New DNA Papers

General discussions regarding DNA and its uses in genealogy research

Posts: 2233
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Sun Jun 03, 2018 7:01 pm
Gioiello wrote:
dartraighe wrote:"It was a given that R1b was in the Steppes long before the various Yamnaya groups coalesced. We have the accepted origin of R (R1?) at least at Mal'ta Buret' Siberia (MA-1) around 24,000 ybp."

The poster who wrote this on another forum is wrong because the ancestors of Native Americans who crossed the Bearing Strait 13,000 years ago did not carry R1b and there was not only the one wave of NA ancestors. There were multiple waves according to all the scientific papers about the NA and no evidence of any R1b lines in the NA. That is the evidence that R1b was a more recent event in eastern Europe.

The L23 samples that were found in ancient dna in eastern Europe were not the ancestors of P312, S1200 and U106. And one has to explain how the Bronze Age R1b in western Europe had Samara autosomal dna when they and their L51 bottlenecked ancestors were not born in Samara. It had to come from Samara females.


Dartraighe, we have to be cautious about all that.
1) Mal’ta boy is certain, but he was only a dead end line, not our line.
2) That R1 was in central Siberia 25000 years ago is possible, above all to me that don’t believe to the “Out of Africa”, thus an origin of Y in East Asia as Shi Huang thinks is likable.
3) That R1 wasn’t in NA doesn’t mean anything about its Asian origin in Central Siberia, because NA arrived in America 13000 years ago but stayed thousands of years in Beringia.
4) We don’t know the expansion of the oldest R1 lines, except that 14000 years ago they were at Villabruna and 12000 years ago at Les Iboussiéres.
5) What happened later is clear to me, and will be clearer when aDNA from Italy is published. We’ll understand also all the pathways. Anyway Western Europe.


No R1b in the Native Americans suggests that no R of any kind survived in Siberia or eastern Europe for that matter. Q1a was not born in Beringia.

It is L23 that is most important to us because R1b M269 went through a huge bottleneck before the birth of L23. We are looking at a very small isolated M269 clan who survived for at least 7,000 years.

L23 expanded in the Neolithic but L51, the branch leading to P312,S1200 and U106, did not expand until the BA. There is not one piece of evidence to suggest that P312,S1200 and U106 expanded in eastern Europe!

Villabruna does not have the correct SNP status for the time that he lived. His dna status could not be resolved and it seems to me that most of the R1b samples before the BA in western/central Europe have not been resolved through ancient dna tests.

Posts: 2233
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Mon Jun 11, 2018 10:43 pm
https://www.nytimes.com/2018/06/11/heal ... osome.html

"Dad genes are particles on the sex-specific Y chromosome, long mocked for being a stunted clump of mostly useless nucleic waste but lately revealed as man’s fastest friend, essential to the health of male bodies and brains no matter the age."

"Researchers have discovered that, contrary to longstanding assumptions, the Y chromosome is not limited to a handful of masculine tasks, like specifying male body parts in a developing embryo or replenishing the sperm supply in an adult man."

"New evidence indicates that the Y chromosome participates in an array of essential, general-interest tasks in men, like stanching cancerous growth, keeping arteries clear and blocking the build up of amyloid plaque in the brain."

Posts: 2233
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Thu Jul 05, 2018 7:34 am
https://www.sciencedirect.com/science/a ... via%3Dihub
The evolutionary history of human populations in Europe
Author links open overlay panel
Iosif Lazaridis




"I review the evolutionary history of human populations in Europe with an emphasis on what has been learned in recent years through the study of ancient DNA. Human populations in Europe ∼430–39 kya (archaic Europeans) included Neandertals and their ancestors, who were genetically differentiated from other archaic Eurasians (such as the Denisovans of Siberia), as well as modern humans. Modern humans arrived to Europe by ∼45 kya, and are first genetically attested by ∼39 kya when they were still mixing with Neandertals. The first Europeans who were recognizably genetically related to modern ones appeared in the genetic record shortly thereafter at ∼37 kya. At ∼15 kya a largely homogeneous set of hunter-gatherers became dominant in most of Europe, but with some admixture from Siberian hunter-gatherers in the eastern part of the continent. These hunter-gatherers were joined by migrants from the Near East beginning at ∼8–9 kya: Anatolian farmers settled most of mainland Europe, and migrants from the Caucasus reached eastern Europe, forming steppe populations. After ∼5 kya there was migration from the steppe into mainland Europe and vice versa. Present-day Europeans (ignoring the long-distance migrations of the modern era) are largely the product of this Bronze Age collision of steppe pastoralists with Neolithic farmers."

The writing I highlighted is a reference to the Villabruna clan. Villabruna has an affinity with everybody including AG3 but excluding MA1, because of there is a 10,000 year separation between them.

Posts: 2233
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Fri Jul 06, 2018 7:50 am
The Genomics of Megaliths: An Irish case study into the reconstruction of prehistoric societal landscapes through ancient DNA analysis

Lara M Cassidy 1

1 Trinity College Dublin (Ireland)

"The Irish Neolithic (circa 3,800-2,500) marks the emergence of complex civilization on the island, alongside the establishment of continued contacts with other Atlantic regions, which intensify in the succeeding Copper and Bronze Ages. In addition to these cultural upheavals, the Neolithic period has been demonstrated to both begin and end with mass migration into the island, potentially from multiple external sources. However, the variable interplay between geography and culture in the catalyzation of these population movements has remained an open question. Indeed, the archaeological record would suggest regional heterogeneity in the uptake of British and continental traditions at both transition points.

Here, the potential social and cultural implications of such events are explored through the prism of ancient genomics. Imputed diploid genotypes for over 50 individuals sampled from the Mesolithic to Bronze Age periods, encompassing a diversity of megalithic structures, are presented and dissected through the use of haplotypic-sharing methods, as well as estimations of kinship and inbreeding. Combined with Y chromosome analysis these provide the first evidence of genetic structure on the island during specific prehistoric time intervals, which can be interpreted along both geographical and cultural lines. Furthermore, candidate refugiums that may recurrently act as reservoirs for older traditions and genetic ancestries are identified, as well as hub regions, which appear more susceptible to demographic disturbances on the continent, highlighting the immovable constraints of geography on both cultural and genomic evolution."

Posts: 2233
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MtDNA:
U5b2b
PostPosted: Sat Aug 11, 2018 9:13 pm
S. V. Ivanova, A. G. Nikitin, D. V. Kiosak
https://www.academia.edu/37141707/С....1089;._101-146


Pendulum migrations in the Circum-Pontic Steppe and Central europe during the Paleometal epoch and the problem of genesis of the yamna Culture

"This article is dedicated to the problem of the origin and spread of the Yamna cultural-historical community (YCHC) in the context of the hypothesis recently expressed by geneticists about the massive migration of population groups genetically related to YCHC and carrying the genetic determinants of the Iranian Neo-lithic agrarians and hunters and fishers of the North Caucasus from the Ponto- Caspian steppe to central and northern Europe at the beginning of the Bronze Age. Based on an in-depth archeological and genetic analysis, we propose that the genetic «invasion» of the Iranian-Caucasian genetic element into Europe at the beginning of the Bronze Age, recently proposed by paleogenetisits on the basis of a large-scale study of ancient DNA, was not the result of a large-scale mi-gration of representatives of YCHC from the Ponto-Caspian steppes to central and northern Europe, but the result of global population and cultural changes in Eurasia at the end of the Atlantic climatic optimum. We further suggest that before the steppe genetics ap-peared in Europe at the beginning of the Bronze Age, central European genetic determinants appeared in the steppe in the Eneolithic, and that the movement of the steppe genetic element to Europe was at least in part the second phase of the «pendular» migration of European expatriates, returning to the historical zone of habitation. We also come to the conclusion that the very concept of distinguishing YCHC as a monolithic entity is inappropriate, and that the groups of nomadic tribes of the Ponto-Caspian steppe most likely existed as discrete communities, although united by a common ideology and a genetic relationship that included both the Iranian-Caucasian (throughout the entire range), and European / Anatolian agricultural (locally) genetic elements."

Posts: 2233
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Sun Sep 09, 2018 6:05 pm
https://theconversation.com/discovering ... tterbutton

"Who spread the CF mutation throughout Europe?
Thus, our newly published data suggest that the F508del mutation arose in the early Bronze Age and spread from west to southeast Europe during ancient migrations.
Moreover, taking the archaeological record into account, our results allow us to introduce a novel concept by suggesting that a population known as the Bell Beaker folk were the probable migrating population responsible for the early dissemination of F508del in prehistoric Europe. They appeared at the transition from the Late Neolithic period, around 4000 B.C., to the Early Bronze Age during the third millennium B.C. somewhere in Western Europe. They were distinguished by their ceramic beakers, pioneering copper and bronze metallurgy north of the Alps and great mobility. All studies, in fact, show that they were into heavy migration, traveling all over Western Europe."

Posts: 2233
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Sat Sep 15, 2018 11:06 am
A Genomic Compendium of an Island: Documenting Continuity and Change across Irish Human Prehistory

Citation:
CASSIDY, LARA, A Genomic Compendium of an Island: Documenting Continuity and Change across Irish Human Prehistory, Trinity College Dublin.School of Genetics & Microbiology.GENETICS, 2018

Link to the full text item Final_Thesis_LM_Cassidy.pdf (PhD Thesis) 16.43Mb

Abstract:
"This thesis provides an initial demographic scaffold for Irish prehistory based on the palaeogenomic analysis of 93 ancient individuals from all major periods of the island's human occupation, sequenced to a median of 1X coverage. ADMIXTURE and principal component analysis identify three ancestrally distinct Irish populations, whose inhabitation of the island corresponds closely to the Mesolithic, Neolithic and Chalcolithic/Early Bronze Age eras, with large scale migration to the island implied during the transitionary periods. Haplotypic-based sharing methods and Y chromosome analysis demonstrate strong continuity between the Early Bronze Age and modern Irish populations, suggesting no substantial population replacement has occurred on the island since this point in time. The Mesolithic population shares high genetic drift with contemporaries from France and Luxembourg and shows evidence of a severe inbreeding bottleneck, apparent through runs of homozygosity (ROH). Substantial contributions from both Mediterranean farming groups and northwestern hunter-gatherers are evident in the Neolithic Irish population. Moreover, evidence for local Mesolithic survival and introgression in southwestern Ireland, long after the commencement of the Neolithic, is also implied in haplotypic-analysis. Societal complexity during the Neolithic is suggested in patterns of Y chromosome and autosomal structure, while the identification of a highly inbred individual through ROH analysis, retrieved from an elite burial context, strongly suggests the elaboration and expansion of megalithic monuments over the course of the Neolithic was accompanied in some regions by dynastic hierarchies. Haplotypic affinities and distributions of steppe-related introgression among samples suggest a potentially bimodal introduction of Beaker culture to the island from both Atlantic and Northern European sources, with southwestern individuals showing inflated levels of Neolithic ancestry relative to individualised burials from the north and east. Signals of genetic continuity and change after this initial establishment of the Irish population are also explored, with haplotypic diversification evident between both the Bronze Age and Iron Age, and the Iron Age and present day. Across these intervals selection pressures related to nutrition appear to have acted, with variants involved in lactase persistence and skin depigmentation showing steady increases in frequency through time."


The dynastic hierarchies in Ireland are associated with R1b so it will be interesting to see the YDNA of this Neolithic individual.
Last edited by dartraighe on Sun Sep 16, 2018 9:01 am, edited 2 times in total.

Posts: 2233
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Sun Sep 16, 2018 6:57 am
dartraighe wrote:A Genomic Compendium of an Island: Documenting Continuity and Change across Irish Human Prehistory

Citation:
CASSIDY, LARA, A Genomic Compendium of an Island: Documenting Continuity and Change across Irish Human Prehistory, Trinity College Dublin.School of Genetics & Microbiology.GENETICS, 2018

Link to the full text item Final_Thesis_LM_Cassidy.pdf (PhD Thesis) 16.43Mb

Abstract:
"This thesis provides an initial demographic scaffold for Irish prehistory based on the palaeogenomic analysis of 93 ancient individuals from all major periods of the island's human occupation, sequenced to a median of 1X coverage. ADMIXTURE and principal component analysis identify three ancestrally distinct Irish populations, whose inhabitation of the island corresponds closely to the Mesolithic, Neolithic and Chalcolithic/Early Bronze Age eras, with large scale migration to the island implied during the transitionary periods. Haplotypic-based sharing methods and Y chromosome analysis demonstrate strong continuity between the Early Bronze Age and modern Irish populations, suggesting no substantial population replacement has occurred on the island since this point in time. The Mesolithic population shares high genetic drift with contemporaries from France and Luxembourg and shows evidence of a severe inbreeding bottleneck, apparent through runs of homozygosity (ROH). Substantial contributions from both Mediterranean farming groups and northwestern hunter-gatherers are evident in the Neolithic Irish population. Moreover, evidence for local Mesolithic survival and introgression in southwestern Ireland, long after the commencement of the Neolithic, is also implied in haplotypic-analysis. Societal complexity during the Neolithic is suggested in patterns of Y chromosome and autosomal structure, while the identification of a highly inbred individual through ROH analysis, retrieved from an elite burial context, strongly suggests the elaboration and expansion of megalithic monuments over the course of the Neolithic was accompanied in some regions by dynastic hierarchies. Haplotypic affinities and distributions of steppe-related introgression among samples suggest a potentially bimodal introduction of Beaker culture to the island from both Atlantic and Northern European sources, with southwestern individuals showing inflated levels of Neolithic ancestry relative to individualised burials from the north and east. Signals of genetic continuity and change after this initial establishment of the Irish population are also explored, with haplotypic diversification evident between both the Bronze Age and Iron Age, and the Iron Age and present day. Across these intervals selection pressures related to nutrition appear to have acted, with variants involved in lactase persistence and skin depigmentation showing steady increases in frequency through time."


https://twitter.com/DebbieKennett/statu ... 8482158593

"93 ancient individuals from all major periods of Ireland's human occupation were sequenced for this PhD project. http://www.tara.tcd.ie/handle/2262/82960 … The thesis is under embargo but you can hear Lara talking about her research at Genetic Genealogy Ireland in October: http://ggi2013.blogspot.com/2018/08/dna ... ublin.html …"

Posts: 2233
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Sun Sep 16, 2018 9:10 am
From the abstract
"while the identification of a highly inbred individual through ROH analysis, retrieved from an elite burial context, strongly suggests the elaboration and expansion of megalithic monuments over the course of the Neolithic was accompanied in some regions by dynastic hierarchies."


The dynastic hierarchies in Ireland are associated with R1b so it will be interesting to see the YDNA of this Neolithic individual.
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