ORCID Profile
0000-0002-5025-2607
Current Organisation
Københavns Universitet
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Genomics | Aboriginal and Torres Strait Islander History | Population, Ecological and Evolutionary Genetics | Genetics | Anthropological Genetics | Biogeography and Phylogeography | Evolutionary Biology | Biological Adaptation
Expanding Knowledge in the Biological Sciences | Aboriginal and Torres Strait Islander Health - Determinants of Health | Understanding Australia's Past | Conserving Aboriginal and Torres Strait Islander Heritage |
Publisher: Springer Science and Business Media LLC
Date: 18-07-2023
DOI: 10.1038/S41467-023-39532-Z
Abstract: Parallel evolution provides strong evidence of adaptation by natural selection due to local environmental variation. Yet, the chronology, and mode of the process of parallel evolution remains debated. Here, we harness the temporal resolution of paleogenomics to address these long-standing questions, by comparing genomes originating from the mid-Holocene (8610-5626 years before present, BP) to contemporary pairs of coastal-pelagic ecotypes of bottlenose dolphin. We find that the affinity of ancient s les to coastal populations increases as the age of the s les decreases. We assess the youngest genome (5626 years BP) at sites previously inferred to be under parallel selection to coastal habitats and find it contained coastal-associated genotypes. Thus, coastal-associated variants rose to detectable frequencies close to the emergence of coastal habitat. Admixture graph analyses reveal a reticulate evolutionary history between pelagic and coastal populations, sharing standing genetic variation that facilitated rapid adaptation to newly emerged coastal habitats.
Publisher: eLife Sciences Publications, Ltd
Date: 26-05-2020
Publisher: American Association for the Advancement of Science (AAAS)
Date: 06-07-2018
Abstract: The past movements and peopling of Southeast Asia have been poorly represented in ancient DNA studies (see the Perspective by Bellwood). Lipson et al. generated sequences from people inhabiting Southeast Asia from about 1700 to 4100 years ago. Screening of more than a hundred in iduals from five sites yielded ancient DNA from 18 in iduals. Comparisons with present-day populations suggest two waves of mixing between resident populations. The first mix was between local hunter-gatherers and incoming farmers associated with the Neolithic spreading from South China. A second event resulted in an additional pulse of genetic material from China to Southeast Asia associated with a Bronze Age migration. McColl et al. sequenced 26 ancient genomes from Southeast Asia and Japan spanning from the late Neolithic to the Iron Age. They found that present-day populations are the result of mixing among four ancient populations, including multiple waves of genetic material from more northern East Asian populations. Science , this issue p. 92 , p. 88 see also p. 31
Publisher: Elsevier BV
Date: 03-2019
DOI: 10.1016/J.CELL.2019.01.052
Abstract: Identifying the causes of similarities and differences in genetic disease prevalence among humans is central to understanding disease etiology. While present-day humans are not strongly differentiated, vast amounts of genomic data now make it possible to study subtle patterns of genetic variation. This allows us to trace our genomic history thousands of years into the past and its implications for the distribution of disease-associated variants today. Genomic analyses have shown that demographic processes shaped the distribution and frequency of disease-associated variants over time. Furthermore, local adaptation to new environmental conditions-including pathogens-has generated strong patterns of differentiation at particular loci. Researchers are also beginning to uncover the genetic architecture of complex diseases, affected by many variants of small effect. The field of population genomics thus holds great potential for providing further insights into the evolution of human disease.
Publisher: Springer Science and Business Media LLC
Date: 15-08-2023
DOI: 10.1186/S13059-023-03023-7
Abstract: The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 × data from 1987 in iduals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility, and genome architecture and function. We report the analysis of 48 M single-nucleotide, indel, and structural variants spanning the autosomes, X chromosome, and mitochondria. We discover more than 75% of variation for 239 s led breeds. Allele sharing analysis indicates that 94.9% of breeds form monophyletic clusters and 25 major clades. German Shepherd Dogs and related breeds show the highest allele sharing with independent breeds from multiple clades. On average, each breed dog differs from the UU_Cfam_GSD_1.0 reference at 26,960 deletions and 14,034 insertions greater than 50 bp, with wolves having 14% more variants. Discovered variants include retrogene insertions from 926 parent genes. To aid functional prioritization, single-nucleotide variants were annotated with SnpEff and Zoonomia phyloP constraint scores. Constrained positions were negatively correlated with allele frequency. Finally, the utility of the Dog10K data as an imputation reference panel is assessed, generating high-confidence calls across varied genotyping platform densities including for breeds not included in the Dog10K collection. We have developed a dense dataset of 1987 sequenced canids that reveals patterns of allele sharing, identifies likely functional variants, informs breed structure, and enables accurate imputation. Dog10K data are publicly available.
Publisher: Annual Reviews
Date: 20-06-2018
DOI: 10.1146/ANNUREV-BIOCHEM-062917-012002
Abstract: Over the past three decades, studies of ancient biomolecules—particularly ancient DNA, proteins, and lipids—have revolutionized our understanding of evolutionary history. Though initially fraught with many challenges, today the field stands on firm foundations. Researchers now successfully retrieve nucleotide and amino acid sequences, as well as lipid signatures, from progressively older s les, originating from geographic areas and depositional environments that, until recently, were regarded as hostile to long-term preservation of biomolecules. S ling frequencies and the spatial and temporal scope of studies have also increased markedly, and with them the size and quality of the data sets generated. This progress has been made possible by continuous technical innovations in analytical methods, enhanced criteria for the selection of ancient s les, integrated experimental methods, and advanced computational approaches. Here, we discuss the history and current state of ancient biomolecule research, its applications to evolutionary inference, and future directions for this young and exciting field.
Publisher: Wiley
Date: 14-02-2020
DOI: 10.1002/AJPA.24023
Publisher: Cold Spring Harbor Laboratory
Date: 04-11-2022
DOI: 10.1101/2022.11.03.515020
Abstract: Parallel evolution provides among the strongest evidence of the role of natural selection in shaping adaptation to the local environment. Yet, the chronology, mode and tempo of the process of parallel evolution remains broadly debated and discussed in the field of evolutionary biology. In this study, we harness the temporal resolution of paleogenomics to understand the tempo and independence of parallel coastal ecotype adaptation in common bottlenose dolphins ( Tursiops truncatus ). For this, we generated whole genome resequencing data from subfossil dolphins (8,610-5,626 years BP) originating from around the formation time of new coastal habitat and compared them with data from contemporary populations. Genomic data revealed a shift in genetic affinity, with the oldest ancient s le being closer to the pelagic populations, while the younger s les had intermediate ancestry that showed greater affinity with the local contemporary coastal populations. We found coastal-associated genotypes in the genome of our highest coverage ancient s le, SP1060, providing rare evidence of rapid adaptation from standing genetic variation. Lastly, using admixture graph analyses, we found a reticulate evolutionary history between pelagic and coastal populations. Ancestral gene flow from coastal populations was the probable source of standing genetic variation present in the pelagic populations that enabled rapid adaptation to newly emerged coastal habitat. The genetic response to past climatic warming provides an understanding of how bottlenose dolphins will respond to ongoing directional climate change and shifting coastlines.
Publisher: University of Michigan Library
Date: 21-10-2022
DOI: 10.3998/PTPBIO.3363
Abstract: The academic journal publishing model is deeply unethical: today, a few major, for-profit conglomerates control more than 50% of all articles in the natural sciences and social sciences, driving subscription and open-access publishing fees above levels that can be sustainably maintained by publicly funded universities, libraries, and research institutions worldwide. About a third of the costs paid for publishing papers is profit for these dominant publishers' shareholders, and about half of them covers costs to keep the system running, including lobbying, marketing fees, and paywalls. The paywalls in turn restrict access of scientific outputs, preventing them from being freely shared with the public and other researchers. Thus, money that the public is told goes into science is actually being funneled away from it, or used to limit access to it. Alternatives to this model exist and have increased in popularity in recent years, including diamond open-access journals and community-driven recommendation models. These are free of charge for authors and minimize costs for institutions and agencies, while making peer-reviewed scientific results publicly accessible. However, for-profit publishing agents have made change difficult, by co-opting open-access schemes and creating journal-driven incentives that prevent an effective collective transition away from profiteering. Here, we give a brief overview of the current state of the academic publishing system, including its most important systemic problems. We then describe alternative systems. We explain the reasons why the move toward them can be perceived as costly to in idual researchers, and we demystify common roadblocks to change. Finally, in view of the above, we provide a set of guidelines and recommendations that academics at all levels can implement, in order to enable a more rapid and effective transition toward ethical publishing.
Publisher: Cold Spring Harbor Laboratory
Date: 23-09-2022
DOI: 10.1101/2022.09.22.509027
Abstract: The Eurasian Holocene (beginning c. 12 thousand years ago) encompassed some of the most significant changes in human evolution, with far-reaching consequences for the dietary, physical and mental health of present-day populations. Using an imputed dataset of complete ancient genome sequences, and new computational methods for locating selection in time and space, we reconstructed the selection landscape of the transition from hunting and gathering, to farming and pastoralism across West Eurasia. We identify major selection signals related to metabolism, possibly associated with the dietary shift occurring in this period. We show that the selection on loci such as the FADS cluster, associated with fatty acid metabolism, and the lactase persistence locus, began earlier than previously thought. A substantial amount of selection is also found in the HLA region and other loci associated with immunity, possibly due to the increased exposure to pathogens during the Neolithic, which may explain the current high prevalence of auto-immune disease, such as psoriasis, due to genetic trade-offs. By using ancient populations to infer local ancestry tracks in hundreds of thousands of s les from the UK Biobank, we find strong genetic differentiation among ancient Europeans in loci associated with anthropometric traits and susceptibility to several diseases that contribute to present-day disease burden. These were previously thought to be caused by local selection, but in fact can be attributed to differential genetic contributions from various source populations that are ancestral to present-day Europeans. Thus, alleles associated with increased height seem to have increased in frequency following the Yamnaya migration into northwestern Europe around 5,000 years ago. Alleles associated with increased risk of some mood-related phenotypes are overrepresented in the farmer ancestry component entering Europe from Anatolia around 11,000 years ago, while western hunter-gatherers show a strikingly high contribution of alleles conferring risk of traits related to diabetes. Our results paint a picture of the combined contributions of migration and selection in shaping the phenotypic landscape of present-day Europeans that suggests a combination of ancient selection and migration, rather than recent local selection, is the primary driver of present-day phenotypic differences in Europe.
Publisher: Oxford University Press (OUP)
Date: 16-03-2017
Publisher: eLife Sciences Publications, Ltd
Date: 23-06-2020
DOI: 10.7554/ELIFE.54967
Abstract: The explosion in population genomic data demands ever more complex modes of analysis, and increasingly, these analyses depend on sophisticated simulations. Recent advances in population genetic simulation have made it possible to simulate large and complex models, but specifying such models for a particular simulation engine remains a difficult and error-prone task. Computational genetics researchers currently re-implement simulation models independently, leading to inconsistency and duplication of effort. This situation presents a major barrier to empirical researchers seeking to use simulations for power analyses of upcoming studies or sanity checks on existing genomic data. Population genetics, as a field, also lacks standard benchmarks by which new tools for inference might be measured. Here, we describe a new resource, stdpopsim, that attempts to rectify this situation. Stdpopsim is a community-driven open source project, which provides easy access to a growing catalog of published simulation models from a range of organisms and supports multiple simulation engine backends. This resource is available as a well-documented python library with a simple command-line interface. We share some ex les demonstrating how stdpopsim can be used to systematically compare demographic inference methods, and we encourage a broader community of developers to contribute to this growing resource.
Publisher: Cold Spring Harbor Laboratory
Date: 05-05-2022
DOI: 10.1101/2022.05.04.490594
Abstract: Several major migrations and population turnover events during the later Stone Age (after c. 11,000 cal. BP) are believed to have shaped the contemporary population genetic ersity in Eurasia. While the genetic impacts of these migrations have been investigated on regional scales, a detailed understanding of their spatiotemporal dynamics both within and between major geographic regions across Northern Eurasia remains largely elusive. Here, we present the largest shotgun-sequenced genomic dataset from the Stone Age to date, representing 317 primarily Mesolithic and Neolithic in iduals from across Eurasia, with associated radiocarbon dates, stable isotope data, and pollen records. Using recent advances, we imputed ,600 ancient genomes to obtain accurate diploid genotypes, enabling previously unachievable fine-grained population structure inferences. We show that 1) Eurasian Mesolitic hunter-gatherers were more genetically erse than previously known, and deeply ergent between the west and the east 2) Hitherto genetically undescribed hunter-gatherers from the Middle Don region contributed significant ancestry to the later Yamnaya steppe pastoralists 3) The genetic impact of the transition from Mesolithic hunter-gatherers to Neolithic farmers was highly distinct, east and west of a “Great Divide” boundary zone extending from the Black Sea to the Baltic, with large-scale shifts in genetic ancestry to the west. This include an almost complete replacement of hunter-gatherers in Denmark, but no substantial shifts during the same period further to the east 4) Within-group relatedness changes substantially during the Neolithic transition in the west, where clusters of Neolithic farmer-associated in iduals show overall reduced relatedness, while genetic relatedness remains high until ~4,000 BP in the east, consistent with a much longer persistence of smaller localised hunter-gatherer groups 5) A fast-paced second major genetic transformation beginning around 5,000 BP, with Steppe-related ancestry reaching most parts of Europe within a 1,000 years span. Local Neolithic farmers admixed with incoming pastoralists in most parts of Europe, whereas Scandinavia experienced another near-complete population replacement, with similar dramatic turnover-patterns also evident in western Siberia 6) Extensive regional differences in the ancestry components related to these early events remain visible to this day, even within countries (research conducted using the UK Biobank resource). Neolithic farmer ancestry is highest in southern and eastern England while Steppe-related ancestry is highest in the Celtic populations of Scotland, Wales, and Cornwall. Overall, our findings show that although the Stone-Age migrations have been important in shaping contemporary genetic ersity in Eurasia, their dynamics and impact were geographically highly heterogeneous.
Publisher: Cold Spring Harbor Laboratory
Date: 20-06-2023
DOI: 10.1101/2023.06.15.23290026
Abstract: The chemokine receptor variant CCR5delta32 is linked to HIV-1 infection resistance and other pathological conditions. In European populations, the allele frequency ranges from 10-16%, and its evolution has been extensively debated throughout the years. We provide a detailed perspective of the evolutionary history of the deletion through time and space. We discovered that the CCR5delta32 allele arose on a pre-existing haplotype consisting of 84 variants. Using this information, we developed a haplotype-aware probabilistic model to screen for this deletion across 860 low-coverage ancient genomes and we found evidence that CCR5delta32 arose at least 7,000 years BP, with a likely origin somewhere in the Western Eurasian Steppe region. We further show evidence that the CCR5delta32 haplotype underwent positive selection between 7,000-2,000 BP in Western Eurasia and that the presence of the haplotype in Latin America can be explained by post-Columbian genetic exchanges. Finally, we point to new complex CCR5delta32 genotype-haplotype-phenotype relationships, which demand consideration when targeting the CCR5 receptor for therapeutic strategies.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 07-12-2018
Abstract: The expansion into the Americas by the ancestors of present day Native Americans has been difficult to tease apart from analyses of present day populations. To understand how humans erged and spread across North and South America, Moreno-Mayar et al. sequenced 15 ancient human genomes from Alaska to Patagonia. Analysis of the oldest genomes suggests that there was an early split within Beringian populations, giving rise to the Northern and Southern lineages. Because population history cannot be explained by simple models or patterns of dispersal, it seems that people moved out of Beringia and across the continents in a complex manner. Science , this issue p. eaav2621
Start Date: 05-2019
End Date: 04-2021
Amount: $364,000.00
Funder: Australian Research Council
View Funded ActivityStart Date: 02-2018
End Date: 06-2021
Amount: $512,688.00
Funder: Australian Research Council
View Funded Activity