| 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. |
- Cappellini, Enrico, et al.
(författare)
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Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny
- 2019
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 574:7776, s. 103-
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Tidskriftsartikel (refereegranskat)abstract
- The sequencing of ancient DNA has enabled the reconstruction of speciation, migration and admixture events for extinct taxa(1). However, the irreversible post-mortem degradation(2) of ancient DNA has so far limited its recovery-outside permafrost areasto specimens that are not older than approximately 0.5 million years (Myr)(3). By contrast, tandem mass spectrometry has enabled the sequencing of approximately 1.5-Myr-old collagen type I-4. and suggested the presence of protein residues in fossils of the Cretaceous period(5)-although with limited phylogenetic use(6). In the absence of molecular evidence, the speciation of several extinct species of the Early and Middle Pleistocene epoch remains contentious. Here we address the phylogenetic relationships of the Eurasian Rhinocerotidae of the Pleistocene epoch(7-9), using the proteome of dental enamel from a Stephanorhinus tooth that is approximately 1.77-Myr old, recovered from the archaeological site of Dmanisi (South Caucasus, Georgia)(10). Molecular phylogenetic analyses place this Stephanorhinus as a sister group to the Glade formed by the woolly rhinoceros (Coelodonta antiquitatis) and Merck's rhinoceros (Stephanorhinus kirchbergensis). We show that Coelodonta evolved from an early Stephanorhinus lineage, and that this latter genus includes at least two distinct evolutionary lines. The genus Stephanorhinus is therefore currently paraphyletic, and its systematic revision is needed. We demonstrate that sequencing the proteome of Early Pleistocene dental enamel overcomes the limitations of phylogenetic inference based on ancient collagen or DNA. Our approach also provides additional information about the sex and taxonomic assignment of other specimens from Dmanisi. Our findings reveal that proteomic investigation of ancient dental enamel-which is the hardest tissue in vertebrates(11), and is highly abundant in the fossil record-can push the reconstruction of molecular evolution further back into the Early Pleistocene epoch, beyond the currently known limits of ancient DNA preservation.
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| 3. |
- Liu, Shanlin, et al.
(författare)
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Ancient and modem genomes unravel the evolutionary history of the rhinoceros family
- 2021
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Ingår i: Cell. - : Elsevier. - 0092-8674 .- 1097-4172. ; 184:19, s. 4874-4885.e16
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Tidskriftsartikel (refereegranskat)abstract
- Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identify an early divergence between extant African and Eurasian lineages, resolving a key debate regarding the phylogeny of extant rhinoceroses. This early Miocene (similar to 16 million years ago [mya]) split post-dates the land bridge formation between the Afro-Arabian and Eurasian landmasses. Our analyses also show that while rhinoceros genomes in general exhibit low levels of genome-wide diversity, heterozygosity is lowest and inbreeding is highest in the modern species. These results suggest that while low genetic diversity is a long-term feature of the family, it has been particularly exacerbated recently, likely reflecting recent anthropogenic-driven population declines.
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| 4. |
- Nolen, Zachary J, et al.
(författare)
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Historical isolation facilitates species radiation by sexual selection : Insights from Chorthippus grasshoppers
- 2020
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Ingår i: Molecular Ecology. - : WILEY. - 0962-1083 .- 1365-294X. ; 29:24, s. 4985-5002
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Tidskriftsartikel (refereegranskat)abstract
- Theoretical and empirical studies have shown that species radiations are facilitated when a trait under divergent natural selection is also involved in sexual selection. It is yet unclear how quick and effective radiations are where assortative mating is unrelated to the ecological environment and primarily results from sexual selection. We address this question using sympatric grasshopper species of the genus Chorthippus, which have evolved strong behavioural isolation while lacking noticeable ecomorphological divergence. Mitochondrial genomes suggest that the radiation is relatively recent, dating to the mid-Pleistocene, which leads to extensive incomplete lineage sorting throughout the mitochondrial and nuclear genomes. Nuclear data shows that hybrids are absent in sympatric localities but that all species have experienced gene flow, confirming that reproductive isolation is strong but remains incomplete. Demographic modelling is most consistent with a long period of geographic isolation, followed by secondary contact and extensive introgression. Such initial periods of geographic isolation might facilitate the association between male signaling and female preference, permitting the coexistence of sympatric species that are genetically, morphologically, and ecologically similar, but otherwise behave mostly as good biological species.
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