple of different methods, the Mingrelians are the only population chosen as a source for the Near Eastern-related ancestry in the Yamnaya.

Keep in mind, this is an unsupervised test and the algorithm has an infinite number of choices, because migration edges can run from any part of the tree, and yet it chooses the Mingrelians. By the way, if anyone's wondering, I did also try the Bronze Age Armenians, to no avail.



This outcome is also more or less reproducible with more complex topologies that include samples from Central Asia. In the graph below the Georgian Mingrelians form a clade with the Near Eastern-related ancestry of the Yamnaya. It'd be interesting to see if other Georgian groups, like the Svans, do even better, if that's actually possible, but they're not available at the moment.


I actually came up with basically the same result earlier this year using qpAdm (see here). But at the time I was skeptical of its usefulness because qpAdm only offers a supervised test, so picking Georgians as a reference population and getting a good statistical fit doesn't mean as much as a reproducible unsupervised migration edge.

Now, judging by their ADMIXTURE results, these Georgian Mingrelians do carry some Early European farmer-related ancestry, which is missing in the Yamnaya (see here). Therefore, it's likely that ancient samples from the west or northwest Caucasus will prove to be even better proxies for the Near Eastern-related ancestry in the Yamnaya.

The samples used to produce the above TreeMix graphs are listed here. They're sourced from the Allentoft et al., Haak et al., and Lazaridis et al. datasets. I limited the markers to ~65K transversion (high confidence) SNPs that overlap between these datasets.

Updates...

Caucasus hunter-gatherers (CHG) and the Indo-European question

'Fourth strand' of European ancestry originated with (Caucasus) hunter-gatherers isolated by Ice Age

Mixed marriages on the early Eneolithic steppe

Saturday, October 3, 2015

Linguistics, Archeology and Genetics (L-A-G) Conference abstracts


The Max Planck Institute is holding a conference in a few days dedicated to the latest developments in the search for the Indo-European homeland.

Linguistics, Archeology and Genetics: Integrating new evidence for the origin and spread of Indo-European languages

A draft book of presentation abstracts is available here. This one from Danish linguist Guus Kroonen looks very promising.

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 and the Steppe hypothesis 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. 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, and thus patterns with the prehistoric migration of Europe’s first farming populations. 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.

Also, we've known for a while now that the good people at Broad MIT/Harvard have analyzed remains from Neolithic Anatolia, but it's nice to see this framed in the context of the Indo-European homeland debate.

Close genetic relationship of Neolithic Anatolians to early European farmers

Iosif Lazaridis et al.

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 (FST=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.

Indeed, my view is that the implications of this data for the Anatolian hypothesis are fatal (see here). It might also have dire implications for the Armenian Plateau hypothesis, although for the time being this hypothesis limps on.

Feel free to post and discuss your favorite abstracts in the comments below. If anyone reading is going to this thing, I'd love to hear more about the Y-haplogroups of the Anatolian farmers.

Friday, October 2, 2015

Essential reading: Paleoecology, Subsistence, and 14C Chronology of the Eurasian Caspian Steppe


To help things run more smoothly in the comments, I urge everyone taking part in the debates here about the colonization of the Eurasian steppe and the Indo-European homeland question to read carefully the following three papers. They're all open access:

1) Paleoecology, Subsistence, and 14C Chronology of the Eurasian Caspian Steppe Bronze Age

2) The Steppe and the Caucasus During the Bronze Age Mutual Relationships and Mutual Enrichments

3) New Radiocarbon Dates and a Review of the Chronology of Prehistoric Populations from the Minusinsk Basin, Southern Siberia, Russia

In particular, please note the latest calibrated radiocarbon-based dates of the main archaeological cultures being discussed:

- Khvalynsk, Eneolithic, 4300–3800 cal BC

- Steppe Maikop, Early Bronze Age, 3800–3000 cal BC

- Yamnaya, Early Bronze Age, 3000–2450 cal BC

- Afanasievo, Early Bronze Age, 2900-2500 cal BC

- Early Catacomb, Early Bronze Age, 2600–2350 cal BC

Of course, Yamnaya are in large part of Eastern European hunter-gatherer (EHG) origin but with roughly 50% of Near Eastern-related ancestry from an unknown population (Haak et al. 2015). Paper #2 linked to above provides tentative isotopic evidence that the latter might be the Steppe Maikop people or their descendants (see paragraph 4 on page 58).

However, the Khvalynsk population from the Samara region harbors around 25% of the same or very similar Near Eastern-related ancestry (unpublished data courtesy of David Anthony). And, as per the dates above, Khvalynsk existed before Steppe Maikop.

Thus, although the increase of the Near Eastern-related ancestry on the steppe from the Khvalynsk to the Yamnaya periods can be tentatively attributed to Maikop influence, this cannot be the initial source of this type of ancestry on the steppe.

Moreover, dates older than 3,000 cal BC for Afanasievo appear to be spurious (see paper #3 above). If so, what this means is that Afanasievo is around the same age as Yamnaya, or perhaps a little younger, and thus the generally accepted hypothesis that Afanasievo derives from Yamnaya or pre-Yamnaya looks safe.

Now, it's especially important that everyone concerned is aware of the key climatic shifts on the steppe, because climatic changes are often invoked as likely causes of major population movements within and out of the steppe. So I'm re-posting here Table 1 from paper #1 (click to enlarge).


I'll update this post as new information comes in, which will hopefully be very soon. There are signals that something big is on the way from the Reich Lab pertaining to the Indo-European homeland debate (for instance, see here).

See also...

Near Eastern admixture in Yamnaya: a couple of graphs + some ideas

Thursday, October 1, 2015

Near Eastern admixture in Yamnaya: a couple of graphs + some ideas


Update 05/10/2015: Yamnaya's exotic ancestry: The Kartvelian connection

...

The Afanasievo and Yamnaya samples published to date are remarkably homogeneous. Hopefully the bar graphs below, based on a couple of my recent ADMIXTURE runs, illustrate this well enough.

The Near Eastern-related ancestry proportions among the Yamnaya individuals do appear to rise steadily from early Yamnaya to late Yamnaya/early Catacomb. But the ancestral components remain the same, and if the increase in the Near Eastern-related admixture is real, the process is very subtle.

What this suggests to me is that groups of a southern provenance - in all likelihood Neolithic farmers seeking new land - arrived somewhere on the Pontic-Caspian steppe very early, perhaps even during the Early Neolithic, to eventually blend with local foragers. That's because the basic Yamnaya genotype had to have existed before the Yamnaya or pre-Yamnaya ancestors of the Afanasievo nomads set off on their 2000 km trek to the Minusinsk Basin in South Siberia, probably around 3,300 BC.

No doubt, the mixing didn't stop after the initial farmer/forger admixture event, and this is probably why the Near Eastern-related ancestry proportions rise gradually throughout the Yamnaya period. Indeed, considering the high mobility of Bronze Age steppe pastoralists, it's likely that long distance trade, alliances and marriages resulted in the genetic homogenization of vast stretches of Eastern Europe during their reign.


In this analysis I used samples from the Allentoft et al., Haak et al. and Lazaridis et al. datasets, all of which are publicly available. The latter two are found at the Reich Lab site here.

Wednesday, September 30, 2015

The 1000 Genomes paper


To be honest, I'm really looking forward to some papers based on the new Simons Genome Diversity Project dataset. Unlike the 1000 Genomes, it includes samples from a wide range of West Eurasian populations sequenced to at least 30x coverage (see here). But for now, open access at Nature:

The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies.

The 1000 Genomes Project Consortium, A global reference for human genetic variation, Nature 526, 68–74 (01 October 2015) doi:10.1038/nature15393

Cranial affinities of Mesolithic populations from Eastern Europe and Siberia (teaser)


This looks like an excellent example of modern physical anthropology work. Unfortunately it's only an abstract. Can't wait to see the paper.

Mesolithic populations from the Eastern Europe and Siberia: cranial shape analysis with the help of geometric morphometric methodology

Ekaterina Bulygina(1), Anna Rasskasova(1), Denis Pezhemski(1)

1 - Research Institute and Museum of Anthropology, Moscow State University, Russia

Several Mesolithic and early Neolithic populations dated to 10,000 – 6,000 years BC from Russia, Romania and Ukraine have been analysed by means of quantifying their 3D cranial shape. The whole sample comprised 85 individuals, including Mesolithic and Neolithic groups from Yuzhny Oleni Ostrov (Russia); Vasilievka, Voloshkoe and Vovnigi (Ukraine); Varasti (Romania); Itkul and Ust-Isha (South Siberia) and Locomotiv (East Siberia). A comparative set of modern populations was sampled to include representatives from Europe, Africa, Eastern Asia and (native) America. Apart from the standard geometric morphometric procedures, we cluster ordinated data to establish potential relationships between groups and use permutation of individual distances to establish the significance of the group differentiation. The method of analysis is first verified with the help of the modern populations that have varied geographical provenance. We establish that no cranial data, whether the face and the neurocranium are analysed together or separately, allow us to recover geographical relationships between the modern populations in our sample. Nevertheless, clusters that have been recovered with the help of the whole cranium data correspond well with the expected generic relationships between the sampled modern groups. As a result, we choose to analyse the shape of the complete cranium, where such is available, in fossil individuals as well. Our results highlight a high level of variation within Mesolithic and within Neolithic populations of the Eastern Europe and Siberia as compared with the pooled sample of the modern humans from different geographical locations worldwide. However, a certain structure among the analysed groups can still be revealed. The results suggest that Mesolithic groups from the Dnieper region have close morphological affinities with each other, while Yushny Oleni Ostrov have a large overlap with modern humans in general and with some of the mongoloid groups in particular. Neolithic groups are, on the whole, closer to modern populations than to the Mesolithic sample. At the same time, Siberian individuals show a complex pattern of morphological relationships which may be revealing of their genetic identity. On the whole, our results invite further discussion on the origins and affinities of the Eastern European Mesolithic and Early Neolithic groups as well as call for the research into the impact that the choice of data has on the results of 3D morphological analyses. Acknowledgements: This work has been supported by the grant of the Russian Foundation for Basic Research No № НК 13-06-00045.

Source: European Society for the study of Human Evolution (ESHE) 5th Annual Meeting PESHE4 final abstracts volume.

Tuesday, September 29, 2015

Domestic cattle in Neolithic Uzbekistan


Below are a few abstracts from a recent conference on Southwest Asian archaeozoology. The full selection is available here.

Early domestic ungulates in Central Asia: archaeozoological results from Ajakagytma (Uzbekistan, Kel’teminar, 9th-7th millennia cal BP)

Jean-Denis Vigne(1), Florian Brunet(2), Karine Debue(1), M. Khudzhanazarov(3)

1. Centre National de la Recherche Scientifique – Muséum national d’Histoire naturelle; France;
2. Centre National de la Recherche Scientifique - Université Panthéon-Sorbonne; France
3. Academy of Sciences of Uzbekistan; Uzbekistan

Ajakagytma is a Neolithic lake shore site located in the central desert of Uzbekistan (Kyzyl-Kum), a region for which the archaeozoological data are rare and sometimes questionable. New excavations conducted since 2005 by the French-Uzbek mission MAFANAC evidenced several successive Kel’teminar occupations dating from the end of the 7th to the 5th millennium. They provided more than 50 000 microlithic artefacts, and smaller series of degraded pottery, stone pendants, bone industry, animal and plant remains. They also provided more than 2000 faunal remains. Most of them are badly preserved, due to the extreme fluctuations in climate (heating and cooling and wetting and drying). However, 580 specimens could be attributed to a taxon, and more than 200 of them could be identified at the level of genus or species. They provide a clear image of the wild large mammals which lived in this area and which were hunted by the Kel’teminar people: the goitered gazelle (34%), aurochs (16%), onager (11%) and the wild camel (11%). We also find 15% of Caprini but, due to the poor preservation of the material, it was impossible to tell if they were hunted wild bezoar goats or early domesticated sheep or goat. Conversely, 13% of the specimens clearly refer to very small size bovids. This is the earliest evidence of domestic cattle in Central Asia. This presentation will discuss the consequences of this observation in the scope of the origin of cattle husbandry between the Iranian Plateau and North China.

Subsistence economy at Kul Tepe (North-Western Iran) from Early Chalcolithic to the Early Bronze Age

S. Davoudi(1), Marjan Mashkour(2) and Akbara Abedi(3)

1. Department of Archaeology; Tarbiat Modares University; Tehran; Iran;
2. UMR 7209 Archaeozoology; Sorbonne Universités; Natural History Museum of Paris; Centre national de la recherché scientifique;
France; 3. Department of Archaeology; University of Tehran; Iran;

The site of Kul Tepe is located near the city of Hadishahr 10 km to the south of the Araxes River in western Azerbaijan (Iran). Excavations were carried out by A. Abedi and H. Khatib Shahidi in 2010, the cultural material including the animal bones belongs to the Early Chalcolithic, to Late Bronze Age, Iron III, and Achaemenid periods. The faunal remains are very well preserved and cover a period from Early Chalcolithic to Early Bronze Age (5000 to 2200 BC) providing a continuous record for animal exploitation at the site. The faunal study was conducted in the archaeozoology laboratory of the University of Tehran. A wide range of domestic and wild animals are present in the faunal remains. Domestic sheep, goat, and cattle are dominant as the main animal resource in all periods, with an increase of cattle proportions during the Kura-Araxes 1 period. Also a rather important number of hunted species, cervids, gazelle, wild goat, sheep and bovids are present in this collection, especially during the Late Chalcolithic and Kura-Araxes 1 (4400-3200 BC). Also equid remains were found among the bones. Horse remains are present in the Kura-Araxes 1 levels and Early Bronze Age (3600-2200 BC). The quasi absence of suid remains is outstanding here. The study of Kul Tepe faunal remains brings a set of novel data for this region and this period and provides a continuous picture of the subsistence economy from the fifth to the third millennium BC, including three important prehistoric cultural transitions. The strategic location of site at the cross roads of major routes linking the Iranian Plateau to Anatolia and the Caucasus to Northern Mesopotamia suggests relations and interactions between human communities of these areas, and makes it possible to compare the results with other contemporaneous sites.

Early animal husbandry in Azerbaijan: Implications for the origin and development of the Neolithic in the Southern Caucasus

Saiji Arai(1), Seiji Kadowaki(2), K. Ohnishi(2), Farhad Guliyev(3) and Yoshihiro Nishiaki(1)

1. The University of Tokyo; Japan
2. Nagoya University; Japan
3. Institute of Archaeology and Ethnology, Azerbaijan Academy of Sciences; Azerbaijan

Recent archaeological research in Armenia, Georgia and Azerbaijan has significantly extended our knowledge about Neolithic cultures in the Southern Caucasus region. Archaeozoological studies to reconstruct general trends of animal economy during the period have also made substantial progress.

In this paper we present new archaeozoological data on the faunal assemblages from two Pottery Neolithic sites in Azerbaijan: Göytepe and Hacı Elamxanlı Tepe. Both sites are located in the Tovuz region, west Azerbaijan. While Göytepe is one of the largest mounds in the region dated to early and mid-6th millennium BC and belongs to Shomutepe-Shulaveri culture, Hacı Elamxanlı Tepe represents a small mound settled during the beginning of 6th millennium BC. Since no earlier Neolithic site has been found, comparative study of these sites is of great importance to trace the establishments of early agricultural villages in the region. Faunal assemblages from these two sites mainly consist of domestic animals. However, significant differences are also present. Firstly, cattle is almost absent at Hacı Elamxanlı Tepe. Secondly, red deer antler objects are more common at Göytepe, reflecting the practice of a more enhanced broad-spectrum economy. This trend, together with the higher frequency of forestial mammals and the increase of stone axes at Göytepe, indicates more intensive exploitation of forest environment. Thirdly, while the culling profile for caprine is little different between these two sites, the measurement data of sheep shows an increase of female individuals at Göytepe, indicating a development of herding technique.

Finally, on the basis of these archaeozoological results as well as analysis of other archaeological data, we will discuss the possible origin and development of Neolithic economy in the Southern Caucasus. Results of a DNA analysis of domestic goats, which suggest a link with eastern Turkey during early 6th millennium BC, will also be reported.