tag:blogger.com,1999:blog-61915654392308248992024-03-12T19:12:47.992-07:00Polishgenes BlogFocusing on Polish and European population genetics and modern physical anthropology.Davidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.comBlogger25125tag:blogger.com,1999:blog-6191565439230824899.post-87830533323804954532023-11-10T21:43:00.004-08:002023-11-11T18:58:16.483-08:00Wielbark Goths were overwhelmingly of Scandinavian originWhen used properly, Principal Component Analysis (PCA) is an extraordinarily powerful tool and one of the best ways to study fine-scale genetic substructures within Europe.
The PCA plot below is based on Global25 data and focuses on the genetic relationship between Wielbark Goths and Medieval Poles, including from the Viking Age, in the context of present-day European genetic variation.
I'd Davidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.com0tag:blogger.com,1999:blog-6191565439230824899.post-24869926311663577442022-01-11T01:03:00.005-08:002022-01-11T01:16:32.350-08:00Population genetics is a state of mindYears of blogging about population genetics has seriously eroded my faith in the peer review process.
During the past decade I've witnessed an inordinate amount of crap published in basically all of the major science journals. Often the work is misguided in some way, sometimes even quite strange, and occasionally outright wrong.
Back in 2014, a team of scientists from the UK published a paper Davidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.com0tag:blogger.com,1999:blog-6191565439230824899.post-46686438515851637032020-07-13T07:34:00.001-07:002020-07-13T07:34:26.942-07:00Don't believe everything you read in peer reviewed papersCase in point, here's a quote from a recent paper at the Journal of Human Genetics (emphasis is mine):
The Mordovian and Csango samples have a moderate to slight orientation toward the Central-Asian and Siberian Turkic groups. This could suggest the more significant East Eurasian or Turkic ancestry of these populations, which should be further investigated. German samples are inhomogeneous, and Davidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.com0tag:blogger.com,1999:blog-6191565439230824899.post-8297669428911782622019-07-17T04:05:00.000-07:002019-11-01T00:03:00.560-07:00Viking invasion at bioRxivA new preprint featuring hundreds of Viking Age genomes has appeared at bioRxiv [LINK]. Titled Population genomics of the Viking world, it looks like a solid effort overall, although I'm skeptical about its conclusions. I might elaborate on that in the comments below, but I'll have a lot more to say on the topic if and when I get to check out the ancient genomes with my own tools. Details about Davidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.com0tag:blogger.com,1999:blog-6191565439230824899.post-2995788598056960442018-01-31T01:54:00.001-08:002019-10-23T03:28:13.644-07:00Modern-day Poles vs Bronze Age peoples of the East BalticBelow are three of my staple Principal Component Analyses (PCA) featuring Baltic Bronze Age (Baltic_BA) samples from the recent Mittnik et al. 2018 paper (open access here). On each of the plots I've also highlighted modern-day Balts and Poles. The latter two PCA also include most of the other ancients from the said paper (listed here). They're not highlighted, but all of the relevant datasheets Davidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.com31tag:blogger.com,1999:blog-6191565439230824899.post-2859085230961292172018-01-02T22:16:00.000-08:002019-10-23T02:10:23.610-07:00On the genomic history of North Eurasia (Triska et al. 2017)Over at BMC Genetics at this LINK. The accompanying dataset is freely available here, although it includes less than 300K SNPs, so the overlap with the Human Origins and EGDP datasets isn't great. Emphasis is mine:
Background: The history of human populations occupying the plains and mountain ridges separating Europe from Asia has been eventful, as these natural obstacles were crossed westward Davidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.com4tag:blogger.com,1999:blog-6191565439230824899.post-73268646611428578102017-06-19T04:17:00.000-07:002019-10-23T02:13:18.501-07:00Polish aDNA PCABelow is a Principal Component Analysis (PCA) that I put together for an upcoming presentation on Polish ancient DNA (aDNA). The five RISE samples are from Allentoft et al. 2015, including RISE569, the early Slavic genome from the Czech Republic, which was initially wrongly labeled as that of a Czech Bell Beaker (see here). PL_N17 is an Early Bronze Age (EBA) sample from Gustorzyn, Northern Davidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.com15tag:blogger.com,1999:blog-6191565439230824899.post-66231915023339713852017-05-20T02:32:00.000-07:002019-10-23T02:14:49.803-07:00Shared maternal ancestry between Slavs and Germanics probably dates to the Metal AgesOver at the Russian Journal of Genetics behind a paywall at this LINK. Emphasis is mine:
Abstract: The structure and diversity of mitochondrial DNA (mtDNA) macrohaplogroup U lineages in Russians from Eastern Europe are studied on the basis of analysis of variation of nucleotide sequences of complete mitochondrial genomes. In total, 132 mitochondrial genomes belonging to haplogroups U1, U2e, U3, Davidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.com10tag:blogger.com,1999:blog-6191565439230824899.post-67744626583153539662017-05-16T06:37:00.000-07:002019-10-23T02:16:04.886-07:00Globular Amphora people were starkly different from Yamnaya peopleThe figure below is from the recent Mathieson et al. 2017 preprint; slightly edited to highlight the results of nine Globular Amphora Culture (GAC) samples from two burial sites in what are now Poland and Ukraine.
Despite living in East Central Europe at about the same time as the nearby Yamnaya people of the Pontic-Caspian Steppe, these GAC individuals show practically zero Yamnaya-related orDavidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.com2tag:blogger.com,1999:blog-6191565439230824899.post-84991798749902630552017-03-28T03:18:00.000-07:002019-10-23T02:17:15.656-07:00Hints of deep genetic substructure in Iron Age PolandA paper at Infection, Genetics and Evolution looks at the susceptibility to infectious diseases in two late Iron Age groups from Central Poland. I can't wait to see genome-wide and Y-chromosome data from these and other ancient Polish populations. Judging by the outcomes presented in this paper, and also rumors that I've heard from Polish labs, we're in for some major surprises. Emphasis is mine:Davidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.com0tag:blogger.com,1999:blog-6191565439230824899.post-68495498629433610342016-07-27T03:55:00.000-07:002019-10-23T02:18:35.342-07:00Lipka Tatars vs Balto-SlavsNote the huge difference in this ADMIXTURE bar graph from the recent Pankratov et al. paper between Lipka Tatars from Belarus and nearby Balts and Slavs. The Lipka Tatars are almost identical to Volga Tatars despite residing in their current homeland for about 500 years. I'm guessing the fact that they're Sunni Muslims might have something to do with it.
Pankratov, V. et al. East Eurasian Davidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.com1tag:blogger.com,1999:blog-6191565439230824899.post-76733959284670576022016-06-18T01:48:00.001-07:002019-10-23T02:19:40.840-07:00Poles in the new Human Origins datasetHarvard's Human Origins dataset is being updated with 238 new samples, including 23 from Poland (15 from Poznan in western Poland and 8 from Lublin in eastern Poland). It should be available for download soon at the Reich Lab website here, although many of the new samples will only be accessible to people who sign a waiver. Below is a Principal Component Analysis (PCA) from Lazaridis et al. 2016 Davidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.com0tag:blogger.com,1999:blog-6191565439230824899.post-32950651934179201632015-07-18T05:03:00.001-07:002021-10-27T17:39:31.666-07:00Around 65% LN/EBA European ancestry in the Hindu Kush (?)One of the toughest nuts to crack in population genetics has proved to be the story of the people of the Hindu Kush. However, using TreeMix and ancient genomes from the recent Allentoft et al. and Haak et al. papers, I'm seeing most of the Kalash and Pathan individuals from the HGDP modeled as ~65% Late Neolithic/Early Bronze Age (LN/EBA) European and ~35% Central Asian. This, to me at least, Davidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.com53tag:blogger.com,1999:blog-6191565439230824899.post-87777245193647558482015-06-23T03:04:00.001-07:002021-10-27T17:32:43.047-07:00Badasses of the Bronze Age: Analysis of Andronovo, Battle-Axe, Corded Ware and Sintashta genomes - part oneFrom the Eneolithic to the Late Bronze Age vast areas of Eurasia were inhabited by a series of highly mobile and innovative groups that mostly relied on pastoralism for subsistence and, judging by their warlike grave goods, didn't mind a bit of biffo.
In Europe, where they first appeared, their archeological remains are generally classified as part of the Corded Ware Culture (or its Battle-Axe Davidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.com25tag:blogger.com,1999:blog-6191565439230824899.post-70212647510851125612015-05-03T12:22:00.000-07:002019-10-23T02:39:51.248-07:00R1a1a from an Early Bronze Age warrior grave in PolandAncient DNA tests on a skeleton from an Early Bronze Age "warrior" grave near Hrubieszow, southeastern Poland, have revealed that the remains belong to Y-haplogroup R1a1a [source].
Mitochondrial sequences were also obtained from seven other samples from the same burial site, and assigned to mt-haplogroups H1a, H1b (two), H2a (two), H6 and U5b1.
R1a1a is by far the most frequent Y-haplogroup in Davidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.com25tag:blogger.com,1999:blog-6191565439230824899.post-19903389111434647352014-10-23T19:08:00.000-07:002019-10-23T02:41:37.825-07:00Ancient DNA from Iron Age and Medieval PolandA new paper at PLoS ONE featuring ancient mitochondrial (mtDNA) data from Wielbark, Przeworsk and early Slavic remains argues for matrilineal continuity in present-day Poland since the Iron Age. It's actually based on a thesis that I blogged about more than two years ago (see here). However, it does include some fresh insights, so it's worth a look even if you read the thesis. RoIA stands for Davidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.com18tag:blogger.com,1999:blog-6191565439230824899.post-32155401253746101532014-08-13T08:23:00.000-07:002019-10-23T02:43:40.809-07:00Male height in EuropeA new paper in the Economics & Human Biology journal argues that male height in Europe is mostly determined by nutrition and genetics. That's not exactly earth shattering news. However, the authors also point out that Y-chromosome haplogroup I-M170 shows a strong correlation with the highest average stature on the continent, and speculate that the link between the two might be Upper Paleolithic Davidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.com14tag:blogger.com,1999:blog-6191565439230824899.post-2084838859346781512014-03-26T18:18:00.000-07:002019-10-23T02:46:56.409-07:00The story of R1a: the academics flounder onThere's been a lot of horseshit published over the years about Y-chromosome haplogroup R1a, which just happens to be my haplogroup. This includes academic papers in journals like PLoS ONE and Nature.
Indeed, a new paper on the phylogeography of R1a appeared at the Nature website today: Underhill et al. 2014. It's actually a much better effort than anything else on the topic at academic level Davidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.com35tag:blogger.com,1999:blog-6191565439230824899.post-45557578080562706882013-12-17T16:57:00.000-08:002019-10-23T02:50:38.943-07:00Near Eastern origin of Ashkenazi Levite R1aOver 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 Davidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.com74tag:blogger.com,1999:blog-6191565439230824899.post-62230660482465409912013-12-06T03:31:00.001-08:002019-10-23T02:51:39.009-07:00The Globular Amphora man from Late Neolithic PolandHe 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 Davidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.com2tag:blogger.com,1999:blog-6191565439230824899.post-57216212298917863582013-03-24T00:46:00.001-07:002019-10-23T02:52:58.590-07:00No Mongolian admixture in PolandOne of the most enduring myths or cliches concerning European genetic structure is that Poles carry Mongolian admixture. This claim has been repeated so often that it's now regarded by many as fact, including at academic level. Poles apparently acquired this admixture during Mongol and Turkic raids on Eastern Europe during the Middle Ages.
For a long time it was impossible to verify or debunkDavidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.com29tag:blogger.com,1999:blog-6191565439230824899.post-77359639045489542462012-06-20T21:02:00.001-07:002014-10-23T18:08:45.152-07:00First direct evidence of genetic continuity in West and Central Poland from the Iron Age to the presentI've just been sent a fascinating thesis on the mtDNA of Iron Age and Medieval samples from Poland. It suggests direct genetic continuity between Iron Age samples belonging to the Przeworsk and Wielbark Cultures, of what is now West and Central Poland, and present-day Poles. Here's the English summary, and a map of the sites under study:
For many years the origin of the Slavs has been the Davidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.com16tag:blogger.com,1999:blog-6191565439230824899.post-62880365270634744432012-01-23T04:53:00.000-08:002019-10-23T02:55:09.218-07:00Eurogenes' North Euro clusters - phase 2, final resultsThis is a continuation of my ChromoPainter analysis of Europeans from north of the Pyrenees, Alps and Balkans (see here). To obtain the most accurate results possible on my laptop, I increased the burn-ins and iterations in fineSTRUCTURE to 500K each (5 hour run in all, which is all I'm willing to put this machine through). The end product looks very similar to my initial analysis, in which I Davidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.com1tag:blogger.com,1999:blog-6191565439230824899.post-14194378600644920662012-01-14T22:01:00.000-08:002015-06-29T15:39:07.368-07:00Eurogenes' North Euro clusters - phase 1, exploring the dataI have some preliminary results from a new intra-North Euro cluster analysis, using a cutting edge tool called ChromoPainter. More than 400 samples and 270K SNPs were tested, in linkage mode, and then the output processed in fineSTRUCTURE at 200K burn-ins and iterations. Like I say, the results should be treated as preliminary, but they already look better than any other cluster analysis I've Davidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.com1tag:blogger.com,1999:blog-6191565439230824899.post-31929958355845745292008-11-19T20:43:00.000-08:002019-10-23T02:06:55.188-07:00Best of 2008: Corded Ware DNA from GermanyOne of the biggest hits of the year for this blogger was the discovery of Y-DNA haplogroup R1a among three Corded Ware skeletons from a burial site in Eulau, eastern Germany. It's an important result, because it links one of Europe's most dominant Y-haplogroups to a major Late Neolithic archeological complex.
All three individuals were confirmed to be paternally related via their shared Y-STR Davidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.com0