A5002611663- Forensic and Genetic Research
- Pleistocene-Era Hominins and Archaeology
- Forensic Anthropology and Bioarchaeology Studies
- Genetic diversity and population structure
- Chromosomal and Genetic Variations
- Archaeology and ancient environmental studies
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Genomics and Phylogenetic Studies
- Linguistics and Cultural Studies
- Linguistics and language evolution
- Genomic variations and chromosomal abnormalities
- Eurasian Exchange Networks
- Evolution and Genetic Dynamics
- Identification and Quantification in Food
- Genomics and Rare Diseases
- Genetic Associations and Epidemiology
- Race, Genetics, and Society
- RNA and protein synthesis mechanisms
- Genetic and phenotypic traits in livestock
- Primate Behavior and Ecology
- Genetic Neurodegenerative Diseases
- Genetic Mapping and Diversity in Plants and Animals
Aarhus University
2015-2024
Max Planck Institute for Evolutionary Anthropology
2020-2024
University of California, Berkeley
2022-2024
Berkeley College
2022
The Francis Crick Institute
2020
Scunthorpe General Hospital
2012
Charles University
2012
To date, the only Neandertal genome that has been sequenced to high quality is from an individual found in Southern Siberia. We of a female ~50,000 years ago Vindija Cave, Croatia, ~30-fold genomic coverage. She carried 1.6 differences per 10,000 base pairs between two copies her genome, fewer than present-day humans, suggesting populations were small size. Our analyses indicate she was more closely related Neandertals mixed with ancestors humans living outside sub-Saharan Africa previously...
Selection, recombination, and hybrid evolution Hybridization is an important force in evolution. The effects of hybridization across the whole genome are not understood. Using a fine-scale genetic map, Schumer et al. examined local ancestry replicate natural populations swordtail fish. Each parental species contributes different proportions material to genomes their descendants. Genes from “minor” (less well-represented) parent occur regions that subject higher recombination rates where...
We sequenced the genome of a Neandertal from Chagyrskaya Cave in Altai Mountains, Russia, to 27-fold genomic coverage. show that this was female and she more related Neandertals western Eurasia [Prüfer et al., Science 358, 655–658 (2017); Hajdinjak Nature 555, 652–656 (2018)] than who lived earlier Denisova 505, 43–49 (2014)], which is located about 100 km away. About 12.9% spanned by homozygous regions are between 2.5 10 centiMorgans (cM) long. This consistent with fact Siberian relatively...
Abstract Modern humans appeared in Europe by at least 45,000 years ago 1–5 , but the extent of their interactions with Neanderthals, who disappeared about 40,000 6 and relationship to broader expansion modern outside Africa are poorly understood. Here we present genome-wide data from three individuals dated between 45,930 42,580 Bacho Kiro Cave, Bulgaria 1,2 . They earliest Late Pleistocene known have been recovered so far, were found association an Initial Upper Palaeolithic artefact...
Abstract Genomic analyses of Neanderthals have previously provided insights into their population history and relationship to modern humans 1–8 , but the social organization Neanderthal communities remains poorly understood. Here we present genetic data for 13 from two Middle Palaeolithic sites in Altai Mountains southern Siberia: 11 Chagyrskaya Cave 9,10 2 Okladnikov —making this one largest studies a date. We used hybridization capture obtain genome-wide nuclear data, as well mitochondrial...
India has been underrepresented in whole genome sequencing studies. We generated 2,762 high coverage genomes from - including individuals most geographic regions, speakers of all major languages, and tribal caste groups providing a comprehensive survey genetic variation India. With these data, we reconstruct the evolutionary history through space time at fine scales. show that Indians derive ancestry three ancestral related to ancient Iranian farmers, Eurasian Steppe pastoralists South Asian...
Hundreds of thousands human genomes are now being sequenced to characterize genetic variation and use this information augment association mapping studies complex disorders other phenotypic traits. Genetic is identified mainly by short reads the reference genome or performing local assembly. However, these approaches biased against discovery structural variants in more parts genome. Hence, large-scale de novo assembly needed. Here we show that it possible construct excellent assemblies from...
Human populations outside of Africa have experienced at least two bouts introgression from archaic humans, Neanderthals and Denisovans. In Papuans there is prior evidence both these introgressions. Here we present a new approach to detect segments individual genomes origin without using an reference genome. The based on hidden Markov model that identifies genomic regions with high density single nucleotide variants (SNVs) not seen in unadmixed populations. We show simulations this provides...
Abstract Gene flow from Neandertals has shaped the landscape of genetic and phenotypic variation in modern humans. We identify location size introgressed Neandertal ancestry segments more than 300 genomes spanning last 50,000 years. study how is shared among individuals to infer time duration gene flow. find correlation segment locations across their divergence sequenced Neandertals, both support a model single major Our catalog through confirms that most natural selection–positive...
We present analyses of the genome a ~34,000-year-old hominin skull cap discovered in Salkhit Valley northeastern Mongolia. show that this individual was female member modern human population that, following split between East and West Eurasians, experienced substantial gene flow from Eurasians. Both she 40,000-year-old Tianyuan outside Beijing carried genomic segments Denisovan ancestry. These derive same admixture event(s) contributed to present-day mainland Asians but are distinct DNA...
Abstract Much remains unknown about the population history of early modern humans in southeast Asia, where archaeological record is sparse and tropical climate inimical to preservation ancient human DNA 1 . So far, only two low-coverage pre-Neolithic genomes have been sequenced from this region. Both are mainland Hòabìnhian hunter-gatherer sites: Pha Faen Laos, dated 7939–7751 calibrated years before present (yr cal bp; taken as ad 1950), Gua Cha Malaysia (4.4–4.2 kyr bp ) Here we report,...
The X chromosome in non-African humans shows less diversity and Neanderthal introgression than expected from neutral evolution. Analyzing 162 human male chromosomes worldwide, we identified fourteen chromosomal regions where nearly identical haplotypes spanning several hundred kilobases are found at high frequencies non-Africans. Genetic drift alone cannot explain the existence of these haplotypes, which must have been associated with strong positive selection partial selective sweeps....
The human Y-chromosome does not recombine across its male-specific part and is therefore an excellent marker of migrations. It also plays important role in male fertility. However, evolution difficult to fully understand because repetitive sequences, inverted repeats the potentially large gene conversion. Here we perform evolutionary analysis 62 Y-chromosomes Danish descent sequenced using a wide range library insert sizes high coverage, thus allowing regions these chromosomes be well...
After the main Out-of-Africa event, humans interbred with Neanderthals leaving 1-2% of Neanderthal DNA scattered in small fragments all non-African genomes today. Here we investigate what can be learned about human demographic processes from size distribution these fragments. We observe differences fragment length across Eurasia 12% longer East Asians than West Eurasians. Comparisons between extant populations ancient samples show that are caused by different rates decay recombination since...
Insights into the admixture history between modern and archaic humans require accurately inferred introgressed fragments within genomes. Here, we introduce two enhancements to hidden Markov models (HMMs) implemented in hmmix. First, develop a method for sampling state sequences conditional on observed genomic data, enabling robust estimation of summary statistics - such as proportion fragment length distributions. This represents an improvement compared relying solely point estimates...
We study genome-wide nucleotide diversity in three subspecies of extant chimpanzees using exome capture. After strict filtering, Single Nucleotide Polymorphisms and indels were called genotyped for greater than 50% exons at a mean coverage 35× per individual. Central (Pan troglodytes troglodytes) are the most polymorphic (nucleotide diversity, θw = 0.0023 site) followed by Eastern (P. t. schweinfurthii) (θw 0.0016) Western verus) 0.0008). A demographic scenario divergence without gene flow...
Abstract Ampliconic genes are multicopy often located on sex chromosomes and enriched for testis-expressed genes. Here, Lucotte et al. developed new bioinformatic approaches to investigate the ampliconic gene copy number their coding... multicopy, with majority found While have been associated emergence of hybrid incompatibilities, we know little about distribution turnover in human populations. explore evolution X- Y-linked by investigating variation (CNV) coding between populations using...
Abstract We sequenced the genome of a Neandertal from Chagyrskaya Cave in Altai Mountains, Russia, to 27-fold genomic coverage. estimate that this individual lived ~80,000 years ago and was more closely related Neandertals western Eurasia (1,2) than who earlier Denisova (3), which is located about 100 km away. About 12.9% spanned by homozygous regions are between 2.5 10 centiMorgans (cM) long. This consistent with Siberian relatively isolated populations less 60 individuals. In contrast,...
Gene flow from Neanderthals has shaped genetic and phenotypic variation in modern humans. We generated a catalog of Neanderthal ancestry segments more than 300 genomes spanning the past 50,000 years. examined how is shared among individuals over time. Our analysis revealed that vast majority gene attributable to single, extended period occurred between 50,500 43,500 years ago, as evidenced by correlation, colocalization across individuals, divergence sequenced Neanderthals. Most natural...
Abstract While hybridization between species is increasingly appreciated to be a common occurrence, little known about the forces that govern subsequent evolution of hybrid genomes. We considered this question in three independent, naturally-occurring populations formed swordtail fish Xiphophorus birchmanni and X. malinche. To end, we built fine-scale genetic map inferred patterns local ancestry along genomes 690 individuals sampled from populations. In all cases, found more regions high...
Abstract Genomic analyses of Neanderthals have previously provided insights into their population history and relationship to modern humans 1–8 , but the social organization Neanderthal communities remains poorly understood. Here, we present genetic data for 13 from two Middle Palaeolithic sites in Altai Mountains southern Siberia: 11 Chagyrskaya Cave 9,10 Okladnikov - making this largest study a date. We used hybridization capture obtain genome-wide nuclear data, as well mitochondrial...
Spinocerebellar ataxia type 10 (SCA10) is a rare autosomal dominant caused by large expansion of the (ATTCT)n repeat in ATXN10. SCA10 was described Native American and Asian individuals which prompted search for an expanded haplotype to confirm common ancestral origin event. All patients with expansions our cohort share single defined at 5'-end minor allele rs41524547, located ~35 kb upstream expansion. Intriguingly, rs41524547 within miRNA gene, MIR4762, its DROSHA cleavage site just...
A major part of the human Y chromosome consists palindromes with multiple copies genes primarily expressed in testis, many which have been claimed to affect male fertility. Here we examine copy number variation these based on whole genome sequence data from 11,527 Icelandic men. Using a subset 7947 men grouped into 1449 patrilineal genealogies, infer 57 large scale de novo mutations affecting palindrome 1. This corresponds mutation rate 2.34 × 10-3 per meiosis, is 4.1 times larger than our...
Abstract We present analyses of the genome a ~34,000-year-old hominin skull cap discovered in Salkhit Valley North East Mongolia. show that this individual was female member modern human population that, following split between and West Eurasians, experienced substantial gene flow from Eurasians. Both she 40,000-year-old Tianyuan outside Beijing carried genomic segments Denisovan ancestry. These derive same admixture event(s) contributed to present-day mainland Asians but are distinct DNA...