1
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Segawa T, Rey-Iglesia A, Lorenzen ED, Westbury MV. The origins and diversification of Holarctic brown bear populations inferred from genomes of past and present populations. Proc Biol Sci 2024; 291:20232411. [PMID: 38264778 PMCID: PMC10806438 DOI: 10.1098/rspb.2023.2411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 12/20/2023] [Indexed: 01/25/2024] Open
Abstract
The brown bear (Ursus arctos) is one of the survivors of the Late Quaternary megafauna extinctions. However, despite being widely distributed across the Holarctic, brown bears have experienced extensive range reductions, and even extirpations in some geographical regions. Previous research efforts using genetic data have provided valuable insights into their evolutionary history. However, most studies have been limited to contemporary individuals or mitochondrial DNA, limiting insights into population processes that preceded the present. Here, we present genomic data from two Late Pleistocene brown bears from Honshu, Japan and eastern Siberia, and combine them with published contemporary and ancient genomes from across the Holarctic range of brown bears to investigate the evolutionary relationships among brown bear populations through time and space. By including genomic data from Late Pleistocene and Holocene individuals sampled outside the current distribution range, we uncover diversity not present in contemporary populations. Notably, although contemporary individuals display geographically structured populations most likely driven by isolation-by-distance, this pattern varies among the ancient samples across different regions. The inclusion of ancient brown bears in our analysis provides novel insights into the evolutionary history of brown bears and contributes to understanding the populations and diversity lost during the Late Quaternary.
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Affiliation(s)
- Takahiro Segawa
- Center for Life Science Research, University of Yamanashi, Chuo, Yamanashi, Japan
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2
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Xiao B, Rey-lglesia A, Yuan J, Hu J, Song S, Hou Y, Chen X, Germonpré M, Bao L, Wang S, Taogetongqimuge, Valentinovna LL, Lister AM, Lai X, Sheng G. Relationships of Late Pleistocene giant deer as revealed by Sinomegaceros mitogenomes from East Asia. iScience 2023; 26:108406. [PMID: 38047074 PMCID: PMC10690636 DOI: 10.1016/j.isci.2023.108406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/26/2023] [Accepted: 11/03/2023] [Indexed: 12/05/2023] Open
Abstract
The giant deer, widespread in northern Eurasia during the Late Pleistocene, have been classified as western Megaloceros and eastern Sinomegaceros through morphological studies. While Megaloceros's evolutionary history has been unveiled through mitogenomes, Sinomegaceros remains molecularly unexplored. Herein, we generated mitogenomes of giant deer from East Asia. We find that, in contrast to the morphological differences between Megaloceros and Sinomegaceros, they are mixed in the mitochondrial phylogeny, and Siberian specimens suggest a range contact or overlap between these two groups. Meanwhile, one deep divergent clade and another surviving until 20.1 thousand years ago (ka) were detected in northeastern China, the latter implying this area as a potential refugium during the Last Glacial Maximum (LGM). Moreover, stable isotope analyses indicate correlations between climate-introduced vegetation changes and giant deer extinction. Our study demonstrates the genetic relationship between eastern and western giant deer and explores the promoters of their extirpation in northern East Asia.
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Affiliation(s)
- Bo Xiao
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China
- School of Earth Sciences, China University of Geosciences, Wuhan 430074, China
| | - Alba Rey-lglesia
- Globe Institute, University of Copenhagen, Copenhagen, 1350 Copenhagen K, Denmark
| | - Junxia Yuan
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, China
| | - Jiaming Hu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China
- School of Earth Sciences, China University of Geosciences, Wuhan 430074, China
| | - Shiwen Song
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China
- School of Environmental Studies, China University of Geosciences, Wuhan 430078, China
| | - Yamei Hou
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Xi Chen
- Department of Cultural Heritage and Museology, Nanjing Normal University, Nanjing 210046, China
| | - Mietje Germonpré
- Royal Belgian Institute of Natural Sciences, 1000 Brussels, Belgium
| | - Lei Bao
- Ordos Institute of Cultural Relics and Archaeology, Ordos 017010, China
| | | | | | - Lbova Liudmila Valentinovna
- Graduate School of International Relations, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Grazhdansky Av., 28, Russia
| | | | - Xulong Lai
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China
- School of Earth Sciences, China University of Geosciences, Wuhan 430074, China
| | - Guilian Sheng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China
- School of Environmental Studies, China University of Geosciences, Wuhan 430078, China
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3
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Seeber PA, Palmer Z, Schmidt A, Chagas A, Kitagawa K, Marinova-Wolff E, Tafelmaier Y, Epp LS. The first European woolly rhinoceros mitogenomes, retrieved from cave hyena coprolites, suggest long-term phylogeographic differentiation. Biol Lett 2023; 19:20230343. [PMID: 37909055 PMCID: PMC10618854 DOI: 10.1098/rsbl.2023.0343] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/09/2023] [Indexed: 11/02/2023] Open
Abstract
The woolly rhinoceros (Coelodonta antiquitatis) is an iconic species of the Eurasian Pleistocene megafauna, which was abundant in Eurasia in the Pleistocene until its demise beginning approximately 10 000 years ago. Despite the early recovery of several specimens from well-known European archaeological sites, including its type specimen (Blumenbach 1799), no genomes of European populations were available so far, and all available genomic data originated exclusively from Siberian populations. Using coprolites of cave hyenas (Crocuta crocuta spelea) recovered from Middle Palaeolithic layers of two caves in Germany (Bockstein-Loch and Hohlenstein-Stadel), we isolated and enriched predator and prey DNA to assemble the first European woolly rhinoceros mitogenomes, in addition to cave hyena mitogenomes. Both coprolite samples produced copious sequences assigned to C. crocuta (27% and 59% mitogenome coverage, respectively) and woolly rhinoceros (Coelodonta antiquitatis; 27% and 81% coverage, respectively). The sequences suggested considerable DNA degradation, which may limit the conclusions to be drawn; however, the mitogenomes of European woolly rhinoceros are genetically distinct from the Siberian woolly rhinoceros, and analyses of the more complete mitogenome suggest a split of the populations potentially coinciding with the earliest fossil records of woolly rhinoceros in Europe.
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Affiliation(s)
- P. A. Seeber
- Limnological Institute, University of Konstanz, Konstanz, Germany
| | - Z. Palmer
- Limnological Institute, University of Konstanz, Konstanz, Germany
| | - A. Schmidt
- Limnological Institute, University of Konstanz, Konstanz, Germany
| | - A. Chagas
- Limnological Institute, University of Konstanz, Konstanz, Germany
| | - K. Kitagawa
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tubingen, Germany
- Institute of Archaeological Sciences, Department of Geosciences, University of Tübingen, Tubingen, Germany
| | - E. Marinova-Wolff
- Laboratory for Archaeobotany Baden-Württemberg, State Office for Cultural Heritage, Gaienhofen-Hemmenhofen, Germany
| | - Y. Tafelmaier
- State Office for Cultural Heritage Baden-Württemberg, Palaeolithic & Mesolithic Research Unit, Gaienhofen-Hemmenhofen, Germany
| | - L. S. Epp
- Limnological Institute, University of Konstanz, Konstanz, Germany
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4
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Teng SN, Svenning JC, Xu C. Large mammals and trees in eastern monsoonal China: anthropogenic losses since the Late Pleistocene and restoration prospects in the Anthropocene. Biol Rev Camb Philos Soc 2023; 98:1607-1632. [PMID: 37102332 DOI: 10.1111/brv.12968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 04/16/2023] [Accepted: 04/18/2023] [Indexed: 04/28/2023]
Abstract
Massive human-induced declines of large-sized animals and trees (megabiota) from the Late Pleistocene to the Anthropocene have resulted in downsized ecosystems across the globe, in which components and functions have been greatly simplified. In response, active restoration projects of extant large-sized species or functional substitutes are needed at large scales to promote ecological processes that are important for ecosystem self-regulation and biodiversity maintenance. Despite the desired global scope of such projects, they have received little attention in East Asia. Here, we synthesise the biogeographical and ecological knowledge of megabiota in ancient and modern China, with relevant data mostly located in eastern monsoonal China (EMC), aiming to assess its potential for restoring functionally intact ecosystems modulated by megabiota. We found that during the Late Pleistocene, 12 mammalian megafaunal (carnivores ≥15 kg and herbivores ≥500 kg) species disappeared from EMC: one carnivore Crocuta ultima (East Asian spotted hyena) and 11 herbivores including six megaherbivores (≥1000 kg). The relative importance of climate change and humans in driving these losses remains debated, despite accumulating evidence in favour of the latter. Later massive depletion of megafauna and large-sized (45-500 kg) herbivores has been closely associated with agricultural expansion and societal development, especially during the late Holocene. While forests rich in large timber trees (33 taxa in written records) were common in the region 2000-3000 years ago, millennial-long logging has resulted in considerable range contractions and at least 39 threatened species. The wide distribution of C. ultima, which likely favoured open or semi-open habitats (like extant spotted hyenas), suggests the existence of mosaic open and closed vegetation in the Late Pleistocene across EMC, in line with a few pollen-based vegetation reconstructions and potentially, or at least partially, reflecting herbivory by herbivorous megafauna. The widespread loss of megaherbivores may have strongly compromised seed dispersal for both megafruit (fleshy fruits with widths ≥40 mm) and non-megafruit plant species in EMC, especially in terms of extra-long-distance (>10 km) dispersal, which is critical for plant species that rely on effective biotic agents to track rapid climate change. The former occurrence of large mammals and trees have translated into rich material and non-material heritages passed down across generations. Several reintroduction projects have been implemented or are under consideration, with the case of Elaphurus davidianus a notable success in recovering wild populations in the middle reaches of the Yangtze River, although trophic interactions with native carnivorous megafauna have not yet been restored. Lessons of dealing with human-wildlife conflicts are key to public support for maintaining landscapes shared with megafauna and large herbivores in the human-dominated Anthropocene. Meanwhile, potential human-wildlife conflicts, e.g. public health risks, need to be scientifically informed and effectively reduced. The Chinese government's strong commitment to improved policies of ecological protection and restoration (e.g. ecological redlines and national parks) provides a solid foundation for a scaling-up contribution to the global scope needed for solving the crisis of biotic downsizing and ecosystem degradation.
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Affiliation(s)
- Shuqing N Teng
- School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Jens-Christian Svenning
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO) & Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, Aarhus, 8000, Denmark
| | - Chi Xu
- School of Life Sciences, Nanjing University, Nanjing, 210023, China
- Key Laboratory of Restoration and Reconstruction of Degraded Ecosystems in northwestern China of Ministry of Education, Ningxia University, Yinchuan, 750021, China
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5
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Westbury MV, Cabrera AA, Rey-Iglesia A, De Cahsan B, Duchêne DA, Hartmann S, Lorenzen ED. A genomic assessment of the marine-speciation paradox within the toothed whale superfamily Delphinoidea. Mol Ecol 2023; 32:4829-4843. [PMID: 37448145 DOI: 10.1111/mec.17069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 06/21/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023]
Abstract
The impact of post-divergence gene flow in speciation has been documented across a range of taxa in recent years, and may have been especially widespread in highly mobile, wide-ranging marine species, such as cetaceans. Here, we studied individual genomes from nine species across the three families of the toothed whale superfamily Delphinoidea (Delphinidae, Phocoenidae and Monodontidae). To investigate the role of post-divergence gene flow in the speciation process, we used a multifaceted approach, including (i) phylogenomics, (ii) the distribution of shared derived alleles and (iii) demographic inference. We found the divergence of lineages within Delphinoidea did not follow a process of pure bifurcation, but was much more complex. Sliding-window phylogenomics reveal a high prevalence of discordant topologies within the superfamily, with further analyses indicating these discordances arose due to both incomplete lineage sorting and gene flow. D-statistics and f-branch analyses supported gene flow between members of Delphinoidea, with the vast majority of gene flow occurring as ancient interfamilial events. Demographic analyses provided evidence that introgressive gene flow has likely ceased between all species pairs tested, despite reports of contemporary interspecific hybrids. Our study provides the first steps towards resolving the large complexity of speciation within Delphinoidea; we reveal the prevalence of ancient interfamilial gene flow events prior to the diversification of each family, and suggest that contemporary hybridisation events may be disadvantageous, as hybrid individuals do not appear to contribute to the parental species' gene pools.
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Affiliation(s)
| | | | | | - Binia De Cahsan
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - David A Duchêne
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Stefanie Hartmann
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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6
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Song S, Xiao B, Hu J, Lin H, Du Z, Xiang K, Pan D, Hou X, Yuan J, Lai X, Sheng G. Ancient Mitogenomes Reveal Stable Genetic Continuity of the Holocene Serows. Genes (Basel) 2023; 14:1187. [PMID: 37372367 DOI: 10.3390/genes14061187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
As one of the remaining species of Caprinae only found in Asia, serows (Capricornis) and their classification and conservation have received increasing attention in recent years. However, their evolutionary history and population dynamics are not yet clear. To shed light on these topics, we report the first near-complete ancient mitochondrial genomes from two serow sub-fossils (CADG839 and CADG946) dating to 8860 ± 30 years and 2450 ± 30 years, and incorporate the newly obtained mitogenomes into the dataset of living serows (18 complete mitochondrial genomes drawn from National Center for Biotechnology Information, NCBI) to investigate their relationships and evolution. Phylogenetic results support four clades of serows that can be further divided into five subclades, indicating higher genetic diversity than previously thought. Notably, our two ancient samples do not form a separate branch but belong to Capricornis sumatraensis clade A together with modern individuals, which suggests genetic continuity between ancient and modern serows. Furthermore, our results suggest that the maternal divergences of serows occurred at the beginning of the Pleistocene. Bayesian estimation indicates that the first divergence among all serows happened approximately 2.37 Ma (95% highest posterior density, HPD: 2.74-2.02 Ma) when Japanese serow (Capricornis crispus) appeared, while the last divergence occurred within the Sumatran serow (C. sumatraensis clade A and B) around 0.37-0.25 Ma. Additionally, we found the effective maternal population size of C. sumatraensis increased around 225-160 and 90-50 ka, then remained stable since 50 ka. Overall, our study provides new insights into serow phylogeny and evolutionary history.
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Affiliation(s)
- Shiwen Song
- School of Environmental Studies, China University of Geosciences, Wuhan 430078, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China
| | - Bo Xiao
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China
- School of Earth Science, China University of Geosciences, Wuhan 430074, China
| | - Jiaming Hu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China
- School of Earth Science, China University of Geosciences, Wuhan 430074, China
| | - Haifeng Lin
- School of Environmental Studies, China University of Geosciences, Wuhan 430078, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China
| | - Zhicheng Du
- School of Environmental Studies, China University of Geosciences, Wuhan 430078, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China
| | - Kunpeng Xiang
- Guizhou Institute of Geological Survey, Guiyang 550081, China
| | - Dong Pan
- Palaeontological Fossil Conservation Center, Qinggang County, Suihua 151600, China
| | - Xindong Hou
- School of Environmental Studies, China University of Geosciences, Wuhan 430078, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China
| | - Junxia Yuan
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, China
| | - Xulong Lai
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China
- School of Earth Science, China University of Geosciences, Wuhan 430074, China
| | - Guilian Sheng
- School of Environmental Studies, China University of Geosciences, Wuhan 430078, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China
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7
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Hempel E, Bibi F, Faith JT, Koepfli KP, Klittich AM, Duchêne DA, Brink JS, Kalthoff DC, Dalén L, Hofreiter M, Westbury MV. Blue Turns to Gray: Paleogenomic Insights into the Evolutionary History and Extinction of the Blue Antelope (Hippotragus leucophaeus). Mol Biol Evol 2022; 39:6794086. [PMID: 36322483 PMCID: PMC9750129 DOI: 10.1093/molbev/msac241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 09/25/2022] [Accepted: 10/31/2022] [Indexed: 11/07/2022] Open
Abstract
The blue antelope (Hippotragus leucophaeus) is the only large African mammal species to have become extinct in historical times, yet no nuclear genomic information is available for this species. A recent study showed that many alleged blue antelope museum specimens are either roan (Hippotragus equinus) or sable (Hippotragus niger) antelopes, further reducing the possibilities for obtaining genomic information for this extinct species. While the blue antelope has a rich fossil record from South Africa, climatic conditions in the region are generally unfavorable to the preservation of ancient DNA. Nevertheless, we recovered two blue antelope draft genomes, one at 3.4× mean coverage from a historical specimen (∼200 years old) and one at 2.1× mean coverage from a fossil specimen dating to 9,800-9,300 cal years BP, making it currently the oldest paleogenome from Africa. Phylogenomic analyses show that blue and sable antelope are sister species, confirming previous mitogenomic results, and demonstrate ancient gene flow from roan into blue antelope. We show that blue antelope genomic diversity was much lower than in roan and sable antelope, indicative of a low population size since at least the early Holocene. This supports observations from the fossil record documenting major decreases in the abundance of blue antelope after the Pleistocene-Holocene transition. Finally, the persistence of this species throughout the Holocene despite low population size suggests that colonial-era human impact was likely the decisive factor in the blue antelope's extinction.
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Affiliation(s)
| | - Faysal Bibi
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
| | - J Tyler Faith
- Natural History Museum of Utah, University of Utah, 301 Wakara Way, Salt Lake City, UT 84108,Department of Anthropology, University of Utah, 260 South Central Campus Drive, Salt Lake City, UT 84112,Origins Centre, University of the Witwatersrand, Johannesburg, Republic of South Africa
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA 22630,Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, 20008, USA
| | - Achim M Klittich
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Department of Mathematics and Natural Sciences, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - David A Duchêne
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark,Centre for Evolutionary Hologenomics, University of Copenhagen, Copenhagen 1352, Denmark
| | | | - Daniela C Kalthoff
- Swedish Museum of Natural History, Department of Zoology, Box 50007, 10405 Stockholm, Sweden
| | - Love Dalén
- Swedish Museum of Natural History, Department of Bioinformatics and Genetics, Box 50007, 10405 Stockholm, Sweden,Centre for Palaeogenetics, Svante Arrhenius väg 20c, 10691 Stockholm, Sweden,Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
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8
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Westbury MV, Lorenzen ED. Iteratively mapping ancient
DNA
to reconstruct highly divergent mitochondrial genomes: An evaluation of software, parameters and bait reference. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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9
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Li X, Ru D, Garber PA, Zhou Q, Li M, Zhao X. Climate change and human activities promoted speciation of two endangered langurs (François' langur and white-headed langur). Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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10
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Extended longevity of DNA preservation in Levantine Paleolithic sediments, Sefunim Cave, Israel. Sci Rep 2022; 12:14528. [PMID: 36008437 PMCID: PMC9411205 DOI: 10.1038/s41598-022-17399-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 07/25/2022] [Indexed: 11/09/2022] Open
Abstract
Paleogenomic research can elucidate the evolutionary history of human and faunal populations. Although the Levant is a key land-bridge between Africa and Eurasia, thus far, relatively little ancient DNA data has been generated from this region, since DNA degrades faster in warm climates. As sediments can be a source of ancient DNA, we analyzed 33 sediment samples from different sedimentological contexts in the Paleolithic layers of Sefunim Cave (Israel). Four contained traces of ancient Cervidae and Hyaenidae mitochondrial DNA. Dating by optical luminescence and radiocarbon indicates that the DNA comes from layers between 30,000 and 70,000 years old, surpassing theoretical expectations regarding the longevity of DNA deposited in such a warm environment. Both identified taxa are present in the zooarchaeological record of the site but have since gone extinct from the region, and a geoarchaeological study suggests little movement of the sediments after their deposition, lending further support to our findings. We provide details on the local conditions in the cave, which we hypothesize were particularly conducive to the long-term preservation of DNA-information that will be pertinent for future endeavors aimed at recovering ancient DNA from the Levant and other similarly challenging contexts.
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11
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Rocha RG, Gonçalves J, Tarroso P, Monterroso P, Godinho R. Multiple Lines of Ecological Evidence Support Ancient Contact Between the African Wild Dog and the Dhole. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.803822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Genomic tools have greatly enhanced our ability to uncover ancient interspecific gene flow, including cases involving allopatric lineages and/or lineages that have gone extinct. Recently, a genomic analysis revealed the unexpected gene flow between the African wild dog (Lycaon pictus) and the dhole (Cuon alpinus). The two species have currently highly disjunct and patchy distributions in Africa and Asia, respectively, which are remnants of a much wider past distribution. Yet, no reported evidence of their past contact has ever been documented. By hindcasting the past potential distribution of both species during the Last Glacial Maximum and the Last Interglacial, validating paleoclimatic reconstructions with fossil evidence, quantifying the intersection of their bioclimatic niches, and assessing interspecific compatibility, we investigate the location and favorable conditions for such contact and its ecological validity. We were able to identify the Levant region in Eastern Mediterranean during the Last Interglacial as the most suitable spatio-ecological context for the co-occurrence of the two canids, and to provide evidence of a highly significant overlap of the African wild dog niche with the wider niche of the dhole. These results, combined with ecologic traits, including key compatibility features such as cooperative breeding and hunting, provide consistent support for the potential co-occurrence of both canids. We suggest that the ranges of these canids came into contact multiple times during periods resembling the Last Interglacial, eventually facilitating gene flow between the African wild dog and the dhole in their post-divergence history. Our results are highly supportive of the key role of the Levant region in providing connectivity between African and Eurasian faunas and provide further impetus to combine different tools and approaches in advancing the understanding of species evolutionary histories.
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12
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Shao Y, Wang XB, Zhang ML, Liu Y, Wang S, Zhang BL, Yang MM, Yang MH, Jia T, Pu TC, Lu Y, Liu H, Xu Z, Li B, Liu N, Onsongo VM, Wu DD, Zhang CL, Ruan J, Li Y. Long-read genome sequencing provides molecular insights into scavenging and societal complexity in spotted hyena Crocuta crocuta. Mol Biol Evol 2022; 39:6509522. [PMID: 35038730 PMCID: PMC8890499 DOI: 10.1093/molbev/msac011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The spotted hyena (Crocuta crocuta) is a large and unique terrestrial carnivore. It is a particularly fascinating species due to its distinct phenotypic traits, especially its complex social structure and scavenging lifestyle, with associated high dietary exposure to microbial pathogens. However, the underlying molecular mechanisms related to these phenotypes remain elusive. Here, we sequenced and assembled a high-quality long-read genome of the spotted hyena, with a contig N50 length of ∼13.75 Mb. Based on comparative genomics, immunoglobulin family members (e.g., IGKV4-1) showed significant adaptive duplications in the spotted hyena and striped hyena. Furthermore, immune-related genes (e.g., CD8A, LAG3, and TLR3) experienced species-specific positive selection in the spotted hyena lineage. These results suggest that immune tolerance between the spotted hyena and closely related striped hyena has undergone adaptive divergence to cope with prolonged dietary exposure to microbial pathogens from scavenging. Furthermore, we provided the potential genetic insights underlying social complexity, hinting at social behavior and cognition. Specifically, the RECNE-associated genes (e.g., UGP2 and ACTR2) in the spotted hyena genome are involved in regulation of social communication. Taken together, our genomic analyses provide molecular insights into the scavenging lifestyle and societal complexity of spotted hyenas.
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Affiliation(s)
- Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Xiao-Bo Wang
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Mei-Ling Zhang
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming, Yunnan, 650022, China
| | - Yan Liu
- Beijing Zoo, Beijing, 100044, China
| | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Bao-Lin Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Min-Min Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | | | - Ting Jia
- Beijing Zoo, Beijing, 100044, China
| | | | - Yan Lu
- Beijing Zoo, Beijing, 100044, China
| | - He Liu
- Beijing Zoo, Beijing, 100044, China
| | - Zhe Xu
- Beijing Zoo, Beijing, 100044, China
| | - Bo Li
- Beijing Zoo, Beijing, 100044, China
| | - Ning Liu
- Beijing Zoo, Beijing, 100044, China
| | - Violet Magoma Onsongo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | | | - Jue Ruan
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yan Li
- State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
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13
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Kardos M, Armstrong EE, Fitzpatrick SW, Hauser S, Hedrick PW, Miller JM, Tallmon DA, Funk WC. The crucial role of genome-wide genetic variation in conservation. Proc Natl Acad Sci U S A 2021; 118:e2104642118. [PMID: 34772759 PMCID: PMC8640931 DOI: 10.1073/pnas.2104642118] [Citation(s) in RCA: 117] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/02/2021] [Indexed: 12/30/2022] Open
Abstract
The unprecedented rate of extinction calls for efficient use of genetics to help conserve biodiversity. Several recent genomic and simulation-based studies have argued that the field of conservation biology has placed too much focus on conserving genome-wide genetic variation, and that the field should instead focus on managing the subset of functional genetic variation that is thought to affect fitness. Here, we critically evaluate the feasibility and likely benefits of this approach in conservation. We find that population genetics theory and empirical results show that conserving genome-wide genetic variation is generally the best approach to prevent inbreeding depression and loss of adaptive potential from driving populations toward extinction. Focusing conservation efforts on presumably functional genetic variation will only be feasible occasionally, often misleading, and counterproductive when prioritized over genome-wide genetic variation. Given the increasing rate of habitat loss and other environmental changes, failure to recognize the detrimental effects of lost genome-wide genetic variation on long-term population viability will only worsen the biodiversity crisis.
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Affiliation(s)
- Marty Kardos
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA 98112;
| | | | - Sarah W Fitzpatrick
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI 49060
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI 48824
| | - Samantha Hauser
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53211
| | - Philip W Hedrick
- School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Joshua M Miller
- San Diego Zoo Wildlife Alliance, Escondido, CA 92027
- Polar Bears International, Bozeman, MT 59772
- Department of Biological Sciences, MacEwan University, Edmonton, AB T5J 4S2, Canada
| | - David A Tallmon
- Biology and Marine Biology Program, University of Alaska Southeast, Juneau, AK 99801
| | - W Chris Funk
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523
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14
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Abstract
The unprecedented rate of extinction calls for efficient use of genetics to help conserve biodiversity. Several recent genomic and simulation-based studies have argued that the field of conservation biology has placed too much focus on conserving genome-wide genetic variation, and that the field should instead focus on managing the subset of functional genetic variation that is thought to affect fitness. Here, we critically evaluate the feasibility and likely benefits of this approach in conservation. We find that population genetics theory and empirical results show that conserving genome-wide genetic variation is generally the best approach to prevent inbreeding depression and loss of adaptive potential from driving populations toward extinction. Focusing conservation efforts on presumably functional genetic variation will only be feasible occasionally, often misleading, and counterproductive when prioritized over genome-wide genetic variation. Given the increasing rate of habitat loss and other environmental changes, failure to recognize the detrimental effects of lost genome-wide genetic variation on long-term population viability will only worsen the biodiversity crisis.
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15
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Pérez-Escobar OA, Bellot S, Przelomska NAS, Flowers JM, Nesbitt M, Ryan P, Gutaker RM, Gros-Balthazard M, Wells T, Kuhnhäuser BG, Schley R, Bogarín D, Dodsworth S, Diaz R, Lehmann M, Petoe P, Eiserhardt WL, Preick M, Hofreiter M, Hajdas I, Purugganan M, Antonelli A, Gravendeel B, Leitch IJ, Torres Jimenez MF, Papadopulos AST, Chomicki G, Renner SS, Baker WJ. Molecular clocks and archaeogenomics of a Late Period Egyptian date palm leaf reveal introgression from wild relatives and add timestamps on the domestication. Mol Biol Evol 2021; 38:4475-4492. [PMID: 34191029 PMCID: PMC8476131 DOI: 10.1093/molbev/msab188] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The date palm, Phoenix dactylifera, has been a cornerstone of Middle Eastern and North African agriculture for millennia. It was first domesticated in the Persian Gulf, and its evolution appears to have been influenced by gene flow from two wild relatives, P. theophrasti, currently restricted to Crete and Turkey, and P. sylvestris, widespread from Bangladesh to the West Himalayas. Genomes of ancient date palm seeds show that gene flow from P. theophrasti to P. dactylifera may have occurred by ∼2,200 years ago, but traces of P. sylvestris could not be detected. We here integrate archeogenomics of a ∼2,100-year-old P. dactylifera leaf from Saqqara (Egypt), molecular-clock dating, and coalescence approaches with population genomic tests, to probe the hybridization between the date palm and its two closest relatives and provide minimum and maximum timestamps for its reticulated evolution. The Saqqara date palm shares a close genetic affinity with North African date palm populations, and we find clear genomic admixture from both P. theophrasti, and P. sylvestris, indicating that both had contributed to the date palm genome by 2,100 years ago. Molecular-clocks placed the divergence of P. theophrasti from P. dactylifera/P. sylvestris and that of P. dactylifera from P. sylvestris in the Upper Miocene, but strongly supported, conflicting topologies point to older gene flow between P. theophrasti and P. dactylifera, and P. sylvestris and P. dactylifera. Our work highlights the ancient hybrid origin of the date palms, and prompts the investigation of the functional significance of genetic material introgressed from both close relatives, which in turn could prove useful for modern date palm breeding.
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Affiliation(s)
| | - Sidonie Bellot
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | - Natalia A S Przelomska
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK.,National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Jonathan M Flowers
- Center for Genomics and Systems Biology, New York University Abu Dhabi, United Arab Emirates
| | - Mark Nesbitt
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | - Philippa Ryan
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | | | - Muriel Gros-Balthazard
- French National Research Institute for Sustainable Development, Montpellier, BP 64501 - 34394 Cedex 5, France
| | - Tom Wells
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3QU, UK
| | | | - Rowan Schley
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | - Diego Bogarín
- Lankester Botanical Garden, University of Costa Rica, San José, 302-7050, Costa Rica
| | - Steven Dodsworth
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK.,School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Rudy Diaz
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | | | - Peter Petoe
- Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Wolf L Eiserhardt
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK.,Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Michaela Preick
- Institute of Biochemistry and Biology, University of Potsdam, 14469 Potsdam, Germany
| | - Michael Hofreiter
- Institute of Biochemistry and Biology, University of Potsdam, 14469 Potsdam, Germany
| | - Irka Hajdas
- Department of Earth Sciences, ETH Zurich, 8092, Switzerland
| | - Michael Purugganan
- Center for Genomics and Systems Biology, New York University Abu Dhabi, United Arab Emirates
| | - Alexandre Antonelli
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK.,Department of Plant Sciences, University of Oxford, Oxford, OX1 3QU, UK.,Gothenburg Global Biodiversity Centre and Department of Biological and Environmental Sciences, University of Gothenburg, 413 19, Sweden
| | | | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | - Maria Fernanda Torres Jimenez
- Gothenburg Global Biodiversity Centre and Department of Biological and Environmental Sciences, University of Gothenburg, 413 19, Sweden
| | - Alexander S T Papadopulos
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, University of Bangor, Bangor LL57 2UW, UK
| | - Guillaume Chomicki
- Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Susanne S Renner
- Department of Biology, Washington University, Saint Louis, MO 63130, USA
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16
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Zavala EI, Jacobs Z, Vernot B, Shunkov MV, Kozlikin MB, Derevianko AP, Essel E, de Fillipo C, Nagel S, Richter J, Romagné F, Schmidt A, Li B, O'Gorman K, Slon V, Kelso J, Pääbo S, Roberts RG, Meyer M. Pleistocene sediment DNA reveals hominin and faunal turnovers at Denisova Cave. Nature 2021; 595:399-403. [PMID: 34163072 PMCID: PMC8277575 DOI: 10.1038/s41586-021-03675-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/27/2021] [Indexed: 12/31/2022]
Abstract
Denisova Cave in southern Siberia is the type locality of the Denisovans, an archaic hominin group who were related to Neanderthals1–4. The dozen hominin remains recovered from the deposits also include Neanderthals5,6 and the child of a Neanderthal and a Denisovan7, which suggests that Denisova Cave was a contact zone between these archaic hominins. However, uncertainties persist about the order in which these groups appeared at the site, the timing and environmental context of hominin occupation, and the association of particular hominin groups with archaeological assemblages5,8–11. Here we report the analysis of DNA from 728 sediment samples that were collected in a grid-like manner from layers dating to the Pleistocene epoch. We retrieved ancient faunal and hominin mitochondrial (mt)DNA from 685 and 175 samples, respectively. The earliest evidence for hominin mtDNA is of Denisovans, and is associated with early Middle Palaeolithic stone tools that were deposited approximately 250,000 to 170,000 years ago; Neanderthal mtDNA first appears towards the end of this period. We detect a turnover in the mtDNA of Denisovans that coincides with changes in the composition of faunal mtDNA, and evidence that Denisovans and Neanderthals occupied the site repeatedly—possibly until, or after, the onset of the Initial Upper Palaeolithic at least 45,000 years ago, when modern human mtDNA is first recorded in the sediments. Ancient mitochondrial DNA from sediments reveals the sequence of Denisovan, Neanderthal and faunal occupation of Denisova Cave, and evidence for the appearance of modern humans at least 45,000 years ago.
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Affiliation(s)
- Elena I Zavala
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Zenobia Jacobs
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia. .,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia.
| | - Benjamin Vernot
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Michael V Shunkov
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Maxim B Kozlikin
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Anatoly P Derevianko
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Elena Essel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Cesare de Fillipo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sarah Nagel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Julia Richter
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Frédéric Romagné
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anna Schmidt
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Bo Li
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia.,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia
| | - Kieran O'Gorman
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia
| | - Viviane Slon
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Shmunis Family Anthropology Institute, The Dan David Center for Human Evolution and Biohistory Research, Tel Aviv University, Tel Aviv, Israel
| | - Janet Kelso
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Richard G Roberts
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia. .,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia.
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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17
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Baleka S, Herridge VL, Catalano G, Lister AM, Dickinson MR, Di Patti C, Barlow A, Penkman KEH, Hofreiter M, Paijmans JLA. Estimating the dwarfing rate of an extinct Sicilian elephant. Curr Biol 2021; 31:3606-3612.e7. [PMID: 34146486 DOI: 10.1016/j.cub.2021.05.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/29/2021] [Accepted: 05/17/2021] [Indexed: 11/18/2022]
Abstract
Evolution on islands, together with the often extreme phenotypic changes associated with it, has attracted much interest from evolutionary biologists. However, measuring the rate of change of phenotypic traits of extinct animals can be challenging, in part due to the incompleteness of the fossil record. Here, we use combined molecular and fossil evidence to define the minimum and maximum rate of dwarfing in an extinct Mediterranean dwarf elephant from Puntali Cave (Sicily).1 Despite the challenges associated with recovering ancient DNA from warm climates,2 we successfully retrieved a mitogenome from a sample with an estimated age between 175,500 and 50,000 years. Our results suggest that this specific Sicilian elephant lineage evolved from one of the largest terrestrial mammals that ever lived3 to an island species weighing less than 20% of its original mass with an estimated mass reduction between 0.74 and 200.95 kg and height reduction between 0.15 and 41.49 mm per generation. We show that combining ancient DNA with paleontological and geochronological evidence can constrain the timing of phenotypic changes with greater accuracy than could be achieved using any source of evidence in isolation.
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Affiliation(s)
- Sina Baleka
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany; Faculty of Life and Environmental Sciences, University of Iceland, Sæmundargata 2, 101 Reykjavik, Iceland.
| | - Victoria L Herridge
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Giulio Catalano
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Laboratory of Anthropology, Università degli Studi di Palermo, 90128 Palermo, Italy
| | - Adrian M Lister
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Marc R Dickinson
- Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - Carolina Di Patti
- Museo Geologico "G.G. Gemmellaro" - Università degli Studi di Palermo, Corso Tukory 131, 90133 Palermo, Italy
| | - Axel Barlow
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - Kirsty E H Penkman
- Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Johanna L A Paijmans
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany.
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18
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Meleshko O, Martin MD, Korneliussen TS, Schröck C, Lamkowski P, Schmutz J, Healey A, Piatkowski BT, Shaw AJ, Weston DJ, Flatberg KI, Szövényi P, Hassel K, Stenøien HK. Extensive Genome-Wide Phylogenetic Discordance Is Due to Incomplete Lineage Sorting and Not Ongoing Introgression in a Rapidly Radiated Bryophyte Genus. Mol Biol Evol 2021; 38:2750-2766. [PMID: 33681996 PMCID: PMC8233498 DOI: 10.1093/molbev/msab063] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The relative importance of introgression for diversification has long been a highly disputed topic in speciation research and remains an open question despite the great attention it has received over the past decade. Gene flow leaves traces in the genome similar to those created by incomplete lineage sorting (ILS), and identification and quantification of gene flow in the presence of ILS is challenging and requires knowledge about the true phylogenetic relationship among the species. We use whole nuclear, plastid, and organellar genomes from 12 species in the rapidly radiated, ecologically diverse, actively hybridizing genus of peatmoss (Sphagnum) to reconstruct the species phylogeny and quantify introgression using a suite of phylogenomic methods. We found extensive phylogenetic discordance among nuclear and organellar phylogenies, as well as across the nuclear genome and the nodes in the species tree, best explained by extensive ILS following the rapid radiation of the genus rather than by postspeciation introgression. Our analyses support the idea of ancient introgression among the ancestral lineages followed by ILS, whereas recent gene flow among the species is highly restricted despite widespread interspecific hybridization known in the group. Our results contribute to phylogenomic understanding of how speciation proceeds in rapidly radiated, actively hybridizing species groups, and demonstrate that employing a combination of diverse phylogenomic methods can facilitate untangling complex phylogenetic patterns created by ILS and introgression.
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Affiliation(s)
- Olena Meleshko
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | | | | | - Paul Lamkowski
- Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
| | - Jeremy Schmutz
- United States Department of Energy, Joint Genome Institute, Berkeley, CA, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Adam Healey
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | | | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Kjell Ivar Flatberg
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Kristian Hassel
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Hans K Stenøien
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
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19
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Pečnerová P, Garcia-Erill G, Liu X, Nursyifa C, Waples RK, Santander CG, Quinn L, Frandsen P, Meisner J, Stæger FF, Rasmussen MS, Brüniche-Olsen A, Hviid Friis Jørgensen C, da Fonseca RR, Siegismund HR, Albrechtsen A, Heller R, Moltke I, Hanghøj K. High genetic diversity and low differentiation reflect the ecological versatility of the African leopard. Curr Biol 2021; 31:1862-1871.e5. [PMID: 33636121 DOI: 10.1016/j.cub.2021.01.064] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/13/2020] [Accepted: 01/19/2021] [Indexed: 12/12/2022]
Abstract
Large carnivores are generally sensitive to ecosystem changes because their specialized diet and position at the top of the trophic pyramid is associated with small population sizes. Accordingly, low genetic diversity at the whole-genome level has been reported for all big cat species, including the widely distributed leopard. However, all previous whole-genome analyses of leopards are based on the Far Eastern Amur leopards that live at the extremity of the species' distribution and therefore are not necessarily representative of the whole species. We sequenced 53 whole genomes of African leopards. Strikingly, we found that the genomic diversity in the African leopard is 2- to 5-fold higher than in other big cats, including the Amur leopard, likely because of an exceptionally high effective population size maintained by the African leopard throughout the Pleistocene. Furthermore, we detected ongoing gene flow and very low population differentiation within African leopards compared with those of other big cats. We corroborated this by showing a complete absence of an otherwise ubiquitous equatorial forest barrier to gene flow. This sets the leopard apart from most other widely distributed large African mammals, including lions. These results revise our understanding of trophic sensitivity and highlight the remarkable resilience of the African leopard, likely because of its extraordinary habitat versatility and broad dietary niche.
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Affiliation(s)
- Patrícia Pečnerová
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Genís Garcia-Erill
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Xiaodong Liu
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Casia Nursyifa
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Ryan K Waples
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Cindy G Santander
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Liam Quinn
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Peter Frandsen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark; Copenhagen Zoo, Research and Conservation, Roskildevej 32, 2000 Frederiksberg, Denmark
| | - Jonas Meisner
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Frederik Filip Stæger
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Malthe Sebro Rasmussen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Anna Brüniche-Olsen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark; Department of Forestry and Natural Resources, Purdue University, 610 Purdue Mall, West Lafayette, IN 47907, USA
| | | | - Rute R da Fonseca
- Center for Macroecology, Evolution and Climate (CMEC), GLOBE Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Anders Albrechtsen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Rasmus Heller
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark.
| | - Ida Moltke
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark.
| | - Kristian Hanghøj
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark.
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20
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Westbury MV, Le Duc D, Duchêne DA, Krishnan A, Prost S, Rutschmann S, Grau JH, Dalen L, Weyrich A, Norén K, Werdelin L, Dalerum F, Schöneberg T, Hofreiter M. Ecological Specialisation and Evolutionary Reticulation in Extant Hyaenidae. Mol Biol Evol 2021; 38:3884-3897. [PMID: 34426844 PMCID: PMC8382907 DOI: 10.1093/molbev/msab055] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
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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Affiliation(s)
- M V Westbury
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, Potsdam, 14476, Germany.,Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Diana Le Duc
- Institute of Human Genetics, University Medical Center Leipzig, Leipzig, 04103, Germany.,Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - David A Duchêne
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark.,Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Arunkumar Krishnan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.,Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Berhampur, Odisha, 760010, India
| | - Stefan Prost
- LOEWE-Center for Translational Biodiversity Genomics, Senckenberg, 60325, Germany. Frankfurt.,South African National Biodiversity Institute, National Zoological Garden, Pretoria, 0184, South Africa
| | - Sereina Rutschmann
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, Potsdam, 14476, Germany
| | - Jose H Grau
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, Potsdam, 14476, Germany.,amedes Genetics, amedes Medizinische Dienstleistungen, Berlin, Germany
| | - Love Dalen
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, Stockholm, 10691, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, Stockholm, 10405, Sweden
| | - Alexandra Weyrich
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, 10315, Germany
| | - Karin Norén
- Department of Zoology, Stockholm University, Stockholm, 106 91, Sweden
| | - Lars Werdelin
- Department of Palaeobiology, Swedish Museum of Natural History, Box 50007, Stockholm, SE-10405, Sweden
| | - Fredrik Dalerum
- Department of Zoology, Stockholm University, Stockholm, 106 91, Sweden.,Research Unit of Biodiversity (UO-CSIC-PA), Mieres Campus, University of Oviedo, Mieres, Asturias, 33600, Spain.,Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, South Africa
| | - Torsten Schöneberg
- Rudolf Schönheimer Institute of Biochemistry, Molecular Biochemistry, Medical Faculty, Johannisallee 30, Leipzig, 04103, Germany
| | - Michael Hofreiter
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, Potsdam, 14476, Germany
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21
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Hu J, Westbury MV, Yuan J, Zhang Z, Chen S, Xiao B, Hou X, Ji H, Lai X, Hofreiter M, Sheng G. Ancient mitochondrial genomes from Chinese cave hyenas provide insights into the evolutionary history of the genus Crocuta. Proc Biol Sci 2021; 288:20202934. [PMID: 33499784 DOI: 10.1098/rspb.2020.2934] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Cave hyenas (genus Crocuta) are extinct bone-cracking carnivores from the family Hyaenidae and are generally split into two taxa that correspond to a European/Eurasian and an (East) Asian lineage. They are close relatives of the extant African spotted hyenas, the only extant member of the genus Crocuta. Cave hyenas inhabited a wide range across Eurasia during the Pleistocene, but became extinct at the end of the Late Pleistocene. Using genetic and genomic datasets, previous studies have proposed different scenarios about the evolutionary history of Crocuta. However, causes of the extinction of cave hyenas are widely speculative and samples from China are severely understudied. In this study, we assembled near-complete mitochondrial genomes from two cave hyenas from northeastern China dating to 20 240 and 20 253 calBP, representing the youngest directly dated fossils of Crocuta in Asia. Phylogenetic analyses suggest a monophyletic clade of these two samples within a deeply diverging mitochondrial haplogroup of Crocuta. Bayesian analyses suggest that the split of this Asian cave hyena mitochondrial lineage from their European and African relatives occurred approximately 1.85 Ma (95% CI 1.62-2.09 Ma), which is broadly concordant with the earliest Eurasian Crocuta fossil dating to approximately 2 Ma. Comparisons of mean genetic distance indicate that cave hyenas harboured higher genetic diversity than extant spotted hyenas, brown hyenas and aardwolves, but this is probably at least partially due to the fact that their mitochondrial lineages do not represent a monophyletic group, although this is also true for extant spotted hyenas. Moreover, the joint female effective population size of Crocuta (both cave hyenas and extant spotted hyenas) has sustained two declines during the Late Pleistocene. Combining this mitochondrial phylogeny, previous nuclear findings and fossil records, we discuss the possible relationship of fossil Crocuta in China and the extinction of cave hyenas.
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Affiliation(s)
- Jiaming Hu
- School of Environmental Studies, China University of Geosciences, Wuhan 430078, People's Republic of China
| | - Michael V Westbury
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Junxia Yuan
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, People's Republic of China
| | - Zhen Zhang
- Zhaoyuan Museum, Daqing, Heilongjiang 166500, People's Republic of China
| | - Shungang Chen
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, People's Republic of China
| | - Bo Xiao
- School of Environmental Studies, China University of Geosciences, Wuhan 430078, People's Republic of China
| | - Xindong Hou
- School of Environmental Studies, China University of Geosciences, Wuhan 430078, People's Republic of China
| | - Hailong Ji
- Paleontological Fossil Conservation Center, Qinggang County, Qinggang, Heilongjiang 151600, People's Republic of China
| | - Xulong Lai
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, People's Republic of China.,School of Earth Science, China University of Geosciences, Wuhan 430074, People's Republic of China
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Guilian Sheng
- School of Environmental Studies, China University of Geosciences, Wuhan 430078, People's Republic of China.,State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, People's Republic of China
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22
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Mitchell KJ, Rawlence NJ. Examining Natural History through the Lens of Palaeogenomics. Trends Ecol Evol 2021; 36:258-267. [PMID: 33455740 DOI: 10.1016/j.tree.2020.10.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/05/2020] [Accepted: 10/07/2020] [Indexed: 12/20/2022]
Abstract
The many high-resolution tools that are uniquely applicable to specimens from the Quaternary period (the past ~2.5 Ma) provide an opportunity to cross-validate data and test hypotheses based on the morphology and distribution of fossils. Among these tools is palaeogenomics - the genome-scale sequencing of genetic material from ancient specimens - that can provide direct insight into ecology and evolution, potentially improving the accuracy of inferences about past ecological communities over longer timescales. Palaeogenomics has revealed instances of over- and underestimation of extinct diversity, detected cryptic faunal migration and turnover, allowed quantification of widespread sex biases and sexual dimorphism in the fossil record, revealed past hybridisation events and hybrid individuals, and has highlighted previously unrecognised routes of zoonotic disease transfer.
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Affiliation(s)
- Kieren J Mitchell
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia; Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.
| | - Nicolas J Rawlence
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
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23
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Barnett R, Westbury MV, Sandoval-Velasco M, Vieira FG, Jeon S, Zazula G, Martin MD, Ho SYW, Mather N, Gopalakrishnan S, Ramos-Madrigal J, de Manuel M, Zepeda-Mendoza ML, Antunes A, Baez AC, De Cahsan B, Larson G, O'Brien SJ, Eizirik E, Johnson WE, Koepfli KP, Wilting A, Fickel J, Dalén L, Lorenzen ED, Marques-Bonet T, Hansen AJ, Zhang G, Bhak J, Yamaguchi N, Gilbert MTP. Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens. Curr Biol 2020; 30:5018-5025.e5. [PMID: 33065008 PMCID: PMC7762822 DOI: 10.1016/j.cub.2020.09.051] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/10/2020] [Accepted: 09/15/2020] [Indexed: 12/17/2022]
Abstract
Homotherium was a genus of large-bodied scimitar-toothed cats, morphologically distinct from any extant felid species, that went extinct at the end of the Pleistocene [1, 2, 3, 4]. They possessed large, saber-form serrated canine teeth, powerful forelimbs, a sloping back, and an enlarged optic bulb, all of which were key characteristics for predation on Pleistocene megafauna [5]. Previous mitochondrial DNA phylogenies suggested that it was a highly divergent sister lineage to all extant cat species [6, 7, 8]. However, mitochondrial phylogenies can be misled by hybridization [9], incomplete lineage sorting (ILS), or sex-biased dispersal patterns [10], which might be especially relevant for Homotherium since widespread mito-nuclear discrepancies have been uncovered in modern cats [10]. To examine the evolutionary history of Homotherium, we generated a ∼7x nuclear genome and a ∼38x exome from H. latidens using shotgun and target-capture sequencing approaches. Phylogenetic analyses reveal Homotherium as highly divergent (∼22.5 Ma) from living cat species, with no detectable signs of gene flow. Comparative genomic analyses found signatures of positive selection in several genes, including those involved in vision, cognitive function, and energy consumption, putatively consistent with diurnal activity, well-developed social behavior, and cursorial hunting [5]. Finally, we uncover relatively high levels of genetic diversity, suggesting that Homotherium may have been more abundant than the limited fossil record suggests [3, 4, 11, 12, 13, 14]. Our findings complement and extend previous inferences from both the fossil record and initial molecular studies, enhancing our understanding of the evolution and ecology of this remarkable lineage. Nuclear genome and exome analyses of extinct scimitar-toothed cat, Homotherium latidens Homotherium was a highly divergent lineage from all living cat species (∼22.5 Ma) Genetic adaptations to cursorial and diurnal hunting behaviors Relatively high levels of genetic diversity in this individual
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Affiliation(s)
- Ross Barnett
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Michael V Westbury
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark.
| | - Marcela Sandoval-Velasco
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Filipe Garrett Vieira
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Sungwon Jeon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea; Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Grant Zazula
- Yukon Palaeontology Program, Department of Tourism and Culture, Government of Yukon, PO Box 2703, Whitehorse, YT Y1A 2C6, Canada
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim NO-7491, Norway
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Niklas Mather
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark; Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, Copenhagen 1352, Denmark
| | - Jazmín Ramos-Madrigal
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark; Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, Copenhagen 1352, Denmark
| | - Marc de Manuel
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, Barcelona 08003, Spain
| | - M Lisandra Zepeda-Mendoza
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark; School of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, Porto 4450-208, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Porto 4169-007, Portugal
| | - Aldo Carmona Baez
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Binia De Cahsan
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
| | - Stephen J O'Brien
- Laboratory of Genomic Diversity, Center for Computer Technologies, ITMO University, 49 Kronverkskiy Pr., St. Petersburg 197101, Russia; Guy Harvey Oceanographic Center, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, 8000 North Ocean Drive. Ft Lauderdale, FL 33004, USA
| | - Eduardo Eizirik
- Laboratory of Genomics and Molecular Biology, Escola de Ciências da Saúde e da Vida, PUCRS, Porto Alegre, RS, Brazil; INCT Ecologia, Evolução e Conservação da Biodiversidade (INCT-EECBio), Goiânia, GO, Brazil; Instituto Pró-Carnívoros, Atibaia, SP, Brazil
| | - Warren E Johnson
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA 22630, USA; The Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, 4210 Silver Hill Rd., Suitland, MD 20746-2863, USA; Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
| | - Klaus-Peter Koepfli
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA 22630, USA
| | - Andreas Wilting
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, Berlin 10315, Germany
| | - Jörns Fickel
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, Berlin 10315, Germany; Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, Potsdam 14476, Germany
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, Stockholm SE-10691, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, Stockholm 10405, Sweden
| | - Eline D Lorenzen
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark; Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, Copenhagen 1352, Denmark
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, Barcelona 08003, Spain; CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain; Institució Catalana de Recerca i Estudis Avançats, ICREA, Barcelona 08003, Spain; Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, Cerdanyola del Vallès, Barcelona 08193, Spain
| | - Anders J Hansen
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, Copenhagen 1352, Denmark; Section for GeoGenetics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Guojie Zhang
- BGI-Shenzhen, Shenzhen 518083, China; Section for Ecology and Evolution, Department of Biology, Faculty of Science, University of Copenhagen, Universitetsparken 15, Copenhagen, Denmark; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Jong Bhak
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea; Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea; Clinomics, Inc., Ulsan 44919, Republic of Korea; Personal Genomics Institute (PGI), Genome Research Foundation (GRF), Osong 28160, Republic of Korea
| | - Nobuyuki Yamaguchi
- Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark; Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim NO-7491, Norway; Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, Copenhagen 1352, Denmark.
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24
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Palaeoproteomic analysis of Pleistocene cave hyenas from east Asia. Sci Rep 2020; 10:16674. [PMID: 33028848 PMCID: PMC7541484 DOI: 10.1038/s41598-020-73542-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/14/2020] [Indexed: 12/19/2022] Open
Abstract
The spotted hyena (Crocuta crocuta) is the only extant species of the genus Crocuta, which once occupied a much wider range during the Pliocene and Pleistocene. However, its origin and evolutionary history is somewhat contentious due to discordances between morphological, nuclear, and mitochondrial data. Due to the limited molecular data from east Asian Crocuta, also known as cave hyena, and the difficulty of extracting ancient DNA from this area, here we present proteomic analysis of cave hyenas from three locations in northern China. This marks the first proteomic data generated from cave hyenas, adding new molecular data to the east Asian populations. Phylogenetic analysis based on these protein sequences reveals two different groups of cave hyenas in east Asia, one of which could not be distinguished from modern spotted hyenas from northern Africa, tentatively the result of previously suggested gene flow between these lineages. With developments of instrumentation and analytical methods, proteomics holds promising potential for molecular phylogenetic reconstructions of ancient fauna previously thought to be unreachable using ancient DNA.
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25
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Early Pleistocene origin and extensive intra-species diversity of the extinct cave lion. Sci Rep 2020; 10:12621. [PMID: 32724178 PMCID: PMC7387438 DOI: 10.1038/s41598-020-69474-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/08/2020] [Indexed: 11/08/2022] Open
Abstract
The cave lion is an extinct felid that was widespread across the Holarctic throughout the Late Pleistocene. Its closest extant relative is the lion (Panthera leo), but the timing of the divergence between these two taxa, as well as their taxonomic ranking are contentious. In this study we analyse 31 mitochondrial genome sequences from cave lion individuals that, through a combination of 14C and genetic tip dating, are estimated to be from dates extending well into the mid-Pleistocene. We identified two deeply diverged and well-supported reciprocally monophyletic mitogenome clades in the cave lion, and an additional third distinct lineage represented by a single individual. One of these clades was restricted to Beringia while the other was prevalent across western Eurasia. These observed clade distributions are in line with previous observations that Beringian and European cave lions were morphologically distinct. The divergence dates for these lineages are estimated to be far older than those between extant lions subspecies. By combining our radiocarbon tip-dates with a split time prior that takes into account the most up-to-date fossil stem calibrations, we estimated the mitochondrial DNA divergence between cave lions and lions to be 1.85 Million ya (95% 0.52- 2.91 Mya). Taken together, these results support previous hypotheses that cave lions existed as at least two subspecies during the Pleistocene, and that lions and cave lions were distinct species.
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