Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers

Modern humans have populated Europe for more than 45,000 years1,2. Our knowledge of the genetic relatedness and structure of ancient hunter-gatherers is however limited, owing to the scarceness and poor molecular preservation of human remains from that period3. Here we analyse 356 ancient hunter-gatherer genomes, including new genomic data for 116 individuals from 14 countries in western and central Eurasia, spanning between 35,000 and 5,000 years ago. We identify a genetic ancestry profile in individuals associated with Upper Palaeolithic Gravettian assemblages from western Europe that is distinct from contemporaneous groups related to this archaeological culture in central and southern Europe4, but resembles that of preceding individuals associated with the Aurignacian culture. This ancestry profile survived during the Last Glacial Maximum (25,000 to 19,000 years ago) in human populations from southwestern Europe associated with the Solutrean culture, and with the following Magdalenian culture that re-expanded northeastward after the Last Glacial Maximum. Conversely, we reveal a genetic turnover in southern Europe suggesting a local replacement of human groups around the time of the Last Glacial Maximum, accompanied by a north-to-south dispersal of populations associated with the Epigravettian culture. From at least 14,000 years ago, an ancestry related to this culture spread from the south across the rest of Europe, largely replacing the Magdalenian-associated gene pool. After a period of limited admixture that spanned the beginning of the Mesolithic, we find genetic interactions between western and eastern European hunter-gatherers, who were also characterized by marked differences in phenotypically relevant variants

Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers

Modern humans have populated Europe for more than 45,000 years. Our knowledge of the genetic relatedness and structure of ancient hunter-gatherers is however limited, owing to the scarceness and poor molecular preservation of human remains from that period. Here we analyse 356 ancient hunter-gatherer genomes, including new genomic data for 116 individuals from 14 countries in western and central Eurasia, spanning between 35,000 and 5,000 years ago. We identify a genetic ancestry profile in individuals associated with Upper Palaeolithic Gravettian assemblages from western Europe that is distinct from contemporaneous groups related to this archaeological culture in central and southern Europe, but resembles that of preceding individuals associated with the Aurignacian culture. This ancestry profile survived during the Last Glacial Maximum (25,000 to 19,000 years ago) in human populations from southwestern Europe associated with the Solutrean culture, and with the following Magdalenian culture that re-expanded northeastward after the Last Glacial Maximum. Conversely, we reveal a genetic turnover in southern Europe suggesting a local replacement of human groups around the time of the Last Glacial Maximum, accompanied by a north-to-south dispersal of populations associated with the Epigravettian culture. From at least 14,000 years ago, an ancestry related to this culture spread from the south across the rest of Europe, largely replacing the Magdalenian-associated gene pool. After a period of limited admixture that spanned the beginning of the Mesolithic, we find genetic interactions between western and eastern European hunter-gatherers, who were also characterized by marked differences in phenotypically relevant variants.Open access funding provided by Max Planck Society. This project has received funding by the European Research Council under the European Union’s Horizon 2020 research and innovation programme under grant agreements no. 803147-RESOLUTION (to S.T.), no. 771234-PALEoRIDER (to W.H.), no. 864358 (to K.M.), no. 724703 and no. 101019659 (to K.H.). K.H. is also supported by the Deutsche Forschungsgemeinschaft (DFG FOR 2237). E.A. has received funding from the Van de Kamp fonds. PACEA co-authors of this research benefited from the scientific framework of the University of Bordeaux’s IdEx Investments for the Future programme/GPR Human Past. A.G.-O. is supported by a Ramón y Cajal fellowship (RYC-2017-22558). L. Sineo, M.L. and D.C. have received funding from the Italian Ministry of University and Research (MUR) PRIN 2017 grants 20177PJ9XF and 20174BTC4R_002. H. Rougier received support from the College of Social and Behavioral Sciences of CSUN and the CSUN Competition for RSCA Awards. C.L.S. and T. Saupe received support from the European Union through the European Regional Development Fund (project no. 2014-2020.4.01.16-0030) and C.L.S. received support from the Estonian Research Council grant PUT (PRG243). S. Shnaider received support from the Russian Science Foundation (no. 19-78-10053).Peer reviewe

Archaeogenetic analysis of Neolithic sheep from Anatolia suggests a complex demographic history since domestication

Yurtman, ozer, Yuncu et al. provide an ancient DNA data set to demonstrate the impact of human activity on the demographic history of domestic sheep. The authors demonstrate that there may have been multiple domestication events with notable changes to the gene pool of European and Anatolian sheep since the Neolithic. Sheep were among the first domesticated animals, but their demographic history is little understood. Here we analyzed nuclear polymorphism and mitochondrial data (mtDNA) from ancient central and west Anatolian sheep dating from Epipaleolithic to late Neolithic, comparatively with modern-day breeds and central Asian Neolithic/Bronze Age sheep (OBI). Analyzing ancient nuclear data, we found that Anatolian Neolithic sheep (ANS) are genetically closest to present-day European breeds relative to Asian breeds, a conclusion supported by mtDNA haplogroup frequencies. In contrast, OBI showed higher genetic affinity to present-day Asian breeds. These results suggest that the east-west genetic structure observed in present-day breeds had already emerged by 6000 BCE, hinting at multiple sheep domestication episodes or early wild introgression in southwest Asia. Furthermore, we found that ANS are genetically distinct from all modern breeds. Our results suggest that European and Anatolian domestic sheep gene pools have been strongly remolded since the Neolithic

Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers

: Modern humans have populated Europe for more than 45,000 years1,2. Our knowledge of the genetic relatedness and structure of ancient hunter-gatherers is however limited, owing to the scarceness and poor molecular preservation of human remains from that period3. Here we analyse 356 ancient hunter-gatherer genomes, including new genomic data for 116 individuals from 14 countries in western and central Eurasia, spanning between 35,000 and 5,000 years ago. We identify a genetic ancestry profile in individuals associated with Upper Palaeolithic Gravettian assemblages from western Europe that is distinct from contemporaneous groups related to this archaeological culture in central and southern Europe4, but resembles that of preceding individuals associated with the Aurignacian culture. This ancestry profile survived during the Last Glacial Maximum (25,000 to 19,000 years ago) in human populations from southwestern Europe associated with the Solutrean culture, and with the following Magdalenian culture that re-expanded northeastward after the Last Glacial Maximum. Conversely, we reveal a genetic turnover in southern Europe suggesting a local replacement of human groups around the time of the Last Glacial Maximum, accompanied by a north-to-south dispersal of populations associated with the Epigravettian culture. From at least 14,000 years ago, an ancestry related to this culture spread from the south across the rest of Europe, largely replacing the Magdalenian-associated gene pool. After a period of limited admixture that spanned the beginning of the Mesolithic, we find genetic interactions between western and eastern European hunter-gatherers, who were also characterized by marked differences in phenotypically relevant variants

Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers

Publisher Copyright: © 2023, The Author(s).Modern humans have populated Europe for more than 45,000 years1,2. Our knowledge of the genetic relatedness and structure of ancient hunter-gatherers is however limited, owing to the scarceness and poor molecular preservation of human remains from that period3. Here we analyse 356 ancient hunter-gatherer genomes, including new genomic data for 116 individuals from 14 countries in western and central Eurasia, spanning between 35,000 and 5,000 years ago. We identify a genetic ancestry profile in individuals associated with Upper Palaeolithic Gravettian assemblages from western Europe that is distinct from contemporaneous groups related to this archaeological culture in central and southern Europe4, but resembles that of preceding individuals associated with the Aurignacian culture. This ancestry profile survived during the Last Glacial Maximum (25,000 to 19,000 years ago) in human populations from southwestern Europe associated with the Solutrean culture, and with the following Magdalenian culture that re-expanded northeastward after the Last Glacial Maximum. Conversely, we reveal a genetic turnover in southern Europe suggesting a local replacement of human groups around the time of the Last Glacial Maximum, accompanied by a north-to-south dispersal of populations associated with the Epigravettian culture. From at least 14,000 years ago, an ancestry related to this culture spread from the south across the rest of Europe, largely replacing the Magdalenian-associated gene pool. After a period of limited admixture that spanned the beginning of the Mesolithic, we find genetic interactions between western and eastern European hunter-gatherers, who were also characterized by marked differences in phenotypically relevant variants.Peer reviewe

Ten millennia of hepatitis B virus evolution

Hepatitis B virus (HBV) has been infecting humans for millennia and remains a global health problem, but its past diversity and dispersal routes are largely unknown. We generated HBV genomic data from 137 Eurasians and Native Americans dated between ~10,500 and ~400 years ago. We date the most recent common ancestor of all HBV lineages to between ~20,000 and 12,000 years ago, with the virus present in European and South American hunter-gatherers during the early Holocene. After the European Neolithic transition, Mesolithic HBV strains were replaced by a lineage likely disseminated by early farmers that prevailed throughout western Eurasia for ~4000 years, declining around the end of the 2nd millennium BCE. The only remnant of this prehistoric HBV diversity is the rare genotype G, which appears to have reemerged during the HIV pandemic

Antik genom dizileme verisi ile genetik akrabalık ilişkisinin belirlenmesi.

One distinct feature of the early Neolithic settlements in the Near East was their burial customs. Both in the Levant and in Anatolia, people dug graves inside their houses, and multiple individuals were buried in these intramural graves; a custom that reached its climax in Çatalhöyük. Archaeological evidence suggests that individuals buried in a house were socially related, which has motivated anthropologists to estimate biological relatedness among individuals who share the same grave. Such information, which could be obtained from ancient DNA data, could shed light on the social structure of these ancient communities, and be valuable for archaeological studies. The challenge of working with ancient DNA is that it is highly degraded and usually in minute amounts, which results in limited DNA data availability. Importantly, in ancient DNA datasets usually only one allele can be detected per individual. There exist a number of meth- ods to estimate genetic relatedness designed for modern high coverage genomic data, but their performance on ancient DNA data has not been tested. Here we vapply two of these methods, KING and PLINK, on low coverage whole genome data from real family pedigrees, as well as ancient DNA data from simulated pedigrees. We further propose a new approach to calculate relatedness between ancient individuals, which would require minimal coverage and SNP numbers to accurately estimate relatedness. We show that our approach can more effi- ciently estimate the relatedness coefficients compared to the KING and PLINK software. Our approach is expected to promote the application of ancient DNA to address new archaeological questions.M.S. - Master of Scienc

Determining the role of mutation load in mammalian senescence

In most multicellular species, aging is accompanied by an increasing risk of disease and mortality, a process termed senescence. The evolutionary causes and genetic bases of senescence are little understood. Senescence is usually associated with accumulating cellular damage, although a number of theories suggest that harmful mutations that are expressed only at late age could also contribute to the aging phenotype. Analyzing primate brain transcriptome data, we recently identified a pattern that would support this latter notion: genes expressed at high levels in old individuals, compared to genes expressed at high levels in young adults, tend to be evolutionarily less conserved, suggesting that they might harbor a higher proportion of deleterious mutations. This result suggests that a deleterious mutation load may indeed play a role in senescence. In this project, we will use a wide array of transcriptome datasets across multiple tissues and mammalian species, to identify the generality of this pattern. Using a new metric, for the first time, we will measure the decrease in negative selection pressure with age. The results will shed light into one highly debated mechanism of senescence

Yeni nesil moleküler veri analizi yoluyla genom ve transkriptom evriminin incelenmesi

Tüm genom dizileme verisi, genom çapında veya ekzom çapında polimorfizm verisi, mikrodizin ve RNA-dizileme verisi, GC-MS metabolit verisi gibi geniş çaplı moleküler veri setlerinin hesaplamalı analizi yoluyla uzun zamandır biyologları meşgul eden çok sayıda sorunun cevaplanması bugün mümkün hale gelmiştir. Araştırma grubumuzda genom ve transkriptom evrimi üzerine şu soruları gelecek yıl içinde cevaplayamaya çalışacağız:- Primatlar arasında testis transkriptomu niye ve nasıl evrilmektedir? - Türler arasında transkriptom farkları arasında en anlamlı olanlar nasıl tespit edilir?- Genom çapında kısa nükleotit homopolimerleri oluşturan mutasyonların insan popülasyonu içinde hızlı yayılmasının sebepleri nelerdir? - Yaşlanma sırasında metabolit ve gen ifadesi değişimlerinin sebepleri nedir?- Anadolu insan popülasyonunda Neandertal karışımı başka popülasyonlardan farklı olabilir mi?- Anadolu’da geçmiş göç örüntüleri nelerdir?- Mesane kanserinde görülen senkronize tümörler akraba mıdır

Benchmarking kinship estimation tools for ancient genomes using pedigree simulations

There is growing interest in identifying genetic kinship levels among ancient individuals buried in physical proximity, from graveyards to archaeological crime scenes. Ancient genome data produced using massively parallel sequencing allow such estimation, albeit with significant limitations owing to the extremely low coverage of ancient genomes, frequently ranging between 0.2x - 0.01x. Estimating the kinship coefficient reliably using such sparse data is a challenge. Both likelihood-based and non-parametric tools have been recently developed to address this question, but their efficiency has not yet been systematically and comparatively studied. Here we present work where we compared the accuracy of three most commonly employed tools, using ancient genome data produced from simulated pedigrees. We studied accuracy with respect to both kinship coefficient estimation, and also Cotterman coefficients. Our results show that genotype data that include >5,000 SNPs allow close kinship coefficients to be relatively reliably estimated, although accuracy falls dramatically beyond the 3rd degree. In addition, we confirm that pedigree relationship estimation (e.g. distinguishing between parent-child pairs vs. siblings) using Cotterman coefficients is a noteworthy problem, and will require alternative, and holistic approaches to address