Sunday, February 23, 2014
The Estonian Biocentre has a new genotype dataset available from the recently released "Khazar" preprint (see here). The samples include Poles from Estonia, so I ran a PCA to see whether there was a clear difference between them and their ethnic kin from Poland in terms of genome-wide genetic structure. This doesn't appear to be the case, except for a few individuals who probably have significant Estonian and/or northwest Russian ancestry (the several northernmost and easternmost Polish_Estonian samples on the plots below). It's an interesting result, considering that, as far as I know, most Estonian Poles are not of recent Polish origin, but have roots in the East Baltic dating back to the Polish-ruled Duchy of Livonia of the 1600s. Please note, the plots were rotated and stretched horizontally to fit with geography.
Behar, Doron M.; Metspalu, Mait; Baran, Yael; Kopelman, Naama M.; Yunusbayev, Bayazit; Gladstein, Ariella; Tzur, Shay; Sahakyan, Havhannes; Bahmanimehr, Ardeshir; Yepiskoposyan, Levon; Tambets, Kristiina; Khusnutdinova, Elza K.; Kusniarevich, Aljona; Balanovsky, Oleg; Balanovsky, Elena; Kovacevic, Lejla; Marjanovic, Damir; Mihailov, Evelin; Kouvatsi, Anastasia; Traintaphyllidis, Costas; King, Roy J.; Semino, Ornella; Torroni, Anotonio; Hammer, Michael F.; Metspalu, Ene; Skorecki, Karl; Rosset, Saharon; Halperin, Eran; Villems, Richard; and Rosenberg, Noah A., No Evidence from Genome-Wide Data of a Khazar Origin for the Ashkenazi Jews (2013). Human Biology Open Access Pre-Prints. Paper 41.
Friday, February 14, 2014
We've turned out French-like. Sacrebleu!
Source: A genetic atlas of human admixture history
Mapping the history of human admixture (paper + website)
Monday, January 27, 2014
This has actually been obvious for a while now, thanks to both modern and ancient DNA. But the figure below from the new Olalde et al. paper on the complete genome of a Mesolithic hunter-gatherer from Iberia illustrates it more effectively than anything else I've seen to date. Note that the Polish reference set (PL) shows significantly higher allele sharing with the ancient Iberian, La Brana 1, than do Germans (DE). In fact, only Swedes (SE) manage to better Poles in this regard. But it's also worth noting that Poles show the highest allele sharing with the two partial genomic sequences of Neolithic hunter-gatherers from Gotland, Ajv70 and Ajv52.
On the other hand, compared to Poles, Germans clearly show higher allele sharing with Gok4, the Neolithic farmer from Southern Sweden, and Otzi the Iceman from the Copper Age Tyrolean Alps. Unlike the hunter-gatherers, who are genetically more Northern European than any Europeans alive today, these ancient samples are more Mediterranean, and indeed more Near Eastern, than most present-day Europeans, which is something that can be seen clearly on the main Principal Component Analysis (PCA) from Olalde et al. below. This suggests that most of their ancestors arrived in Europe from the Near East during the Neolithic.
It's an intriguing outcome between these two large neighbouring European countries, but perhaps easily explained by geography and climate? Germany is situated west of Poland, so it has a warmer climate, and thus its territory was more heavily settled by early farmers from the Mediterranean Basin during the Neolithic. Moreover, much of what is now Germany was part of the Roman Empire, which might have facilitated gene flow between the ancestors of present-day Germans and southern Europeans.
Poles, on the other hand, show stronger genetic links to Baltic populations, especially Lithuanians and Estonians, who are arguably the most Mesolithic-like Europeans alive today (see here). In fact, if they were present on the graphs above, they'd probably easily top the allele-sharing list with La Brana 1 and all of the hunter-gatherers from Gotland. This might be due to the almost impenetrable primeval forests that once covered the areas just south and east of the Baltic, as well as the relatively cold climate in these regions.
Olalde et al., Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European, Nature (2014), doi:10.1038/nature12960
Prehistoric Scandinavians genetically most similar to modern Poles
Mesolithic genome from Spain reveals markers for blue eyes, dark skin and Y-haplogroup C6
Tuesday, December 17, 2013
Over at Nature Communications, Rootsi et al. report on a newly discovered Ashkenazi-specific subclade of R1a, defined by the M582 mutation. They argue that it's a marker of Near Eastern origin, and based on the comprehensive data in their paper, I'd say they're correct. However, it's important to note that this doesn't preclude an ultimate Eastern European or Central Asian source of M582 in the Near East. For instance, an R1a mutation ancestral to M582 might have been introduced by the proto-Iranians from the steppe into what is now Iran during the early Indo-European dispersals. Indeed, that's actually what Figure 1a from the study suggests (phylogenetic tree of R1a below). The paper is open access, but here are a few quotes anyway:
Haplogroup R1a-M582 was only sporadically observed in Europe, the Diaspora residence of Ashkenazi Jews. Notably, it was not identified among 2,149 samples (including 922 R1a-M198) of non-Jews from East Europe, where the Ashkenazi Jewish community flourished in recent centuries (Table 1).
Within 1,068 West/North European samples (106 R1a-M198), M582 was observed in just one German sample, and among 3,756 Central/South European samples (710 R1a-M198), it was found only in one Hungarian and one Slovakian sample (Table 1).
Among 3,739 Near Eastern samples (303 R1a-M198), R1a-M582 was identified in various populations, with the highest frequency occurring within Iranians collected from the southeastern Kerman population who self-identified as Persians, northwestern Iranian Azeri and in Cilician Anatolian Kurds, at 2.86%, 2.50% and 2.83%, respectively (Table 1). In contrast, among 2,164 samples from the Caucasus (211 R1a-M198), R1a-M582 was found in just one Nogay sample (Table 1).
Considering the historical records of Ashkenazi Jews, three potential geographic sources should be considered: the Near East, which was the geographic location for the ancient Hebrews; Europe, which was the residence of the Ashkenazi Jewish Diaspora and the region in which they evolved for nearly two millennia; and the region overlapping with the no longer extant mid-11th Century Khazarian Khaganate, whose ruling class has been suggested to have converted to Judaism18. Our data render the latter source highly unlikely since the Khazarian Khaganate overlapped with the Northern Pontic-Caspian steppe and the North Caucasus region, in which just one Nogay sample carried the R1a-M582 haplogroup (Table 1). Furthermore, the Nogays, formerly a powerful Kipchak Turkic-speaking nomadic confederation, are relatively recent inhabitants of the Caucasus, and the STR haplotype of the sole R1a-M582 Nogay sample lies outside of the Levite cluster. Had the Caucasus region been the source for the Ashkenazi modal lineage, we likely would have found R1a-M582 Y-chromosomes in some of its 20 local populations examined in our sample of more than 2,000 Y-chromosomes (Table 1).
Near Eastern populations are the only populations in which haplogroup R1a-M582 was found at significant frequencies (Table 1). Moreover, the representative samples displayed substantial diversity even within this geographic region (Fig. 1b). Higher frequencies and diversities often suggest lineage autochthony.
Rootsi, S. et al. Phylogenetic applications of whole Y-chromosome sequences and the Near Eastern origin of Ashkenazi Levites. Nat. Commun. 4:2928 doi: 10.1038/ncomms3928 (2013).
Origins of R1a1a in or near Europe (aka. R1a1a out of India theory looks like a dud)
R1a and R1b as markers of the Proto-Indo-European expansion: a review of ancient DNA evidence
Ancient Siberians carrying R1a1 had light eyes - take 2
New R1a1a tree
Saturday, December 7, 2013
The results from the first study on the eating habits of the people of the Wielbark Culture are now out in a peer-reviewed article: Diet and society in Poland before the state: stable isotope evidence from a Wielbark population (2nd c. AD). They were originally published back in 2012 as part of a thesis, which also included data on the diet of suspected Viking settlers in Medieval Poland (see here).
The δ13Cca values from Rogowo [the Wielbark site in question] suggest millet contributed between 0% and 35% to overall diet, depending on the individual. This corroborates archaeobotanical evidence for a broad-spectrum agricultural strategy including millet, barley, rye, oats and wheat (Wasylikowa et al. 1991).
Unlike in Eastern and Southern Europe, millet is not widespread in Western Europe. With its occurrence following cultural distribution patterns rather than geography or climate, millet appears to characterize diets of Slavic populations. In her book documenting the history of Polish cuisine, Maria Dembińska posits that “… the Polish preference for millet was cultural and that millet must have arrived with the earliest Slavic migrants” (104). That millet might be used as a proxy for Slavic migrations is an interesting possibility, given the controversy surrounding the relationship between the Wielbark culture and the issue of Slavic ethnogenesis (c.f., Dąbrowski 2006). Millet consumption among Wielbark and early medieval Polish populations represents a potentially significant continuity between the Roman era and the medieval period in Poland.
Diet at Rogowo was based on terrestrial foods (meat, milk, and plants), but with supplemental input from fish (likely low- δ15N anadromous or littoral fish), indicating an overall broad-spectrum subsistence economy. Millet was consumed at Rogowo, and in greater amounts than during the medieval period to follow (c.f., Fig. 6; Reitsema et al. 2010; Reitsema 2012). Stable isotope differences between the sexes indicate that men and women may have consumed different foods, although there is a possibility that women migrated to Rogowo from an isotopically different region of Europe.
Ancient DNA has already been extracted from some of the Rogowo samples, and the results presented in a thesis focusing on the ethnogenesis of Slavs, and in particular the question of genetic continuity in present-day Poland from the Iron Ago to the early Medieval period (see here). The outcome was somewhat inconclusive, because the study was based on low resolution mtDNA haplotypes. However, the most informative haplotypes showed greatest affinity to those of the present-day Polish population. A more detailed genetic analysis of Wielbark and many other ancient Polish samples, using next-generation sequencing, is on the way (see here).
Laurie J. Reitsema, Tomasz Kozłowski, Diet and society in Poland before the state: stable isotope evidence from a Wielbark population (2nd c. AD), Anthropological Review. Volume 0, Issue 0, Pages 1–22, ISSN (Online) 2083-4594, ISSN (Print) 1898-6773, DOI: 10.2478/anre-2013-0010, November 2013
Friday, December 6, 2013
He was short (<160 cm), probably lactose intolerant, had an exceedingly long melon (cranial index = 72.6), and belonged to mtDNA haplogroup K2a. In other words, he was a typical Neolithic farmer, and clearly different from the average modern-day inhabitant of the North European Plain.
No doubt, his people were largely replaced by newcomers from the east and also west during the frequent population shifts in the region after the Neolithic (see here). However, the stable isotope analysis suggests that he ate a lot of millet, which is known as a typically Slavic cultigen in Europe.
ABSTRACT: In 2007 a ceremonial complex representing the Globular Amphora Culture was discovered in Kowal (the Kuyavia region, Poland). Radiocarbon dating demonstrated that the human remains associated with the complex are of similar antiquity, i.e. 4.105 ± 0.035 conv. and 3.990 ± 0.050 conv. Kyrs. After calibration, this suggests a period between 2850 and 2570 BC (68.2% likelihood), or more specifically, 2870 to 2500 BC (95.4% likelihood). Morphological data indicate that the skeleton belonged to a male who died at 27–35 years of age. The unusual morphology of his hard palate suggests this individual may have had a speech disorder. Stable oxygen isotope values of the individual's teeth are above the locally established oxygen isotope range of precipitation, but due to sample limitations we cannot conclusively say whether the individual is of non-local origin. Stable carbon and nitrogen isotope ratios were analyzed to reconstruct the diet of the studied individual, and show a terrestrial-based diet. Through ancient DNA (aDNA) analysis, the mtDNA haplogroup K2a* and lactose intolerance as evidenced by homozygous C-13910 allele were identified. These aDNA results are the first sequences reported for an individual representing the Globular Amphora Culture, enriching the still modest pool of human genetic data from the Neolithic.
Kozłowski T., Stepańczak B., Laurie J. Reitsama, Osipowicz G., Szostek K., Płoszaj T., Jędryhowska-Dańska K., Pawlyta J., Paluszkiewicz C., Witas H.W. Osteological, chemical and genetic analyses of the human skeleton from a Neolithic site representing the Globular Amphora Culture (Kowal, Kuyavia region, Poland), Anthropologie [In Press]
Polish "Goths" enjoyed their millet, while Polish "Vikings" did not
Friday, November 22, 2013
Update 7/12/2013: 23andMe's Ancestry Composition is now better, but still not great
Almost a year ago, amidst great marketing fanfare and expectations from customers, 23andMe rolled out the Ancestry Composition (AC). This wasn't just supposed to be an updated Ancestry Painting (the company's previous main ancestry tool), but a state-of-the-art global and local ancestry deconvolution analysis that would put all competitors to shame.
Alas, not everything went according to plan.
For one, 23andMe's decision to represent Europe as ten ancestral regions, but not break up Sub-Saharan Africa or eastern Asia, was met with disbelief from many of the punters. Secondly, the AC suffered from an overfitting problem.
Overfitting happens when the individuals being tested are also used as reference samples, so they end up with inflated ancestry proportions based on their self-reported ancestry. For more info check out these threads at the 23andMe forums here and here. I was one of the overfitted customers, and it really pissed me off.
23andMe tried to fix the overfitting problem about six weeks after the launch, but that didn't go too well at all. See here.
Last week 23andMe announced that it would again attempt to fix the overfitting problem, and also break up Sub-Saharan Africa and eastern Asia into three and five regions, respectively. I'm not sure if the process has started yet, but you can get updates on how things are going here. You'll see these question marks next to the new reference sets in the AC until your updated ancestry proportions have been computed.
I was very excited about the AC when it was first announced, but now, after a year of waiting for the overfitting fix, I find the whole thing very underwhelming. I might, at some stage, write a review and user guide, but then again I might not.