Eupedia Forum - Paleogenetics Debate new studies about ancient DNA (Y-DNA, mtDNA or autosomal DNA). en Fri, 18 Oct 2019 07:30:13 GMT vBulletin 60 Eupedia Forum - Paleogenetics Genomic game of thrones: Ancient DNA analysis of European and Asian royal dynasties Tue, 15 Oct 2019 09:25:48 GMT Abstract In most societies, aristocracy has a marriage pattern different from that of the general population. Dynasties of rulers often had foreign origin and thus might be genetically distant. Moreover, they tend to marry their relatives (which genetically would result in elevated inbreeding)... Abstract

In most societies, aristocracy has a marriage pattern different from that of the general population. Dynasties of rulers often had foreign origin and thus might be genetically distant. Moreover, they tend to marry their relatives (which genetically would result in elevated inbreeding) and partners from other countries (genetically counteractive). A genomic analysis of royal families is therefore interesting not only for the sake of accurate historical identification, but also for addressing population genetic questions on an “aristocratic subpopulation”.

We analyzed genomic data representing three dynasties: the medieval North European Rurikid dynasty, the 19th century Russian Romanov dynasty, and Genghis Khan’s descendants.

The chronicles indicate that Rurikid princes, which ruled Russia over seven centuries, descent from the Viking Rurik. The genetic-genealogical analysis of the present-day princes identified the core genetic lineage rooted in Scandinavia. We analyzed the ancient DNA of medieval princes including Vladimir (11th century) who is placed in traditional genealogy just five generations apart from the Rurik, and compared the ancient and modern members of the Rurikid dynasty.

The second study was performed in parallel by the two ancient DNA labs which were approached by the Russian Church requesting kinship analyses of the anonymous bone samples. The analysis was made as a blind test, the investigation was paralleled, and the results matched. The mtDNA profiles coincided with the published data on the last Russian emperor and empress (Rogaev et al., 2009), but the new results included also the preceding generations of the dynasty. The genomic results corroborate previous PCR-based findings and will settle the remaining doubts around the authenticity of Royal family remains. Genetically, these individuals are consistent with being Central Europeans, in agreement with the genealogical records, as they were close relatives of the Danish king, Queen Victoria of the United Kingdom, and other Central European dynasties.

Finally, we analyzed Y-chromosomes of several clans claiming their origin from Genghis Khan. Surprisingly, the genetic variation in this sample was even higher than in general population. While the Nyru’un tribe (Genghis Khan belonged to) in general carried high frequency of the “star-cluster” (C-F3796), most studied aristocratic clans from Kazakhstan, Mongolia, and China carried two other lineages (C-F1756 and C-M407).
Paleogenetics Jovialis
The genetics of the second plague pandemic Wed, 02 Oct 2019 17:36:10 GMT Max Planck again. It's really the genetics of the "Black Death" and going forward.


"Analysis of 34 ancient plague genomes from the Black Death and succeeding plague epidemics in Europe between the 14th and 17th centuries, reveals how the bacterium diversified after a single introduction."

Insufficient coverage of Italy, ONE sample, when it killed so many of us. There was a 90% death rate in Fivizzano in the Lunigiana, one of the highest I've ever seen.

An international team of researchers has analyzed remains from ten archaeological sites in England, France, Germany, Russia, and Switzerland to gain insight into the different stages of the second plague pandemic (14th-18th centuries) and the genetic diversity of Yersinia pestis during and after the Black Death. In a study published in Nature Communications, the researchers reconstructed 34 Y. pestis genomes, tracing the genetic history of the bacterium, which revealed key insights into the initiation and progression of the second plague pandemic in Europe."

It's the steppe again, but the spread was, from historical accounts, from the Crimea to Italy aboard Genovese ships. Do geneticists never read history? If they knew that you'd think they would have looked for more samples from Italy. They're ubiquitous. That would have given a clearer idea of the spread. Even with only the one sample from Italy (Siena), it's suggestive that the historical accounts are true.

This is what comes of educating scientists as if they're car mechanics and university is a trade school. There should be MANDATORY classes in Western Civilization for two years.

Despite the ubiquity of the Black Death in historical texts and the popular imagination, the entry point of the
Y. pestis bacterium at this time and the route it traveled through Europe remain unclear, due to a lack of data from early outbreaks and a general scarcity of published ancient Y. pestis genomes. In the current study, researchers reconstructed plague genomes from the teeth of 34 individuals, including two from Laishevo, in the Volga region of Russia, and found a single strain that is ancestral to all second pandemic strains. In addition, the researchers observe an absence of genomic diversity from samples during the Black Death. “These findings indicate a single entry of Y. pestis into Europe through the east”, explains first author Maria Spyrou of the Max Planck Institute for the Science of Human History. “However, it is possible that additional interpretations may be revealed with future discoveries of un-sampled diversity in western Eurasia”, she notes.

This disease has been pivotal in human history. First it facilitated the arrival of the Europeans, a variant may have helped bring down the Roman Empire, and then it paved the way for the changes in the late Medieval period and Renaissance.

Burial pits in second plague pandemic
Paleogenetics Angela
Projectile-weapons enter Europe 20,000 years earlier than previously thought Mon, 30 Sep 2019 16:35:42 GMT A team of Japanese and Italian researchers, including from Tohoku University, have evidenced mechanically delivered projectile weapons in Europe dating to 45,000-40,000 years—more than 20,000 years than previously thought. This study, titled "The earliest evidence for mechanically delivered projectile weapons in Europe," published in Nature Ecology & Evolution, indicated that the spearthrower and bow-and-arrow technologies allowed modern humans to hunt more successfully than Neanderthals—giving them a competitive advantage. This discovery offered important insight to understand the reasons for the replacement of Neanderthals by modern humans.
Apparently, Neanderthals and modern humans coexisted in Europe for at least 5,000 years. However, little is known about why modern humans could increase their population size after migrating to Europe and successfully occupy new territories, while autochthonous Neanderthals went extinct ~ 40,000 years ago.



The backed pieces were macroscopically and microscopically analyzed using a Hirox digital microscope and results were compared with use-wear patterns on experimental samples. Through this analysis, diagnostic impact fractures and microscopic impact linear traces were found on numerous backed pieces, demonstrating that they were used as hunting weapons. "The diagnostic impact fractures showed the similar patterns of experimental samples delivered by a spearthrower and a bow, but significantly different from those observed on throwing and thrusting samples," said Katsuhiro Sano. "Modern humans migrating into Europe equipped themselves with mechanically delivered projectile weapons, such as a spearthrower-darts or a bow-and-arrows, which had higher impact energy hunting strategy and offered modern humans a substantive advantage over Neanderthals," concluded Sano.

Paper: ]]>
Paleogenetics Jovialis
Removing reference bias in ancient DNA Fri, 27 Sep 2019 17:53:26 GMT *Abstract* During the last decade, the analysis of ancient DNA (aDNA) sequence has become a powerful tool for the study of past human populations. However, the degraded nature of aDNA means that aDNA sequencing reads are short, single-ended and frequently mutated by post-mortem chemical... Abstract

During the last decade, the analysis of ancient DNA (aDNA) sequence has become a powerful tool for the study of past human populations. However, the degraded nature of aDNA means that aDNA sequencing reads are short, single-ended and frequently mutated by post-mortem chemical modifications. All these features decrease read mapping accuracy and increase reference bias, in which reads containing non-reference alleles are less likely to be mapped than those containing reference alleles. Recently, alternative approaches for read mapping and genetic variation analysis have been developed that replace the linear reference by a variation graph which includes all the alternative variants at each genetic locus. Here, we evaluate the use of variation graph software vg to avoid reference bias for ancient DNA. We used vg to align multiple previously published aDNA samples to a variation graph containing 1000 Genome Project variants, and compared these with the same data aligned with bwa to the human linear reference genome. We show that use of vg leads to a much more balanced allelic representation at polymorphic sites and better variant detection in comparison with bwa, especially in the presence of post-mortem changes, effectively removing reference bias. A recently published approach that filters bwa alignments using modified reads also removes bias, but has lower sensitivity than vg. Our findings demonstrate that aligning aDNA sequences to variation graphs allows recovering a higher fraction of non-reference variation and effectively mitigates the impact of reference bias in population genetics analyses using aDNA, while retaining mapping sensitivity.
Paleogenetics Jovialis
Adaptive evolution in humans-A Review Fri, 27 Sep 2019 14:48:24 GMT Very handy review of the current state of knowledge about adaptation in a number of areas: pigmentation, lactase persistence, high fat, high starch diets, malaria, etc.

Although they don't explain their reasoning, they are locating the emergence of the complete package of skin lightening snps around Hungary, which makes sense to me as the place where the different alleles "met". We saw that as far back as Cristina Gamba et al, discussed here:

They place lactase persistence in the extreme northeast, i.e. Finland. That also makes sense to me. Certainly not on the steppe, as people vehemently insisted for years, but as the ancient samples showed, was not possible.


"Going Global by Adapting Local"

"The spread of modern humans across the globe has led to genetic adaptations to diverse local environments. Recent developments in genomic technologies, statistical analyses, and expanded sampled populations have led to improved identification and fine-mapping of genetic variants associated with adaptations to regional living conditions and dietary practices. Ongoing efforts in sequencing genomes of indigenous populations, accompanied by the growing availability of “-omics” and ancient DNA data, promises a new era in our understanding of recent human evolution and the origins of variable traits and disease risks."

[IMG][/IMG] ]]>
Paleogenetics Angela
Corsican analysis with Central and North Italians Tue, 24 Sep 2019 05:55:07 GMT Genome-wide analysis of Corsican population reveals a close affinity with Northern and Central Italy * Erika Tamm (, * Julie Di Cristofaro...


Scientific Reportsvolume 9, Article number: 13581 (2019)

Despite being the fourth largest island in the Mediterranean basin, the genetic variation of Corsica has not been explored as exhaustively as Sardinia, which is situated only 11 km South. However, it is likely that the populations of the two islands shared, at least in part, similar demographic histories. Moreover, the relative small size of the Corsica may have caused genetic isolation, which, in turn, might be relevant under medical and translational perspectives. Here we analysed genome wide data of 16 Corsicans, and integrated with newly (33 individuals) and previously generated samples from West Eurasia and North Africa. Allele frequency, haplotype-based, and ancient genome analyses suggest that although Sardinia and Corsica may have witnessed similar isolation and migration events, the latter is genetically closer to populations from continental Europe, such as Northern and Central Italians. ]]>
Paleogenetics torzio
ETHNOGENE results Sun, 22 Sep 2019 21:18:04 GMT Did you find it accurate for you ??? Did you find it accurate for you ??? ]]> Paleogenetics Tilly7 DNA Land Mediterranian islander Sun, 22 Sep 2019 21:16:46 GMT Have you tested with DNA land . I bet yes!
I wonder why they assign so much Mediterranian islander - in my case 30% .

I heard other people asking similar questions.
Any idea ? Is it some indigenous Balkan market that they translate mislead?

I don't know any ancestry of mine from Crete or Cyprus etc... ]]>
Paleogenetics Tilly7
D4J Mtd6 Sun, 22 Sep 2019 21:10:40 GMT Hi everyone! Anyone in here with EU DNA but EA mtdna- D4j??? Hi everyone!

Anyone in here with EU DNA but EA mtdna- D4j??? ]]>
Paleogenetics Tilly7
Proto-Albanians and proto-Romanians (Y-DNA) Fri, 20 Sep 2019 06:38:37 GMT An interesting discussion started in the thread dedicated to Minoan and Mycenean origins, so let's continue in a more focused manner here. What can Y-DNA data tell us about affinities between proto-Albanian and proto-Romanian and the regions where their speakers might have lived? There seems to a consensus that Moldavian paternal lines are sufficiently different from Albanians to exclude a significant Carpi contribution to the Albanian ethnogenesis, so I will talk just about Albanian-Romanian connections.

According to linguists proto-Albanians and proto-Romanians had intense contacts for several centuries in the early Middle Ages, maybe up to the 10th. So to guess where this area of contacts was, we should look at paleo-Balkan Y-DNA lines younger 1200-1800 years old, that both Albanians and Romanians have. We already know the most common and likely paleo-Balkan haplogroups in Albanians are E-V13, J2b-L283 and R1b. Data I gathered from Bosch 2006, Stanciu 2010, Netea 2012 & Varzari 2013 (total n=363) show Romanians have 16.3% E, 12.1% R1b (<1% BY611), 3.6% J2b2.

Regarding E-V13, as I mentioned, it is difficult to classify short haplotypes into early medieval subclades, but, looking at the main Albanian clusters: PH2180, Y93102, BY4461 and 2 clusters under FGC11450, it seems unlikely that Romanians will show significant connections within 1200-1400 years with them. Nonetheless, because Romanians are so poorly tested, I would say that a thorough analysis of E-V13 needs more data.


Originally Posted by Demetrios View Post
Even if we consider the common J2b-L283 lines of Romanians and Albanians as western rather than generally Balkanic lines, this doesn't erase the fact that E-V13 looks more central, southern and eastern, in a Balkanic context

Why do you think that? And how does that play into the early medieval contacts between proto-Albanians & proto-Romanians? Have you found any E-V13 Albanian-Romanian clades with a mrca of 1200-1800?

When it comes to J2b-L283 and R1b-BY611, even though Romanians are not well-tested, the data is already one-sided. The main J2b-L283 Albanian clusters Z38300>Y20899, Y82533, CTS11100 and even smaller ones, like that J-Z631 haplotype found in some Romanians, all have western distributions. J2b-L283 is even more frequent and diverse in Apulia than in Romania or SE Serbia. Btw some Vlachs from Albania have been found to belong to Y20899, a diverse Albanian cluster also found in Apulia.


Originally Posted by Demetrios View Post
You write, "There is no reason at all to exclude J2b-L283. J2b-L283 in Tosks actually has some good diversity, and it is still more frequent than in neighboring countries.". Maybe there is not a reason to exclude it, bearing in mind that it is the second most prevalent haplogroup among Ghegs (which are also the ones living the closest to the proto-Albanian homeland), but we also have to consider the frequency among Tosks.

J2b-L283 frequency among Tosks is lower than in Ghegs, even though more frequent than elsewhere. However, the main indicator or historical presence is diversity, and in Tosks it is diverse, albeit less than in Ghegs. But this might not even be a Tosk-Gheg, as much as a highland-lowland difference: if you look at the largest highland of the South, Laberia, J2b-L283 is close to 15%. Other paleo-Balkan lines are also more frequent in mountainous areas, which makes perfect sense because we know the Slavic incomers were mainly settling in agricultural, flat lands, and the native element of the Albanian language has a strong pastorial, highland character. So, I don't see how proto-Albanians might not have had a significant % of J2b-L283.

R1b-BY611 it is at minimal frequency in Romanians. More importantly, I can classify the few haplotypes I have seen until today into either R-Z2705>BY105603>BY61976 or R-Z2705>BY38894>Y32147. Vlachs and some areas in Bulgaria have higher frequency than Romanians, but similar diversity, lacking 393=12 & 392=13 haplotypes (no such haplotypes have been found in Bulgarians, SE Serbs or Vlachs either).


Originally Posted by Demetrios View Post
Indeed, most Albanian R1b-Z2103 is R1b-Z2705, and i see that its earliest lines seem to be concentrated in the Dinaric Alps. In any case, the group's predecessor lived approximately 1450 years ago, which was a period of great upheaval and subsequent migrations in the Balkans. Is there any possibility he could have come from the eastern and central Balkans, subsequently pushed to the west by the newcomers? Do we have any significant information on R1b-Y10789 and R1b-Y23373?

Yes, the age of the branch is not high (although it should increase a bit soon), but the likeliest location of tmrca is NW Albania or Montenegro. And the closest relatives whose ancestry we know, at 3300 ybp, are in the W Mediterranean. A few unconfirmed, potential R-BY611 haplotypes, are mostly concentrated in North Italy and NW Balkans (check the thread I linked). Of course, we cannot say with 100% confidence that Moesia can be excluded. But right now, I do not see a single point of evidence suggesting the eastern half of the Balkans.


Originally Posted by Demetrios View Post
You write, "So, as I said, there is little shared paleo-Balkan paternal ancestry in the best researched branches, and current data suggests that this small amount spread from the western half of the Balkans.". But shouldn't there have been some, bearing in mind that you are also a proponent of the "Immigrationist theory" and Schramm? As for the current genetic data suggesting that it spread from the west, allow me to view it as more obscure. In any case it is very probable, not just because of genetics, but folklore does give some hints likewise.

Yes, there definitely is some, but not too much. Looking at the current data, it seems likely that proto-Romanian developed south of the Danube, as we agreed, and most linguists and historians suggest. I think there the likeliest scenario that can explain why the shared Y-DNA lines of Albanians and Romanians are relatively rare and more diverse in the west, is that the proto-Romanians lived in an area stretching through Moesia and further west, only the western part being in contact with proto-Albanians, and absorbing a limited number of proto-Albanian Y-DNA lines. Of course, if new data is revlead and it contradicts what we have until now, I might change my mind. ]]>
Paleogenetics Ownstyler
What Denisovans may have looked like Thu, 19 Sep 2019 18:41:27 GMT Image: Image: Image:
Paleogenetics Jovialis
Rome as a genetic melting pot: Population dynamics over 12,000 years. Mon, 16 Sep 2019 17:05:12 GMT this is the abstract Nearly 2000 years ago, Rome was the largest urban center of the ancient world and the capital of an empire with over... this is the abstract

surrounding regions closely mirrors Rome’s geopolitical interactions. Interestingly, Rome’s population

the study is to be published soon it seems

they mention only neolithic and bronze age steppe turnovers

no mention of DNA from the Aegean, from the Eastern Meditterranean nor from bronze age Anatolia, at least not in or around Rome ]]>
Paleogenetics bicicleur
The genetic legacy of pre-contact Puerto Rico Sat, 14 Sep 2019 15:22:46 GMT This is the other side of the story, and an important one.


"Indigenous peoples have occupied the island of Puerto Rico since at least 3000 B.C. Due to the demographic shifts that occurred after European contact, the origin(s) of these ancient populations, and their genetic relationship to present-day islanders, are unclear. We use ancient DNA to characterize the population history and genetic legacies of pre-contact Indigenous communities from Puerto Rico. Bone, tooth and dental calculus samples were collected from 124 individuals from three pre-contact archaeological sites: Tibes, Punta Candelero and Paso del Indio. Despite poor DNA preservation, we used target enrichment and high-throughput sequencing to obtain complete mitochondrial genomes (mtDNA) from 45 individuals and autosomal genotypes from two individuals. We found a high proportion of Native American mtDNA haplogroups A2 and C1 in the pre-contact Puerto Rico sample (40% and 44%, respectively). This distribution, as well as the haplotypes represented, support a primarily Amazonian South American origin for these populations, and mirrors the Native American mtDNA diversity patterns found in present-day islanders. Three mtDNA haplotypes from pre-contact Puerto Rico persist among Puerto Ricans and other Caribbean islanders, indicating that present-day populations are reservoirs of pre-contact mtDNA diversity. Lastly, we find similarity in autosomal ancestry patterns between pre-contact individuals from Puerto Rico and the Bahamas, suggesting a shared component of Indigenous Caribbean ancestry with close affinity to South American populations. Our findings contribute to a more complete reconstruction of pre-contact Caribbean population history and explore the role of Indigenous peoples in shaping the biocultural diversity of present-day Puerto Ricans and other Caribbean islanders." ]]>
Paleogenetics Angela
Pioneer of paleogenetics: Max Planck researcher Svante Pääboääbo?goto=newpost Thu, 12 Sep 2019 12:45:07 GMT

Here's a new video from the Max Planck Society YouTube page. ]]>
Paleogenetics Jovialisääbo
The genetic landscape of Ethiopia Fri, 06 Sep 2019 16:36:57 GMT *Abstract* The rich linguistic, ethnic and cultural diversity of Ethiopia provides an unprecedented opportunity to understand the level to which cultural factors correlate with -- and shape -- genetic structure in human populations. Using primarily novel genetic variation data covering 1,268... Abstract

The rich linguistic, ethnic and cultural diversity of Ethiopia provides an unprecedented opportunity to understand the level to which cultural factors correlate with -- and shape -- genetic structure in human populations. Using primarily novel genetic variation data covering 1,268 Ethiopians representing 68 different ethnic groups, together with information on individuals' birthplaces, linguistic/religious practices and 31 cultural practices, we disentangle the effects of geographic distance, elevation, and social factors upon shaping the genetic structure of Ethiopians today. We provide examples of how social behaviours have directly -- and strongly -- increased genetic differences among present-day peoples. We also show the fluidity of intermixing across linguistic and religious groups. We identify correlations between cultural and genetic patterns that likely indicate a degree of social selection involving recent intermixing among individuals that have certain practices in common. In addition to providing insights into the genetic structure and history of Ethiopia, including how they correlate with current linguistic classifications, these results identify the most important cultural and geographic proxies for genetic differentiation and provide a resource for designing sampling protocols for future genetic studies involving Ethiopians.
Paleogenetics Jovialis