PCA/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.

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

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

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

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

Ancient DNA from early Medieval Muslim graves in France

A new paper at PLoS ONE reveals that three individuals from early Medieval burials in southern France belong to Y-chromosome haplogroup E1b1b1b-M81 and mtDNA haplogroups H1, K1a4a and L1c3a, and thus were probably of North African origin.

Abstract: The rapid Arab-Islamic conquest during the early Middle Ages led to major political and cultural changes in the Mediterranean world. Although the early medieval Muslim presence in the Iberian Peninsula is now well documented, based in the evaluation of archeological and historical sources, the Muslim expansion in the area north of the Pyrenees has only been documented so far through textual sources or rare archaeological data. Our study provides the first archaeo-anthropological testimony of the Muslim establishment in South of France through the multidisciplinary analysis of three graves excavated at Nimes. First, we argue in favor of burials that followed Islamic rites and then note the presence of a community practicing Muslim traditions in Nimes. Second, the radiometric dates obtained from all three human skeletons (between the 7th and the 9th centuries AD) echo historical sources documenting an early Muslim presence in southern Gaul (i.e., the first half of 8th century AD). Finally, palaeogenomic analyses conducted on the human remains provide arguments in favor of a North African ancestry of the three individuals, at least considering the paternal lineages. Given all of these data, we propose that the skeletons from the Nimes burials belonged to Berbers integrated into the Umayyad army during the Arab expansion in North Africa. Our discovery not only discusses the first anthropological and genetic data concerning the Muslim occupation of the Visigothic territory of Septimania but also highlights the complexity of the relationship between the two communities during this period.

Gleize Y, Mendisco F, Pemonge M-H, Hubert C, Groppi A, Houix B, et al. (2016) Early Medieval Muslim Graves in France: First Archaeological, Anthropological and Palaeogenomic Evidence. PLoS ONE 11(2): e0148583. doi:10.1371/journal.pone.0148583

CHG admixture in early western Anatolian farmers

Anatolian Neolithic farmer I0708 from the Mathieson et al. 2015 dataset belongs to Y-haplogroup J2a and is the most Caucasus-shifted of the early Anatolian farmers in my Principal Component Analysis (PCA) of West Eurasia (see below). This is unlikely to be a coincidence and provides strong evidence that at least some Neolithic farmers in western Anatolia harbored Caucasus Hunter-Gatherer (CHG) ancestry.

Note that the two CHG genomes sequenced to date courtesy of Jones et al. 2015, Kotias and Satsurblia, belonged to Y-haplogroups J and J2a. Moreover, J2 today shows peaks in frequency and diversity in and around the Caucasus. In other words, Y-haplogroup J, and in particular J2, appear to represent paternal signals of CHG admixture.

Unfortunately, it's not yet possible to demonstrate with formal tests beyond any doubt that I0708 has CHG admixture.

For instance, the D-stats below, in which a couple of the least Caucasus-shifted Anatolian farmers are Anatolia Neolithic1, while I0708 is Anatolia Neolithic2, fail to reach significance (Z=3). Please note, I ran the stats with the Amerindian and Siberian samples to test for Ancient North Eurasian (ANE) admixture, which appears to be a feature of CHG.

However, the results are all clearly positive, and might reach significance with higher quality data and/or a better reference than Anatolia Neolithic1.

Indeed, the subtle difference in ANE affinity between Anatolia Neolithic1 and Anatolia Neolithic2 is underlined by the D-stats below. Note that here Kotias shows significant signals of admixture when paired with Anatolia Neolithic1, but not when paired with Anatolia Neolithic2. This is despite the fact that Anatolia Neolithic2 is a higher coverage sequence (6.95x vs 2.66x) and offers more markers.

I0708 is unlikely to be the only early western Anatolian farmer with CHG/ANE admixture. The PCA above show that a couple of others are also pulling strongly towards the Caucasus. Indeed, all of the Anatolian and European Neolithic samples might harbor low levels of CHG ancestry. The problem with testing this idea at present is a lack of more basal Near Eastern ancient genomes from core areas of the Near East, like, say, the Levant.

Hopefully they're on their way, but in any case, it's almost certain now that CHG was already expanding west, and in all likelihood east, during the early Neolithic. This probably has some important implications for the peopling of West Eurasia and their linguistic affinities. Feel free to post what these might be in the comments.

Update 11/02/2016: I came up with new Anatolia Neolithic1 and Anatolia Neolithic2 sets using D-stats (by comparing each of the Anatolians to Kotias versus sample I0708). For a breakdown see here. Anatolia Neolithic2 now shows significant signals of admixture from Kotias, Dai, Surui and Han. This implies that it not only harbors CHG ancestry, but also ANE and East Asian-related admixtures.

Ancient Greeks and Romans may have imported a whole new genetic cline into Europe (or not)

Is anyone else thinking what I'm thinking? The Principal Component Analysis (PCA) below should be self-explanatory. But if you're having problems with the abbreviations and acronyms, consult the list of definitions here.

See also...

First Neolithic genomes from Greece

The enigmatic headless Romans from York

Greeks in a Longobard cemetery

The enigmatic headless Romans from York

My dataset was recently enriched with six ancient individuals from Roman York, courtesy of Martiniano et al. 2016.

They were either gladiators or soldiers. Each one was decapitated. This may have been a coup de grâce or a burial rite. At least one, 3DRIF-26, was not native to Britian.

In fact, isotopic evidence suggests that he spent his childhood in a region with a hot and dry climate such as North Africa or the Levant. Moreover, his top matching population in terms of pairwise Identical-by-State (IBS) allele sharing are present-day Saudis (see here).

However, I thought it might be useful to revisit 3DRIF-26's genetic affinities after taking into account his non-trivial Sub-Saharan admixture. This can be done with qpAdm. The best ten models are listed below.

Please note that in the last model I had to use 3DRIF-26 as a mixture source for present-day Egyptians, because he has less Yoruba-related admixture than the Egyptians.

Anatolia_Neolithic 0.528
Caucasus_HG Kotias 0.379
Yoruba 0.093
chisq 2.813 tail prob 0.421347

Samaritan 0.940
Yoruba 0.060
chisq 3.706 tail prob 0.447229

Cypriot 0.915
Yoruba 0.085
chisq 4.564 tail prob 0.334981

Lebanese_Druze 0.933
Yoruba 0.067
chisq 5.961 tail prob 0.202081

BedouinB 0.998
Yoruba 0.002
chisq 6.311 tail prob 0.17709

Lebanese_Christian 0.929
Yoruba 0.071
chisq 6.660 tail prob 0.155006

Lebanese_Muslim 0.943
Yoruba 0.057
chisq 6.874 tail prob 0.142671

Druze 0.933
Yoruba 0.067
chisq 8.235 tail prob 0.0833513

Iraqi_Jew 0.924
Yoruba 0.076
chisq 8.443 tail prob 0.0766321

Egyptian
Roman_outlier 0.900
Yoruba 0.100
chisq 9.262 tail prob 0.0548746

I'd say these results provide rather convincing evidence that 3DRIF-26's West Eurasian ancestry is derived from the Levant. Moreover, his relatively high level of Sub-Saharan admixture suggests that he came from the southern Levant or perhaps a nearby region, like the Sinai Peninsula.

Interestingly, the best models feature a couple of religious minorities (Samaritans and Lebanese Druze), an island population (Cypriots), and a fairly unique group in terms of genetic structure from Israel's Negev Desert (BedouinB). This suggests that 3DRIF-26 may have belonged to a similar religious or geographic isolate population, or, alternatively, that most of the Levant has experienced significant genetic shifts since he was alive.

The rest of the headless Romans were, in all likelihood, born and raised in or near Britain. However, two of the individuals, 3DRIF-16 and 6DRIF-3, show elevated IBS affinity to Lithuanians and Poles. At the same time, they both belong to Y-chromosome haplogroup R1b-U106 (aka M405), which is a marker generally thought to have arrived in Britain with Anglo-Saxons and Scandinavians. This might be a coincidence, but probably not.

D-stats confirm that they do show elevated Northeastern European affinity relative to the other three Romans. Only one of the Z-scores is statistically significant (>3), but most of the others would probably also reach significance with more SNPs and higher quality sequences.

My guess is that 3DRIF-16 and 6DRIF-3 were Britons of mixed origin, with recent ancestry from Scandinavia and/or East Central Europe. Indeed, they can be modeled with qpAdm as part Swedish and Polish.

England_Roman 0.869
Swedish 0.131
chisq 1.784 tail prob 0.775339

England_Roman 0.884
Polish 0.116
chisq 1.971 tail prob 0.741124

Data source and citation...

Martiniano, R. et al. Genomic signals of migration and continuity in Britain before the Anglo-Saxons. Nat. Commun. 7:10326 doi: 10.1038/ncomms10326 (2016).

Ancient genomes from Iron Age, Roman and Anglo-Saxon Britain (Martiniano et al. & Schiffels et al. 2016)

Open access at Nature Communications at this LINK:

The purported migrations that have formed the peoples of Britain have been the focus of generations of scholarly controversy. However, this has not benefited from direct analyses of ancient genomes. Here we report nine ancient genomes (~1 ×) of individuals from northern Britain: seven from a Roman era York cemetery, bookended by earlier Iron-Age and later Anglo-Saxon burials. Six of the Roman genomes show affinity with modern British Celtic populations, particularly Welsh, but significantly diverge from populations from Yorkshire and other eastern English samples. They also show similarity with the earlier Iron-Age genome, suggesting population continuity, but differ from the later Anglo-Saxon genome. This pattern concords with profound impact of migrations in the Anglo-Saxon period. Strikingly, one Roman skeleton shows a clear signal of exogenous origin, with affinities pointing towards the Middle East, confirming the cosmopolitan character of the Empire, even at its northernmost fringes.

Martiniano, R. et al. Genomic signals of migration and continuity in Britain before the Anglo-Saxons. Nat. Commun. 7:10326 doi: 10.1038/ncomms10326 (2016).

And another one at this LINK:

British population history has been shaped by a series of immigrations, including the early Anglo-Saxon migrations after 400 CE. It remains an open question how these events affected the genetic composition of the current British population. Here, we present whole-genome sequences from 10 individuals excavated close to Cambridge in the East of England, ranging from the late Iron Age to the middle Anglo-Saxon period. By analysing shared rare variants with hundreds of modern samples from Britain and Europe, we estimate that on average the contemporary East English population derives 38% of its ancestry from Anglo-Saxon migrations. We gain further insight with a new method, rarecoal, which infers population history and identifies fine-scale genetic ancestry from rare variants. Using rarecoal we find that the Anglo-Saxon samples are closely related to modern Dutch and Danish populations, while the Iron Age samples share ancestors with multiple Northern European populations including Britain.

Schiffels, S. et al. Iron Age and Anglo-Saxon genomes from East England reveal British migration history. Nat. Commun. 7:10408 doi: 10.1038/ncomms10408 (2016).

See also...

The enigmatic headless Romans from York

Hinxton ancient genomes roundup