Tuesday, February 2, 2016
Due to their low SNP counts, I wasn't confident enough to run these three ancient genomes in Principal Component Analyses (PCA) when they were first published last year. But since then I've discovered a few things about how to get the most out of low quality samples with PCA projection, so here goes: 101 ancient Eurasian genomes (Allentoft et al. 2015)
Monday, December 21, 2015
Reich Lab et al. are now targeting more than 1.2 million sites in the ancient samples that they genotype, including over one million from the Illumina genotype array. This is great because it means that I can now run analyses with these ancients on the present-day populations in my Illumina array-based dataset using as many as 500K SNPs, which makes things more accurate and interesting. Below are a few sets of D-statistics of the form D(Outgroup,X)(Population1,Population2), featuring several ancient populations from the recent Allentoft et al., Haak et al. and Mathieson et al. papers. I'm basically testing how much closer X is to either Population1 or Population2. The results look very solid considering the spatio-temporal and archaeological origins of the samples. However, the outcomes for the smaller Northern European nations perhaps look slightly inflated. This is probably due to their peculiar demographic histories and resulting relative genetic homogeneity. At this stage, I don't know how to test this and limit its effects, if indeed it is a problem.
Afanasievo Poltavka 0.4678 Yamnaya_Kalmykia 0.4667 Yamnaya_Samara 0.4659 Srubnaya 0.4583 Corded_Ware_Germany 0.4554 Full output here Andronovo Sintashta 0.4584 Poltavka 0.4571 Srubnaya 0.4566 Yamnaya_Samara 0.4556 Afanasievo 0.455 Full output here Khvalynsk Poltavka 0.4617 Yamnaya_Samara 0.4594 Afanasievo 0.4556 Yamnaya_Kalmykia 0.454 Srubnaya 0.4522 Full output here Poltavka Yamnaya_Samara 0.4658 Afanasievo 0.4616 Yamnaya_Kalmykia 0.4602 Corded_Ware_Germany 0.4555 Srubnaya 0.4551 Full output here Poltavka_outlier Srubnaya 0.4572 Poltavka 0.4568 Sintashta 0.4534 Yamnaya_Samara 0.4518 Corded_Ware_Germany 0.4514 Full output here Potapovka Poltavka 0.4555 Srubnaya 0.454 Andronovo 0.4537 Yamnaya_Samara 0.4536 Corded_Ware_Germany 0.4523 Full output here Sintashta Andronovo 0.4567 Srubnaya 0.4553 Poltavka 0.4526 Yamnaya_Kalmykia 0.4507 Unetice_EBA 0.4506 Full output here Srubnaya Poltavka 0.4571 Yamnaya_Samara 0.4565 Afanasievo 0.454 Corded_Ware_Germany 0.4538 Unetice_EBA 0.4528 Full output here Yamnaya_Kalmykia Afanasievo 0.4644 Poltavka 0.464 Yamnaya_Samara 0.463 Srubnaya 0.4523 Andronovo 0.4513 Full output here Yamnaya_Samara Poltavka 0.4669 Yamnaya_Kalmykia 0.4615 Afanasievo 0.4612 Srubnaya 0.4554 Corded_Ware_Germany 0.4542 Full output hereSee also... qpAdm tour of the Eneolithic/Bronze Age steppe At least three genetically distinct Indo-European migrations into South Asia
Sunday, October 11, 2015
The recently revised Mathieson et al. preprint has some interesting comments about genetic ties between Bronze Age Eastern Europe and South Asia:
After the Poltavka period, population change occurred in Samara: the Late Bronze Age Srubnaya have ~17% Anatolian Neolithic or EEF ancestry (Extended Data Fig. 2). Previous work documented that such ancestry appeared east of the Urals beginning at least by the time of the Sintashta culture, and suggested that it reflected an eastward migration from the Corded Ware peoples of central Europe5. However, the fact that the Srubnaya also harbored such ancestry indicates that the Anatolian Neolithic or EEF ancestry could have come into the steppe from a more eastern source. Further evidence that migrations originating as far west as central Europe may not have had an important impact on the Late Bronze Age steppe comes from the fact that the Srubnaya possess exclusively (n=6) R1a Y chromosomes (Extended Data Table 1), and four of them (and one Poltavka male) belonged to haplogroup R1a-Z93 which is common in central/south Asians12, very rare in present-day Europeans, and absent in all ancient central Europeans studied to date.
This represents a direct link between the European steppe and central/south Asia, an intriguing observation that may be related to the spread of Indo-European languages in that direction.
Actually, several Corded Ware samples from previous studies carried the M417 and Z645 mutations, which are ancestral to Z93. So who's to say that the main patriarch of the Sintashta and Srubnaya cultures, both of which appear to have been rich in R1a-Z93, didn't live somewhere within the Corded Ware horizon, even as far west as Germany or Poland?
In any case, it's nice to see academia finally mention R1a-Z93 in the context of the Indo-European expansion into South Asia. I've been saying for years that this looks like the marker of the Proto-Indo-Iranians and Proto-Indo-Aryans (see here and here).
I also recently wrote how the early Indo-Europeans, all the way from Scandinavia to South Asia, were obsessed with the sun and the moon, otherwise known as the Divine Twins (see here). After seeing the results in Mathieson et al., I did some Googling about the Srubnaya Culture, and found these news features:
Illuminating! Ancient Slab May Be Sundial-Moondial
Photos: Ancient Sundial-Moondial Discovered
Fascinating stuff. Anyone know if similar Sundial-Moondials dating to the Bronze or Iron Age have been found in South Asia?
Lactase persistence and ancient DNA
The Poltavka outlier
Friday, September 18, 2015
A new open access paper at Current Biology looks at the role of recent admixture in the formation of the present-day West Eurasian gene pool. It appears to be an updated version of a paper from last year which I found somewhat disappointing (see here). This effort is a lot better; it's more detailed and sophisticated, and the authors are more cautious with their interpretations of the data.
That's it for now, but I'll have a lot more to say about these results soon at my other blog when more ancient DNA data rolls in from southern Europe and the Near East.
Below is Figure 4A from the paper, which shows the proportions of admixture from outside of Europe and West Asia among a wide variety of West Eurasian groups.
Busby et al., The Role of Recent Admixture in Forming the Contemporary West Eurasian Genomic Landscape, Current Biology, DOI: http://dx.doi.org/10.1016/j.cub.2015.08.007
Wednesday, September 2, 2015
PLoS One has just put out a major paper on the genetic structure of Balto-Slavs, and unfortunately I have to say it's a major disappointment.
Kushniarevich A, Utevska O, Chuhryaeva M, Agdzhoyan A, Dibirova K, Uktveryte I, et al. (2015) Genetic Heritage of the Balto-Slavic Speaking Populations: A Synthesis of Autosomal, Mitochondrial and Y-Chromosomal Data. PLoS ONE 10(9):e0135820. doi:10.1371/journal.pone.0135820
The authors used a very small number of Polish samples for their genome-wide analysis, mostly from the Estonian Biocentre (see here and here). At least 10 of these Poles come from Estonia, and some even resemble northern Russians with their unusual ancestry proportions. Note the dichotomy in the levels of the lemon yellow "Siberian/Volga-region" component within the Polish set in the ADMIXTURE bar graph from the paper.
I raised this issue with Estonian Biocentre Research Director Mait Metspalu a while ago when these samples were first published, and this was his response.
What we have is self identity. As you can see from Supplementary table 1 these samples have been collected in Estonia and the donors are self reported Poles.
Well, I'm sure there are people in South America who identify as Spanish. But would anyone in their right mind use them to make inferences about the genetic structure and history of the people of Spain?
Fine-scale population genetic analyses like this should only be done with lots of samples from the right places. Self-reported Poles from Estonia, and perhaps also Russia, who clearly don't resemble Poles from Poland aren't good enough. Estonian Biocentre scientists do a lot of useful work, but in this particular instance they were rather sloppy in labeling these Estonian Poles as simply Polish.
Kushniarevich et al. were very sloppy in not stating where their Polish samples were really from (their map shows the middle of Poland) and not bothering to remove obvious outliers from their dataset.
Recent admixture in West Eurasia (including Europe)
Friday, August 14, 2015
The recent Allentoft et al. paper on the ancient genomics of Eurasia featured an Early Bronze Age Corded Ware/proto-Unetice individual belonging to Y-haplogroup R1a. His remains came from a kurgan burial in present-day Greater Poland, or Wielkopolska, known as one of the four Pyramids of Wielkopolska.
Of course, R1a is by far the most common Y-haplogroup in Poland today, and Greater Poland is generally accepted to be the cradle of the Polish nation.
It's tempting to think that all of this isn't just a happy coincidence, and that this kurgan man and/or his close relatives are the ancestors of modern-day Poles. Considering that we have some of his genome, can we actually test this hypothesis?
Unfortunately, the sequence by itself is too limited to allow such a high resolution analysis. However, the Allentoft et al. dataset includes six other Bronze Age samples from Poland; one other Corded Ware individual from Greater Poland, and five Unetice individuals from Silesia. Thus, it's possible to combine these samples and at least run a preliminary analysis comparing them to present-day Europeans, including Poles, to test their affinities.
The only reliable way to do this is to use formal statistics, and specifically D-statistics. That's because, unlike model-based analyses, D-stats ignore recent genetic drift and, unlike f3-stats, they're able to discriminate correctly at a very fine scale between samples with somewhat different numbers of markers. Below are two sets of results of the form D(Outgroup, PopulationTest) (Population1, Population2).
D(Ju_hoan_North, Poland_Bronze_Age) (BedouinB, European)Basically, what the results show is that western Poland was inhabited by a very northern people during the Bronze Age. They were similar to present-day Balts, Scandinavians, Irish, and...Poles.
D(Ju_hoan_North, Poland_Bronze_Age) (Polish, European)
Indeed, in these sorts of tests small Northern European countries tend to get the best scores with most prehistoric Europeans. I believe that this isn't just because of shared ancestry, but also relative isolation and homogeneity. So the fact that Poland is the only really big country at the top of the list above might be very important.
That's pretty much it for now. As far as I can see, there's nothing to suggest that present-day Poles can't be the direct descendants of these ancients. But as I say, this was a preliminary analysis and a work in progress. I'll revisit this issue when more samples come in. By the way, I also ran a bunch of other D-stats that might be of interest.
D(Ju_hoan_North, Bell_Beaker) (BedouinB, European)
D(Ju_hoan_North, Corded_Ware) (BedouinB, European)
D(Ju_hoan_North, EHG) (BedouinB, European)
D(Ju_hoan_North, Hungary_BA) (BedouinB, European)
D(Ju_hoan_North, Loschbour) (BedouinB, European)
D(Ju_hoan_North, Motala_HG) (BedouinB, European)
D(Ju_hoan_North, Stuttgart) (BedouinB, European)
D(Ju_hoan_North, Unetice_EBA) (BedouinB, European)
D(Ju_hoan_North, Yamnaya) (BedouinB, European)
It's useful to plot D-stats against each other when looking for patterns in the data. For instance, in the graphs below Basques and southern French often look like obvious outliers. What this means is that there's something peculiar about their genetic history. What might that be I wonder? Any suggestions?
The present-day Polish samples, eleven in all, came from here. Most of the other samples are from the Allentoft et al. (Rise Project), Haak et al. and Lazaridis et al. datasets, all of which are publicly available.
R1a1a from an Early Bronze Age warrior grave in Poland
Monday, July 27, 2015
I never knew that corded ware penetrated deep into the Balkans. According to this recent paper, it certainly did, even as far as present-day Greece.
Abstract: The analysis of corded ware and accompanying artifacts reveals the nature of its appearance across the Central and Southern Balkan Eneolithic during three cultural-chronological horizons. The first horizon corresponds to the Early Eneolithic, namely the Bubanj-Salcuta-Krivodol cultural complex (BSK), while the second corresponds to the Cotofeni culture. The third horizon, showing chronological continuity with the second, and set within the Late Eneolithic/Early Bronze Age, has a site distribution that encompasses the territory of nearly the entire Balkan Peninsula, where corded ware is found together with other steppe elements which are present in large numbers, such are burials under mounds and the appearance of the domestic horse.
Aleksandar Bulatovic, Corded Ware in the Central and Southern Balkans: A Consequence of Cultural Interaction or an Indication of Ethnic Change?, The Journal of Indo-European Studies, Volume 42, Number 1 & 2, Spring/Summer 2014
Population genomics of Early Bronze Age Europe in three simple graphs