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Thursday, December 8, 2016

Middle Ages: rotten time to be a spotted horse


Scientific Reports has a new paper on the history of coat patterns in domesticated horses and the domestication process itself. Emphasis is mine:

Horses have been valued for their diversity of coat colour since prehistoric times; this is especially the case since their domestication in the Caspian steppe in ~3,500 BC. Although we can assume that human preferences were not constant, we have only anecdotal information about how domestic horses were influenced by humans. Our results from genotype analyses show a significant increase in spotted coats in early domestic horses (Copper Age to Iron Age). In contrast, medieval horses carried significantly fewer alleles for these phenotypes, whereas solid phenotypes (i.e., chestnut) became dominant. This shift may have been supported because of (i) pleiotropic disadvantages, (ii) a reduced need to separate domestic horses from their wild counterparts, (iii) a lower religious prestige, or (iv) novel developments in weaponry. These scenarios may have acted alone or in combination. However, the dominance of chestnut is a remarkable feature of the medieval horse population.

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In addition, we discovered that tobiano spotting, which only occurs in domestic horses and had thus far only been detected after 1500 BC, was present in the Eneolithic/Copper Age (Kazakhstan, cal. 3654–3630 BC, and Germany, cal. 3368–3101 BC). Similar to chestnut and sabino spotting, the tobiano phenotype appears to arise shortly after domestication, which is assumed to have started approximately 4000–3500 BC in the Ponto-Caspian steppe region (modern day Kazakhstan and Ukraine) [17].

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Moreover, the detection of the tobiano phenotype in two Eneolithic domestic horses from distant regions has important implications regarding the origins of horse domestication [17] and their subsequent distribution. It also supports previous claims that the emergence of domestic horses in Central Europe at the end of the fourth millennium BC was facilitated by introduced horses from the Ponto-Caspian steppe [19].

Wutke, S. et al. Spotted phenotypes in horses lost attractiveness in the Middle Ages. Sci. Rep. 6, 38548; doi: 10.1038/srep38548 (2016).

Wednesday, December 7, 2016

Population history of Sardinia from 3,514 whole genomes


Just in at bioRxiv:

Abstract: The population of the Mediterranean island of Sardinia has made important contributions to genome-wide association studies of traits and diseases. The history of the Sardinian population has also been the focus of much research, and in recent ancient DNA (aDNA) studies, Sardinia has provided unique insight into the peopling of Europe and the spread of agriculture. In this study, we analyze whole-genome sequences of 3,514 Sardinians to address hypotheses regarding the founding of Sardinia and its relation to the peopling of Europe, including examining fine-scale substructure, population size history, and signals of admixture. We find the population of the mountainous Gennargentu region shows elevated genetic isolation with higher levels of ancestry associated with mainland Neolithic farmers and depleted ancestry associated with more recent Bronze Age Steppe migrations on the mainland. Notably, the Gennargentu region also has elevated levels of pre-Neolithic hunter-gatherer ancestry and increased affinity to Basque populations. Further, allele sharing with pre-Neolithic and Neolithic mainland populations is larger on the X chromosome compared to the autosome, providing evidence for a sex-biased demographic history in Sardinia. These results give new insight to the demography of ancestral Sardinians and help further the understanding of sharing of disease risk alleles between Sardinia and mainland populations.

Charleston et al., Population history of the Sardinian people inferred from whole-genome sequencing, bioRxiv, Posted December 7, 2016, doi: http://dx.doi.org/10.1101/092148

Tuesday, December 6, 2016

Iberian Bell Beaker teaser (Roth 2016)


Before we get to chew on the Bell Beaker behemoth, probably early next year if not sooner, here's an appetizer on a similar topic. Thanks to Bell Beaker blogger for catching it.

Roth, Christina, Once upon a time in the West : paleogenetic analyses on Mesolithic to Early Bronze Age individuals from the Iberian Peninsula, Dissertation, Mainz : Univ. 236 Seiten, 2016

Not really sure what to make of these mtDNA results or the author's conclusions. But this part is interesting, because mtDNA U5a is relatively common in ancient groups with inflated Eastern European Hunter-Gatherer (EHG) genome-wide ancestry, such as Yamnaya and Corded Ware.

The two Bell Beaker groups show significant differences on haplogroup level to Chalcolithic non-Bell Beaker from the Southern Meseta and all Early and Late Neolithic groups with strong genetic hunter-gatherer background (NSE, CPE, and EVN) (see table 13, p.91). They are clearly separated from all other Chalcolithic groups in PCA, cluster analysis, and MDS (see fig. 16–18, pp.89–96). Furthermore, AMOVA supports – though not significant – separation of Bell Beaker and non-Bell Beaker groups (see table 21, p.104). The Fisher-test with superordinate groups supports significant differences between Chalcolithic Bell Beaker and non-Bell Beaker groups as well (see table 14, p.92). Genetic differences between the two Bell Beaker groups are low but not significant while higher and mostly significant FST values to the Chalcolithic groups of the Southern Meseta and East Spain can be observed (see table 16, p.94).

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A common feature that is shared between the two Bell Beaker groups and that separates them from other Chalcolithic groups is the low amount of haplogroup H and the presence of haplogroup U5a, which was – apart from the Bell Beaker groups – only found in one Late Neolithic individual from Portugal and the Portuguese Chalcolithic site of Perdigões.


Friday, December 2, 2016

Bell Beaker behemoth coming real soon


Interesting post here by author Jean Manco. Emphasis is mine:

Reporting back on the lecture on Bell Beaker by Volker Heyd this evening in Dorchester. The expected two aDNA papers on Bell Beaker have been delayed for the best possible reason. The two teams, one from Harvard and the other from Copenhagen, have agreed to amalgamate their results into one huge paper, which will give the results of over 200 samples. It is due to be published in a couple of months. Until then all the results are embargoed. Volker Heyd would only say that they are exciting.

He would also prefer me not to divulge everything he said at the lecture on the archaeological side, since he has a paper coming out in the March issue of Antiquity on Bell Beaker; while in the same issue will be one by Kristiansen on Corded Ware. So I'll be brief. He went through the various theories of the origins of Bell Beaker: the Dutch model prevalent until the 1990s, the change wrought by the Muller and Van Willigen radiocarbon date compilation of 2001 and subsequent publications of early dates in Iberia, the various attempts to make sense of an Iberian origin. The problem of the latter and of the idea of a North African origin are the same in his view. There is no prior usage of cord in pottery decoration of either. So he sticks by the Yamnaya link to a pre-BB culture proposed in Harrison and Heyd 2007. The icing on the cake lies in two significant new discoveries, which are not entirely published as yet.

See also...

The man with the flat occiput

Population genomics of Early Bronze Age Europe in three simple graphs

Wednesday, November 30, 2016

Five foot Philistines


Vilified in biblical texts and even ridiculed by Iggy Pop, the Iron Age pagan seafarers known as the Philistines were basically the East Mediterranean version of the Vikings, except apparently much smaller:

Relatively short average heights for people buried at Ashkelon — about 5 feet, 1 inch for men and 4 feet, 10 inches for women — also fit a scenario of biological stress, Fox said. Short stature and minimal height differences between men and women occur with population-wide stresses such as malnutrition, she said.

...

The Philistines were a famously combative crowd. Archaeologist Eric Meyers of Duke University, who was not a member of the Ashkelon team, wondered if at least some of those buried at Ashkelon had been killed in battles or fights. But no head injuries or other skeletal signs of violent encounters appeared among the dead at Ashkelon, Fox said. Neither did any skeletons contain evidence of tumors or cancers.

If DNA can be extracted from the Ashkelon skeletons, scientists may get a glimpse of where the Philistines originally came from. Evolutionary geneticist Johannes Krause of the Max Planck Institute for the Science of Human History in Jena, Germany, is currently directing efforts to retrieve genetic sequences from the Ashkelon bones.


Source: Ancient cemetery provides peek into Philistines’ lives, health, ScienceNews, November 22, 2016

See also...

American Schools of Oriental Research 2016 paper abstracts (PDF link)

Monday, November 28, 2016

Fund-raising offer: Basal-rich K7 and/or Global 10 genetic map


I'm now taking donations for 2017. Anyone who donates $12 USD or $16 AUD, or more, will get the Basal-rich K7 ancestry proportions. Of course, you'll need to send me your genotype data for that to happen (Ancestry.com, FTDNA or 23andMe).

The Basal-rich K7

Please send your non-tax deductible donations via PayPal to eurogenesblog at gmail dot com. E-mail your genotype data to the same address. Please don't assume that I already have your data. I'll try and get back to everyone within a day and will put things on hold if that becomes an unrealistic target.

Using your Basal-rich K7 ancestry proportions, I'll show you where you cluster in the new and improved Fateful Triangle. Many people will probably land somewhere along the cline made up of Late Neolithic/Early Bronze Age Europeans and Middle/Late Bronze Age steppe herders and warriors. This, to me, looks like a cline produced by the expansion of early Indo-Europeans into Western and Central Europe.


For an extra donation of $16 USD or $21 AUD, those of you feeling more adventurous will also receive the Global 10 genetic map, and, more importantly, coordinates for ten dimensions.

A fresh look at global genetic diversity

The Basal-rich K7 is the best ancient ancestry test that I've been able to come up with. It correlates strongly with latest research reported in scientific literature. And, in fact, in some instances it probably trumps latest scientific literature.

For instance, Broushaki et al. 2016 characterized Early Neolithic farmers from the Zagros Mountains, Iran, as 62% Basal Eurasian and 38% Ancient North Eurasian-related (Figure S52). This, considering formal statistics like the D-stat below, with AfontovaGora3 (AG3) as the ANE proxy, is unlikely to be correct, despite the fact that AG3 is a relatively low quality sample.

D(Yoruba,Iran_Neolithic)(Villabruna,AfontovaGora3) 0.0223 Z 2.812

On the other hand, the Basal-rich K7 models the early Zagros farmers as 39.05% Ancient North Eurasian and 56.67% Basal-rich (which is probably a composite of Basal Eurasian and something Villabruna-related). To me this appears to be the more sensible solution.

Moreover, Lazaridis et al. 2016 characterized South Caspian forager Iran_HotuIIIb as more Basal Eurasian than the early Zagros farmers (Supplementary Information 4). The Basal-rich K7, on the other hand, shows the opposite. The D-stat below suggests that the Basal-rich K7 is closer to the truth.

D(Chimp,Ust_Ishim)(Iran_Neolithic,Iran_Hotu) 0.0156 Z 1.337

There are other such examples, and I might post them in the comments. In any case, the point I'm making is that the Basal-rich K7 is a solid piece of work and it's likely to remain relevant for a long time. Indeed, I'll be updating the Basal-rich K7 spreadsheet regularly as new ancient samples roll in, which means that you'll be able to model yourself as newly sampled ancient populations using the Basal-rich K7 ancestry proportions (for instance, see here).

The only problem with this test is that it's optimized for Eurasians. As a result, it might be sensible for anyone with significant (>5%) Sub-Saharan ancestry to skip the Basal-rich K7 and just ask for the Global 10 genetic map and coordinates.


You can use the Global 10 coordinates to model your ancient and recent fine-scale ancestry, just as you would using mixture proportions. In fact, I'd say the Global 10 coordinates are more useful in this respect than any mixture test, including the Basal-rich K7.

Thanks in advance for your support. Keep in mind that the more cash I raise the busier things will be on this blog in 2017, which, by all accounts, is shaping up to be the year for ancient DNA.

Saturday, November 26, 2016

Big deal of 2016: the territory of present-day Iran cannot be the Indo-European homeland


It's been a pretty big year. Not as big as many of us had hoped for, but there's still a few more weeks till 2017, so who knows what will happen?

In any case, for me 2016 will be the year in which we finally saw hard data - courtesy of Lazaridis et al. and Broushaki at al. - that crossed off the territory of present-day Iran from the list of potential Proto-Indo-European (PIE) homelands.

Now, it's true, Lazaridis et al. and Broushaki et al. were somewhat vague in what their data meant in this context, and indeed, both sets of authors left open the possibility that what is now Iran might prove to be the PIE homeland. However, their data left no doubt: look elsewhere for the PIE Urheimat.

Why? Here it is, in point form, as simply as I can put it:

- the Mesolithic and Neolithic peoples of the Zagros range and South Caspian region were highly distinct both in terms of genome-wide genetic structure and uniparental markers, and clearly only contributed meaningful gene flow to South Asia, not to Europe or Anatolia

- after the descendants of Neolithic farmers from the Zagros range, or at least their very close relatives, migrated to South Asia, the territory of present-day Iran, as per the data in Lazaridis et al. and Broushaki et al., saw waves of migrations from the west and north that dramatically shifted the population structure of the region, bringing it closer in this respect to the Levant and Europe

- most of the Neolithic samples from Iran in Lazaridis et al. and Broushaki et al. came from near the proto-Elamite homeland in the Kor River basin in central Fars, which strongly suggests that their close relatives who streamed into South Asia were not Indo-Europeans, but rather speakers of languages closely related to Elamite

- even though Lazaridis et al. successfully modeled Early/Middle Bronze Age steppe populations, including Yamnaya, as largely of Iran Chalcolithic origin, this appeared to be a coincidence, because the Chalcolithic samples from Iran showed fairly typical South Caspian uniparental markers, such as Y-chromosome haplogroups J and G1 and mitochondrial (mtDNA) haplogroup U7, which are conspicuous by their absence from an exceptionally wide range of Bronze Age steppe samples.

I do realize that many readers won't accept these arguments for emotional reasons, because the PIE homeland debate is an emotional one for a lot of people. Nevertheless, if you decide to argue with me in the comments, make sure you have a coherent argument.

Actually, the territory of present-day Iran has never been a serious contender in the PIE homeland debate. This is something that many Iranian scholars will freely admit.

Not only was central Fars the proto-Elamite homeland, but much of what is now western Iran was the stomping ground of the Hurrians. The Indo-Europeans, in the form of Indo-Iranians such as the Medes, only got there late in the game, in all likelihood from the Eurasian steppes.

But a lot of newbies to the PIE debate don't know this, or they don't want to know it. I guess to them, Iran makes sense because it's in between Europe and South Asia? Or maybe it's the fact that the word Iran is kind of similar to the word Aryan? No idea, really, but like I say, it's now all over.

Friday, November 25, 2016

First news of Hunnic and Botai aDNA


According to this Kazakh press report, remains from an elite Hunnic burial in what is now Hungary belonged to Y-chromosome haplogroup L and mitochondrial (mtDNA) haplogroup D4j12.

КАЗАХСТАНСКИЙ ДНК-ПРОЕКТ

These markers are extremely rare in modern-day Europeans, including Hungarians. Indeed, mtDNA D is fairly common in Central Asian groups with high levels of East Eurasian admixture, while Y-hg L peaks in frequency in South Central Asia. However, the latter was found in three Chalcolithic individuals from the Areni-1 cave complex in Armenia (see here), so it may have been more common in and around Europe in ancient times.

The article also mentions that a sample from an Botai culture burial in present-day Kazakhstan belonged to mtDNA K1b2. This marker is today found at low but appreciable frequencies throughout Northern and Eastern Europe. One of the Samara Srubnaya samples from Mathieson et al. 2015 belonged to K1b2a.

Unfortunately, as per the article, the Y-hg of the Botai individual remains a mystery, due to a lack of supplies and funding. Perhaps the Reich Lab or GeoGenetics can help out?

Thursday, November 24, 2016

Multiple Holocene Eurasian migrations into north central Africa


The AJHG has a new open access paper on the population history of Chad. It lays out a reasonable hypothesis for the sources and timing of Eurasian gene flow into north central Africa. Just wondering, though, if the authors considered the possibility that R1b-V88 may have expanded into Africa from Iberia? After all, the oldest instance of a probable R1b-V88 to date is from an Iberian Early Neolithic sample (ID I0410, Els Trocs, Spain, Haak et al. 2015). But I don't have a strong opinion on the issue at the moment. From the paper (emphasis is mine):

Understanding human genetic diversity in Africa is important for interpreting the evolution of all humans, yet vast regions in Africa, such as Chad, remain genetically poorly investigated. Here, we use genotype data from 480 samples from Chad, the Near East, and southern Europe, as well as whole-genome sequencing from 19 of them, to show that many populations today derive their genomes from ancient African-Eurasian admixtures. We found evidence of early Eurasian backflow to Africa in people speaking the unclassified isolate Laal language in southern Chad and estimate from linkage-disequilibrium decay that this occurred 4,750–7,200 years ago. It brought to Africa a Y chromosome lineage (R1b-V88) whose closest relatives are widespread in present-day Eurasia; we estimate from sequence data that the Chad R1b-V88 Y chromosomes coalesced 5,700–7,300 years ago. This migration could thus have originated among Near Eastern farmers during the African Humid Period. We also found that the previously documented Eurasian backflow into Africa, which occurred ∼3,000 years ago and was thought to be mostly limited to East Africa, had a more westward impact affecting populations in northern Chad, such as the Toubou, who have 20%–30% Eurasian ancestry today. We observed a decline in heterozygosity in admixed Africans and found that the Eurasian admixture can bias inferences on their coalescent history and confound genetic signals from adaptation and archaic introgression.

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It is important to note that in this work we inevitably invoke Occam’s razor to support the simplest model consistent with our data; the history of the populations studied here, including the time and sources of the Eurasian admixture in Africa, could be more complex. aDNA from Chad and neighboring regions remains a challenge given the poor DNA preservation in hot climates, but future successful efforts in aDNA research could provide additional insights and reveal additional complexities not considered by the modern-DNA-based models favored here.

Haber at al., Chad Genetic Diversity Reveals an African History Marked by Multiple Holocene Eurasian Migrations, AJHG, Published Online: November 23, 2016, DOI: http://dx.doi.org/10.1016/j.ajhg.2016.10.012 show

Saturday, November 12, 2016

Days of high adventure


I've redesigned and streamlined my Principal Component Analysis (PCA) plot of West Eurasia in anticipation of the arrival of many more ancient samples. Rumor has it we'll not only get stuff from the Balkans, but also finally from the steppes north of the Black Sea.

Moreover, apparently 12 of the 15 skeletons recently unearthed at the Harappan-era Rakhigarhi site have been genotyped, and we should see a paper, as well as hopefully the genotype data, by the middle of next year.

I'd say my new plot does a better job of highlighting relationships between the different prehistoric groups and population shifts across space and time. The datasheet is available here.
It should be pretty clear from this plot how the modern-day European gene pool came about. So I don't expect any major surprises when the new samples come in. Nevertheless, the wait is killing me, and many others I'm sure.