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      A mitochondrial genetic divergence proxy predicts the reproductive compatibility of mammalian hybrids

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          Abstract

          Numerous pairs of evolutionarily divergent mammalian species have been shown to produce hybrid offspring. In some cases, F 1 hybrids are able to produce F 2 s through matings with F 1 s. In other instances, the hybrids are only able to produce offspring themselves through backcrosses with a parent species owing to unisexual sterility (Haldane's Rule). Here, we explicitly tested whether genetic distance, computed from mitochondrial and nuclear genes, can be used as a proxy to predict the relative fertility of the hybrid offspring resulting from matings between species of terrestrial mammals. We assessed the proxy's predictive power using a well-characterized felid hybrid system, and applied it to modern and ancient hominins. Our results revealed a small overlap in mitochondrial genetic distance values that distinguish species pairs whose calculated distances fall within two categories: those whose hybrid offspring follow Haldane's Rule, and those whose hybrid F 1 offspring can produce F 2 s. The strong correlation between genetic distance and hybrid fertility demonstrated here suggests that this proxy can be employed to predict whether the hybrid offspring of two mammalian species will follow Haldane's Rule.

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          The complete genome sequence of a Neandertal from the Altai Mountains

          We present a high-quality genome sequence of a Neandertal woman from Siberia. We show that her parents were related at the level of half siblings and that mating among close relatives was common among her recent ancestors. We also sequenced the genome of a Neandertal from the Caucasus to low coverage. An analysis of the relationships and population history of available archaic genomes and 25 present-day human genomes shows that several gene flow events occurred among Neandertals, Denisovans and early modern humans, possibly including gene flow into Denisovans from an unknown archaic group. Thus, interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene. In addition, the high quality Neandertal genome allows us to establish a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neandertals and Denisovans.
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            A high-coverage genome sequence from an archaic Denisovan individual.

            We present a DNA library preparation method that has allowed us to reconstruct a high-coverage (30×) genome sequence of a Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation of Denisovan heterozygosity indicating that genetic diversity in these archaic hominins was extremely low. It also allows tentative dating of the specimen on the basis of "missing evolution" in its genome, detailed measurements of Denisovan and Neandertal admixture into present-day human populations, and the generation of a near-complete catalog of genetic changes that swept to high frequency in modern humans since their divergence from Denisovans.
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              Is Open Access

              Tree of Life Reveals Clock-Like Speciation and Diversification

              Genomic data are rapidly resolving the tree of living species calibrated to time, the timetree of life, which will provide a framework for research in diverse fields of science. Previous analyses of taxonomically restricted timetrees have found a decline in the rate of diversification in many groups of organisms, often attributed to ecological interactions among species. Here, we have synthesized a global timetree of life from 2,274 studies representing 50,632 species and examined the pattern and rate of diversification as well as the timing of speciation. We found that species diversity has been mostly expanding overall and in many smaller groups of species, and that the rate of diversification in eukaryotes has been mostly constant. We also identified, and avoided, potential biases that may have influenced previous analyses of diversification including low levels of taxon sampling, small clade size, and the inclusion of stem branches in clade analyses. We found consistency in time-to-speciation among plants and animals, ∼2 My, as measured by intervals of crown and stem species times. Together, this clock-like change at different levels suggests that speciation and diversification are processes dominated by random events and that adaptive change is largely a separate process.
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                Author and article information

                Journal
                Proceedings of the Royal Society B: Biological Sciences
                Proc. R. Soc. B.
                The Royal Society
                0962-8452
                1471-2954
                June 10 2020
                June 03 2020
                June 10 2020
                : 287
                : 1928
                : 20200690
                Affiliations
                [1 ]Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK
                [2 ]Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
                [3 ]Department of Archaeology, Durham University, Science Site, Durham DH1 3LE, UK
                [4 ]Department of Anatomy, University of Otago, Great King Street, Dunedin 9016, New Zealand
                [5 ]School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
                [6 ]Lundbeck GeoGenetics Centre, The Globe Institute, University of Copenhagen, 1350 Copenhagen, Denmark
                [7 ]Department of Anthropology, Texas A&M University, College Station, TX 77843-4352, USA
                [8 ]Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
                [9 ]Department of Archaeology, Classics and Egyptology, University of Liverpool, 12-14 Abercromby Square, Liverpool L69 7WZ, UK
                [10 ]Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 IJF, UK
                [11 ]Institute of Geography, School of Geosciences, University of Edinburgh, Drummond Street, Edinburgh EH9 3PX, UK
                Article
                10.1098/rspb.2020.0690
                32486979
                874dc6b6-4b98-494c-872c-2e70a1eeb258
                © 2020

                https://royalsociety.org/-/media/journals/author/Licence-to-Publish-20062019-final.pdf

                https://royalsociety.org/journals/ethics-policies/data-sharing-mining/

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