| 1. |
- Gopalakrishnan, Shyam, et al.
(författare)
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The population genomic legacy of the second plague pandemic
- 2022
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Ingår i: Current Biology. - : Elsevier. - 0960-9822 .- 1879-0445. ; 32:21, s. 4743-4751.e6
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Tidskriftsartikel (refereegranskat)abstract
- Human populations have been shaped by catastrophes that may have left long-lasting signatures in their genomes. One notable example is the second plague pandemic that entered Europe in ca. 1,347 CE and repeatedly returned for over 300 years, with typical village and town mortality estimated at 10%–40%.1 It is assumed that this high mortality affected the gene pools of these populations. First, local population crashes reduced genetic diversity. Second, a change in frequency is expected for sequence variants that may have affected survival or susceptibility to the etiologic agent (Yersinia pestis).2 Third, mass mortality might alter the local gene pools through its impact on subsequent migration patterns. We explored these factors using the Norwegian city of Trondheim as a model, by sequencing 54 genomes spanning three time periods: (1) prior to the plague striking Trondheim in 1,349 CE, (2) the 17th–19th century, and (3) the present. We find that the pandemic period shaped the gene pool by reducing long distance immigration, in particular from the British Isles, and inducing a bottleneck that reduced genetic diversity. Although we also observe an excess of large FST values at multiple loci in the genome, these are shaped by reference biases introduced by mapping our relatively low genome coverage degraded DNA to the reference genome. This implies that attempts to detect selection using ancient DNA (aDNA) datasets that vary by read length and depth of sequencing coverage may be particularly challenging until methods have been developed to account for the impact of differential reference bias on test statistics.
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| 2. |
- Margaryan, Ashot, et al.
(författare)
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Population genomics of the Viking world
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 585:7825, s. 390-396
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Tidskriftsartikel (refereegranskat)abstract
- The maritime expansion of Scandinavian populations during the Viking Age (about ad750–1050) was a far-flung transformation in world history1,2. Here we sequenced the genomes of 442humans from archaeological sites across Europe and Greenland (to a median depth of about 1×) to understand the global influence of this expansion. We find the Viking period involved gene flow into Scandinavia from the south and east. We observe genetic structure within Scandinavia, with diversity hotspots in the south and restricted gene flow within Scandinavia. We find evidence for a major influx of Danish ancestry into England; a Swedish influx into the Baltic; and Norwegian influx into Ireland, Iceland and Greenland. Additionally, we see substantial ancestry from elsewhere in Europe entering Scandinavia during the Viking Age. Our ancient DNA analysis also revealed that a Viking expedition included close family members. By comparing with modern populations, we find that pigmentation-associated loci have undergone strong population differentiation during the past millennium, and trace positively selected loci—including the lactase-persistence allele of LCT and alleles of ANKA that are associated with the immune response—in detail. We conclude that the Viking diaspora was characterized by substantial transregional engagement: distinct populations influenced the genomic makeup of different regions of Europe, and Scandinavia experienced increased contact with the rest of the continent.
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| 3. |
- McKenna, James, 1987-
(författare)
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Divergence, admixture and continuity in the human past : Demographic inference using ancient and modern genomes
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Demographic forces shaping the genetic variation we observe today can include population divergences, admixture events and continuity through time. The advancement of high-throughput sequencing technologies, together with developments in molecular and bio-informatics methods, mean the number of ancient genomes available for inference has risen steeply. To make effective use of aDNA however, inference tools need to be developed that account for temporal as well as geographic sampling of genomes. Here I have developed, evaluated and applied methods for estimating divergence times between ancient and modern populations. I used simulation to study the sensitivity of these approaches to violations of model assumptions, before applying them to study the history of population divergence between pairs of populations from a global panel. Non-tree-like demography is common in the human past, with evidence of ancestral structure in the form of archaic admixture in the genomes of all non-African modern humans. Using SNP-array data collected from 118 ethnic groups in the Philippines, I show that the highest levels of Denisovan ancestry are found among the Ayta Magbukon, further highlighting the complex history between modern human groups and the archaic hominins occupying Eurasia before our arrival. Among the most important contributions population genetics has made to the study of the human past is the demonstration that cultural transitions and spread of technologies were often associated with migrating groups of people. This can result in the admixture, displacement or replacement of populations, and aDNA provides us with the opportunity to assess these trends directly through time. I developed a statistical tool to detect population continuity through time, evaluating its performance using simulation. Applied to a dataset of ancient genomes from Early Neolithic Scandinavia, I demonstrate population continuity in the hunter-gathering Pitted Ware culture, despite these people overlapping both geographically and temporally with farmers of the Funnel Beaker culture. In another study of the hunter-gatherer ancestors of the San people of southern Africa, I show evidence that this group exhibited long-term population isolation, remaining unaffected by admixture from outside southern Africa until surprisingly recent times. Using these ancient genomes, I provide further evidence that all modern Khoe-San populations exhibit significant levels of admixture with people of non-Khoe-San ancestry, demonstrating the strong impact migrations in this region have had in the past ~2,000 years.
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| 4. |
- Pečnerová, Patrícia, et al.
(författare)
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Population genomics of the muskox' resilience in the near absence of genetic variation
- 2024
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Ingår i: Molecular Ecology. - 0962-1083 .- 1365-294X. ; 33:2
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Tidskriftsartikel (refereegranskat)abstract
- Genomic studies of species threatened by extinction are providing crucial information about evolutionary mechanisms and genetic consequences of population declines and bottlenecks. However, to understand how species avoid the extinction vortex, insights can be drawn by studying species that thrive despite past declines. Here, we studied the population genomics of the muskox (Ovibos moschatus), an Ice Age relict that was at the brink of extinction for thousands of years at the end of the Pleistocene yet appears to be thriving today. We analysed 108 whole genomes, including present-day individuals representing the current native range of both muskox subspecies, the white-faced and the barren-ground muskox (O. moschatus wardi and O. moschatus moschatus) and a ~21,000-year-old ancient individual from Siberia. We found that the muskox' demographic history was profoundly shaped by past climate changes and post-glacial re-colonizations. In particular, the white-faced muskox has the lowest genome-wide heterozygosity recorded in an ungulate. Yet, there is no evidence of inbreeding depression in native muskox populations. We hypothesize that this can be explained by the effect of long-term gradual population declines that allowed for purging of strongly deleterious mutations. This study provides insights into how species with a history of population bottlenecks, small population sizes and low genetic diversity survive against all odds.
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