Benjamin M. Peter's research while affiliated with Max Planck Institute for Evolutionary Anthropology and other places
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Publications (28)
Genetic kinship of ancient individuals can provide insights into their culture and social hierarchy, and is relevant for downstream genetic analyses. However, estimating relatedness from ancient DNA is difficult due to low-coverage, ascertainment bias, or contamination from various sources. Here, we present KIN, a method to estimate the relatedness...
Genetic kinship of ancient individuals can provide insights into their culture and social hierarchy, and is relevant for downstream genetic analyses. However, estimating relatedness from ancient DNA is difficult due to low-coverage, ascertainment bias, or contamination from various sources. Here, we present KIN, a method to estimate the relatedness...
Genomic analyses of Neanderthals have previously provided insights into their population history and relationship to modern humans1–8, but the social organization of Neanderthal communities remains poorly understood. Here we present genetic data for 13 Neanderthals from two Middle Palaeolithic sites in the Altai Mountains of southern Siberia: 11 fr...
The Massim, a cultural region that includes the southeastern tip of mainland Papua New Guinea (PNG) and nearby PNG offshore islands, is renowned for a trading network called Kula, in which different valuable items circulate in different directions among some of the islands. While the Massim has been a focus of anthropological investigation since th...
Proteins associated with the spindle apparatus, a cytoskeletal structure that ensures the proper segregation of chromosomes during cell division, experienced an unusual number of amino acid substitutions in modern humans after the split from the ancestors of Neandertals and Denisovans. Here, we analyze the history of these substitutions and show th...
Principal component analysis (PCA) and F -statistics sensu Patterson are two of the most widely used population genetic tools to study human genetic variation. Here, I derive explicit connections between the two approaches and show that these two methods are closely related. F -statistics have a simple geometrical interpretation in the context of P...
The Massim, a cultural region encompassing the southeastern tip of mainland Papua New Guinea (PNG) and nearby islands, is famous for the Kula trading network, in which different valuables circulate in different directions among the islands. To explore Massim genetic history, we generated genome-wide data from across the region and found variable le...
Proteins associated with the spindle apparatus, a cytoskeletal structure that ensures the proper segregation of chromosomes during cell division, experienced an unusual number of amino acid substitutions in modern humans after the split from the ancestors of Neandertals and Denisovans. Here, we analyze the history of these substitutions and show th...
In most macaques, females are philopatric and males migrate from their natal ranges, which results in pronounced divergence of mitochondrial genomes within and among species. We therefore predicted that some nuclear genes would have to acquire compensatory mutations to preserve compatibility with diverged interaction partners from the mitochondria....
After the main Out-of-Africa event, humans interbred with Neanderthals leaving 1–2% of Neanderthal DNA scattered in small fragments in all non-African genomes today. Here we investigate what can be learned about human demographic processes from the size distribution of these fragments. We observe differences in fragment length across Eurasia with 1...
Much remains unknown about the population history of early modern humans in southeast Asia, where the archaeological record is sparse and the tropical climate is inimical to the preservation of ancient human DNA ¹ . So far, only two low-coverage pre-Neolithic human genomes have been sequenced from this region. Both are from mainland Hòabìnhian hunt...
Neandertal DNA makes up 2-3% of the genomes of all non-African individuals. The patterns of Neandertal ancestry in modern humans have been used to estimate that this is the result of gene flow that occurred during the expansion of modern humans into Eurasia, but the precise dates of this event remain largely unknown. Here, we introduce an extended...
The value of dirty DNA
Environmental DNA can identify the presence of species, even from the distant past. Surveying three cave sites in western Europe and southern Siberia, Vernot et al. identified nuclear DNA and confirmed that it is from the close relatives of anatomically modern humans—Neanderthal and Denisovan individuals. A phylogenetic analy...
Modern humans appeared in Europe by at least 45,000 years ago1–5, but the extent of their interactions with Neanderthals, who disappeared by about 40,000 years ago6, and their relationship to the broader expansion of modern humans outside Africa are poorly understood. Here we present genome-wide data from three individuals dated to between 45,930 a...
Neandertal DNA makes up 2-3 % of the genomes of all non-African individuals on average. The length of Neandertal ancestry segments in modern humans has been used to estimate that the mean time of gene flow occurred during the expansion of modern humans into Eurasia, but the precise dates of this gene flow remain largely unknown. Here, we introduce...
After the main out-of-Africa event, humans interbred with Neanderthals leaving 1-2% of Neanderthal DNA scattered in small fragments in all non-African genomes today1,2. Here we investigate the size distribution of these fragments in non-African genomes3. We find consistent differences in fragment length distributions across Eurasia with 11% longer...
We generated induced excitatory neurons (iNeurons, iNs) from chimpanzee, bonobo and human stem cells by expressing the transcription factor neurogenin‑2 (NGN2). Single cell RNA sequencing (scRNAseq) showed that genes involved in dendrite and synapse development are expressed earlier during iNs maturation in the chimpanzee and bonobo than the human...
DNA analyses of an early East Asian
Ancient, anatomically modern humans interbred with the archaic hominins Neanderthals and Denisovans. However, the extent of this interbreeding and how it affects modern populations is not well understood. Massilani et al. generated genome-wide data from a 34,000-year-old female individual from the Salkhit Valley...
Contamination from present-day DNA is a fundamental issue when studying ancient DNA from historical or archaeological material, and quantifying the amount of contamination is essential for downstream analyses. We present AuthentiCT, a command-line tool to estimate the proportion of present-day DNA contamination in ancient DNA datasets generated fro...
We sequenced the genome of a Neandertal from Chagyrskaya Cave in the Altai Mountains, Russia, to 27-fold genomic coverage. We show that this Neandertal was a female and that she was more related to Neandertals in western Eurasia [Prüfer et al., Science 358, 655–658 (2017); Hajdinjak et al., Nature 555, 652–656 (2018)] than to Neandertals who lived...
We present analyses of the genome of a ~34,000-year-old hominin skull cap discovered in the Salkhit Valley in North East Mongolia. We show that this individual was a female member of a modern human population that, following the split between East and West Eurasians, experienced substantial gene flow from West Eurasians. Both she and a 40,000-year-...
We generated induced excitatory sensory neurons (iNeurons, iNs) from chimpanzee, bonobo and human stem cells by expressing the transcription factor neurogenin 2 (NGN2). Single cell-RNA sequencing showed that genes involved in dendrite and synapse development are expressed earlier during iNs maturation in the chimpanzee than the human cells. In acco...
Contamination from present-day DNA is a fundamental issue when studying ancient DNA from historical or archaeological material, and quantifying the amount of contamination is essential for downstream analyses. We present AuthentiCT, a command-line tool to estimate the proportion of present-day DNA contamination in ancient DNA datasets generated fro...
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The Siberian Altai mountains have been intermittently occupied by both Neandertals and Denisovans, two extinct hominin groups 1,2 . While they diverged at least 390,000 years ago 3,4 , later contacts lead to gene flow from Neandertals into Denisovans 5,6 . Using a new population genetic method that is capable of inferring signatures of ad...
We sequenced the genome of a Neandertal from Chagyrskaya Cave in the Altai Mountains, Russia, to 27-fold genomic coverage. We estimate that this individual lived ~80,000 years ago and was more closely related to Neandertals in western Eurasia than to Neandertals who lived earlier in Denisova Cave, which is located about 100 km away. About 12.9% of...
Geographic patterns in human genetic diversity carry footprints of population history 1,2 and provide insights for genetic medicine and its application across human populations 3,4 . Summarizing and visually representing these patterns of diversity has been a persistent goal for human geneticists 5–10 , and has revealed that genetic differentiation...
Indigenous populations of the Tibetan plateau have attracted much attention for their good performance at extreme high altitude. Most genetic studies of Tibetan adaptations have used genetic variation data at the genome scale, while genetic inferences about their demography and population structure are largely based on uniparental markers. To provi...
Citations
... To test the performance of BREADR, we performed analyses on simulated data as described in [14] 1 , and on published empirical data from a population genetic and relatedness study by villalba2022kinship 2 , and compared our results to those obtained from READ. ...
... The data analysed in this study was obtained from the following archive study accessions: PRJEB54831 (ENA) 9 , PRJEB51180 (ENA) 10 , PRJCA005576 (GSA) 11 , PRJEB52849 (ENA) 12 , PRJEB42656 (ENA) 13 , PRJEB49291 (ENA) 14 , PRJEB42781 (ENA) 15 , PRJEB46734 (ENA) 16 , PRJNA798381 (SRA) 17 , PRJEB42269 (ENA) 18 , PRJEB47891 (ENA) 19 , PRJEB54899 (ENA) 20 , PRJEB43715 (ENA) 21 , PRJEB39134 (ENA) 22 , PRJEB46162 (ENA) 23 , PRJEB46875 (ENA) 24 , PRJEB44430 (ENA) 25 , PRJEB42199 (ENA) 26 , PRJEB38555 (ENA) 27 , PRJEB55327 (ENA) 28 , PRJEB50368 (ENA) 29 , PRJEB50857 (ENA) 30 , PRJCA003870 (GSA) 31 , PRJCA003699 (GSA) 32 , PRJEB53475 (ENA) 33 , PRJEB37782 (ENA) 34 , PRJNA687817 (SRA) 35 , PRJEB42372 (ENA) 36 . ...
... Recent evidence indicates possible early Homo sapiens incursions into southern Europe, overlapping (France (Slimak et al. 2022)) or predating (Southern Greece (Harvati et al. 2019)) the time frame of the Königsaue birch tar artefacts. These findings are supported by paleo-genetic analyses (Peyrégne et al. 2022;Posth et al. 2017). Thus, the possibility of cultural exchange cannot be completely excluded and should be further investigated. ...
... However, the observed distance between the ancient and present-day Brazilian samples is likely the result of strong genetic drift effects experienced by the Amazonian populations [6,12] (figure 1b) since they split with the ancient individuals. It is known that changes in allele frequencies due to drift in a given population might affect its position in PCspace [27] relative to other populations. The exception to this observation is when the referred population is not part of the principal components' (PCs) construction [27], which is not the case for Surui and Karitiana. ...
... Downloaded from https://academic.oup.com/sysbio/advance-article/doi/10.1093/sysbio/syad020/7130943 by guest on 12 May 2023 most plausible explanation for mitochondrial breaks within rhesus and pig-tailed macaques (Tosi et al. 2003;Evans et al. 2021). We find both of these mechanisms to be implausible explanations for at least two of the three Draco intraspecific mitochondrial boundaries based on key deviations from model expectations. ...
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... Instead, it categorizes individuals who satisfy certain criteria and then divides generations based on the temporal aggregation that corresponds to the features [26]. In medical research, generation is defned as the biological activity, such as relationship between children and parents, or several ofsprings as a generation with diferences in biological traits [27][28][29]. Unlike sociology, intergeneration divisions in medicine are not refected in the same time interval but rather in diferent features. Nevertheless, both two types of studies are characterized by the fact that evolution produces intergeneration. ...
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... The data analysed in this study was obtained from the following archive study accessions: PRJEB54831 (ENA) 9 , PRJEB51180 (ENA) 10 , PRJCA005576 (GSA) 11 , PRJEB52849 (ENA) 12 , PRJEB42656 (ENA) 13 , PRJEB49291 (ENA) 14 , PRJEB42781 (ENA) 15 , PRJEB46734 (ENA) 16 , PRJNA798381 (SRA) 17 , PRJEB42269 (ENA) 18 , PRJEB47891 (ENA) 19 , PRJEB54899 (ENA) 20 , PRJEB43715 (ENA) 21 , PRJEB39134 (ENA) 22 , PRJEB46162 (ENA) 23 , PRJEB46875 (ENA) 24 , PRJEB44430 (ENA) 25 , PRJEB42199 (ENA) 26 , PRJEB38555 (ENA) 27 , PRJEB55327 (ENA) 28 , PRJEB50368 (ENA) 29 , PRJEB50857 (ENA) 30 , PRJCA003870 (GSA) 31 , PRJCA003699 (GSA) 32 , PRJEB53475 (ENA) 33 , PRJEB37782 (ENA) 34 , PRJNA687817 (SRA) 35 , PRJEB42372 (ENA) 36 . ...
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... Over the last decades, multiple approaches have been designed to study introgresion [3][4][5][6][7][8][9] . ...
... The data analysed in this study was obtained from the following archive study accessions: PRJEB54831 (ENA) 9 , PRJEB51180 (ENA) 10 , PRJCA005576 (GSA) 11 , PRJEB52849 (ENA) 12 , PRJEB42656 (ENA) 13 , PRJEB49291 (ENA) 14 , PRJEB42781 (ENA) 15 , PRJEB46734 (ENA) 16 , PRJNA798381 (SRA) 17 , PRJEB42269 (ENA) 18 , PRJEB47891 (ENA) 19 , PRJEB54899 (ENA) 20 , PRJEB43715 (ENA) 21 , PRJEB39134 (ENA) 22 , PRJEB46162 (ENA) 23 , PRJEB46875 (ENA) 24 , PRJEB44430 (ENA) 25 , PRJEB42199 (ENA) 26 , PRJEB38555 (ENA) 27 , PRJEB55327 (ENA) 28 , PRJEB50368 (ENA) 29 , PRJEB50857 (ENA) 30 , PRJCA003870 (GSA) 31 , PRJCA003699 (GSA) 32 , PRJEB53475 (ENA) 33 , PRJEB37782 (ENA) 34 , PRJNA687817 (SRA) 35 , PRJEB42372 (ENA) 36 . ...
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... pnas.org latitudes of Eurasia from ~54 to 51 ka (Fig. 4 and SI Appendix, Table S9 and Supplemental Materials 2). The earliest observations of eight sweeps occur in genomes from the first analyzed European and Asian AMH populations, which are associated with the Initial Upper Paleolithic culture, ~45 to 40 ka; (83). Following the IUP, early West Eurasian individuals dated between 38 and 18 ka subsequently recorded an additional 10 sweeps (Fig. 4 and SI Appendix, Table S9). ...
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