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Monday, March 28, 2016

Higher than expected Denisovan admixture in South Asia

We've seen a lot of papers in recent years on South Asian genetic history. Unfortunately, most of them have not been very useful. The only way to remedy this sad state of affairs is with at least a few prehistoric genomes from the Indian subcontinent. If this ever happens, we'll probably be treated to some surprises. A new paper at Current Biology suggests that inflated Denisovan-related ancestry in South Asian hunter-gatherers will be one of them:

Summary: Some present-day humans derive up to ∼5% [ 1 ] of their ancestry from archaic Denisovans, an even larger proportion than the ∼2% from Neanderthals [ 2 ]. We developed methods that can disambiguate the locations of segments of Denisovan and Neanderthal ancestry in present-day humans and applied them to 257 high-coverage genomes from 120 diverse populations, among which were 20 individual Oceanians with high Denisovan ancestry [ 3 ]. In Oceanians, the average size of Denisovan fragments is larger than Neanderthal fragments, implying a more recent average date of Denisovan admixture in the history of these populations (p = 0.00004). We document more Denisovan ancestry in South Asia than is expected based on existing models of history, reflecting a previously undocumented mixture related to archaic humans (p = 0.0013). Denisovan ancestry, just like Neanderthal ancestry, has been deleterious on a modern human genetic background, as reflected by its depletion near genes. Finally, the reduction of both archaic ancestries is especially pronounced on chromosome X and near genes more highly expressed in testes than other tissues (p = 1.2 × 10−7 to 3.2 × 10−7 for Denisovan and 2.2 × 10−3 to 2.9 × 10−3 for Neanderthal ancestry even after controlling for differences in level of selective constraint across gene classes). This suggests that reduced male fertility may be a general feature of mixtures of human populations diverged by >500,000 years.

Sankararaman et al., The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans, Current Biology (2016),

PC/nMonte open thread

Below are a few nMonte models of ancient individuals based on 25 principal components (PCs). The relevant datasheet and nMonte R script can be downloaded here and here, respectively.

Many of the outcomes are basically perfect. Others could certainly be better. But they all make sense.

The more complex the ancestry, the more difficult it is to model. Also, deamination, low coverage and missing markers are probably skewing things to some degree for most of these samples. So although time consuming, it might be a good idea to use population averages minus the most obvious outliers.

Are there any other ways to improve the analysis? Is 25 dimensions too much or too little? Let's run plenty of tests and see where this takes us.

I can update the datasheet with many more populations and dimensions later this week. Feel free to post your requests in the comments and I'll run them if I have them. Also, if anyone's wondering, I don't know yet which commercial genotype files I can run in this test, if any. I'll check.

Update 04/04/2016: A modified datasheet with 50 dimensions and many more samples is available here. It should be more useful in modeling South Central Asians, especially the Kalash. However, as far as I can tell, using just 9 dimensions, like in the version here, is faster and produces more accurate results.

Friday, March 25, 2016

Epic Bronze Age battle near the Baltic

There's a fascinating feature at Science about a surprisingly large-scale Bronze Age battle in present-day North Germany. It's great to see ancient DNA being tested. Can't wait for the results.

Ancient DNA could potentially reveal much more: When compared to other Bronze Age samples from around Europe at this time, it could point to the homelands of the warriors as well as such traits as eye and hair color. Genetic analysis is just beginning, but so far it supports the notion of far-flung origins. DNA from teeth suggests some warriors are related to modern southern Europeans and others to people living in modern-day Poland and Scandinavia. “This is not a bunch of local idiots,” says University of Mainz geneticist Joachim Burger. “It’s a highly diverse population.”

As University of Aarhus’s Vandkilde puts it: “It’s an army like the one described in Homeric epics, made up of smaller war bands that gathered to sack Troy”—an event thought to have happened fewer than 100 years later, in 1184 B.C.E. That suggests an unexpectedly widespread social organization, Jantzen says. “To organize a battle like this over tremendous distances and gather all these people in one place was a tremendous accomplishment,” he says.

Source: Andrew Curry, Slaughter at the bridge: Uncovering a colossal Bronze Age battle, DOI: 10.1126/science.aaf4033

Some more details about the project:

The human skeletal material from the Tollense Valley, Mecklenburg West-Pomerania, represents an unparalleled archaeological discovery: the anthropological and biomolecular preservation of the bones is remarkably good, and the large number of individuals from a putative Bronze Age battlefield context is a rare find. A pilot study carried out by the applicants confirmed that the preservation of mitochondrial and nuclear DNA is excellent. The latest developments in DNA sequencing technology (next generation sequencing, NGS), and especially the progress in modeling prehistoric population structure through computer simulations, enables the precise reconstruction of the population history of such a large coherent site. Additionally, the hypothesis of intergroup conflict can be tested. Previous studies on Holocene population dynamics focused on the Neolithic transition. The prevailing hypothesis suggests that the European gene pool resulted from a complex and regionally differentiated admixture pattern between local hunter-gatherers and immigrant farmers. Bronze Age populations are the key to testing this hypothesis, which we propose to do using our newly-developed multi locus system of 319 neutral chromosomal markers. Furthermore, the excellent preservation of these samples will allow us to conduct a population- genetic analysis of paternal lineages. Not least, this is an opportunity to retrace evolutionary adaptation processes (e.g. Calcium- and Vitamin D metabolism) originating in the Neolithic transition. We plan to use mitochondrial and nuclear aDNA capture essays and next generation sequencing technology to generate the most comprehensive prehistoric DNA data set to date. This study will be the first to combine multi locus aDNA capture assays and spatially explicit coalescence analyses of prehistoric DNA, and will undoubtedly set a new standard for human population genetics. The relevance of these results will extend far beyond the archaeological site of the Tollense Valley, and our data will be interpreted within the diachronic and supra-regional context of European population history.

Source: Population genetics of the Bronze Age site in the Tollense Valley, Mechlenburg-Pomerania

Monday, March 21, 2016

R1a in Yamnaya

Do you ever get the feeling when reading some of the ancient DNA papers that the authors know more than they're willing to admit? That's probably because they do.

It looks like Y-chromosome haplogroup R1a has already been found in Yamnaya remains, which, I believe, was something that was hinted at by David Reich and colleagues last year. It's just that, for some reason, the result hasn't yet been published. Crank up Google translate and navigate to here.

Что касается различий в преобладании R1a у Corded Ware Culture и R1b у ямников, то хочу напомнить — в статье приводится всего 5 определений гаплогрупп ямников, что конечно же мало! И уже после выхода статьи мы получили новый образец уже гаплогруппы R1aдля ямного погребения. Все определения, которыми мы сейчас оперируем получены из маленькой и далёкой территории – северной части степного Поволжья. Я же с большим оптимизмом жду определений ямников из Причерноморских степей.


Александр, дорый день! Надеждинка — это погребение 1 кургана 1. Оно основное. В глубокой яме лежал подросток — мальчик: Y-hapl. R1a1a1d2a. Лежал на спине, ноги подогнуты, руки не сохранились. Голова была посыпана тёмно-красной охрой, у левого плечал стоял круглодонный сосуд, лежала створка раковины. И обряд и инвентарь — типичные для ямной культуры Поволжья. Курган стоял на берегу р. Б.Иргиз (левый приток р. Волга) — N 52 град 12 минут, Е 48 град 39 мин. Должен заметить, что Восточное крыло ямников (Волго-Уралье) охватывает период 3400 — 2900 ВС. Западное крыло 3100-2400 ВС. Александр, а где вы встретили информацию о гаплогруппах энеолитических хвалынцев?


Уважаемая Елена, результат прислал Девид Райх (David Reih). Он возглавляет департамент в медицинской школе Гарварда. Увы, он ещё не опубликован. Ваш КП

Yep, the Corded Ware people were closely related to the Yamnaya folk. No doubt about it. I'd say it's just a matter a time before an early Yamnaya or proto-Yamnaya group is found on the steppe with R1a lineages ancestral to those present among Corded Ware males, and indeed many millions of present-day Europeans.

Sunday, March 20, 2016

Rakhigarhi ancient DNA paper probably a while away

Back in December The Guardian published an article saying that ancient DNA results from the Harappan site of Rakhigarhi, northern India, "may come within weeks" (see here).

I'm guessing now that it was just a slow news day feature, because we've seen nothing since, and the Korean team entrusted with doing the paleogenomics work has just come back from another dig at Rakhigarhi (see here). Best case scenario, it'll take them months to process the remains, analyze the DNA, and get something published.

On a more positive note, National Geographic is now backing the effort, I'm guessing with funds and/or equipment, which might mean more sophisticated outcomes, like hopefully a few full genomes.

My lab performed excavation in Rakhigarhi/India for Feb 19 to Mar 8 (Hong JH); Mar 4 to Mar 13 (Shin DH), 2016. The excavation is supported by National Geographic Foundation.


As regards our plans for the relevant human remains, they will be collected via a procedure specifically designed to minimize contamination by modern DNA. They will then be moved to and maintained at Deccan College. Subsequent anthropological analyses will proceed as follows: 1) gross anthropological study (determination of sex and age, identification of any pathological signs in bones, forensic investigation for race determination, etc.); 2) paleoparasitological study (analysis of soil sediments on hipbones, determination of any presence of parasite eggs, drawing of tentative conclusions on parasitic infection of Harappan people); 3) aDNA mitochondrial, Y-chromosomal, autosomal and stable-isotope analyses (obtainment of information on maternal and paternal lineages); 4) first-ever facial reconstruction of approximately 4,500-year-old Harappan person, a member of one of the greatest civilizations in human history (based on DNA and forensic data obtained in this study). It is anticipated that by the proposed research and the various advanced techniques entailed, a full and very detailed biological and anthropological picture of the Harappan people will be obtained.

Source: Excavation in Rakhigarhi on March

Update 25/03/2016: However, this talk will be presented later this year at the WAC-8 conference in Kyoto, which suggests that a paper with ancient DNA results from some of the Rakhigarhi remains is basically ready.

Harappan Burial Sites in India: Recent Research Trends

Astha Dibyopama1, Vasant Shinde1, Dong Hoon Shin2, Chang Seok Oh2 and Nilesh P. Jadhav1

1Department of Archaeology, Deccan College Post Graduate and Research Institute, India 2Institute of Forensic Science, Seoul National University, Korea

Harappan civilization flourished mainly in northwestern province of Indian subcontinent, roughly between 4000 to 1500 BCE. There are about more than fifty burial sites of the Harappa Civilization discovered so far. Of them, Lothal, Kalibangan, Rupar, Rakhigarhi, Farmana, Tarkhanwala Dera, Sanauli, Bedwa, Puthi Seman, Bhorgarh etc. are major sites yielding the remains of Harappan burial. Until the early 1980’s, the study of human skeletons was primarily focused to answer specific questions pertaining to establishing the ethnic or racial identity of the concerned population and was used primarily to complement archaeological hypotheses of cultural migration or diffusion. Recently, however, more efforts are also made to study diet, health and genetics of Harappan population. The aim of present paper is to show how these scientific methods that are recently applied to Harappan burial studies are useful for the complete reconstruction of Harappan civilization and its people.

Source: Papers presented in WAC8, Kyoto

Saturday, March 19, 2016

Indo-European phylogeny + Y-DNA R subclades

Here's one of the most sensible Indo-European phylogenetic trees of this type that I've seen to date. It comes from a recent paper from Tuebingen University (see here). I added the red Y-chromosome haplogroup R subclade labels. Can something like this work as well, or even better, with other haplogroups?

My decision to mark the Tocharian branch with R-M417* is based on the latest available information on the paternal markers of the Tarim Basin mummies (scroll down to the second part of the post here). The rest of my choices should be self explanatory.


Taraka Rama, Ancestry sampling for Indo-European phylogeny and dates, InProceedings (Aufsatz / Paper einer Konferenz etc.), 2016-03-07

Friday, March 18, 2016

New insights into human adaptation and population structure thanks to ancient genomes

Open access at Nature Communications:

Abstract: The influence of positive selection sweeps in human evolution is increasingly debated, although our ability to detect them is hampered by inherent uncertainties in the timing of past events. Ancient genomes provide snapshots of allele frequencies in the past and can help address this question. We combine modern and ancient genomic data in a simple statistic (DAnc) to time allele frequency changes, and investigate the role of drift and adaptation in population differentiation. Only 30% of the most strongly differentiated alleles between Africans and Eurasians changed in frequency during the colonization of Eurasia, but in Europe these alleles are enriched in genic and putatively functional alleles to an extent only compatible with local adaptation. Adaptive alleles—especially those associated with pigmentation—are mostly of hunter-gatherer origin, although lactose persistence arose in a haplotype present in farmers. These results provide evidence for a role of local adaptation in human population differentiation.

Key, F. M. et al. Human adaptation and population differentiation in the light of ancient genomes. Nat. Commun. 7:10775 doi: 10.1038/ncomms10775 (2016).

See also...

Lactase persistence and ancient DNA

Extracting Neandertal and Denisovan DNA from the genomes of present-day Melanesians

Open access at Science:

Abstract: Although Neandertal sequences that persist in the genomes of modern humans have been identified in Eurasians, comparable studies in people whose ancestors hybridized with both Neandertals and Denisovans are lacking. We developed an approach to identify DNA inherited from multiple archaic hominin ancestors and applied it to whole-genome sequences from 1523 geographically diverse individuals, including 35 new Island Melanesian genomes. In aggregate, we recovered 1.34 Gb and 303 Mb of the Neandertal and Denisovan genome, respectively. We leverage these maps of archaic sequence to show that Neandertal admixture occurred multiple times in different non-African populations, characterize genomic regions that are significantly depleted of archaic sequence, and identify signatures of adaptive introgression.

Vernot et al., Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals, Science 17 Mar 2016, DOI: 10.1126/science.aad9416

Wednesday, March 16, 2016

Sintashta, BMAC and the Indo-Iranians

I'm perusing the online archives of Harvard Sanskrit Professor Michael Witzel. The links below are worth checking out for some background info on the prehistory of Eastern Europe and Central Asia. There's a very cool map on page 6 of the second PDF.

Sintashta, BMAC and the Indo-Iranians. A query.

Linguistic Evidence for Cultural Exchange in Prehistoric Western Central Asia.

The Home of the Aryans.

Autochthonous Aryans? The Evidence from Old Indian and Iranian Texts.

Looking back, these old school linguistics articles make a lot more sense than most of the supposedly cutting-edge population genetics papers coming out at around the same time dealing with the Indo-Aryan question.

Many population geneticists back then took the view that the ancestors of the Indo-Aryans could not have spread from the European steppes to India because Y-chromosome haplogroup R1a apparently showed the greatest haplotype diversity in the Indus Valley. Well, what a load of crock that turned out to be.

See also...

The Poltavka outlier

Friday, March 11, 2016

D-stats/nMonte open thread

I'll start the ball rolling with a 9-way mixture analysis of 93 European, Near Eastern and Central Asian present-day and ancient populations. The relevant datasheet and R script are available here and here.

Below is a simple tree/cluster analysis based on the results, using the freely available Past3 software. Makes perfect sense, I'd say.

It's important to understand that these sorts of tests are basically designed to estimate ancient ancestry proportions, rather than calculate minor admixtures. With that in mind, here are a few observations:

- Karasuk outlier RISE497 (the most eastern Karasuk individual) is surprisingly important for Near Eastern populations

- Nordic LNBA and Sintashta look very similar in terms of overall ancestry proportions, suggesting that they perhaps derive from the same ancestral population

- The effects of postmortem deaminantion or DNA damage appear to be expressed in many of the non-UDG treated ancient samples as minor Sub-Saharan admixture

Can anyone put together a better model for West Eurasians? Also, I'd really like to see a well thought out D-stats/nMonte analysis of South Central Asia.

See also...

Yamnaya = Khvalynsk + extra CHG + maybe something else

D-stats/nMonte open thread #2

Sunday, March 6, 2016

D-stats/4mix tour of ancient Eurasia

This 4mix experiment is based on a series of statistics of the form D(Chimp,Reference_pop/Test_pop)(Mbuti,X), where X represents one of 9 ancient and present-day outgroups. The input data is available here. Feel free to try it yourself and post your models in the comments below.

Here's a Principal Component Analysis (PCA) based on the D-stats. As far as I can see, it makes very good sense. Click to enlarge.

See also...

Yamnaya = Khvalynsk + extra CHG + maybe something else

PC/nMonte open thread

Thursday, March 3, 2016

Irano-Turko-Slavic roots of Ashkenazi Jews?

As far as I've been able to discern, Ashkenazi Jews are very similar to Sephardic Jews, except with minor admixture from Central and Eastern Europe, and perhaps Central Asia (via the Silk Road). So the hypothesis presented in this new paper at Genome Biology and Evolution doesn't work for me:

The Yiddish language is over one thousand years old and incorporates German, Slavic, and Hebrew elements. The prevalent view claims Yiddish has a German origin, whereas the opposing view posits a Slavic origin with strong Iranian and weak Turkic substrata. One of the major difficulties in deciding between these hypotheses is the unknown geographical origin of Yiddish speaking Ashkenazic Jews (AJs). An analysis of 393 Ashkenazic, Iranian, and mountain Jews and over 600 non-Jewish genomes demonstrated that Greeks, Romans, Iranians, and Turks exhibit the highest genetic similarity with AJs. The Geographic Population Structure (GPS) analysis localized most AJs along major primeval trade routes in northeastern Turkey adjacent to primeval villages with names that may be derived from "Ashkenaz." Iranian and mountain Jews were localized along trade routes on the Turkey's eastern border. Loss of maternal haplogroups was evident in non-Yiddish speaking AJs. Our results suggest that AJs originated from a Slavo-Iranian confederation, which the Jews call "Ashkenazic" (i.e., "Scythian"), though these Jews probably spoke Persian and/or Ossete. This is compatible with linguistic evidence suggesting that Yiddish is a Slavic language created by Irano-Turko-Slavic Jewish merchants along the Silk Roads as a cryptic trade language, spoken only by its originators to gain an advantage in trade. Later, in the 9th century, Yiddish underwent relexification by adopting a new vocabulary that consists of a minority of German and Hebrew and a majority of newly coined Germanoid and Hebroid elements that replaced most of the original Eastern Slavic and Sorbian vocabularies, while keeping the original grammars intact.

Das et al., Localizing Ashkenazic Jews to primeval villages in the ancient Iranian lands of Ashkenaz, Genome Biol Evol (2016), doi: 10.1093/gbe/evw046

See also...

Khazar shmazar

Khazar shmazar #2