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  • 1. Brantberg, Krister
    et al.
    Babak, F.
    Kalthoff, Daniela
    Swedish Museum of Natural History, Department of Zoology.
    Do extant elephants have superior canal dehiscence syndrome?2015In: Acta Oto-Laryngologica, ISSN 0001-6489, E-ISSN 1651-2251Article in journal (Refereed)
  • 2. Brealey, Jaelle C.
    et al.
    Leitao, Henrique G.
    Department of Ecology and Genetics/Animal Ecology, Uppsala University.
    Hofstede, Thijs
    Department of Ecology and Genetics/Animal Ecology, Uppsala University.
    Kalthoff, Daniela C.
    Swedish Museum of Natural History, Department of Zoology.
    Guschanski, Katerina
    Department of Ecology and Genetics/Animal Ecology, Uppsala University.
    The oral microbiota of wild bears in Sweden reflects the history of antibiotic use by humans2021In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 31, no 20, p. 4650-4658.e6Article in journal (Refereed)
    Abstract [en]

    Following the advent of industrial-scale antibiotic production in the 1940s,1 antimicrobial resistance (AMR) has been on the rise and now poses a major global health threat in terms of mortality, morbidity, and economic burden.2,3 Because AMR can be exchanged between humans, livestock, and wildlife, wild animals can be used as indicators of human-associated AMR contamination of the environment.4 However, AMR is a normal function of natural environments and is present in host-associated microbiomes, which makes it challenging to distinguish between anthropogenic and natural sources.4,5 One way to overcome this difficulty is to use historical samples that span the period from before the mass production of antibiotics to today. We used shotgun metagenomic sequencing of dental calculus, the calcified form of the oral microbial biofilm, to determine the abundance and repertoire of AMR genes in the oral microbiome of Swedish brown bears collected over the last 180 years. Our temporal metagenomics approach allowed us to establish a baseline of natural AMR in the pre-antibiotics era and to quantify a significant increase in total AMR load and diversity of AMR genes that is consistent with patterns of national human antibiotic use. We also demonstrated a significant decrease in total AMR load in bears in the last two decades, which coincides with Swedish strategies to mitigate AMR. Our study suggests that public health policies can be effective in limiting human-associated AMR contamination of the environment and wildlife.

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  • 3.
    Gharibi, Hassan
    et al.
    Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden.
    Chernobrovkin, Alexey L.
    Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden;Pelago Bioscience, SE-171 48 Solna, Sweden.
    Eriksson, Gunilla
    Department of Archaeology and Classical Studies, Stockholm University, SE-114 19 Stockholm, Sweden.
    Saei, Amir Ata
    Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden;Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States.
    Timmons, Zena
    Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, U.K..
    Kitchener, Andrew C.
    Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, U.K..
    Kalthoff, Daniela C.
    Swedish Museum of Natural History, Department of Zoology.
    Lidén, Kerstin
    Department of Archaeology and Classical Studies, Stockholm University, SE-114 19 Stockholm, Sweden.
    Makarov, Alexander A.
    Thermo Fisher Scientific GmbH, 28199 Bremen, Germany.
    Zubarev, Roman A.
    Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden;Department of Pharmacological & Technological Chemistry, I. M. Sechenov First Moscow State Medical University, Moscow 119991, Russia;The National Medical Research Center for Endocrinology, Moscow 115478, Russia.
    Abnormal (Hydroxy)proline Deuterium Content Redefines Hydrogen Chemical Mass2022In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 144, no 6, p. 2484-2487Article in journal (Refereed)
    Abstract [en]

    Analyzing the δ2H values in individual amino acids of proteins extracted from vertebrates, we unexpectedly found insome samples, notably bone collagen from seals, more than twice as much deuterium in proline and hydroxyproline residues than inseawater. This corresponds to at least 4 times higher δ2H than in any previously reported biogenic sample. We ruled out diet as aplausible mechanism for such anomalous enrichment. This finding puts into question the old adage that “you are what you eat”.

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  • 4.
    Granell-Ruiz, Maria
    et al.
    Department of Zoology, Stockholm University, Stockholm, Sweden.
    Norén, Karin
    Department of Zoology, Stockholm University, Stockholm, Sweden.
    Kalthoff, Daniela C.
    Swedish Museum of Natural History, Department of Zoology.
    Le Roux, Aliza
    Department of Zoology and Entomology, University of the Free State, Phuthaditjhaba, South Africa.
    Dalerum, Fredrik
    Department of Zoology, Stockholm University, Stockholm, Sweden;Research Unit of Biodiversity (UO-CSIC-PA), Spanish National Research Council, University of Oviedo, Mieres, Spain;Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa.
    Genetic variation between and within two populations of bat-eared foxes (Otocyon megalotis Desmarest, 1822) in South Africa2021In: African Zoology, ISSN 1562-7020, E-ISSN 2224-073X, Vol. 56, no 3, p. 165-172Article in journal (Refereed)
    Abstract [en]

    Information on genetic variation within and among populations is relevant for a broad range of topics in biology. We use a combination of mitochondrial and nuclear microsatellite markers to evaluate genetic variation within and between two populations of bat-eared foxes (Otocyon megalotis Desmarest, 1822) in South Africa. The bat-eared fox is a small canid occurring in southern and eastern Africa. The species is currently not threatened with extinction, but a lack of information on genetic diversity has been identified as a deficit for its future conservation. We observed low to moderate genetic differentiation between the two geographically separated populations, but neither mitochondrial nor nuclear microsatellite markers suggested that there have been dispersal barriers between them. Similar genetic diversity within both populations was contrasted by interpopulational differences in relatedness variation among males and females. A high genetic relatedness within both populations, indicated by mitochondrial data, is likely caused by a common historical origin or a combination of species-specific social organization and environmental dispersal constraints. We call for further research on the genetic divergence of bat-eared fox populations as well as on the genetic consequences of interactions between environmental characteristics and social organization in this species.

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  • 5. Green, Jeremy
    et al.
    Kalthoff, Daniela C.
    Swedish Museum of Natural History, Department of Zoology.
    Xenarthran tooth architecture and dietary adaptations from analyses of dental microstructure and microwear, with new data for the giant sloth Megatherium americanum (Megatheriidae)2015In: Journal of Mammalogy, ISSN 0022-2372, E-ISSN 1545-1542, Vol. 96, no 4, p. 645-657Article in journal (Refereed)
  • 6.
    Hempel, Elisabeth
    et al.
    Universität Potsdam, Evolutionary Adaptive Genomics, Germany.
    Bibi, Faysal
    Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany.
    Faith, J. Tyler
    Natural History Museum of Utah, University of Utah, USA.
    Brink, James S.
    National Museum Bloemfontein, Republic of South Africa.
    Kalthoff, Daniela C.
    Swedish Museum of Natural History, Department of Zoology.
    Kamminga, Pepijn
    Naturalis Biodiversity Center, Leiden, The Netherlands.
    Paijmans, Johanna L. A.
    Department of Genetics and Genome Biology, University of Leicester, UK.
    Westbury, Michael V.
    Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Denmark.
    Hofreiter, Michael
    Universität Potsdam, Evolutionary Adaptive Genomics, Germany.
    Zachos, Frank E.
    Natural History Museum Vienna, Austria.
    Identifying the true number of specimens of the extinct blue antelope (Hippotragus leucophaeus)2021In: Scientific Reports, E-ISSN 2045-2322, Vol. 11, no 2100Article in journal (Refereed)
    Abstract [en]

    Native to southern Africa, the blue antelope (Hippotragus leucophaeus) is the only large African mammal species known to have become extinct in historical times. However, it was poorly documented prior to its extinction ~ 1800 AD, and many of the small number of museum specimens attributed to it are taxonomically contentious. This places limitations on our understanding of its morphology, ecology, and the mechanisms responsible for its demise. We retrieved genetic information from ten of the sixteen putative blue antelope museum specimens using both shotgun sequencing and mitochondrial genome target capture in an attempt to resolve the uncertainty surrounding the identification of these specimens. We found that only four of the ten investigated specimens, and not a single skull, represent the blue antelope. This indicates that the true number of historical museum specimens of the blue antelope is even smaller than previously thought, and therefore hardly any reference material is available for morphometric, comparative and genetic studies. Our study highlights how genetics can be used to identify rare species in natural history collections where other methods may fail or when records are scarce. Additionally, we present an improved mitochondrial reference genome for the blue antelope as well as one complete and two partial mitochondrial genomes. A first analysis of these mitochondrial genomes indicates low levels of maternal genetic diversity in the ‘museum population’, possibly confirming previous results that blue antelope population size was already low at the time of the European colonization of South Africa.

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    Hempel et al 2021_Identifying the true number of specimens of the extinct blue antelope.pdf
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    Hempel et al 2021_Supplementary Information.pdf
  • 7.
    Kalthoff, Daniela
    Swedish Museum of Natural History, Department of Zoology.
    Extinctions, genetic erosion and conservation options for the black rhinoceros (Diceros bicornis)2017In: Scientific Reports, E-ISSN 2045-2322, article id 41417Article in journal (Refereed)
    Abstract [en]

    The black rhinoceros is again on the verge of extinction due to unsustainable poaching in its nativerange. Despite a wide historic distribution, the black rhinoceros was traditionally thought of asdepauperate in genetic variation, and with very little known about its evolutionary history. Thisknowledge gap has hampered conservation efforts because hunting has dramatically reduced thespecies' once continuous distribution, leaving five surviving gene pools of unknown genetic affinity.Here we examined the range-wide genetic structure of historic and modern populations using thelargest and most geographically representative sample of black rhinoceroses ever assembled. Usingboth mitochondrial and nuclear datasets, we described a staggering loss of 69% of the species'mitochondrial genetic variation, including the most ancestral lineages that are now absent frommodern populations. Genetically unique populations in countries such as Nigeria, Cameroon, Chad,Eritrea, Ethiopia, Somalia, Mozambique, Malawi and Angola no longer exist. We found that the historicrange of the West African subspecies (D. b. longipes), declared extinct in 2011, extends into southernKenya, where a handful of individuals survive in the Masai Mara. We also identify conservation unitsthat will help maintain evolutionary potential. Our results suggest a complete re-evaluation of currentconservation management paradigms for the black rhinoceros.

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  • 8.
    Kalthoff, Daniela
    Swedish Museum of Natural History, Department of Zoology.
    Feeding Ecology in Oligocene Mylodontoid Sloths (Mammalia,Xenarthra) as Revealed by Orthodentine Microwear Analysis2018In: Journal of mammalian evolution, ISSN 1064-7554, E-ISSN 1573-7055, Vol. 25, no 4, p. 551-564-Article in journal (Refereed)
    Abstract [en]

    Recently, dental microwear analysis has been successfully employed to xenarthran teeth. Here, we present new data on use wear features on 16 molariforms of Orophodon hapaloides and Octodontotherium grande. These taxa count among the earliest sloths and are known from the Deseadan SALMA (late Oligocene). Modern phylogenetic analyses classify Octodontotherium and Orophodon within Mylodontoidea with whom they share lobate cheek teeth with an outer layer of cementum and a thick layer of orthodentine. Similar target areas of 100 μm2 were analyzed on the orthodentine surface of each tooth by stereomicroscopic microwear and by SEM microwear. Results were unlike those of extant sloths (stereomicroscopic microwear: Bradypus, Choloepus) and published data from fossil sloths (SEM microwear: Acratocnus, Megalonyx, Megatherium, Thinobadistes); thus, both approaches independently indicate a different feeding ecology for the Oligocene taxa. The unique microwear results suggest that both taxa fed on plant material with low to moderate intrinsic toughness (foliage, twigs) but also proposes intake of tougher food items (e.g., seeds). Frequent gouging of the tooth surfaces can be explained by exogenous influence on microwear, such as possible intake of abrasive grit. We suggest an unspecialized herbivorous diet for Octodontotherium and Orophodon utilizing diverse food resources of their habitat. These interpretations support the reconstruction of (1) Deseadan environments as open habitats with spreading savannas/grasslands and (2) both taxa as wide muzzled bulk feeders at ground level.

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  • 9.
    Kalthoff, Daniela
    Swedish Museum of Natural History, Department of Zoology.
    Modular Wear Facet Nomenclature for Mammalian post-canine dentitions2017In: Historical Biology, ISSN 0891-2963, E-ISSN 1029-2381, Vol. 30, no 1-2, p. 30-41Article in journal (Refereed)
    Abstract [en]

    Dental wear facets on the occlusal surface of premolars and molars are traces of their main function, themastication and therefore reflect masticatory movements and also paramasticatory (i.e. non-dietary useof teeth) behavior. Here we present the Modular Wear Facet Nomenclature applicable to most mammaliandentitions. Topographic positions of wear facets in relation to the major cusps and crests of the teeth areused to designate the areas of the occlusal surface the facets occupy (e.g. their mesial, distal, lingual, orbuccal position). Previous published systems for labeling wear facets have been inconsistent with eachother. Therefore, we provide a synoptic review of the most widely-used terminologies, and introducethe alternative Modular Wear Facet Nomenclature. This nomenclature aims to overcome the difficultiescaused by the existing inconsistent wear facet terminologies. Our new approach is applicable to dentitionswhere the occlusal morphology does not change significantly for most of the lifetime of the animal. Inthose dentitions, the primary occlusal surfaces are not significantly modified as wear facets become moreextensive with wearing. This appears to be a common pattern in pre-tribosphenic, tribosphenic molars,and the teeth derived from tribosphenic precursors (e.g. bunodont molar morphologies). In teeth wherethe secondary occlusal surface is functionally intensely modified (i.e. high-crowned and evergrowingteeth with large areas of dentine exposed) any facet labeling system appears to be challenging, since theidentification of individual facets is blurred and their spatial position may be indeterminable.

  • 10.
    Kalthoff, Daniela
    Swedish Museum of Natural History, Department of Zoology.
    Short review of dental microstructure and dental microwear in xenarthran teeth2020In: Mammalian Teeth – Form and Function / [ed] Thomas Martin and Wighart von Koenigswald, München: Verlag Dr. Friedrich Pfeil , 2020, 1, p. 231-241Chapter in book (Refereed)
    Abstract [en]

    There is no abstract.

  • 11.
    Kalthoff, Daniela C.
    et al.
    Swedish Museum of Natural History, Department of Zoology. Department of Zoology Swedish Museum of Natural History Stockholm Sweden.
    Fejfar, Oldrich
    Geological‐Paleontological Institute Karls University Prague Czech Republic.
    Kimura, Yuri
    Department of Geology and Paleontology National Museum of Nature and Science Tsukuba Japan;Institut Català de Paleontologia Miquel Crusafont Universitat Autònoma de Barcelona Barcelona Spain.
    Bailey, Bruce E.
    Division of Vertebrate Paleontology University of Nebraska State Museum Lincoln Nebraska USA.
    Mörs, Thomas
    Swedish Museum of Natural History, Department of Paleobiology. Department of Paleobiology Swedish Museum of Natural History Stockholm Sweden.
    Incisor enamel microstructure places New and Old World Eomyidae outside Geomorpha (Rodentia, Mammalia)2022In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 51, no 4, p. 381-400Article in journal (Refereed)
    Abstract [en]

    The lower incisor enamel microstructure of the fossil rodent family Eomyidae was believed to be three-layered and highly derived but rather uniform throughout the clade. Here, we describe a new four-layered schmelzmuster in Eomyidae consisting of a three-fold portio interna with longitudinal oriented, uniserial Hunter-Schreger bands and a one-fold portio externa, accounting for a unique enamel microstructure character combination in Rodentia. This new schmelzmuster type has developed early in eomyid evolution and is detectable already in the late Eocene (Chadronian) of North America. In European eomyids, it first occurs in the early Miocene (MN 3), implying that this four-layered schmelzmuster was not present in all members of the family but restricted to species included in Eomyini and some genera currently considered Eomyidae incertae sedis within Eomyidae. Additionally, our analysis recognizes three taxa with schmelzmuster divergent from all other eomyids. Incisor enamel microstructure does not advocate a close phylogenetic relationship of Eomyidae to either fossil or extant Heteromyidae and Geomyidae, nor to fossil Heliscomyidae and Florentiamyidae. Our results rather support the view that Eomyidae are placed outside Geomorpha.

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  • 12.
    Kalthoff, Daniela C.
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Mörs, Thomas
    Swedish Museum of Natural History, Department of Paleobiology.
    Biomechanical adaptations for burrowing in the incisor enamel microstructure of Geomyidae and Heteromyidae (Rodentia: Geomyoidea)2021In: Ecology and Evolution, E-ISSN 2045-7758, Vol. 11, p. 9447-9459Article in journal (Refereed)
    Abstract [en]

    The enamel microstructure of fossil and extant Geomyoidea (Geomyidae, Heteromyidae) lower incisors incorporates three- or two-layered schmelzmusters with uniserial, transverse Hunter-Schreger bands having parallel and perpendicular or exclusively perpendicular oriented interprismatic matrix. Phylogenetically, these schmelzmusters are regarded as moderately (enamel type 2) to highly derived (enamel type 3). Our analysis detected a zone of modified radial enamel close to the enamel–dentine junction. Modified radial enamel shows a strong phylogenetic signal within the clade Geomorpha as it is restricted to fossil and extant Geomyoidea and absent in Heliscomyidae, Florentiamyidae, and Eomyidae. This character dates back to at least the early Oligocene (early Arikareean, 29 Ma), where it occurs in entoptychine gophers. We contend that this specialized incisor enamel architecture developed as a biomechanical adaptation to regular burrowing activities including chisel-tooth digging and a fiber-rich diet and was probably present in the common ancestor of the clade. We regard the occurrence of modified radial enamel in lower incisors of scratch-digging Geomyidae and Heteromyidae as the retention of a plesiomorphic character that is selectively neutral. The shared occurrence of modified radial enamel is a strong, genetically anchored argument for the close phylogenetic relationship of Geomyidae and Heteromyidae on the dental microstructure level.

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  • 13.
    Kalthoff, Daniela
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Lindsay, Everett H.
    Koenigswald, Wighart von
    Paciculus walshi, new species, (Rodentia, Cricetidae), the origin of Cricetidae and an Oligocene intercontinental mammal dispersal event2016In: Historical Biology, Vol. 28, p. 78-94Article in journal (Refereed)
  • 14.
    Kalthoff, Daniela
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    O'Connor, Patrick M.
    Ohio Center for Ecology and Evolutionary Studies, Athens, Ohio, USA.
    Roberts, Eric M.
    James Cook University, Townsville, Australia.
    A new mammal from the Turonian–Campanian (Upper Cretaceous) Galula Formation, southwestern Tanzania2019In: Acta Palaeontologica Polonica, Vol. 64, no 1, p. 65-84Article in journal (Refereed)
    Abstract [en]

    We here establish a newmammaliaform genus and species, Galulatheriumjenkinsi (Mammalia), from the UpperCretaceous Galula Formation in the Rukwa Rift Basin of southwestern Tanzania. Thisrepresents the first named taxon of a mammaliaform from the entire Late Cretaceous,an interval of 34 million years, of continental Afro-Africa. Preliminary studyof the holotype (a partial dentary) resulted in tentative assignation to the Gondwanatheria,a poorly known, enigmatic clade of Late Cretaceous–Paleogene Gondwanan mammals (Krauseet al. 2003). The application of advanced imaging (µCT) and visualizationtechniques permits a more detailed understanding of key anatomical features of thenew taxon. CT analysis reveals that the lower dentition consisted of a large,procumbent lower incisor and four cheek teeth, all which are ever growing(hypselodont). Importantly, all of the teeth appear to have been devoid ofenamel during life. Comparisons conducted with a range of Mesozoic and selectedCenozoic mammaliaform groups demonstrates that a number of features (e.g.,enamel-less and ever-growing teeth, columnar cheek teeth with relatively simpleocclusal morphology) expressed in Galulatheriumare reminiscent of disparate groups, making taxonomic assignment difficult. Hereinwe retain the provisional referral of Galulatherium(RRBP 02067) to Gondwanatheria; it is most similar to sudamericids such as Lavanify and Bharratherium from the Late Cretaceous of Madagascar and India,respectively, which exhibit relatively simple, high-crowned, columnar cheek teeth.Other features (e.g., enamel-less dentition) shared with disparate forms suchas the Late Jurassic Fruitafossor andvarious xenarthrans (e.g., sloths) are attributed to convergence. Detailed analysesof the depositional context for the type and only specimen place it as havinglived sometime between the late Turonian and latest Campanian (roughly 91–72million years ago). This enhanced geochronological context helps to refine thepalaeobiogeographical significance of Galulatheriumamong Cretaceous mammals in general and those of Gondwanan landmassesspecifically.

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  • 15.
    Kalthoff, Daniela
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Schulz-Kornas, Ellen
    Max Planck Institute for Evolutionary Anthropology.
    Corfe, Ian
    University of Helsinki.
    Martin, Thomas
    Universität Bonn.
    McLoughlin, Stephen
    Swedish Museum of Natural History, Department of Paleobiology.
    Schultz, Julia A.
    Universität Bonn.
    Complementary approaches to tooth wear analysisin Tritylodontidae (Synapsida, Mammaliamorpha)reveal a generalist diet.2019In: PLOS ONE, E-ISSN 1932-6203, Vol. 14, no 7, p. 1-24, article id e0220188Article in journal (Refereed)
    Abstract [en]

    Stereoscopic microwear and 3D surface texture analyses on the cheek teeth of ten Upper Triassic to Lower Cretaceous tritylodontid (Mammaliamorpha) taxa of small/medium to large body size suggest that all were generalist feeders and none was a dietary specialist adapted to herbivory. There was no correspondence between body size and food choice. Stereomicroscopic microwear analysis revealed predominantly fine wear features with numerous small pits and less abundant fine scratches as principal components. Almost all analyzed facets bear some coarser microwear features, such as coarse scratches, large pits, puncture pits and gouges pointing to episodic feeding on harder food items or exogenous effects (contamination of food with soil grit and/or dust), or both. 3D surface texture analysis indicates predominantly fine features with large void volume, low peak densities, and various stages of roundness of the peaks. We interpret these features to indicate consumption of food items with low to moderate intrinsic abrasiveness and can exclude regular rooting, digging or caching behavior. Possible food items include plant vegetative parts, plant reproductive structures (seeds and seed-bearing organs), and invertebrates (i.e., insects). Although the tritylodontid tooth morphology and auto-occlusion suggest plants as the primary food resource, our results imply a wider dietary range including animal matter.

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  • 16.
    Kalthoff, Daniela
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Trocheri, M.W.
    Jungers, W.L.
    The evolutionary origin and population history of the grauer gorilla2016In: Yearbook of Physical Anthropology, Vol. 159, p. S4-S18Article in journal (Refereed)
  • 17.
    KIMURA, Yuri
    et al.
    Department of Geology and Paleontology, National Museum of Nature and Science.
    CASANOVAS-VILAR, Isaac
    Institut Català de Paleontologia Miquel Crusafont, ICTA-ICP.
    MARIDET, OLIVIER
    JURASSICA Museum, Route de Fontenais 21, CH-2900 Porrentruy, Switzerland.
    KALTHOFF, Daniela
    Swedish Museum of Natural History, Department of Zoology.
    Mörs, Thomas
    Swedish Museum of Natural History, Department of Paleobiology.
    TOMIDA, Yukimitsu
    The Eomyidae in Asia: Biogeography, diversity and dispersals2020In: Fossil Imprint, Vol. 76, no 1, p. 181-200Article in journal (Refereed)
    Abstract [en]

    In Asia, the first find of an eomyid rodent was reported almost one century after the first studies of the family Eomyidae in North America and Europe. Since then, eomyid rodents have been increasingly found in Asia particularly over the past two decades. Here, we review the Asian record of this family at the genus level. Currently, 22 species within 14 genera were reported from Asia, including seven endemic genera and rare materials of apeomyine eomyids. Eomyids emphasize the palaeogeographic importance of Asia in considering intercontinental dispersal events of small mammals. With newly compiled data for Asian eomyids, we also compare genus-level diversity trends through time among North America, Europe, and Asia. Despite data standardizations limited with respect to potential biases in the fossil record, we found that the Asian eomyid diversity closely follows ecological shifts induced by climate changes. In general, Asian eomyid genera disappeared earlier than their European counterparts. We suggest that this pattern is not dictated by differences in the quality of the fossil record and is related to the expansion of drier habitats over large areas of Asia.

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  • 18. KIMURA, Yuri
    et al.
    TOMIDA, Yukimitsu
    Kalthoff, Daniela
    Swedish Museum of Natural History, Department of Zoology.
    CASANOVAS-VILAR, Isaac
    Mörs, Thomas
    Swedish Museum of Natural History, Department of Paleobiology.
    A new endemic genus of eomyid rodents from the early Miocene of Japan2019In: Acta Palaeontologica Polonica, ISSN 0567-7920, E-ISSN 1732-2421Article in journal (Refereed)
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  • 19.
    Lagerholm, Vendela
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Sandoval-Castellanos, E.
    Ehrich, D.
    Abramson, N.
    Nadachowski, A.
    Kalthoff, Daniela C.
    Swedish Museum of Natural History, Department of Zoology.
    Germonpré, M.
    Angerbjörn, A.
    Stewart, J.
    Dalén, L.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    On the Origin of the Norwegian Lemming2014In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 23, no 8, p. 2060-2071Article in journal (Refereed)
  • 20.
    Loch, Carolona
    et al.
    University of Otago, Dunedin.
    BUONO, Monica
    Instituto Patagónico de Geología y Paleontología, CONICET, Puerto Madryn.
    KALTHOFF, Daniela
    Swedish Museum of Natural History, Department of Zoology.
    Mörs, Thomas
    Swedish Museum of Natural History, Department of Paleobiology.
    FERNANDEZ, Martha
    Universidad Nacional de La Plata, CONICET, La Plata.
    Enamel microstructure in Eocene cetaceans from Antarctica (Archaeoceti and Mysticeti)2020In: Journal of mammalian evolution, ISSN 1064-7554, E-ISSN 1573-7055, Vol. 27, p. 289-298Article in journal (Refereed)
    Abstract [en]

    Modern baleen whales have no adult teeth, whereas dolphins and porpoises have a homodont and polydont dentition, with simplified enamel microstructure. However, archaic cetaceans (archaeocetes and early mysticetes and odontocetes) had a complexand ornamented dentition, with complex enamel microstructure as in terrestrial mammals. This study describes the morphology of teeth and enamel microstructure in two fossil cetaceans from Antarctica: a basilosaurid archaeocete from the La Meseta Formation (middle Eocene); and Llanocetus sp. from the Submeseta Formation (late Eocene), one of the oldest mysticetes known. The two teeth analyzed were lower premolars, with transversely compressed triangular crowns composed of a main cuspand accessory denticles. The enamel microstructure of the basilosaurid and Llanocetus sp. is prismatic with Hunter-Schreger bands (HSB) and an outer zone of radial enamel. In the basilosaurid, the enamel is relatively thin and measures 150–180 μm, whereas in Llanocetus sp. it is considerably thicker, measuring 830–890 μm in the cusp area and 350–380 μm near the crown base. This is one of the thickest enamel layers among cetaceans, extinct and living. Structures resembling enamel tufts and lamellae were observed in both fossils at the enamel-dentine junction (EDJ) and extending along the thickness of the enamel layer, respectively. The presence of HSB and biomechanical reinforcing structures such as tufts and lamellae suggests prominent occlusal loads during feeding, consistent with raptorial feeding habits. Despite the simplification or absence of teeth in modern cetaceans, their ancestors had complex posterior teeth typical of most mammals, with a moderately thick enamel layer with prominent HSB.

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  • 21. Meadows, Jennifer R. S.
    et al.
    Kidd, Jeffrey M.
    Wang, Guo-Dong
    Parker, Heidi G.
    Schall, Peter Z.
    Bianchi, Matteo
    Christmas, Matthew J.
    Bougiouri, Katia
    Buckley, Reuben M.
    Hitte, Christophe
    Nguyen, Anthony K.
    Wang, Chao
    Jagannathan, Vidhya
    Niskanen, Julia E.
    Frantz, Laurent A. F.
    Arumilli, Meharji
    Hundi, Sruthi
    Lindblad-Toh, Kerstin
    Ginja, Catarina
    Agustina, Kadek Karang
    André, Catherine
    Boyko, Adam R.
    Davis, Brian W.
    Drögemüller, Michaela
    Feng, Xin-Yao
    Gkagkavouzis, Konstantinos
    Iliopoulos, Giorgos
    Harris, Alexander C.
    Hytönen, Marjo K.
    Kalthoff, Daniela C.
    Swedish Museum of Natural History, Department of Zoology.
    Liu, Yan-Hu
    Lymberakis, Petros
    Poulakakis, Nikolaos
    Pires, Ana Elisabete
    Racimo, Fernando
    Ramos-Almodovar, Fabian
    Savolainen, Peter
    Venetsani, Semina
    Tammen, Imke
    Triantafyllidis, Alexandros
    vonHoldt, Bridgett
    Wayne, Robert K.
    Larson, Greger
    Nicholas, Frank W.
    Lohi, Hannes
    Leeb, Tosso
    Zhang, Ya-Ping
    Ostrander, Elaine A.
    Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture2023In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 24, no 1, article id 187Article in journal (Refereed)
    Abstract [en]

    Background

    The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 × data from 1987 individuals, 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.

    Results

    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 sampled 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.

    Conclusions

    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.

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  • 22.
    Mörs, Thomas
    et al.
    Swedish Museum of Natural History, Department of Paleobiology.
    Tomida, Yukimitsu
    Kalthoff, Daniela
    Swedish Museum of Natural History, Department of Zoology.
    A new large beaver (Mammalia, Castoridae) from the Early Miocene of Japan2016In: Journal of Vertebrate Paleontology, ISSN 0272-4634, E-ISSN 1937-2809Article in journal (Refereed)
    Abstract [en]

    A new early Miocene large castorid, Minocastor godai gen. et sp. nov., from the Dota locality, Gifu Prefecture in central Japan, is described on the basis of dentaries and teeth. The material comes from the Kani basin, where limnofluviatile clay and sandstones of the Nakamura Formation (Mizunami Group) are exposed on the southern (left) bank of the Kiso River. It represents the richest sample of a Miocene small mammal in the Japanese fossil record thus far known. Based on jaw and tooth morphology, this new castorid most likely represents a primitive anchitheriomyine. However, it lacks the marked striations on the incisors that are characteristic of the advanced large, middle Miocene anchitheriomyines like Anchitheriomys and Amblycastor. The new castorid shares this dental feature with other primitive anchitheriomyines from Asia and North America, like Propalaeocastor, Oligotheriomys, and Miotheriomys. For these genera, a new tribe, Minocastorini, is proposed as sister group to the Anchitheriomyini. The incisor enamel microstructure of the new castorid largely exhibits plesiomorphic characters but also apomorphic features such as pseudo-pauciserial Hunter-Schreger bands. Additionally, the outer portion of the enamel band is rather thick in comparison to that of other beavers. Based on the rodent taxa associated with Minocastor godai gen. et sp. nov., Dota can be correlated with European Neogene mammal units MN 3/4. Magnetostratigraphic studies and radiometric dates obtained from the Mizunami Group indicate that Dota is more likely correlated with MN 3, with an absolute age of around 18.5 Ma.

  • 23. Palkopoulou, Eleftheria
    et al.
    Baca, Mateusz
    Abramson, Natalia I.
    Sablin, Mikhail
    Socha, Pawel
    Nadachowski, Adam
    Prost, Stefan
    Germonpre, Mietje
    Kosintsev, Pavel
    Smirnov, Nickolay G.
    Vartanyan, Sergey
    Ponomarev, Dmitry
    Nystroem, Johanna
    Nikolskiy, Pavel
    Jass, Christopher N.
    Litvinov, Yuriy N.
    Kalthoff, Daniela C.
    Grigoriev, Semyon
    Fadeeva, Tatyana
    Douka, Aikaterini
    Higham, Thomas F. G.
    Ersmark, Erik
    Pitulko, Vladimir
    Pavlova, Elena
    Stewart, John R.
    Weglenski, Piotr
    Stankovic, Anna
    Dalen, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Synchronous genetic turnovers across Western Eurasia in Late Pleistocene collared lemmings2016In: Global Change Biology, ISSN 1354-1013, E-ISSN 1365-2486, Vol. 22, no 5, p. 1710-1721Article in journal (Refereed)
    Abstract [en]

    Recent palaeogenetic studies indicate a highly dynamic history in collared lemmings (Dicrostonyx spp.), with several demographical changes linked to climatic fluctuations that took place during the last glaciation. At the western range margin of D.torquatus, these changes were characterized by a series of local extinctions and recolonizations. However, it is unclear whether this pattern represents a local phenomenon, possibly driven by ecological edge effects, or a global phenomenon that took place across large geographical scales. To address this, we explored the palaeogenetic history of the collared lemming using a next-generation sequencing approach for pooled mitochondrial DNA amplicons. Sequences were obtained from over 300 fossil remains sampled across Eurasia and two sites in North America. We identified five mitochondrial lineages of D.torquatus that succeeded each other through time across Europe and western Russia, indicating a history of repeated population extinctions and recolonizations, most likely from eastern Russia, during the last 50000years. The observation of repeated extinctions across such a vast geographical range indicates large-scale changes in the steppe-tundra environment in western Eurasia during the last glaciation. AllHolocene samples, from across the species' entire range, belonged to only one of the five mitochondrial lineages. Thus, extant D.torquatus populations only harbour a small fraction of the total genetic diversity that existed across different stages of the Late Pleistocene. In North American samples, haplotypes belonging to both D.groenlandicus and D.richardsoni were recovered from a Late Pleistocene site in south-western Canada. This suggests that D.groenlandicus had a more southern and D.richardsoni a more northern glacial distribution than previously thought. This study provides significant insights into the population dynamics of a small mammal at a large geographical scale and reveals a rather complex demographical history, which could have had bottom-up effects in the Late Pleistocene steppe-tundra ecosystem.

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  • 24.
    Sandoval, Eluzai Dinai Pinto
    et al.
    Faculdade de Ciências Agrárias e Veterinárias da Universidade Estadual Paulista (UNESP), Brazil.
    Queiroz Vacari, Gabrielle
    Faculdade de Ciências Agrárias e Veterinárias da Universidade Estadual Paulista (UNESP), Brazil.
    Juliá, Juan Pablo
    Universidad Nacional de Tucumán, Argentina.
    González, Susana
    Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay.
    Vozdova, Miluse
    Veterinary Research Institute, Brno, Czech Republic.
    Cernohorska, Halina
    Veterinary Research Institute, Brno, Czech Republic.
    Kubickova, Svatav
    Veterinary Research Institute, Brno, Czech Republic.
    Kalthoff, Daniela C.
    Swedish Museum of Natural History, Department of Zoology.
    Barbanti Duarte, José Mauricio
    Faculdade de Ciências Agrárias e Veterinárias da Universidade Estadual Paulista (UNESP), Brazil.
    Assessing the taxonomic status of the Gray Brocket Mazama simplicicornis argentina Lönnberg, 1919 (Artiodactyla: Cervidae)2023In: Zoological Studies, ISSN 1021-5506, E-ISSN 1810-522X, Vol. 62, article id 30Article in journal (Refereed)
    Abstract [en]

    Mazama simplicicornis argentina is the name that was given to describe a gray brocket collected by Lönberg in 1919 in the central Chaco region of Argentina. Subsequent authors, based on morphological similarities, considered this name to be a synonym for the species Subulo gouazoubira Fischer, 1814 from Paraguay. In the absence of genetic analyses to compare the Argentinian and Paraguayan gray brockets, we aimed to clarify the taxonomy of M. simplicicornis argentina through an integrative assessment using morphological, cytogenetical, and molecular data from its holotype and a current topotype. Qualitative skull features and cranio-morphometric results of M. simplicicornis argentina showed a great similarity with the S. gouazoubira neotype characters. The diploid chromosome number of M. simplicicornis argentinatopotype corresponded with the karyotypical pattern of S. gouazoubira with 2n = 70 and FN = 70, showing a great similarity in all classic and molecular cytogenetic results and revealing the homologies between karyotypes. The phylogenetic analysis of mitochondrial genes used in this study (concatenated partial ND5 and Cytb gene) allocated the M. simplicicornis argentina specimens in the monophyletic clade of S. gouazoubira with a branch value of 100%. These results show that there is no discontinuity between the Argentinian and Paraguayan gray brockets. Therefore, the individuals originally described as M. simplicicornis argentina should be recognized as S. gouazoubira.

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  • 25.
    Schultz, Julia A.
    et al.
    Institute of Geosciences, Section Palaeontology, University of Bonn, Germany.
    Braune, Caroline
    Brinkkötter, Janka J.
    Anders, Ulrike
    Calandra, Ivan
    Monrepos Archaeological Research Centre and Museum.
    Engels, Sandra
    Findeisen, Eva
    Gailer, Juan-Pablo
    Universität Hamburg, Department of Mammalogy/Paleoanthropology.
    Hummel, Jürgen
    Georg-August-Universität Göttingen.
    Jäger, Kai
    Rheinische Friedrich-Wilhelms-Universität Bonn, Section Palaeontology, Institute of Geosciences.
    Kaiser, Thomas M.
    Universität Hamburg, Department of Mammalogy/Paleoanthropology.
    Kalthoff, Daniela
    Swedish Museum of Natural History, Department of Zoology.
    Koenigswald, Wighart von
    Rheinische Friedrich-Wilhelms-Universität Bonn, Section Palaeontology, Institute of Geosciences.
    Kullmer, Ottmar
    Senckenberg Forschungsinstitut und Naturmuseum Frankfurt.
    Landwehr, Christina
    Mau, Markus
    Menz, Ulrike
    Ruf, Irina
    Senckenberg Forschungsinstitut und Naturmuseum Frankfurt.
    Schubert, Anna M.
    Schulz-Kornas, Ellen
    Poliklinik für Zahnerhaltung und Parodontologie, Universität Leipzig.
    Schwermann, Achim H.
    LWL-Museum für Naturkunde, Westfälisches Landesmuseum mit Planetarium.
    Schwermann, Leonie C.
    LWL-Museum für Naturkunde, Westfälisches Landesmuseum mit Planetarium.
    Skiba, Mirella
    Steuer, Patrick
    Senzyme GmbH.
    Südekum, Karl-Heinz
    Rheinische Friedrich-Wilhelms-Universität Bonn, Institute of Animal Science.
    Winkler, Daniela E.
    Johannes Gutenberg-Universität Mainz, Institute for Geosciences.
    Martin, Thomas
    Rheinische Friedrich-Wilhelms-Universität Bonn, Section Palaeontology, Institute of Geosciences.
    A new wear facet terminology for mammalian dentitions2020In: Mammalian Teeth – Form and Function / [ed] Thomas Martin and Wighart von Koenigswald, München: Verlag Dr. Friedrich Pfeil , 2020, 1, p. 11-24Chapter in book (Refereed)
    Abstract [en]

    There is no abstract.

  • 26.
    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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  • 27.
    Sánchez‐Barreiro, Fátima
    et al.
    GLOBE Institute University of Copenhagen Copenhagen Denmark.
    Gopalakrishnan, Shyam
    GLOBE Institute University of Copenhagen Copenhagen Denmark;DTU Bioinformatics Kongens Lyngby Hovedstaden Denmark;Center for Evolutionary Hologenomics University of Copenhagen Copenhagen Denmark.
    Ramos‐Madrigal, Jazmín
    GLOBE Institute University of Copenhagen Copenhagen Denmark.
    Westbury, Michael V.
    GLOBE Institute University of Copenhagen Copenhagen Denmark.
    Manuel, Marc
    Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas–Universitat Pompeu Fabra) Barcelona Biomedical Research Park Barcelona Spain.
    Margaryan, Ashot
    GLOBE Institute University of Copenhagen Copenhagen Denmark;Center for Evolutionary Hologenomics University of Copenhagen Copenhagen Denmark.
    Ciucani, Marta M.
    GLOBE Institute University of Copenhagen Copenhagen Denmark.
    Vieira, Filipe G.
    GLOBE Institute University of Copenhagen Copenhagen Denmark.
    Patramanis, Yannis
    GLOBE Institute University of Copenhagen Copenhagen Denmark.
    Kalthoff, Daniela C.
    Swedish Museum of Natural History, Department of Zoology.
    Timmons, Zena
    Department of Natural Sciences National Museums Scotland Edinburgh UK.
    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.
    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.
    Ryder, Oliver A.
    San Diego Zoo Institute for Conservation Research Escondido CA USA.
    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 ZoologyChinese Academy of Sciences Kunming China;Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China;BGI‐Shenzhen Shenzhen China.
    Marquès‐Bonet, Tomás
    Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas–Universitat Pompeu Fabra) Barcelona Biomedical Research Park Barcelona Spain;National Centre for Genomic Analysis–Centre for Genomic Regulation Barcelona Institute of Science and Technology Barcelona Spain;Institucio Catalana de Recerca i Estudis Avançats (ICREA) Barcelona Spain.
    Moodley, Yoshan
    Department of Zoology University of Venda Thohoyandou South Africa.
    Gilbert, M. Thomas P.
    GLOBE Institute University of Copenhagen Copenhagen Denmark;Center for Evolutionary Hologenomics University of Copenhagen Copenhagen Denmark;Norwegian University of Science and Technology University Museum Trondheim Norway.
    Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros ( Ceratotherium simum )2021In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 30, no 23, p. 6355-6369Article in journal (Refereed)
    Abstract [en]

    Large vertebrates are extremely sensitive to anthropogenic pressure, and their populations are declining fast. The white rhinoceros (Ceratotherium simum) is a paradigmatic case: this African megaherbivore has suffered a remarkable decline in the last 150 years due to human activities. Its subspecies, the northern (NWR) and the southern white rhinoceros (SWR), however, underwent opposite fates: the NWR vanished quickly, while the SWR recovered after the severe decline. Such demographic events are predicted to have an erosive effect at the genomic level, linked to the extirpation of diversity, and increased genetic drift and inbreeding. However, there is little empirical data available to directly reconstruct the subtleties of such processes in light of distinct demographic histories. Therefore, we generated a whole-genome, temporal data set consisting of 52 resequenced white rhinoceros genomes, representing both subspecies at two time windows: before and during/after the bottleneck. Our data reveal previously unknown population structure within both subspecies, as well as quantifiable genomic erosion. Genome-wide heterozygosity decreased significantly by 10% in the NWR and 36% in the SWR, and inbreeding coefficients rose significantly by 11% and 39%, respectively. Despite the remarkable loss of genomic diversity and recent inbreeding it suffered, the only surviving subspecies, the SWR, does not show a significant accumulation of genetic load compared to its historical counterpart. Our data provide empirical support for predictions about the genomic consequences of shrinking populations, and our findings have the potential to inform the conservation efforts of the remaining white rhinoceroses.

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  • 28. van der Valk, Tom
    et al.
    Sandoval-Castellanos, Edson
    Caillaud, Damien
    Ngobobo, Urbain
    Binyinyi, Escobar
    Nishuli, Radar
    Stoinski, Tara
    Gilissen, Emmanuel
    Sonet, Gontran
    Semal, Patrick
    Kalthoff, Daniela C.
    Swedish Museum of Natural History, Department of Zoology.
    Dalén, Love
    Guschanski, Katerina
    Significant loss of mitochondrial diversity within the last century due to extinction of peripheral populations in eastern gorillas2018In: Scientific Reports, E-ISSN 2045-2322, Vol. 8, article id 6551Article in journal (Refereed)
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