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  • 1. Brace, Selina
    et al.
    Thomas, Jessica A.
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Burger, Joachim
    MacPhee, Ross D. E.
    Barnes, Ian
    Turvey, Samuel T.
    Evolutionary History of the Nesophontidae, the Last Unplaced Recent Mammal Family2016In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 33, no 12, p. 3095-3103Article in journal (Refereed)
    Abstract [en]

    The mammalian evolutionary tree has lost several major clades through recent human-caused extinctions. This process of historical biodiversity loss has particularly affected tropical island regions such as the Caribbean, an area of great evolutionary diversification but poor molecular preservation. The most enigmatic of the recently extinct endemic Caribbean mammals are the Nesophontidae, a family of morphologically plesiomorphic lipotyphlan insectivores with no consensus on their evolutionary affinities, and which constitute the only major recent mammal clade to lack any molecular information on their phylogenetic placement. Here, we use a palaeogenomic approach to place Nesophontidae within the phylogeny of recent Lipotyphla. We recovered the near-complete mitochondrial genome and sequences for 17 nuclear genes from a similar to 750-year-old Hispaniolan Nesophontes specimen, and identify a divergence from their closest living relatives, the Solenodontidae, more than 40 million years ago. Nesophontidae is thus an older distinct lineage than many extant mammalian orders, highlighting not only the role of island systems as "museums" of diversity that preserve ancient lineages, but also the major human-caused loss of evolutionary history.

  • 2. Brealey, Jaelle C
    et al.
    Leitão, Henrique G
    van der Valk, Tom
    Xu, Wenbo
    Bougiouri, Katia
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Guschanski, Katerina
    Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral Microbiome2020In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 37, no 10, p. 3003-3022Article in journal (Refereed)
    Abstract [en]

    Dental calculus, the calcified form of the mammalian oral microbial plaque biofilm, is a rich source of oral microbiome, host, and dietary biomolecules and is well preserved in museum and archaeological specimens. Despite its wide presence in mammals, to date, dental calculus has primarily been used to study primate microbiome evolution. We establish dental calculus as a valuable tool for the study of nonhuman host microbiome evolution, by using shotgun metagenomics to characterize the taxonomic and functional composition of the oral microbiome in species as diverse as gorillas, bears, and reindeer. We detect oral pathogens in individuals with evidence of oral disease, assemble near-complete bacterial genomes from historical specimens, characterize antibiotic resistance genes, reconstruct components of the host diet, and recover host genetic profiles. Our work demonstrates that metagenomic analyses of dental calculus can be performed on a diverse range of mammalian species, which will allow the study of oral microbiome and pathogen evolution from a comparative perspective. As dental calculus is readily preserved through time, it can also facilitate the quantification of the impact of anthropogenic changes on wildlife and the environment.

  • 3.
    Dalen, Love
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Orlando, Ludovic
    Shapiro, Beth
    Brandstrom-Durling, Mikael
    Quam, Rolf
    Gilbert, M. Thomas P.
    Diez Fernandez-Lomana, J. Carlos
    Willerslev, Eske
    Luis Arsuaga, Juan
    Goetherstrom, Anders
    Partial Genetic Turnover in Neandertals: Continuity in the East and Population Replacement in the West2012In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 29, no 8, p. 1893-1897Article in journal (Refereed)
  • 4. Malmstrom, H
    et al.
    Stora, J
    Dalen, L
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Holmlund, G
    Gotherstrom, A
    Extensive human DNA contamination in extracts from ancient dog bones and teeth2005In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 22, no 10, p. 2040-2047Article in journal (Refereed)
  • 5. Miranda, I
    et al.
    Giska, I
    Farelo, L
    Pimenta, J
    Zimova, M
    Bryk, J
    Dalen, L
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Mills, L S
    Zub, K
    Melo-Ferreira, J
    Museomics Dissects the Genetic Basis for Adaptive Seasonal Coloration in the Least Weasel2021In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 38, no 10, p. 4388-4402Article in journal (Refereed)
  • 6. Moodley, Yoshan
    et al.
    Westbury, Michael V
    Russo, Isa-Rita M
    Gopalakrishnan, Shyam
    Rakotoarivelo, Andrinajoro
    Olsen, Remi-Andre
    Prost, Stefan
    Tunstall, Tate
    Ryder, Oliver A
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Bruford, Michael W
    Interspecific Gene Flow and the Evolution of Specialization in Black and White Rhinoceros2020In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 37, no 11, p. 3105-3117Article in journal (Refereed)
    Abstract [en]

    Africa’s black (Diceros bicornis) and white (Ceratotherium simum) rhinoceros are closely related sister-taxa that evolved highly divergent obligate browsing and grazing feeding strategies. Although their precursor species Diceros praecox and Ceratotherium mauritanicum appear in the fossil record ∼5.2 Ma, by 4 Ma both were still mixed feeders, and were even spatiotemporally sympatric at several Pliocene sites in what is today Africa’s Rift Valley. Here, we ask whether or not D. praecox and C. mauritanicum were reproductively isolated when they came into Pliocene secondary contact. We sequenced and de novo assembled the first annotated black rhinoceros reference genome and compared it with available genomes of other black and white rhinoceros. We show that ancestral gene flow between D. praecox and C. mauritanicum ceased sometime between 3.3 and 4.1 Ma, despite conventional methods for the detection of gene flow from whole genome data returning false positive signatures of recent interspecific migration due to incomplete lineage sorting. We propose that ongoing Pliocene genetic exchange, for up to 2 My after initial divergence, could have potentially hindered the development of obligate feeding strategies until both species were fully reproductively isolated, but that the more severe and shifting paleoclimate of the early Pleistocene was likely the ultimate driver of ecological specialization in African rhinoceros.

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  • 7.
    Sánchez-Barreiro, Fátima
    et al.
    Globe Institute, University of Copenhagen , Copenhagen , Denmark.
    De Cahsan, Binia
    Globe Institute, University of Copenhagen , Copenhagen , Denmark.
    Westbury, Michael V
    Globe Institute, University of Copenhagen , Copenhagen , Denmark.
    Sun, Xin
    Globe Institute, University of Copenhagen , Copenhagen , Denmark.
    Margaryan, Ashot
    Globe Institute, University of Copenhagen , Copenhagen , Denmark.
    Fontsere, Claudia
    Globe Institute, University of Copenhagen , Copenhagen , Denmark;Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas–Universitat Pompeu Fabra), Barcelona Biomedical Research Park , Barcelona, Catalonia , Spain.
    Bruford, Michael W
    Cardiff School of Biosciences, Cardiff University , Cardiff , UK.
    Russo, Isa-Rita M
    Cardiff School of Biosciences, Cardiff University , Cardiff , UK.
    Kalthoff, Daniela C
    Swedish Museum of Natural History, Department of Zoology. Swedish Museum of Natural History.
    Sicheritz-Pontén, Thomas
    Globe Institute, University of Copenhagen , Copenhagen , Denmark;Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University , Kedah , Malaysia.
    Petersen, Bent
    Globe Institute, University of Copenhagen , Copenhagen , Denmark;Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University , Kedah , Malaysia.
    Dalén, Love
    Department of Zoology, Centre for Palaeogenetics , Stockholm University, Stockholm , Sweden;Department of Bioinformatics and Genetics, Swedish Museum of Natural History , Stockholm , Sweden.
    Zhang, Guojie
    Section for Ecology and Evolution, Department of Biology, University of Copenhagen , Copenhagen , Denmark;State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming , People's Republic of China;Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences , Kunming , People's Republic of China;BGI Research, BGI-Shenzhen , Shenzhen , People's Republic of China.
    Marquès-Bonet, Tomás
    Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas–Universitat Pompeu Fabra), Barcelona Biomedical Research Park , Barcelona, Catalonia , Spain;National Centre for Genomic Analysis–Centre for Genomic Regulation, Barcelona Institute of Science and Technology , Barcelona , Spain;Life & Medical Sciences, Institucio Catalana de Recerca i Estudis Avançats (ICREA) , Barcelona, Catalonia , Spain.
    Gilbert, M Thomas P
    Globe Institute, University of Copenhagen , Copenhagen , Denmark;Department of Natural History, NTNU University Museum , Trondheim , Norway.
    Moodley, Yoshan
    Department of Biological Sciences, University of Venda , Thohoyandou , Republic of South Africa.
    Historic Sampling of a Vanishing Beast: Population Structure and Diversity in the Black Rhinoceros2023In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 40, no 9, article id msad180Article in journal (Refereed)
    Abstract [en]

    The black rhinoceros (Diceros bicornis L.) is a critically endangered species historically distributed across sub-Saharan Africa. Hunting and habitat disturbance have diminished both its numbers and distribution since the 19th century, but a poaching crisis in the late 20th century drove them to the brink of extinction. Genetic and genomic assessments can greatly increase our knowledge of the species and inform management strategies. However, when a species has been severely reduced, with the extirpation and artificial admixture of several populations, it is extremely challenging to obtain an accurate understanding of historic population structure and evolutionary history from extant samples. Therefore, we generated and analyzed whole genomes from 63 black rhinoceros museum specimens collected between 1775 and 1981. Results showed that the black rhinoceros could be genetically structured into six major historic populations (Central Africa, East Africa, Northwestern Africa, Northeastern Africa, Ruvuma, and Southern Africa) within which were nested four further subpopulations (Maasailand, southwestern, eastern rift, and northern rift), largely mirroring geography, with a punctuated north–south cline. However, we detected varying degrees of admixture among groups and found that several geographical barriers, most prominently the Zambezi River, drove population discontinuities. Genomic diversity was high in the middle of the range and decayed toward the periphery. This comprehensive historic portrait also allowed us to ascertain the ancestry of 20 resequenced genomes from extant populations. Lastly, using insights gained from this unique temporal data set, we suggest management strategies, some of which require urgent implementation, for the conservation of the remaining black rhinoceros diversity.

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  • 8. Westbury, Michael, V
    et al.
    Hartmann, Stefanie
    Barlow, Axel
    Wiesel, Ingrid
    Leo, Viyanna
    Welch, Rebecca
    Parker, Daniel M.
    Sicks, Florian
    Ludwig, Arne
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Hofreiter, Michael
    Extended and Continuous Decline in Effective Population Size Results in Low Genomic Diversity in the World's Rarest Hyena Species, the Brown Hyena2018In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 35, no 5, p. 1225-1237Article in journal (Refereed)
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  • 9.
    Westbury, Michael V
    et al.
    Department of Mathematics and Natural Sciences, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany;Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
    Le Duc, Diana
    Institute of Human Genetics, University Medical Center Leipzig, Leipzig, Germany;Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
    Duchêne, David A
    Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark;Research School of Biology, Australian National University, Canberra, ACT, Australia.
    Krishnan, Arunkumar
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA;Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Berhampur, Odisha, India.
    Prost, Stefan
    LOEWE-Center for Translational Biodiversity Genomics, Senckenberg, Frankfurt, Germany;South African National Biodiversity Institute, National Zoological Garden, Pretoria, South Africa.
    Rutschmann, Sereina
    Department of Mathematics and Natural Sciences, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
    Grau, Jose H
    Department of Mathematics and Natural Sciences, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany;Amedes Genetics, amedes Medizinische Dienstleistungen, Berlin, Germany.
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. Centre for Palaeogenetics, Stockholm, Sweden;Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
    Weyrich, Alexandra
    Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany.
    Norén, Karin
    Department of Zoology, Stockholm University, Stockholm, Sweden.
    Werdelin, Lars
    Swedish Museum of Natural History, Department of Paleobiology.
    Dalerum, Fredrik
    Department of Zoology, Stockholm University, Stockholm, Sweden;Research Unit of Biodiversity (UO-CSIC-PA), Mieres Campus, University of Oviedo, Mieres, Asturias, Spain;Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, South Africa.
    Schöneberg, Torsten
    Rudolf Schönheimer Institute of Biochemistry, Molecular Biochemistry, Medical Faculty, Leipzig, Germany.
    Hofreiter, Michael
    Department of Mathematics and Natural Sciences, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
    Ecological Specialization and Evolutionary Reticulation in Extant Hyaenidae2021In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 38, no 9, p. 3884-3897Article in journal (Refereed)
    Abstract [en]

    During the Miocene, Hyaenidae was a highly diverse family of Carnivora that has since been severely reduced to four species: the bone-cracking spotted, striped, and brown hyenas, and the specialized insectivorous aardwolf. Previous studies investigated the evolutionary histories of the spotted and brown hyenas, but little is known about the remaining two species. Moreover, the genomic underpinnings of scavenging and insectivory, defining traits of the extant species, remain elusive. Here, we generated an aardwolf genome and analyzed it together with the remaining three species to reveal their evolutionary relationships, genomic underpinnings of their scavenging and insectivorous lifestyles, and their respective genetic diversities and demographic histories. High levels of phylogenetic discordance suggest gene flow between the aardwolf lineage and the ancestral brown/striped hyena lineage. Genes related to immunity and digestion in the bone-cracking hyenas and craniofacial development in the aardwolf showed the strongest signals of selection, suggesting putative key adaptations to carrion and termite feeding, respectively. A family-wide expansion in olfactory receptor genes suggests that an acute sense of smell was a key early adaptation. Finally, we report very low levels of genetic diversity within the brown and striped hyenas despite no signs of inbreeding, putatively linked to their similarly slow decline in effective population size over the last ∼2 million years. High levels of genetic diversity and more stable population sizes through time are seen in the spotted hyena and aardwolf. Taken together, our findings highlight how ecological specialization can impact the evolutionary history, demographics, and adaptive genetic changes of an evolutionary lineage.

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