New DNA Papers

General discussions regarding DNA and its uses in genealogy research

Posts: 1757
Joined: Fri Mar 16, 2012 5:43 pm
PostPosted: Tue Mar 07, 2017 12:52 am
https://rd.springer.com/article/10.1007 ... 017-1769-8

Abstract
"The great apes (orangutans, gorillas, chimpanzees, bonobos and humans) descended from a common ancestor around 13 million years ago, and since then their sex chromosomes have followed very different evolutionary paths. While great-ape X chromosomes are highly conserved, their Y chromosomes, reflecting the general lability and degeneration of this male-specific part of the genome since its early mammalian origin, have evolved rapidly both between and within species. Understanding great-ape Y chromosome structure, gene content and diversity would provide a valuable evolutionary context for the human Y, and would also illuminate sex-biased behaviours, and the effects of the evolutionary pressures exerted by different mating strategies on this male-specific part of the genome. High-quality Y-chromosome sequences are available for human and chimpanzee (and low-quality for gorilla). The chromosomes differ in size, sequence organisation and content, and while retaining a relatively stable set of ancestral single-copy genes, show considerable variation in content and copy number of ampliconic multi-copy genes. Studies of Y-chromosome diversity in other great apes are relatively undeveloped compared to those in humans, but have nevertheless provided insights into speciation, dispersal, and mating patterns. Future studies, including data from larger sample sizes of wild-born and geographically well-defined individuals, and full Y-chromosome sequences from bonobos, gorillas and orangutans, promise to further our understanding of population histories, male-biased behaviours, mutation processes, and the functions of Y-chromosomal genes."

Posts: 1757
Joined: Fri Mar 16, 2012 5:43 pm
PostPosted: Tue Mar 07, 2017 8:50 am
dartraighe wrote:https://rd.springer.com/article/10.1007%2Fs00439-017-1769-8

Abstract
"The great apes (orangutans, gorillas, chimpanzees, bonobos and humans) descended from a common ancestor around 13 million years ago, and since then their sex chromosomes have followed very different evolutionary paths. While great-ape X chromosomes are highly conserved, their Y chromosomes, reflecting the general lability and degeneration of this male-specific part of the genome since its early mammalian origin, have evolved rapidly both between and within species. Understanding great-ape Y chromosome structure, gene content and diversity would provide a valuable evolutionary context for the human Y, and would also illuminate sex-biased behaviours, and the effects of the evolutionary pressures exerted by different mating strategies on this male-specific part of the genome. High-quality Y-chromosome sequences are available for human and chimpanzee (and low-quality for gorilla). The chromosomes differ in size, sequence organisation and content, and while retaining a relatively stable set of ancestral single-copy genes, show considerable variation in content and copy number of ampliconic multi-copy genes. Studies of Y-chromosome diversity in other great apes are relatively undeveloped compared to those in humans, but have nevertheless provided insights into speciation, dispersal, and mating patterns. Future studies, including data from larger sample sizes of wild-born and geographically well-defined individuals, and full Y-chromosome sequences from bonobos, gorillas and orangutans, promise to further our understanding of population histories, male-biased behaviours, mutation processes, and the functions of Y-chromosomal genes."



The estimated ancestor of all modern humans originated 350,000 ybp , so the above does not make one ounce of sense. The replication process today is 99% accurate. In the past the accuracy must have been greater, so it is not possible that humans and apes had the same ancestor if the replication process is near perfect. The more births the more mutations is what the scientists tell us. Will the chimps rule the world in 350,000 years and humans will become extinct, I asked the question already. The reply I got was that we are in the final phase of evolution. For those who believe in evolution there is no such state as the final phase. Evolution is either in a perpetual state or it isn't.

The 1% difference in our dna is mostly due to regional variation. That is what the scientists state.

Posts: 1757
Joined: Fri Mar 16, 2012 5:43 pm
PostPosted: Tue Mar 14, 2017 10:16 am
https://link.springer.com/article/10.10 ... 017-1770-2

Abstract
"Y-chromosomal variation in West Asian populations has so far been studied in less detail than in the neighboring Europe. Here, we analyzed 598 Y-chromosomes from two West Asian subregions—Transcaucasia and the Armenian plateau—using 40 Y-SNPs and 17 Y-STRs and combined them with previously published data from the region. The West Asian populations fell into two clusters: upland populations from the Anatolian, Armenian and Iranian plateaus, and lowland populations from the Levant, Mesopotamia and the Arabian Peninsula. This geographic subdivision corresponds with the linguistic difference between Indo-European and Turkic speakers, on the one hand, and Semitic speakers, on the other. This subdivision could be traced back to the Neolithic epoch, when upland populations from the Anatolian and Iranian plateaus carried similar haplogroup spectra but did not overlap with lowland populations from the Levant. We also found that the initial gene pool of the Armenian motherland population has been well preserved in most groups of the Armenian Diaspora. In view of the contribution of West Asians to the autosomal gene pool of the steppe Yamnaya archaeological culture, we sequenced a large portion of the Y-chromosome in haplogroup R1b samples from present-day East European steppe populations. The ancient Yamnaya samples are located on the “eastern” R-GG400 branch of haplogroup R1b-L23, showing that the paternal descendants of the Yamnaya still live in the Pontic steppe and that the ancient Yamnaya population was not an important source of paternal lineages in present-day West Europeans."

Posts: 1757
Joined: Fri Mar 16, 2012 5:43 pm
PostPosted: Wed Mar 15, 2017 1:32 pm
dartraighe wrote:More of the same old mantra. 40-50% of the males in western Europe today are descended from one man who lived 5000 years ago in western Europe. That is the reason that this paper is rubbish if they are referring to R1b.



"Thousands of horsemen may have swept into Bronze Age Europe, transforming the local population"

http://www.sciencemag.org/news/2017/02/ ... population

"The finding that Yamnaya men migrated for many generations also suggests that all was not right back home in the steppe. “It would imply a continuing strongly negative push factor within the steppes, such as chronic epidemics or diseases,” says archaeologist David Anthony of Hartwick College in Oneonta, New York, who was not an author of the new study. Or, he says it could be the beginning of cultures that sent out bands of men to establish new politically aligned colonies in distant lands, as in later groups of Romans or Vikings."

Why did the epidemics not push the women out of the Steppe????????????????? Were they immune to epidemics and diseases????????????????

The Romans and the Vikings had very little genetic impact on the regions they invaded!!!!!!!!!!!!!!



http://www.biorxiv.org/content/early/2017/03/14/114124

Abstract
"We fail to replicate a genetic signal for sex bias in the steppe migration to central Europe after ~5,000 years proposed by Goldberg et al. PNAS 114(10):2657-2662. Estimation of X-chromosome steppe ancestry in the Bronze Age central European population with the qpAdm method (Haak et al. Nature 522, 207-11) does not indicate lower steppe ancestry on the X-chromosome than in the autosomes. We perform a simulation which indicates presence of estimation bias of -19.5% in the inference of X-chromosome admixture proportions using the method used by Goldberg et al., largely eliminating the observed sex bias."

Posts: 1757
Joined: Fri Mar 16, 2012 5:43 pm
PostPosted: Wed Mar 22, 2017 3:09 pm
Reconciling evidence from ancient and contemporary genomes: a major source for the European Neolithic within Mediterranean Europe
Joana B. Pereira, Marta D. Costa, Daniel Vieira, Maria Pala, Lisa Bamford, Nourdin Harich, Lotfi Cherni, Farida Alshamali, Jiři Hatina, Sergey Rychkov, Gheorghe Stefanescu, Turi King, Antonio Torroni, Pedro Soares, Luísa Pereira, Martin B. Richards
Abstract

"Important gaps remain in our understanding of the spread of farming into Europe, due partly to apparent contradictions between studies of contemporary genetic variation and ancient DNA. It seems clear that farming was introduced into central, northern, and eastern Europe from the south by pioneer colonization. It is often argued that these dispersals originated in the Near East, where the potential source genetic pool resembles that of the early European farmers, but clear ancient DNA evidence from Mediterranean Europe is lacking, and there are suggestions that Mediterranean Europe may have resembled the Near East more than the rest of Europe in the Mesolithic. Here, we test this proposal by dating mitogenome founder lineages from the Near East in different regions of Europe. We find that whereas the lineages date mainly to the Neolithic in central Europe and Iberia, they largely date to the Late Glacial period in central/eastern Mediterranean Europe. This supports a scenario in which the genetic pool of Mediterranean Europe was partly a result of Late Glacial expansions from a Near Eastern refuge, and that this formed an important source pool for subsequent Neolithic expansions into the rest of Europe."

Posts: 1757
Joined: Fri Mar 16, 2012 5:43 pm
PostPosted: Thu Mar 30, 2017 9:54 am
First evidence of a Late Upper Palaeolithic human presence in Ireland.


Abstract
"The colonisation of North West Europe by humans and fauna following the Last Glacial Maximum (LGM) has been the subject of considerable discussion in recent decades and within multiple disciplines. Here we present new evidence that pushes back the date of human footfall in Ireland by up to 2500 cal BP to the Upper Palaeolithic. An assemblage of animal bones recovered from a cave in the west of Ireland during antiquarian excavations in 1903 included a butchered brown bear bone (patella) which was recently subjected to two independent radiocarbon dating processes; the resultant dates were in agreement: 12,810-12,590 cal BP and 12,810-12,685 cal BP. This find rewrites the antiquity of human occupation of Ireland and challenges the traditional paradigm that certain biota may have naturally colonised the island prior to human arrival."

First evidence of a Late Upper Palaeolithic human presence in Ireland (PDF Download Available). Available from: https://www.researchgate.net/publicatio ... in_Ireland [accessed Mar 30, 2017].

Posts: 1757
Joined: Fri Mar 16, 2012 5:43 pm
PostPosted: Fri Mar 31, 2017 6:55 pm
http://www.ucl.ac.uk/archaeology/calend ... t_book.pdf

The Hole Story: Ancient DNA, stable isotope and
radiocarbon analysis of human remains from the
'Mesolithic' cemetery at Aveline's Hole
T. Booth1
; S. Brace1
; Z. Faltyskova2
; Y. Diekmann2
; L. Wilson3
; G. Mullan3
;
R. Schulting4
; M. Thomas2
; I. Barnes1
1 Natural History Museum, 2 University College London, 3 University of Bristol Spelaeological
Society, 4 University of Oxford
"Aveline's Hole Cave in the Mendip Hills, Somerset, England, which was
originally excavated in 1860, is renowned as the earliest known cemetery
in Britain. Up to 50 individuals were interred in the cave, although remains
of only around 21 individuals have survived. Dozens of radiocarbon dates
obtained from this assemblage are tightly clustered in the mid-late 9th
Millennium BC, the Early Mesolithic. These tight dates suggest that whole
bodies were interred over a relatively short period, after which the cave was
sealed, perhaps deliberately. Here we present Next Generation
Sequencing whole genome data, as well as further stable isotope and
radiocarbon dating results from the Aveline's Hole human assemblage. Our
results suggest that the assemblage includes human remains which date
to the early 4th Millennium BC, show dietary signals more consistent with a
farming than a hunter-gathering lifestyle and which have genetic affinities
with European Middle Neolithic populations ultimately deriving from
Anatolia. These results not only inform on the nature of the British
Mesolithic-Neolithic transition, but also overturn the conventional
archaeological narrative of this unique and important site."

Posts: 1757
Joined: Fri Mar 16, 2012 5:43 pm
PostPosted: Tue Apr 04, 2017 11:32 am
Open access, click on PDF.
https://www.cambridge.org/core/search?f ... Code=SE-AU

Abstract
"Recent genetic, isotopic and linguistic research has dramatically changed our understanding of how the Corded Ware Culture in Europe was formed. Here the authors explain it in terms of local adaptations and interactions between migrant Yamnaya people from the Pontic-Caspian steppe and indigenous North European Neolithic cultures. The original herding economy of the Yamnaya migrants gradually gave way to new practices of crop cultivation, which led to the adoption of new words for those crops. The result of this hybridisation process was the formation of a new material culture, the Corded Ware Culture, and of a new dialect, Proto-Germanic. Despite a degree of hostility between expanding Corded Ware groups and indigenous Neolithic groups, stable isotope data suggest that exogamy provided a mechanism facilitating their integration. This article should be read in conjunction with that by Heyd (2017, in this issue)."

Posts: 2138
Joined: Sun Mar 18, 2012 7:08 am
Location: Pisa (Italy)
YDNA:
R- Z2110 (KV7Y2)
MtDNA:
K1a1b1e/HQ176413
PostPosted: Tue Apr 04, 2017 12:41 pm
dartraighe wrote:Open access, click on PDF.
https://www.cambridge.org/core/search?f ... Code=SE-AU

Abstract
"Recent genetic, isotopic and linguistic research has dramatically changed our understanding of how the Corded Ware Culture in Europe was formed. Here the authors explain it in terms of local adaptations and interactions between migrant Yamnaya people from the Pontic-Caspian steppe and indigenous North European Neolithic cultures. The original herding economy of the Yamnaya migrants gradually gave way to new practices of crop cultivation, which led to the adoption of new words for those crops. The result of this hybridisation process was the formation of a new material culture, the Corded Ware Culture, and of a new dialect, Proto-Germanic. Despite a degree of hostility between expanding Corded Ware groups and indigenous Neolithic groups, stable isotope data suggest that exogamy provided a mechanism facilitating their integration. This article should be read in conjunction with that by Heyd (2017, in this issue)."


Gioiello has left a new comment on the post "Latest on Bell Beaker and Corded Ware":

@ Davidski

Where have you read in this (ridiculous) paper that Bell Beakers derived from Yamnaya and its R-L51 and subclades?
After, perhaps it will be demonstrated that my R-L23-Z2110* came with Alans linked with Longobards, it is possible, but nothing will be taken away from my analyses.

Posts: 1757
Joined: Fri Mar 16, 2012 5:43 pm
PostPosted: Tue Apr 04, 2017 7:05 pm
Gioiello wrote:
dartraighe wrote:Open access, click on PDF.
https://www.cambridge.org/core/search?f ... Code=SE-AU

Abstract
"Recent genetic, isotopic and linguistic research has dramatically changed our understanding of how the Corded Ware Culture in Europe was formed. Here the authors explain it in terms of local adaptations and interactions between migrant Yamnaya people from the Pontic-Caspian steppe and indigenous North European Neolithic cultures. The original herding economy of the Yamnaya migrants gradually gave way to new practices of crop cultivation, which led to the adoption of new words for those crops. The result of this hybridisation process was the formation of a new material culture, the Corded Ware Culture, and of a new dialect, Proto-Germanic. Despite a degree of hostility between expanding Corded Ware groups and indigenous Neolithic groups, stable isotope data suggest that exogamy provided a mechanism facilitating their integration. This article should be read in conjunction with that by Heyd (2017, in this issue)."


Gioiello has left a new comment on the post "Latest on Bell Beaker and Corded Ware":

@ Davidski

Where have you read in this (ridiculous) paper that Bell Beakers derived from Yamnaya and its R-L51 and subclades?
After, perhaps it will be demonstrated that my R-L23-Z2110* came with Alans linked with Longobards, it is possible, but nothing will be taken away from my analyses.


We know from the ancient dna that the CWC were 100% YDNA R1a in Germany. Did they carry the pre-proto- Germanic ( whatever that is supposed to be)language? Looks like more fairy tales. They made this paper public so that we could rip it to shreds before the BB paper becomes public and to warn us of the impending unusual ancient dna results in the BB paper. They are stating that there was no male dominated migration after all. They exchanged females and that is a surprise. Does that mean that the R1a in western Europe is indigenous?

"CWC is not descended from Yamnaya, not directly and not partly. "
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