Post by djoser-xyyman on Aug 27, 2018 10:02:08 GMT -5
New papers of interest....from crazy, fat white people to African ghost population.
New papers of interest....from crazy, fat white people to African ghost population
Positive selection in Europeans and East-Asians at the ABCA12 gene - Roberto Sirica1
ABSTRACT
Natural selection acts on genetic variants by increasing the frequency of alleles responsible for a cellular function that is
favorable in a certain environment. In a previous genome-wide scan for positive selection in contemporary humans, we
identified a signal of positive selection in European and Asians at the genetic variant rs10180970. The variant is located in the
second intron of the ABCA12 gene, which is implicated in the lipid barrier formation and down-regulated by UVB radiation.
We studied the signal of selection in the genomic region surrounding rs10180970 in a larger dataset that includes DNA
sequences from ancient samples. We also investigated the functional consequences of gene expression of the alleles of
rs10180970 and another genetic variant in its proximity in healthy volunteers exposed to similar UV radiation.
We confirmed the selection signal and refine its location that extends over 35 kb and includes the first intron, the first two exons
and the transcription starting site of ABCA12. We found ***no obvious*** effect of rs10180970 alleles on ABCA12 gene expression.
We reconstructed the trajectory of the T allele over the last 80,000 years to discover that it was specific to H. sapiens and
frequent among non-Africans already 45,000 years ago. xyyman comment: another lie exposed?? About lipid metabolism found in Euroepans are attributed to Neanderthal admixture
Positive and balancing selection on SLC18A1 gene associated with psychiatric disorders and human-unique personality traits - Daiki X. Sato1 and Masakado Kawata1
Maintenance of genetic variants susceptible to psychiatric disorders is one of the intriguing evolutionary enigmas. The present
study detects three psychiatric disorder-relevant genes (CLSTN2, FAT1, and SLC18A1) that have been under positive selection
during the human evolution. In particular, SLC18A1 (vesicular monoamine transporter 1; VMAT1) gene has a human-unique variant
(rs1390938, Thr136Ile), which is associated with bipolar disorders and/or the anxiety-related personality traits. 136Ile shows
relatively high (20–61%) frequency in non-African populations, and Tajima’s D reports a significant peak around the Thr136Ile site,
suggesting that this polymorphism has been positively maintained by balancing selection in non-African populations. Moreover,
Coalescent simulations predict that 136Ile originated around 100,000 years ago, the time being generally associated with the
Out-of-Africa migration of modern humans. Our study sheds new light on a gene in monoamine pathway as a strong candidate
contributing to human-unique psychological traits.
xyyman comment: confirmation on why Eurasians are psycho crazy ??
Reconstruction of human subsistence and husbandry strategies from the Iberian Early Neolithic: A stable isotope approach
Abstract
Objectives
The Early Neolithic involved an important social and economic shift that can be tested not only with the material culture, but also through biomolecular approaches. The Iberian Peninsula presents few Early Neolithic sites where fauna and humans can be analyzed together from an isotopic perspective. Here we present an isotopic study on the site of Cueva de Chaves as an example for understanding the dietary and economical changes that took place during Early Neolithic in Iberia.
Material and methods
Here we apply carbon and nitrogen stable isotope analysis to bone collagen from 4 humans and 64 faunal samples from 14 different species. The large dataset belongs to the same unique chrono‐cultural context secured by 20 radiocarbon dates. Three direct new radiocarbon dates were carried out on the human remains analyzed.
Results
Faunal isotope values show no significant differences between wild and domestic herbivores, although the latter have more homogeneous values. Domestic pigs, potentially considered omnivorous, also show signatures of a herbivore diet. Human isotopic results show a diet mainly based on terrestrial C3 resources and possibly high meat consumption. The only individual found buried with a special funerary treatment presents a slightly different protein intake, when taking into account the long contemporaneous baseline analyzed.
Discussion
Similar values between wild and domestic species could be the result of common feeding resources and/or grazing on the same parts of the landscape. The herbivore diet seen amongst domestic pigs rules out feeding on household leftovers. High meat consumption by humans would support the hypothesis of the existence of a specialized animal husbandry management community in which agriculture was not intensively developed. Our results suggest that the development of agricultural practices and animal husbandry were not necessarily associated together in the early stages of the Western Mediterranean Neolithic.
xyyman comment: was the "individual" from Africa?
Implementing a biogeographic ancestry inference service for forensic casework
Soulbee Jin
Abstract
The Centre of Forensic Sciences has validated The Precision ID Ancestry Panel on the Ion S5™ Massively Parallel Sequencing instrument for use in forensic casework. The focus of this paper is the development of reporting guidelines for implementation of the biogeographic ancestry (BGA) inference service based on Admixture Prediction results produced using the Torrent Suite™ Software (Thermo Fisher Scientific). The Admixture Prediction algorithm estimates the genetic ancestry of a sample using seven root populations (Europe, East Asia, Oceania, America, Africa, South Asia, Southwest Asia). For individuals that declared a single ancestry, there was a high correlation between the declared ancestry and the ancestry predicted by the algorithm. However, some individuals with declared ancestries of Southern Europe, Southwest Asia, South Asia and the Horn of Africa had Admixture Predictions that were composed of two or more root populations at 20% or greater. For individuals with known admixed ancestry, the major component of their declaration was included in their results in all but one case. Based on these results, reporting guidelines were developed and subsequently evaluated using the Admixture Predictions of additional samples. This paper discusses the development and evaluation of these reporting guidelines, along with an implementation plan for forensic casework.
xyyman comment: Better toool for predicting admixture
Reconciling the father tongue and mother tongue hypotheses in Indo-European populations
Menghan Zhang Hong-Xiang Zheng Shi Yan Li Jin
\
Abstract
In opposite to the Mother Tongue Hypothesis, the Father Tongue Hypothesis states that humans tend to speak their fathers' language, based on a stronger correlation of languages to paternal lineages (Y-chromosome) than to maternal lineages (mitochondria). . To reassess these two competing hypotheses, we conducted a genetic-linguistic study of 34 modern Indo-European (IE) populations. In this study, genetic histories of paternal and maternal migrations in these IE populations were elucidated using phylogenetic networks of Y-chromosomal and mitochondrial DNA haplogroups, respectively. Unlike previous studies, we quantitatively characterized the languages based on lexical and phonemic systems, separately. We showed that genetic and linguistic distances are significantly correlated with each other and that both are correlated with geographic distances among these populations. However, when controlling for geographic factors, only the correlation between the distances of paternal and lexical characteristics and between those of maternal and phonemic remained. These unbalanced correlations reconciled the two seemingly conflicting hypotheses.
xyyman comment: Isloation by Distance is a FACT
Phylogeny Estimation by Integration over Isolation with Migration Models - Jody Hey
Abstract
Phylogeny estimation is difficult for closely related populations and species, especially if they have been exchanging genes. We present a hierarchical Bayesian, Markov-chain Monte Carlo method with a state space that includes all possible phylogenies in a full Isolation-with-Migration model framework. The method is based on a new type of genealogy augmentation called a ‘hidden genealogy’ that enables efficient updating of the phylogeny. This is the first likelihood-based method to fully incorporate **"directional" gene flow ***and genetic drift for estimation of a species or population phylogeny. Application to human hunter-gatherer populations from Africa revealed a clear phylogenetic history, with strong support for gene exchange with an un-sampled ghost population, and relatively ancient divergence between a ghost population and modern human populations, consistent with human/archaic divergence. In contrast, a study of five chimpanzee populations reveals a clear phylogeny with several pairs of populations having exchanged DNA, but does not support a history with an unsampled ghost population.
xyyman comment: similar or improved tool to Treemix which can predict DIRECTION of migration?
Enrichment of genetic markers of recent human evolution in educational and cognitive traits
Saurabh Srinivasan, Francesco Bettella, Oleksandr Frei, W. David Hill, Yunpeng Wang, Aree Witoelar, Andrew J. Schork, Wesley K. Thompson, Gail Davies, Rahul S. Desikan, Ian J. Deary, Ingrid Melle, Torill Ueland, Anders M. Dale, Srdjan Djurovic, Olav B. Smeland & Ole A. Andreassen
Scientific Reportsvolume 8, Article number: 12585 (2018) | Download Citation
Abstract
Higher cognitive functions are regarded as one of the main distinctive traits of humans. Evidence for the cognitive evolution of human beings is mainly based on fossil records of an expanding cranium and an increasing complexity of material culture artefacts. However, the molecular genetic factors involved in the evolution are still relatively unexplored. Here, we investigated whether genomic regions that underwent positive selection in humans after divergence from Neanderthals are enriched for genetic association with phenotypes related to cognitive functions. We used genome wide association data from a study of college completion (N = 111,114), one of educational attainment (N = 293,623) and two different studies of general cognitive ability (N = 269,867 and 53,949). We found nominally significant polygenic enrichment of associations with college completion (p = 0.025), educational attainment (p = 0.043) and general cognitive ability (p = 0.015 and 0.025, respectively), suggesting that variants influencing these phenotypes are more prevalent in evolutionarily salient regions. The enrichment remained significant after controlling for other known genetic enrichment factors, and for affiliation to genes highly expressed in the brain. These findings support the notion that phenotypes related to higher order cognitive skills typical of humans have a recent genetic component that originated AFTER the separation of the human and Neanderthal lineages.
xyyman comment: Sorry Eurasians did not inherits their 'smarts" from Neanderthal but from Africans
Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation
Éadaoin Harney, Hila May, Dina Shalem, Nadin Rohland, Swapan Mallick, Iosif Lazaridis, Rachel Sarig, Kristin Stewardson, Susanne Nordenfelt, Nick Patterson, Israel Hershkovitz & David Reich
Nature Communicationsvolume 9, Article number: 3336 (2018) | Download Citation
Abstract
The material culture of the Late Chalcolithic period in the southern Levant (4500–3900/3800 BCE) is qualitatively distinct from previous and subsequent periods. Here, to test the hypothesis that the advent and decline of this culture was influenced by movements of people, we generated genome-wide ancient DNA from 22 individuals from Peqi’in Cave, Israel. These individuals were part of a homogeneous population that can be modeled as deriving ~57% of its ancestry from groups related to those of the local Levant Neolithic, ~17% from groups related to those of the Iran Chalcolithic, and ~26% from groups related to those of the Anatolian Neolithic. The Peqi’in population also appears to have contributed differently to later Bronze Age groups, one of which we show cannot plausibly have descended from the same population as that of Peqi’in Cave. These results provide an example of how population movements propelled cultural changes in the deep past.
xyyman comment: who is the Levant Neolithic? Bedouions. The Levant is an extension of Africa...@57%?
ANCIENT DNA ANALYSIS OF ARCHAEOLOGICAL REMAINS - Maria A. Nieves‐Colón
Summary
Ancient DNA has become a powerful tool to investigate human population history, social patterns within archaeological sites, plant and animal domestication, as well as the pathogens that have impacted us through time. Recent technical advances in DNA capture and sequencing have made it possible to obtain complete genome sequences in a relatively short time from small amounts of biological material such as bone, dental calculus, and coprolites. This has led to several startling discoveries and a deeper understanding of our past.
xyyman comment: should be an interesting paper
New papers of interest....from crazy, fat white people to African ghost population
Positive selection in Europeans and East-Asians at the ABCA12 gene - Roberto Sirica1
ABSTRACT
Natural selection acts on genetic variants by increasing the frequency of alleles responsible for a cellular function that is
favorable in a certain environment. In a previous genome-wide scan for positive selection in contemporary humans, we
identified a signal of positive selection in European and Asians at the genetic variant rs10180970. The variant is located in the
second intron of the ABCA12 gene, which is implicated in the lipid barrier formation and down-regulated by UVB radiation.
We studied the signal of selection in the genomic region surrounding rs10180970 in a larger dataset that includes DNA
sequences from ancient samples. We also investigated the functional consequences of gene expression of the alleles of
rs10180970 and another genetic variant in its proximity in healthy volunteers exposed to similar UV radiation.
We confirmed the selection signal and refine its location that extends over 35 kb and includes the first intron, the first two exons
and the transcription starting site of ABCA12. We found ***no obvious*** effect of rs10180970 alleles on ABCA12 gene expression.
We reconstructed the trajectory of the T allele over the last 80,000 years to discover that it was specific to H. sapiens and
frequent among non-Africans already 45,000 years ago. xyyman comment: another lie exposed?? About lipid metabolism found in Euroepans are attributed to Neanderthal admixture
Positive and balancing selection on SLC18A1 gene associated with psychiatric disorders and human-unique personality traits - Daiki X. Sato1 and Masakado Kawata1
Maintenance of genetic variants susceptible to psychiatric disorders is one of the intriguing evolutionary enigmas. The present
study detects three psychiatric disorder-relevant genes (CLSTN2, FAT1, and SLC18A1) that have been under positive selection
during the human evolution. In particular, SLC18A1 (vesicular monoamine transporter 1; VMAT1) gene has a human-unique variant
(rs1390938, Thr136Ile), which is associated with bipolar disorders and/or the anxiety-related personality traits. 136Ile shows
relatively high (20–61%) frequency in non-African populations, and Tajima’s D reports a significant peak around the Thr136Ile site,
suggesting that this polymorphism has been positively maintained by balancing selection in non-African populations. Moreover,
Coalescent simulations predict that 136Ile originated around 100,000 years ago, the time being generally associated with the
Out-of-Africa migration of modern humans. Our study sheds new light on a gene in monoamine pathway as a strong candidate
contributing to human-unique psychological traits.
xyyman comment: confirmation on why Eurasians are psycho crazy ??
Reconstruction of human subsistence and husbandry strategies from the Iberian Early Neolithic: A stable isotope approach
Abstract
Objectives
The Early Neolithic involved an important social and economic shift that can be tested not only with the material culture, but also through biomolecular approaches. The Iberian Peninsula presents few Early Neolithic sites where fauna and humans can be analyzed together from an isotopic perspective. Here we present an isotopic study on the site of Cueva de Chaves as an example for understanding the dietary and economical changes that took place during Early Neolithic in Iberia.
Material and methods
Here we apply carbon and nitrogen stable isotope analysis to bone collagen from 4 humans and 64 faunal samples from 14 different species. The large dataset belongs to the same unique chrono‐cultural context secured by 20 radiocarbon dates. Three direct new radiocarbon dates were carried out on the human remains analyzed.
Results
Faunal isotope values show no significant differences between wild and domestic herbivores, although the latter have more homogeneous values. Domestic pigs, potentially considered omnivorous, also show signatures of a herbivore diet. Human isotopic results show a diet mainly based on terrestrial C3 resources and possibly high meat consumption. The only individual found buried with a special funerary treatment presents a slightly different protein intake, when taking into account the long contemporaneous baseline analyzed.
Discussion
Similar values between wild and domestic species could be the result of common feeding resources and/or grazing on the same parts of the landscape. The herbivore diet seen amongst domestic pigs rules out feeding on household leftovers. High meat consumption by humans would support the hypothesis of the existence of a specialized animal husbandry management community in which agriculture was not intensively developed. Our results suggest that the development of agricultural practices and animal husbandry were not necessarily associated together in the early stages of the Western Mediterranean Neolithic.
xyyman comment: was the "individual" from Africa?
Implementing a biogeographic ancestry inference service for forensic casework
Soulbee Jin
Abstract
The Centre of Forensic Sciences has validated The Precision ID Ancestry Panel on the Ion S5™ Massively Parallel Sequencing instrument for use in forensic casework. The focus of this paper is the development of reporting guidelines for implementation of the biogeographic ancestry (BGA) inference service based on Admixture Prediction results produced using the Torrent Suite™ Software (Thermo Fisher Scientific). The Admixture Prediction algorithm estimates the genetic ancestry of a sample using seven root populations (Europe, East Asia, Oceania, America, Africa, South Asia, Southwest Asia). For individuals that declared a single ancestry, there was a high correlation between the declared ancestry and the ancestry predicted by the algorithm. However, some individuals with declared ancestries of Southern Europe, Southwest Asia, South Asia and the Horn of Africa had Admixture Predictions that were composed of two or more root populations at 20% or greater. For individuals with known admixed ancestry, the major component of their declaration was included in their results in all but one case. Based on these results, reporting guidelines were developed and subsequently evaluated using the Admixture Predictions of additional samples. This paper discusses the development and evaluation of these reporting guidelines, along with an implementation plan for forensic casework.
xyyman comment: Better toool for predicting admixture
Reconciling the father tongue and mother tongue hypotheses in Indo-European populations
Menghan Zhang Hong-Xiang Zheng Shi Yan Li Jin
\
Abstract
In opposite to the Mother Tongue Hypothesis, the Father Tongue Hypothesis states that humans tend to speak their fathers' language, based on a stronger correlation of languages to paternal lineages (Y-chromosome) than to maternal lineages (mitochondria). . To reassess these two competing hypotheses, we conducted a genetic-linguistic study of 34 modern Indo-European (IE) populations. In this study, genetic histories of paternal and maternal migrations in these IE populations were elucidated using phylogenetic networks of Y-chromosomal and mitochondrial DNA haplogroups, respectively. Unlike previous studies, we quantitatively characterized the languages based on lexical and phonemic systems, separately. We showed that genetic and linguistic distances are significantly correlated with each other and that both are correlated with geographic distances among these populations. However, when controlling for geographic factors, only the correlation between the distances of paternal and lexical characteristics and between those of maternal and phonemic remained. These unbalanced correlations reconciled the two seemingly conflicting hypotheses.
xyyman comment: Isloation by Distance is a FACT
Phylogeny Estimation by Integration over Isolation with Migration Models - Jody Hey
Abstract
Phylogeny estimation is difficult for closely related populations and species, especially if they have been exchanging genes. We present a hierarchical Bayesian, Markov-chain Monte Carlo method with a state space that includes all possible phylogenies in a full Isolation-with-Migration model framework. The method is based on a new type of genealogy augmentation called a ‘hidden genealogy’ that enables efficient updating of the phylogeny. This is the first likelihood-based method to fully incorporate **"directional" gene flow ***and genetic drift for estimation of a species or population phylogeny. Application to human hunter-gatherer populations from Africa revealed a clear phylogenetic history, with strong support for gene exchange with an un-sampled ghost population, and relatively ancient divergence between a ghost population and modern human populations, consistent with human/archaic divergence. In contrast, a study of five chimpanzee populations reveals a clear phylogeny with several pairs of populations having exchanged DNA, but does not support a history with an unsampled ghost population.
xyyman comment: similar or improved tool to Treemix which can predict DIRECTION of migration?
Enrichment of genetic markers of recent human evolution in educational and cognitive traits
Saurabh Srinivasan, Francesco Bettella, Oleksandr Frei, W. David Hill, Yunpeng Wang, Aree Witoelar, Andrew J. Schork, Wesley K. Thompson, Gail Davies, Rahul S. Desikan, Ian J. Deary, Ingrid Melle, Torill Ueland, Anders M. Dale, Srdjan Djurovic, Olav B. Smeland & Ole A. Andreassen
Scientific Reportsvolume 8, Article number: 12585 (2018) | Download Citation
Abstract
Higher cognitive functions are regarded as one of the main distinctive traits of humans. Evidence for the cognitive evolution of human beings is mainly based on fossil records of an expanding cranium and an increasing complexity of material culture artefacts. However, the molecular genetic factors involved in the evolution are still relatively unexplored. Here, we investigated whether genomic regions that underwent positive selection in humans after divergence from Neanderthals are enriched for genetic association with phenotypes related to cognitive functions. We used genome wide association data from a study of college completion (N = 111,114), one of educational attainment (N = 293,623) and two different studies of general cognitive ability (N = 269,867 and 53,949). We found nominally significant polygenic enrichment of associations with college completion (p = 0.025), educational attainment (p = 0.043) and general cognitive ability (p = 0.015 and 0.025, respectively), suggesting that variants influencing these phenotypes are more prevalent in evolutionarily salient regions. The enrichment remained significant after controlling for other known genetic enrichment factors, and for affiliation to genes highly expressed in the brain. These findings support the notion that phenotypes related to higher order cognitive skills typical of humans have a recent genetic component that originated AFTER the separation of the human and Neanderthal lineages.
xyyman comment: Sorry Eurasians did not inherits their 'smarts" from Neanderthal but from Africans
Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation
Éadaoin Harney, Hila May, Dina Shalem, Nadin Rohland, Swapan Mallick, Iosif Lazaridis, Rachel Sarig, Kristin Stewardson, Susanne Nordenfelt, Nick Patterson, Israel Hershkovitz & David Reich
Nature Communicationsvolume 9, Article number: 3336 (2018) | Download Citation
Abstract
The material culture of the Late Chalcolithic period in the southern Levant (4500–3900/3800 BCE) is qualitatively distinct from previous and subsequent periods. Here, to test the hypothesis that the advent and decline of this culture was influenced by movements of people, we generated genome-wide ancient DNA from 22 individuals from Peqi’in Cave, Israel. These individuals were part of a homogeneous population that can be modeled as deriving ~57% of its ancestry from groups related to those of the local Levant Neolithic, ~17% from groups related to those of the Iran Chalcolithic, and ~26% from groups related to those of the Anatolian Neolithic. The Peqi’in population also appears to have contributed differently to later Bronze Age groups, one of which we show cannot plausibly have descended from the same population as that of Peqi’in Cave. These results provide an example of how population movements propelled cultural changes in the deep past.
xyyman comment: who is the Levant Neolithic? Bedouions. The Levant is an extension of Africa...@57%?
ANCIENT DNA ANALYSIS OF ARCHAEOLOGICAL REMAINS - Maria A. Nieves‐Colón
Summary
Ancient DNA has become a powerful tool to investigate human population history, social patterns within archaeological sites, plant and animal domestication, as well as the pathogens that have impacted us through time. Recent technical advances in DNA capture and sequencing have made it possible to obtain complete genome sequences in a relatively short time from small amounts of biological material such as bone, dental calculus, and coprolites. This has led to several startling discoveries and a deeper understanding of our past.
xyyman comment: should be an interesting paper
