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Buss DL, Atmore LM, Zicos MH, Goodall-Copestake WP, Brace S, Archer FI, Baker CS, Barnes I, Carroll EL, Hart T, Kitchener AC, Sabin R, Sremba AL, Weir CR, Jackson JA. Historical Mitogenomic Diversity and Population Structuring of Southern Hemisphere Fin Whales. Genes (Basel) 2023; 14:1038. [PMID: 37239398 PMCID: PMC10218396 DOI: 10.3390/genes14051038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
Fin whales Balaenoptera physalus were hunted unsustainably across the globe in the 19th and 20th centuries, leading to vast reductions in population size. Whaling catch records indicate the importance of the Southern Ocean for this species; approximately 730,000 fin whales were harvested during the 20th century in the Southern Hemisphere (SH) alone, 94% of which were at high latitudes. Genetic samples from contemporary whales can provide a window to past population size changes, but the challenges of sampling in remote Antarctic waters limit the availability of data. Here, we take advantage of historical samples in the form of bones and baleen available from ex-whaling stations and museums to assess the pre-whaling diversity of this once abundant species. We sequenced 27 historical mitogenomes and 50 historical mitochondrial control region sequences of fin whales to gain insight into the population structure and genetic diversity of Southern Hemisphere fin whales (SHFWs) before and after the whaling. Our data, both independently and when combined with mitogenomes from the literature, suggest SHFWs are highly diverse and may represent a single panmictic population that is genetically differentiated from Northern Hemisphere populations. These are the first historic mitogenomes available for SHFWs, providing a unique time series of genetic data for this species.
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Affiliation(s)
- Danielle L. Buss
- British Antarctic Survey, National Environment Research Council, Cambridge CB3 0ET, UK
- Department of Archaeology, University of Cambridge, Downing Street, Cambridge CB2 3DZ, UK
| | - Lane M. Atmore
- Department of Archaeology, University of Cambridge, Downing Street, Cambridge CB2 3DZ, UK
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Maria H. Zicos
- The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - William P. Goodall-Copestake
- British Antarctic Survey, National Environment Research Council, Cambridge CB3 0ET, UK
- Scottish Association for Marine Science, Oban PA37 1QA, UK
| | - Selina Brace
- The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Frederick I. Archer
- National Oceanic and Atmospheric Administration, Southwest Fisheries Science Center, La Jolla, CA 92037, USA
| | - C. Scott Baker
- Marine Mammal Institute and Department of Fisheries and Wildlife, Hatfield Marine Science Center, Oregon State University, Newport, OR 97365, USA
| | - Ian Barnes
- The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Emma L. Carroll
- Te Kura Mātauranga Koiora—School of Biological Sciences, University of Auckland Waipapa Taumata Rau, Auckland 1010, New Zealand
| | - Tom Hart
- Department of Zoology, University of Oxford, Mansfield Road, Oxford OX1 3SZ, UK
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK
- School of Geosciences, University of Edinburgh, Drummond Street, Edinburgh EH8 9XP, UK
| | - Richard Sabin
- The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Angela L. Sremba
- Marine Mammal Institute and Department of Fisheries and Wildlife, Hatfield Marine Science Center, Oregon State University, Newport, OR 97365, USA
| | - Caroline R. Weir
- Falklands Conservation, Ross Road, Stanley F1QQ 1ZZ, Falkland Islands
| | - Jennifer A. Jackson
- British Antarctic Survey, National Environment Research Council, Cambridge CB3 0ET, UK
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2
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Marsh WA, Brace S, Barnes I. Inferring biological kinship in ancient datasets: comparing the response of ancient DNA-specific software packages to low coverage data. BMC Genomics 2023; 24:111. [PMID: 36918761 PMCID: PMC10015695 DOI: 10.1186/s12864-023-09198-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 02/20/2023] [Indexed: 03/16/2023] Open
Abstract
BACKGROUND The inference of biological relations between individuals is fundamental to understanding past human societies. Caregiving, resource sharing and sexual behaviours are often mediated by biological kinship and yet the identification and interpretation of kin relationships in prehistoric human groups is difficult. In recent years, the advent of archaeogenetic techniques have offered a fresh approach, and when combined with more traditional osteological and interpretive archaeological methods, allows for improved interpretation of the burial practices, cultural behaviours, and societal stratification in ancient societies. Although archaeogenetic techniques are developing at pace, questions remain as to their accuracy, particularly when applied to the low coverage datasets that results from the sequencing of DNA derived from highly degraded ancient material. RESULTS The performance of six of the most commonly used kinship identifcation software methods was explored at a range of low and ultra low genome coverages. An asymmetrical response was observed across packages, with decreased genome coverage resulting in differences in both direction and degree of change of calculated kinship scores and thus pairwise relatedness estimates are dependant on both package used and genome coverage. Methods reliant upon genotype likelihoods methods (lcMLkin, NGSrelate and NGSremix) show a decreased level of prediction at coverage below 1x, although were consistent in the particular relationships identified at these coverages when compared to the pseudohaploid reliant methods tested (READ, the Kennett 2017 method and TKGWV2.0). The three pseudohaploid methods show predictive potential at coverages as low as 0.05x, although the accuracy of the relationships identified is questionable given the increase in the number of relationships identifIed at the low coverage (type I errors). CONCLUSION Two pseudohaploid methods (READ and Kennett 2017) show relatively consistent inference of kin relationships at low coverage (0.5x), with READ only showing a significant performance drop off at ultralow coverages (< 0.2x). More generally, our results reveal asymmetrical kinship classifications in some software packages even at high coverages, highlighting the importance of applying multiple methods to authenticate kin relationships in ancient material, along with the continuing need to develop laboratory methods that maximise data output for downstream analyses.
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Affiliation(s)
- William A Marsh
- Natural History Museum, Cromwell Road, SW7 5BD, London, England. .,BioArCh, University of York, YO10 5NG, York, England.
| | - Selina Brace
- Natural History Museum, Cromwell Road, SW7 5BD, London, England
| | - Ian Barnes
- Natural History Museum, Cromwell Road, SW7 5BD, London, England
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3
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Arce AN, Cantwell-Jones A, Tansley M, Barnes I, Brace S, Mullin VE, Notton D, Ollerton J, Eatough E, Rhodes MW, Bian X, Hogan J, Hunter T, Jackson S, Whiffin A, Blagoderov V, Broad G, Judd S, Kokkini P, Livermore L, Dixit MK, Pearse WD, Gill RJ. Signatures of increasing environmental stress in bumblebee wings over the past century: Insights from museum specimens. J Anim Ecol 2023; 92:297-309. [PMID: 35978494 PMCID: PMC10086799 DOI: 10.1111/1365-2656.13788] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 06/22/2022] [Indexed: 11/27/2022]
Abstract
Determining when animal populations have experienced stress in the past is fundamental to understanding how risk factors drive contemporary and future species' responses to environmental change. For insects, quantifying stress and associating it with environmental factors has been challenging due to a paucity of time-series data and because detectable population-level responses can show varying lag effects. One solution is to leverage historic entomological specimens to detect morphological proxies of stress experienced at the time stressors emerged, allowing us to more accurately determine population responses. Here we studied specimens of four bumblebee species, an invaluable group of insect pollinators, from five museums collected across Britain over the 20th century. We calculated the degree of fluctuating asymmetry (FA; random deviations from bilateral symmetry) between the right and left forewings as a potential proxy of developmental stress. We: (a) investigated whether baseline FA levels vary between species, and how this compares between the first and second half of the century; (b) determined the extent of FA change over the century in the four bumblebee species, and whether this followed a linear or nonlinear trend; (c) tested which annual climatic conditions correlated with increased FA in bumblebees. Species differed in their baseline FA, with FA being higher in the two species that have recently expanded their ranges in Britain. Overall, FA significantly increased over the century but followed a nonlinear trend, with the increase starting c. 1925. We found relatively warm and wet years were associated with higher FA. Collectively our findings show that FA in bumblebees increased over the 20th century and under weather conditions that will likely increase in frequency with climate change. By plotting FA trends and quantifying the contribution of annual climate conditions on past populations, we provide an important step towards improving our understanding of how environmental factors could impact future populations of wild beneficial insects.
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Affiliation(s)
- Andres N Arce
- Georgina Mace Centre for The Living Planet, Department of Life Sciences, Silwood Park, Imperial College London, Ascot, UK.,School of Engineering, Arts, Science & Technology, University of Suffolk, Ipswich, UK
| | - Aoife Cantwell-Jones
- Georgina Mace Centre for The Living Planet, Department of Life Sciences, Silwood Park, Imperial College London, Ascot, UK
| | - Michael Tansley
- Georgina Mace Centre for The Living Planet, Department of Life Sciences, Silwood Park, Imperial College London, Ascot, UK.,Department of Zoology, University of Oxford, Oxford, UK
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Victoria E Mullin
- Department of Earth Sciences, Natural History Museum, London, UK.,Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - David Notton
- Department of Earth Sciences, Natural History Museum, London, UK.,National Museum Scotland, Edinburgh, UK
| | - Jeff Ollerton
- Faculty of Arts, Science and Technology, University of Northampton, Northampton, UK
| | - Emma Eatough
- Georgina Mace Centre for The Living Planet, Department of Life Sciences, Silwood Park, Imperial College London, Ascot, UK
| | - Marcus W Rhodes
- Georgina Mace Centre for The Living Planet, Department of Life Sciences, Silwood Park, Imperial College London, Ascot, UK
| | - Xueni Bian
- Georgina Mace Centre for The Living Planet, Department of Life Sciences, Silwood Park, Imperial College London, Ascot, UK.,Department of Earth Sciences, Natural History Museum, London, UK
| | - James Hogan
- Oxford University Museum of Natural History, Oxford, UK
| | | | - Simon Jackson
- Tullie House Museum and Art Gallery Trust, Cumbria, UK.,Ipswich Museum (Colchester and Ipswich Museums), Ipswich, UK
| | | | | | - Gavin Broad
- Department of Earth Sciences, Natural History Museum, London, UK
| | | | - Phaedra Kokkini
- Department of Earth Sciences, Natural History Museum, London, UK
| | | | - Mahika K Dixit
- Georgina Mace Centre for The Living Planet, Department of Life Sciences, Silwood Park, Imperial College London, Ascot, UK
| | - William D Pearse
- Georgina Mace Centre for The Living Planet, Department of Life Sciences, Silwood Park, Imperial College London, Ascot, UK
| | - Richard J Gill
- Georgina Mace Centre for The Living Planet, Department of Life Sciences, Silwood Park, Imperial College London, Ascot, UK
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4
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Sampaio FL, Day JJ, Mendis Wickramasinghe LJ, Cyriac VP, Papadopoulou A, Brace S, Rajendran A, Simon-Nutbrown C, Flouris T, Kapli P, Ranga Vidanapathirana D, Kotharambath R, Kodandaramaiah U, Gower DJ. A near-complete species-level phylogeny of uropeltid snakes harnessing historical museum collections as a DNA source. Mol Phylogenet Evol 2023; 178:107651. [PMID: 36306995 DOI: 10.1016/j.ympev.2022.107651] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 10/09/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022]
Abstract
Uropeltidae is a clade of small fossorial snakes (ca. 64 extant species) endemic to peninsular India and Sri Lanka. Uropeltid taxonomy has been confusing, and the status of some species has not been revised for over a century. Attempts to revise uropeltid systematics and undertake evolutionary studies have been hampered by incompletely sampled and incompletely resolved phylogenies. To address this issue, we take advantage of historical museum collections, including type specimens, and apply genome-wide shotgun (GWS) sequencing, along with recent field sampling (using Sanger sequencing) to establish a near-complete multilocus species-level phylogeny (ca. 87% complete at species level). This results in a phylogeny that supports the monophyly of all genera (if Brachyophidium is considered a junior synonym of Teretrurus), and provides a firm platform for future taxonomic revision. Sri Lankan uropeltids are probably monophyletic, indicating a single colonisation event of this island from Indian ancestors. However, the position of Rhinophis goweri (endemic to Eastern Ghats, southern India) is unclear and warrants further investigation, and evidence that it may nest within the Sri Lankan radiation indicates a possible recolonisation event. DNA sequence data and morphology suggest that currently recognised uropeltid species diversity is substantially underestimated. Our study highlights the benefits of integrating museum collections in molecular genetic analyses and their role in understanding the systematics and evolutionary history of understudied organismal groups.
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Affiliation(s)
- Filipa L Sampaio
- Natural History Museum, Cromwell Road, London SW7 5BD, UK; Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK.
| | - Julia J Day
- Natural History Museum, Cromwell Road, London SW7 5BD, UK; Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | | | - Vivek P Cyriac
- IISER-TVM Centre for Research and Education in Ecology and Evolution, Indian Institute of Science Education and Research Thiruvananthapuram, Kerala 695 551, India
| | - Anna Papadopoulou
- Department of Biological Sciences, University of Cyprus, 2109 Nicosia, Cyprus
| | - Selina Brace
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Albert Rajendran
- Research Department of Zoology, St. John's College, Tirunelveli, Tamil Nadu, India
| | - Cornelia Simon-Nutbrown
- The Lyell Centre for Earth and Marine Science and Technology, Heriot-Watt University, Edinburgh EH14 4BA, UK; Royal Botanic Garden Edinburgh, Edinburgh, UK
| | - Tomas Flouris
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Paschalia Kapli
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | | | - Ramachandran Kotharambath
- Natural History Museum, Cromwell Road, London SW7 5BD, UK; Department of Zoology, Central University of Kerala, Tejaswini Hills, Kasaragod, Kerala, India
| | - Ullasa Kodandaramaiah
- IISER-TVM Centre for Research and Education in Ecology and Evolution, Indian Institute of Science Education and Research Thiruvananthapuram, Kerala 695 551, India
| | - David J Gower
- Natural History Museum, Cromwell Road, London SW7 5BD, UK; Department of Zoology, Central University of Kerala, Tejaswini Hills, Kasaragod, Kerala, India.
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5
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Charlton S, Brace S, Hajdinjak M, Kearney R, Booth T, Reade H, Tripp JA, Sayle KL, Grimm SB, Bello SM, Walker EA, Gilardet A, East P, Glocke I, Larson G, Higham T, Stringer C, Skoglund P, Barnes I, Stevens RE. Dual ancestries and ecologies of the Late Glacial Palaeolithic in Britain. Nat Ecol Evol 2022; 6:1658-1668. [PMID: 36280785 PMCID: PMC9630104 DOI: 10.1038/s41559-022-01883-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 08/16/2022] [Indexed: 11/09/2022]
Abstract
Genetic investigations of Upper Palaeolithic Europe have revealed a complex and transformative history of human population movements and ancestries, with evidence of several instances of genetic change across the European continent in the period following the Last Glacial Maximum (LGM). Concurrent with these genetic shifts, the post-LGM period is characterized by a series of significant climatic changes, population expansions and cultural diversification. Britain lies at the extreme northwest corner of post-LGM expansion and its earliest Late Glacial human occupation remains unclear. Here we present genetic data from Palaeolithic human individuals in the United Kingdom and the oldest human DNA thus far obtained from Britain or Ireland. We determine that a Late Upper Palaeolithic individual from Gough's Cave probably traced all its ancestry to Magdalenian-associated individuals closely related to those from sites such as El Mirón Cave, Spain, and Troisième Caverne in Goyet, Belgium. However, an individual from Kendrick's Cave shows no evidence of having ancestry related to the Gough’s Cave individual. Instead, the Kendrick’s Cave individual traces its ancestry to groups who expanded across Europe during the Late Glacial and are represented at sites such as Villabruna, Italy. Furthermore, the individuals differ not only in their genetic ancestry profiles but also in their mortuary practices and their diets and ecologies, as evidenced through stable isotope analyses. This finding mirrors patterns of dual genetic ancestry and admixture previously detected in Iberia but may suggest a more drastic genetic turnover in northwestern Europe than in the southwest. The authors report genetic, archaeological and stable isotopic data from two late Palaeolithic individuals in Britain, from Gough's Cave and Kendrick's Cave. The individuals differ not only in their ancestry but also their diets, ecologies and mortuary practices, revealing diverse origins and lifeways among inhabitants of late Pleistocene Britain.
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6
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Brace S, Diekmann Y, Booth T, Macleod R, Timpson A, Stephen W, Emery G, Cabot S, Thomas MG, Barnes I. Genomes from a medieval mass burial show Ashkenazi-associated hereditary diseases pre-date the 12th century. Curr Biol 2022; 32:4350-4359.e6. [PMID: 36044903 PMCID: PMC10499757 DOI: 10.1016/j.cub.2022.08.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/26/2022] [Accepted: 08/12/2022] [Indexed: 11/16/2022]
Abstract
We report genome sequence data from six individuals excavated from the base of a medieval well at a site in Norwich, UK. A revised radiocarbon analysis of the assemblage is consistent with these individuals being part of a historically attested episode of antisemitic violence on 6 February 1190 CE. We find that four of these individuals were closely related and all six have strong genetic affinities with modern Ashkenazi Jews. We identify four alleles associated with genetic disease in Ashkenazi Jewish populations and infer variation in pigmentation traits, including the presence of red hair. Simulations indicate that Ashkenazi-associated genetic disease alleles were already at appreciable frequencies, centuries earlier than previously hypothesized. These findings provide new insights into a significant historical crime, into Ashkenazi population history, and into the origins of genetic diseases associated with modern Jewish populations.
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Affiliation(s)
- Selina Brace
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Yoan Diekmann
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK; Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, 55099 Mainz, Germany
| | - Thomas Booth
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; Francis Crick Institute, London NW1 1AT, UK; UCL Genetics Institute, University College London, London, UK
| | - Ruairidh Macleod
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK; Department of Archaeology, University of Cambridge, Downing Street, Cambridge CB2 3DZ, UK
| | - Adrian Timpson
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Will Stephen
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Giles Emery
- Norvic Archaeology, 7 Foxburrow Road, Norwich NR7 8QU, UK
| | - Sophie Cabot
- Norfolk Record Office, The Archive Centre, Martineau Lane, Norwich, Norfolk NR1 2DQ, UK
| | - Mark G Thomas
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK.
| | - Ian Barnes
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK.
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7
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Adler GH, Brace S, Christenhusz MJM, Dittel JW, Hansford JP. Integrative approaches to mammalian systematics, ecomorphology and biomechanics. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Gregory H Adler
- Biology Department, University of Wisconsin - Oshkosh, 800 Algoma Boulevard, Oshkosh , WI 54901-3551 , USA
| | - Selina Brace
- Earth Sciences, Natural History Museum , Cromwell Road, London SW7 5BD , UK
| | | | - Jacob W Dittel
- Department of Biology, University of North Alabama , Box 5048, Florence, AL 35632-0001 , USA
| | - James P Hansford
- Institute of Zoology of the Zoological Society of London , Regent’s Park, London NW1 4RY , UK
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8
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Struebig MJ, Aninta SG, Beger M, Bani A, Barus H, Brace S, Davies ZG, Brauwer M, Diele K, Djakiman C, Djamaluddin R, Drinkwater R, Dumbrell A, Evans D, Fusi M, Herrera-Alsina L, Iskandar DT, Jompa J, Juliandi B, Lancaster LT, Limmon G, Lo MGY, Lupiyaningdyah P, McCannon M, Meijaard E, Mitchell SL, Mumbunan S, O'Connell D, Osborne OG, Papadopulos AST, Rahajoe JS, Rossiter SJ, Rustiami H, Salzmann U, Sudiana IM, Sukara E, Tasirin JS, Tjoa A, Travis JMJ, Trethowan L, Trianto A, Utteridge T, Voigt M, Winarni N, Zakaria Z, Edwards DP, Frantz L, Supriatna J. Safeguarding Imperiled Biodiversity and Evolutionary Processes in the Wallacea Center of Endemism. Bioscience 2022; 72:1118-1130. [PMID: 36325105 PMCID: PMC9618277 DOI: 10.1093/biosci/biac085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Wallacea-the meeting point between the Asian and Australian fauna-is one of the world's largest centers of endemism. Twenty-three million years of complex geological history have given rise to a living laboratory for the study of evolution and biodiversity, highly vulnerable to anthropogenic pressures. In the present article, we review the historic and contemporary processes shaping Wallacea's biodiversity and explore ways to conserve its unique ecosystems. Although remoteness has spared many Wallacean islands from the severe overexploitation that characterizes many tropical regions, industrial-scale expansion of agriculture, mining, aquaculture and fisheries is damaging terrestrial and aquatic ecosystems, denuding endemics from communities, and threatening a long-term legacy of impoverished human populations. An impending biodiversity catastrophe demands collaborative actions to improve community-based management, minimize environmental impacts, monitor threatened species, and reduce wildlife trade. Securing a positive future for Wallacea's imperiled ecosystems requires a fundamental shift away from managing marine and terrestrial realms independently.
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9
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Gretzinger J, Sayer D, Justeau P, Altena E, Pala M, Dulias K, Edwards CJ, Jodoin S, Lacher L, Sabin S, Vågene ÅJ, Haak W, Ebenesersdóttir SS, Moore KHS, Radzeviciute R, Schmidt K, Brace S, Bager MA, Patterson N, Papac L, Broomandkhoshbacht N, Callan K, Harney É, Iliev L, Lawson AM, Michel M, Stewardson K, Zalzala F, Rohland N, Kappelhoff-Beckmann S, Both F, Winger D, Neumann D, Saalow L, Krabath S, Beckett S, Van Twest M, Faulkner N, Read C, Barton T, Caruth J, Hines J, Krause-Kyora B, Warnke U, Schuenemann VJ, Barnes I, Dahlström H, Clausen JJ, Richardson A, Popescu E, Dodwell N, Ladd S, Phillips T, Mortimer R, Sayer F, Swales D, Stewart A, Powlesland D, Kenyon R, Ladle L, Peek C, Grefen-Peters S, Ponce P, Daniels R, Spall C, Woolcock J, Jones AM, Roberts AV, Symmons R, Rawden AC, Cooper A, Bos KI, Booth T, Schroeder H, Thomas MG, Helgason A, Richards MB, Reich D, Krause J, Schiffels S. The Anglo-Saxon migration and the formation of the early English gene pool. Nature 2022; 610:112-119. [PMID: 36131019 PMCID: PMC9534755 DOI: 10.1038/s41586-022-05247-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 08/17/2022] [Indexed: 11/09/2022]
Abstract
The history of the British Isles and Ireland is characterized by multiple periods of major cultural change, including the influential transformation after the end of Roman rule, which precipitated shifts in language, settlement patterns and material culture1. The extent to which migration from continental Europe mediated these transitions is a matter of long-standing debate2-4. Here we study genome-wide ancient DNA from 460 medieval northwestern Europeans-including 278 individuals from England-alongside archaeological data, to infer contemporary population dynamics. We identify a substantial increase of continental northern European ancestry in early medieval England, which is closely related to the early medieval and present-day inhabitants of Germany and Denmark, implying large-scale substantial migration across the North Sea into Britain during the Early Middle Ages. As a result, the individuals who we analysed from eastern England derived up to 76% of their ancestry from the continental North Sea zone, albeit with substantial regional variation and heterogeneity within sites. We show that women with immigrant ancestry were more often furnished with grave goods than women with local ancestry, whereas men with weapons were as likely not to be of immigrant ancestry. A comparison with present-day Britain indicates that subsequent demographic events reduced the fraction of continental northern European ancestry while introducing further ancestry components into the English gene pool, including substantial southwestern European ancestry most closely related to that seen in Iron Age France5,6.
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Affiliation(s)
- Joscha Gretzinger
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | | | | | - Maria Pala
- University of Huddersfield, Huddersfield, UK
| | - Katharina Dulias
- University of Huddersfield, Huddersfield, UK
- Institute of Geosystems and Bioindication, Technische Universität Braunschweig, Braunschweig, Germany
| | - Ceiridwen J Edwards
- University of Huddersfield, Huddersfield, UK
- University of Oxford, Oxford, UK
| | | | - Laura Lacher
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Susanna Sabin
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
| | - Åshild J Vågene
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Wolfgang Haak
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - S Sunna Ebenesersdóttir
- deCODE Genetics/AMGEN Inc., Reykjavík, Iceland
- Department of Anthropology, School of Social Sciences, University of Iceland, Reykjavík, Iceland
| | | | - Rita Radzeviciute
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Martina Abenhus Bager
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nick Patterson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Luka Papac
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Kimberly Callan
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Éadaoin Harney
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Lora Iliev
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Megan Michel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Frank Both
- Landesmuseum Natur und Mensch, Oldenburg, Germany
| | | | | | - Lars Saalow
- Landesamt für Kultur und Denkmalpflege Mecklenburg-Vorpommern, Schwerin, Germany
| | - Stefan Krabath
- Institute for Historical Coastal Research (NIhK), Wilhelmshaven, Germany
| | - Sophie Beckett
- Sedgeford Historical and Archaeological Research Project, Sedgeford, UK
- Cranfield Forensic Institute, Cranfield Defence and Security, Cranfield University, Cranfield, UK
- Melbourne Dental School, University of Melbourne, Melbourne, Victoria, Australia
| | - Melanie Van Twest
- Sedgeford Historical and Archaeological Research Project, Sedgeford, UK
| | - Neil Faulkner
- Sedgeford Historical and Archaeological Research Project, Sedgeford, UK
| | - Chris Read
- The Atlantic Technological University, Sligo, Ireland
| | | | | | | | | | | | - Verena J Schuenemann
- University of Zurich, Zurich, Switzerland
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London, UK
| | | | | | - Andrew Richardson
- Canterbury Archaeological Trust, Canterbury, UK
- Isle Heritage CIC, Sandgate, UK
| | | | | | | | | | - Richard Mortimer
- Oxford Archaeology East, Cambridge, UK
- Cotswold Archaeology, Needham Market, UK
| | - Faye Sayer
- University of Birmingham, Birmingham, UK
| | - Diana Swales
- Centre for Anatomy and Human Identification (CAHID), University of Dundee, Dundee, UK
| | | | | | - Robert Kenyon
- East Dorset Antiquarian Society (EDAS), West Bexington, UK
| | - Lilian Ladle
- Department of Archaeology and Anthropology, Bournemouth University, Poole, UK
| | - Christina Peek
- Institute for Historical Coastal Research (NIhK), Wilhelmshaven, Germany
| | | | | | | | | | | | | | | | | | - Anooshka C Rawden
- Fishbourne Roman Palace, Fishbourne, UK
- South Downs Centre, Midhurst, UK
| | - Alan Cooper
- BlueSkyGenetics, Adelaide, South Australia, Australia
| | - Kirsten I Bos
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Hannes Schroeder
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Agnar Helgason
- deCODE Genetics/AMGEN Inc., Reykjavík, Iceland
- Department of Anthropology, School of Social Sciences, University of Iceland, Reykjavík, Iceland
| | | | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Johannes Krause
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Stephan Schiffels
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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10
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Mullin VE, Stephen W, Arce AN, Nash W, Raine C, Notton DG, Whiffin A, Blagderov V, Gharbi K, Hogan J, Hunter T, Irish N, Jackson S, Judd S, Watkins C, Haerty W, Ollerton J, Brace S, Gill RJ, Barnes I. First large‐scale quantification study of DNA preservation in insects from natural history collections using genome‐wide sequencing. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Victoria E. Mullin
- Department of Earth Sciences The Natural History Museum London UK
- Smurfit Institute of Genetics Trinity College Dublin Dublin Ireland
| | - William Stephen
- Department of Earth Sciences The Natural History Museum London UK
| | - Andres N. Arce
- Georgina Mace Centre for The Living Planet Department of Life Sciences, Silwood Park, Imperial College London Berks UK
- School of Engineering, Arts, Science & Technology University of Suffolk Ipswich UK
| | - Will Nash
- The Earlham Institute Norwich Research Park, Colney Lane Norwich UK
| | - Calum Raine
- The Earlham Institute Norwich Research Park, Colney Lane Norwich UK
| | | | | | | | - Karim Gharbi
- The Earlham Institute Norwich Research Park, Colney Lane Norwich UK
| | - James Hogan
- Oxford University Museum of Natural History Oxford UK
| | | | - Naomi Irish
- The Earlham Institute Norwich Research Park, Colney Lane Norwich UK
| | - Simon Jackson
- Tullie House Museum and Art Gallery Trust Carlisle UK
- Ipswich Museum (Colchester and Ipswich Museums) Ipswich UK
| | | | - Chris Watkins
- The Earlham Institute Norwich Research Park, Colney Lane Norwich UK
| | - Wilfried Haerty
- The Earlham Institute Norwich Research Park, Colney Lane Norwich UK
| | - Jeff Ollerton
- Faculty of Arts, Science and Technology University of Northampton Northampton UK
| | - Selina Brace
- Department of Earth Sciences The Natural History Museum London UK
| | - Richard J. Gill
- Georgina Mace Centre for The Living Planet Department of Life Sciences, Silwood Park, Imperial College London Berks UK
| | - Ian Barnes
- Department of Earth Sciences The Natural History Museum London UK
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11
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Bergström A, Stanton DWG, Taron UH, Frantz L, Sinding MHS, Ersmark E, Pfrengle S, Cassatt-Johnstone M, Lebrasseur O, Girdland-Flink L, Fernandes DM, Ollivier M, Speidel L, Gopalakrishnan S, Westbury MV, Ramos-Madrigal J, Feuerborn TR, Reiter E, Gretzinger J, Münzel SC, Swali P, Conard NJ, Carøe C, Haile J, Linderholm A, Androsov S, Barnes I, Baumann C, Benecke N, Bocherens H, Brace S, Carden RF, Drucker DG, Fedorov S, Gasparik M, Germonpré M, Grigoriev S, Groves P, Hertwig ST, Ivanova VV, Janssens L, Jennings RP, Kasparov AK, Kirillova IV, Kurmaniyazov I, Kuzmin YV, Kosintsev PA, Lázničková-Galetová M, Leduc C, Nikolskiy P, Nussbaumer M, O'Drisceoil C, Orlando L, Outram A, Pavlova EY, Perri AR, Pilot M, Pitulko VV, Plotnikov VV, Protopopov AV, Rehazek A, Sablin M, Seguin-Orlando A, Storå J, Verjux C, Zaibert VF, Zazula G, Crombé P, Hansen AJ, Willerslev E, Leonard JA, Götherström A, Pinhasi R, Schuenemann VJ, Hofreiter M, Gilbert MTP, Shapiro B, Larson G, Krause J, Dalén L, Skoglund P. Grey wolf genomic history reveals a dual ancestry of dogs. Nature 2022; 607:313-320. [PMID: 35768506 PMCID: PMC9279150 DOI: 10.1038/s41586-022-04824-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 04/28/2022] [Indexed: 01/01/2023]
Abstract
The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived1–8. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000–30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located. DNA from ancient wolves spanning 100,000 years sheds light on wolves’ evolutionary history and the genomic origin of dogs.
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Affiliation(s)
- Anders Bergström
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK.
| | - David W G Stanton
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden.,School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Ulrike H Taron
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Laurent Frantz
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.,Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
| | - Mikkel-Holger S Sinding
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland.,The Qimmeq Project, University of Greenland, Nuuk, Greenland.,Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Erik Ersmark
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Saskia Pfrengle
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.,Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Molly Cassatt-Johnstone
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Ophélie Lebrasseur
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Linus Girdland-Flink
- Department of Archaeology, School of Geosciences, University of Aberdeen, Aberdeen, UK.,School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | - Daniel M Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.,CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Morgane Ollivier
- University of Rennes, CNRS, ECOBIO (Ecosystèmes, biodiversité, évolution)-UMR 6553, Rennes, France
| | - Leo Speidel
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK.,Genetics Institute, University College London, London, UK
| | | | - Michael V Westbury
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.,The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Tatiana R Feuerborn
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,The Qimmeq Project, University of Greenland, Nuuk, Greenland.,Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Ella Reiter
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Joscha Gretzinger
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.,Max Planck Institute for the Science of Human History, Jena, Germany
| | - Susanne C Münzel
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Pooja Swali
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Nicholas J Conard
- Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Tübingen, Germany.,Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Christian Carøe
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - James Haile
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Anna Linderholm
- Centre for Palaeogenetics, Stockholm, Sweden.,The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.,Texas A&M University, College Station, TX, USA.,Department of Geological Sciences, Stockholm University, Stockholm, Sweden
| | | | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Chris Baumann
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany.,Department of Geosciences and Geography, Faculty of Science, University of Helsinki, Helsinki, Finland
| | | | - Hervé Bocherens
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany.,Biogeology, Department of Geosciences, University of Tübingen, Tübingen, Germany
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Ruth F Carden
- School of Archaeology, University College Dublin, Dublin, Ireland
| | - Dorothée G Drucker
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Sergey Fedorov
- North-Eastern Federal University, Yakutsk, Russian Federation
| | | | | | | | - Pam Groves
- University of Alaska, Fairbanks, AK, USA
| | - Stefan T Hertwig
- Naturhistorisches Museum Bern, Bern, Switzerland.,Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | | | | | - Richard P Jennings
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | - Aleksei K Kasparov
- Institute for the History of Material Culture, Russian Academy of Sciences, St Petersburg, Russian Federation
| | - Irina V Kirillova
- Ice Age Museum, Shidlovskiy National Alliance 'Ice Age', Moscow, Russian Federation
| | - Islam Kurmaniyazov
- Department of Archaeology, Ethnology and Museology, Al-Farabi Kazakh State University, Almaty, Kazakhstan
| | - Yaroslav V Kuzmin
- Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | | | | | | | - Pavel Nikolskiy
- Geological Institute, Russian Academy of Sciences, Moscow, Russian Federation
| | | | - Cóilín O'Drisceoil
- National Monuments Service, Department of Housing, Local Government and Heritage, Dublin, Ireland
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse UMR 5288, CNRS, Faculté de Médecine Purpan, Université Paul Sabatier, Toulouse, France
| | - Alan Outram
- Department of Archaeology, University of Exeter, Exeter, UK
| | - Elena Y Pavlova
- Arctic & Antarctic Research Institute, St Petersburg, Russian Federation
| | - Angela R Perri
- PaleoWest, Henderson, NV, USA.,Department of Anthropology, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Małgorzata Pilot
- Museum & Institute of Zoology, Polish Academy of Sciences, Gdańsk, Poland
| | - Vladimir V Pitulko
- Institute for the History of Material Culture, Russian Academy of Sciences, St Petersburg, Russian Federation
| | | | | | | | - Mikhail Sablin
- Zoological Institute of the Russian Academy of Sciences, St. Petersburg, Russian Federation
| | - Andaine Seguin-Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse UMR 5288, CNRS, Faculté de Médecine Purpan, Université Paul Sabatier, Toulouse, France
| | - Jan Storå
- Stockholm University, Stockholm, Sweden
| | | | - Victor F Zaibert
- Institute of Archaeology and Steppe Civilizations, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Grant Zazula
- Yukon Palaeontology Program, Whitehorse, Yukon Territories, Canada.,Collections and Research, Canadian Museum of Nature, Ottawa, Ontario, Canada
| | | | - Anders J Hansen
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Eske Willerslev
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Zoology, University of Cambridge, Cambridge, UK
| | | | - Anders Götherström
- Centre for Palaeogenetics, Stockholm, Sweden.,Stockholm University, Stockholm, Sweden
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.,Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
| | - Verena J Schuenemann
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.,Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland.,Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - M Thomas P Gilbert
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,University Museum, NTNU, Trondheim, Norway
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA.,Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Greger Larson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Johannes Krause
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Pontus Skoglund
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK.
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12
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Woods R, Barnes I, Brace S, Turvey ST. Ancient DNA Suggests Single Colonization and Within-Archipelago Diversification of Caribbean Caviomorph Rodents. Mol Biol Evol 2021; 38:84-95. [PMID: 33035304 PMCID: PMC7783164 DOI: 10.1093/molbev/msaa189] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Reconstructing the evolutionary history of island biotas is complicated by unusual morphological evolution in insular environments. However, past human-caused extinctions limit the use of molecular analyses to determine origins and affinities of enigmatic island taxa. The Caribbean formerly contained a morphologically diverse assemblage of caviomorph rodents (33 species in 19 genera), ranging from ∼0.1 to 200 kg and traditionally classified into three higher-order taxa (Capromyidae/Capromyinae, Heteropsomyinae, and Heptaxodontidae). Few species survive today, and the evolutionary affinities of living and extinct Caribbean caviomorphs to each other and to mainland taxa are unclear: Are they monophyletic, polyphyletic, or paraphyletic? We use ancient DNA techniques to present the first genetic data for extinct heteropsomyines and heptaxodontids, as well as for several extinct capromyids, and demonstrate through analysis of mitogenomic and nuclear data sets that all sampled Caribbean caviomorphs represent a well-supported monophyletic group. The remarkable morphological and ecological variation observed across living and extinct caviomorphs from Cuba, Hispaniola, Jamaica, Puerto Rico, and other islands was generated through within-archipelago evolutionary radiation following a single Early Miocene overwater colonization. This evolutionary pattern contrasts with the origination of diversity in many other Caribbean groups. All living and extinct Caribbean caviomorphs comprise a single biologically remarkable subfamily (Capromyinae) within the morphologically conservative living Neotropical family Echimyidae. Caribbean caviomorphs represent an important new example of insular mammalian adaptive radiation, where taxa retaining “ancestral-type” characteristics coexisted alongside taxa occupying novel island niches. Diversification was associated with the greatest insular body mass increase recorded in rodents and possibly the greatest for any mammal lineage.
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Affiliation(s)
- Roseina Woods
- School of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom.,Department of Earth Sciences, Natural History Museum, London, United Kingdom
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London, United Kingdom
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London, United Kingdom
| | - Samuel T Turvey
- Institute of Zoology, Zoological Society of London, London, United Kingdom
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13
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Rey-Iglesia A, Lister AM, Campos PF, Brace S, Mattiangeli V, Daly KG, Teasdale MD, Bradley DG, Barnes I, Hansen AJ. Exploring the phylogeography and population dynamics of the giant deer ( Megaloceros giganteus) using Late Quaternary mitogenomes. Proc Biol Sci 2021; 288:20201864. [PMID: 33977786 DOI: 10.1098/rspb.2020.1864] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Late Quaternary climatic fluctuations in the Northern Hemisphere had drastic effects on large mammal species, leading to the extinction of a substantial number of them. The giant deer (Megaloceros giganteus) was one of the species that became extinct in the Holocene, around 7660 calendar years before present. In the Late Pleistocene, the species ranged from western Europe to central Asia. However, during the Holocene, its range contracted to eastern Europe and western Siberia, where the last populations of the species occurred. Here, we generated 35 Late Pleistocene and Holocene giant deer mitogenomes to explore the genetics of the demise of this iconic species. Bayesian phylogenetic analyses of the mitogenomes suggested five main clades for the species: three pre-Last Glacial Maximum clades that did not appear in the post-Last Glacial Maximum genetic pool, and two clades that showed continuity into the Holocene. Our study also identified a decrease in genetic diversity starting in Marine Isotope Stage 3 and accelerating during the Last Glacial Maximum. This reduction in genetic diversity during the Last Glacial Maximum, coupled with a major contraction of fossil occurrences, suggests that climate was a major driver in the dynamics of the giant deer.
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Affiliation(s)
- Alba Rey-Iglesia
- Centre for Geogenetics, Natural History Museum Denmark, University of Copenhagen, Østervoldgade 5-7, 1350 Copenhagen, Denmark
| | - Adrian M Lister
- Earth Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Paula F Campos
- Centre for Geogenetics, Natural History Museum Denmark, University of Copenhagen, Østervoldgade 5-7, 1350 Copenhagen, Denmark.,CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, 4450-208 Matosinhos, Portugal
| | - Selina Brace
- Earth Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Valeria Mattiangeli
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin Dublin 2, Ireland
| | - Kevin G Daly
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin Dublin 2, Ireland
| | - Matthew D Teasdale
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin Dublin 2, Ireland.,McDonald Institute for Archaeological Research, Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin Dublin 2, Ireland
| | - Ian Barnes
- Earth Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Anders J Hansen
- Centre for Geogenetics, Natural History Museum Denmark, University of Copenhagen, Østervoldgade 5-7, 1350 Copenhagen, Denmark
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14
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von Seth J, Dussex N, Díez-Del-Molino D, van der Valk T, Kutschera VE, Kierczak M, Steiner CC, Liu S, Gilbert MTP, Sinding MHS, Prost S, Guschanski K, Nathan SKSS, Brace S, Chan YL, Wheat CW, Skoglund P, Ryder OA, Goossens B, Götherström A, Dalén L. Genomic insights into the conservation status of the world's last remaining Sumatran rhinoceros populations. Nat Commun 2021; 12:2393. [PMID: 33896938 PMCID: PMC8071806 DOI: 10.1038/s41467-021-22386-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 03/01/2021] [Indexed: 02/02/2023] Open
Abstract
Small populations are often exposed to high inbreeding and mutational load that can increase the risk of extinction. The Sumatran rhinoceros was widespread in Southeast Asia, but is now restricted to small and isolated populations on Sumatra and Borneo, and most likely extinct on the Malay Peninsula. Here, we analyse 5 historical and 16 modern genomes from these populations to investigate the genomic consequences of the recent decline, such as increased inbreeding and mutational load. We find that the Malay Peninsula population experienced increased inbreeding shortly before extirpation, which possibly was accompanied by purging. The populations on Sumatra and Borneo instead show low inbreeding, but high mutational load. The currently small population sizes may thus in the near future lead to inbreeding depression. Moreover, we find little evidence for differences in local adaptation among populations, suggesting that future inbreeding depression could potentially be mitigated by assisted gene flow among populations.
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Affiliation(s)
- Johanna von Seth
- Centre for Palaeogenetics, Stockholm, Sweden.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
- Department of Zoology, Stockholm University, Stockholm, Sweden.
| | - Nicolas Dussex
- Centre for Palaeogenetics, Stockholm, Sweden.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
- Department of Zoology, Stockholm University, Stockholm, Sweden.
| | - David Díez-Del-Molino
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Tom van der Valk
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
| | - Verena E Kutschera
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Marcin Kierczak
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Cynthia C Steiner
- San Diego Zoo Wildlife Alliance, Beckman Center for Conservation Research, Escondido, CA, USA
| | - Shanlin Liu
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Norwegian University of Science and Technology, University Museum, Trondheim, Norway
| | - Mikkel-Holger S Sinding
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Stefan Prost
- LOEWE-Centre for Translational Biodiversity Genomics, Senckenberg, Frankfurt, Germany
- South African National Biodiversity Institute, National Zoological Garden, Pretoria, South Africa
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Yvonne L Chan
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | | | | | - Oliver A Ryder
- San Diego Zoo Wildlife Alliance, Beckman Center for Conservation Research, Escondido, CA, USA
| | - Benoit Goossens
- Sabah Wildlife Department, Kota Kinabalu, Sabah, Malaysia
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff, UK
- Sustainable Places Research Institute, Cardiff University, Cardiff, UK
- Danau Girang Field Centre, c/o Sabah Wildlife Department, Kota Kinabalu, Sabah, Malaysia
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm, Sweden.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
- Department of Zoology, Stockholm University, Stockholm, Sweden.
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15
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Perri AR, Mitchell KJ, Mouton A, Álvarez-Carretero S, Hulme-Beaman A, Haile J, Jamieson A, Meachen J, Lin AT, Schubert BW, Ameen C, Antipina EE, Bover P, Brace S, Carmagnini A, Carøe C, Samaniego Castruita JA, Chatters JC, Dobney K, Dos Reis M, Evin A, Gaubert P, Gopalakrishnan S, Gower G, Heiniger H, Helgen KM, Kapp J, Kosintsev PA, Linderholm A, Ozga AT, Presslee S, Salis AT, Saremi NF, Shew C, Skerry K, Taranenko DE, Thompson M, Sablin MV, Kuzmin YV, Collins MJ, Sinding MHS, Gilbert MTP, Stone AC, Shapiro B, Van Valkenburgh B, Wayne RK, Larson G, Cooper A, Frantz LAF. Dire wolves were the last of an ancient New World canid lineage. Nature 2021; 591:87-91. [PMID: 33442059 DOI: 10.1038/s41586-020-03082-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 11/12/2020] [Indexed: 11/09/2022]
Abstract
Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America1, yet relatively little is known about their evolution or extinction. Here, to reconstruct the evolutionary history of dire wolves, we sequenced five genomes from sub-fossil remains dating from 13,000 to more than 50,000 years ago. Our results indicate that although they were similar morphologically to the extant grey wolf, dire wolves were a highly divergent lineage that split from living canids around 5.7 million years ago. In contrast to numerous examples of hybridization across Canidae2,3, there is no evidence for gene flow between dire wolves and either North American grey wolves or coyotes. This suggests that dire wolves evolved in isolation from the Pleistocene ancestors of these species. Our results also support an early New World origin of dire wolves, while the ancestors of grey wolves, coyotes and dholes evolved in Eurasia and colonized North America only relatively recently.
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Affiliation(s)
- Angela R Perri
- Department of Archaeology, Durham University, Durham, UK.
| | - Kieren J Mitchell
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.
| | - Alice Mouton
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | | | - Ardern Hulme-Beaman
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK.,School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK
| | - James Haile
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, Oxford, UK
| | - Alexandra Jamieson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, Oxford, UK
| | - Julie Meachen
- Department of Anatomy, Des Moines University, Des Moines, IA, USA
| | - Audrey T Lin
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, Oxford, UK.,Department of Zoology, University of Oxford, Oxford, UK.,Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Blaine W Schubert
- Center of Excellence in Paleontology & Department of Geosciences, East Tennessee State University, Johnson City, TN, USA
| | - Carly Ameen
- Department of Archaeology, University of Exeter, Exeter, UK
| | | | - Pere Bover
- ARAID Foundation, Instituto Universitario de Investigación en Ciencias Ambientales (IUCA) - Aragosaurus Group, Universidad de Zaragoza, Zaragoza, Spain
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Alberto Carmagnini
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Christian Carøe
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Keith Dobney
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK.,Department of Archaeology, University of Sydney, Sydney, New South Wales, Australia.,Department of Archaeology, University of Aberdeen, Aberdeen, UK.,Department of Archaeology, Simon Fraser University, Burnaby, Canada
| | - Mario Dos Reis
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Allowen Evin
- Institut des Sciences de l'Evolution - Montpellier, CNRS, Université de Montpellier, IRD, EPHE, Montpellier, France
| | - Philippe Gaubert
- Laboratoire Evolution & Diversité Biologique, UPS/CNRS/IRD, Université Paul Sabatier, Toulouse, France
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Graham Gower
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Holly Heiniger
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Kristofer M Helgen
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Josh Kapp
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Pavel A Kosintsev
- Institute of Plant and Animal Ecology, Urals Branch of the Russian Academy of Sciences, Yekaterinburg, Russia.,Ural Federal University, Yekaterinburg, Russia
| | - Anna Linderholm
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, Oxford, UK.,Department of Anthropology, Texas A&M University, College Station, TX, USA
| | - Andrew T Ozga
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.,School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Halmos College of Arts and Sciences, Nova Southeastern University, Fort Lauderdale, FL, USA
| | | | - Alexander T Salis
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Nedda F Saremi
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Colin Shew
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Katherine Skerry
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Dmitry E Taranenko
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Mary Thompson
- Idaho Museum of Natural History, Idaho State University, Pocatello, ID, USA
| | - Mikhail V Sablin
- Zoological Institute of the Russian Academy of Sciences, St Petersburg, Russia
| | - Yaroslav V Kuzmin
- Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Tomsk State University, Tomsk, Russia
| | - Matthew J Collins
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
| | - Mikkel-Holger S Sinding
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Greenland Institute of Natural Resources, Nuuk, Greenland
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,NTNU University Museum, Trondheim, Norway
| | - Anne C Stone
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.,School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Institute of Human Origins, Arizona State University, Tempe, AZ, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Blaire Van Valkenburgh
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Greger Larson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, Oxford, UK
| | - Alan Cooper
- South Australian Museum, Adelaide, South Australia, Australia
| | - Laurent A F Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK. .,Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany.
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16
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Woods R, Turvey ST, Brace S, McCabe CV, Dalén L, Rayfield EJ, Brown MJF, Barnes I. Rapid size change associated with intra-island evolutionary radiation in extinct Caribbean "island-shrews". BMC Evol Biol 2020; 20:106. [PMID: 32811443 PMCID: PMC7437022 DOI: 10.1186/s12862-020-01668-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 08/04/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Caribbean offers a unique opportunity to study evolutionary dynamics in insular mammals. However, the recent extinction of most Caribbean non-volant mammals has obstructed evolutionary studies, and poor DNA preservation associated with tropical environments means that very few ancient DNA sequences are available for extinct vertebrates known from the region's Holocene subfossil record. The endemic Caribbean eulipotyphlan family Nesophontidae ("island-shrews") became extinct ~ 500 years ago, and the taxonomic validity of many Nesophontes species and their wider evolutionary dynamics remain unclear. Here we use both morphometric and palaeogenomic methods to clarify the status and evolutionary history of Nesophontes species from Hispaniola, the second-largest Caribbean island. RESULTS Principal component analysis of 65 Nesophontes mandibles from late Quaternary fossil sites across Hispaniola identified three non-overlapping morphometric clusters, providing statistical support for the existence of three size-differentiated Hispaniolan Nesophontes species. We were also able to extract and sequence ancient DNA from a ~ 750-year-old specimen of Nesophontes zamicrus, the smallest non-volant Caribbean mammal, including a whole-mitochondrial genome and partial nuclear genes. Nesophontes paramicrus (39-47 g) and N. zamicrus (~ 10 g) diverged recently during the Middle Pleistocene (mean estimated divergence = 0.699 Ma), comparable to the youngest species splits in Eulipotyphla and other mammal groups. Pairwise genetic distance values for N. paramicrus and N. zamicrus based on mitochondrial and nuclear genes are low, but fall within the range of comparative pairwise data for extant eulipotyphlan species-pairs. CONCLUSIONS Our combined morphometric and palaeogenomic analyses provide evidence for multiple co-occurring species and rapid body size evolution in Hispaniolan Nesophontes, in contrast to patterns of genetic and morphometric differentiation seen in Hispaniola's extant non-volant land mammals. Different components of Hispaniola's mammal fauna have therefore exhibited drastically different rates of morphological evolution. Morphological evolution in Nesophontes is also rapid compared to patterns across the Eulipotyphla, and our study provides an important new example of rapid body size change in a small-bodied insular vertebrate lineage. The Caribbean was a hotspot for evolutionary diversification as well as preserving ancient biodiversity, and studying the surviving representatives of its mammal fauna is insufficient to reveal the evolutionary patterns and processes that generated regional diversity.
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Affiliation(s)
- Roseina Woods
- Department of Earth Sciences, Natural History Museum, London, SW7 5BD, UK
- Department of Biological Sciences, Royal Holloway University of London, Egham, TW20 0EX, UK
| | - Samuel T Turvey
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK.
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London, SW7 5BD, UK
| | - Christopher V McCabe
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
- School of Earth Sciences, University of Bristol, Bristol, BS8 1RL, UK
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405, Stockholm, Sweden
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-106 91, Stockholm, Sweden
| | - Emily J Rayfield
- School of Earth Sciences, University of Bristol, Bristol, BS8 1RL, UK
| | - Mark J F Brown
- Department of Biological Sciences, Royal Holloway University of London, Egham, TW20 0EX, UK
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London, SW7 5BD, UK
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17
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Scott MF, Botigué LR, Brace S, Stevens CJ, Mullin VE, Stevenson A, Thomas MG, Fuller DQ, Mott R. A 3,000-year-old Egyptian emmer wheat genome reveals dispersal and domestication history. Nat Plants 2019; 5:1120-1128. [PMID: 31685951 PMCID: PMC6858886 DOI: 10.1038/s41477-019-0534-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 09/22/2019] [Indexed: 05/05/2023]
Abstract
Tetraploid emmer wheat (Triticum turgidum ssp. dicoccon) is a progenitor of the world's most widely grown crop, hexaploid bread wheat (Triticum aestivum), as well as the direct ancestor of tetraploid durum wheat (T. turgidum subsp. turgidum). Emmer was one of the first cereals to be domesticated in the old world; it was cultivated from around 9700 BC in the Levant1,2 and subsequently in south-western Asia, northern Africa and Europe with the spread of Neolithic agriculture3,4. Here, we report a whole-genome sequence from a museum specimen of Egyptian emmer wheat chaff, 14C dated to the New Kingdom, 1130-1000 BC. Its genome shares haplotypes with modern domesticated emmer at loci that are associated with shattering, seed size and germination, as well as within other putative domestication loci, suggesting that these traits share a common origin before the introduction of emmer to Egypt. Its genome is otherwise unusual, carrying haplotypes that are absent from modern emmer. Genetic similarity with modern Arabian and Indian emmer landraces connects ancient Egyptian emmer with early south-eastern dispersals, whereas inferred gene flow with wild emmer from the Southern Levant signals a later connection. Our results show the importance of museum collections as sources of genetic data to uncover the history and diversity of ancient cereals.
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Affiliation(s)
- Michael F Scott
- Genetics Institute, Research Department of Genetics, Evolution and Environment, University College London, London, UK.
| | - Laura R Botigué
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Chris J Stevens
- Institute of Archaeology, University College London, London, UK
| | | | - Alice Stevenson
- Institute of Archaeology, University College London, London, UK
| | - Mark G Thomas
- Genetics Institute, Research Department of Genetics, Evolution and Environment, University College London, London, UK
- Research Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Dorian Q Fuller
- Institute of Archaeology, University College London, London, UK
| | - Richard Mott
- Genetics Institute, Research Department of Genetics, Evolution and Environment, University College London, London, UK.
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18
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Turvey ST, Marr MM, Barnes I, Brace S, Tapley B, Murphy RW, Zhao E, Cunningham AA. Historical museum collections clarify the evolutionary history of cryptic species radiation in the world's largest amphibians. Ecol Evol 2019; 9:10070-10084. [PMID: 31624538 PMCID: PMC6787787 DOI: 10.1002/ece3.5257] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/02/2019] [Accepted: 04/13/2019] [Indexed: 11/06/2022] Open
Abstract
Inaccurate taxonomic assessment of threatened populations can hinder conservation prioritization and management, with human-mediated population movements obscuring biogeographic patterns and confounding reconstructions of evolutionary history. Giant salamanders were formerly distributed widely across China, and are interpreted as a single species, Andrias davidianus. Previous phylogenetic studies have identified distinct Chinese giant salamander lineages but were unable to associate these consistently with different landscapes, probably because population structure has been modified by human-mediated translocations for recent commercial farming. We investigated the evolutionary history and relationships of allopatric Chinese giant salamander populations with Next-Generation Sequencing methods, using historical museum specimens and late 20th-century samples, and retrieved partial or near-complete mitogenomes for 17 individuals. Samples from populations unlikely to have been affected by translocations form three clades from separate regions of China, spatially congruent with isolation by either major river drainages or mountain ranges. Pliocene-Pleistocene divergences for these clades are consistent with topographic modification of southern China associated with uplift of the Qinghai-Tibet Plateau. General Mixed Yule Coalescent model analysis indicates that these clades represent separate species: Andrias davidianus (Blanchard, 1871) (northern Yangtze/Sichuan), Andrias sligoi (Boulenger, 1924) (Pearl/Nanling), and an undescribed species (Huangshan). Andrias sligoi is possibly the world's largest amphibian. Inclusion of additional reportedly wild samples from areas of known giant salamander exploitation and movement leads to increasing loss of biogeographic signal. Wild Chinese giant salamander populations are now critically depleted or extirpated, and conservation actions should be updated to recognize the existence of multiple species.
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Affiliation(s)
| | | | - Ian Barnes
- Earth Sciences DepartmentNatural History MuseumLondonUK
| | - Selina Brace
- Earth Sciences DepartmentNatural History MuseumLondonUK
| | | | - Robert W. Murphy
- Centre for Biodiversity and Conservation BiologyRoyal Ontario MuseumTorontoOntarioCanada
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Ermi Zhao
- Chengdu Institute of BiologyChinese Academy of SciencesChengduChina
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19
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Bokelmann L, Hajdinjak M, Peyrégne S, Brace S, Essel E, de Filippo C, Glocke I, Grote S, Mafessoni F, Nagel S, Kelso J, Prüfer K, Vernot B, Barnes I, Pääbo S, Meyer M, Stringer C. A genetic analysis of the Gibraltar Neanderthals. Proc Natl Acad Sci U S A 2019; 116:15610-15615. [PMID: 31308224 PMCID: PMC6681707 DOI: 10.1073/pnas.1903984116] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Forbes' Quarry and Devil's Tower partial crania from Gibraltar are among the first Neanderthal remains ever found. Here, we show that small amounts of ancient DNA are preserved in the petrous bones of the 2 individuals despite unfavorable climatic conditions. However, the endogenous Neanderthal DNA is present among an overwhelming excess of recent human DNA. Using improved DNA library construction methods that enrich for DNA fragments carrying deaminated cytosine residues, we were able to sequence 70 and 0.4 megabase pairs (Mbp) nuclear DNA of the Forbes' Quarry and Devil's Tower specimens, respectively, as well as large parts of the mitochondrial genome of the Forbes' Quarry individual. We confirm that the Forbes' Quarry individual was a female and the Devil's Tower individual a male. We also show that the Forbes' Quarry individual is genetically more similar to the ∼120,000-y-old Neanderthals from Scladina Cave in Belgium (Scladina I-4A) and Hohlenstein-Stadel Cave in Germany, as well as to a ∼60,000- to 70,000-y-old Neanderthal from Russia (Mezmaiskaya 1), than to a ∼49,000-y-old Neanderthal from El Sidrón (El Sidrón 1253) in northern Spain and other younger Neanderthals from Europe and western Asia. This suggests that the Forbes' Quarry fossil predates the latter Neanderthals. The preservation of archaic human DNA in the warm coastal climate of Gibraltar, close to the shores of Africa, raises hopes for the future recovery of archaic human DNA from regions in which climatic conditions are less than optimal for DNA preservation.
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Affiliation(s)
- Lukas Bokelmann
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany;
| | - Mateja Hajdinjak
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Stéphane Peyrégne
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Selina Brace
- Centre for Human Evolution Research, Department of Earth Sciences, The Natural History Museum, London SW7 5BD, United Kingdom
| | - Elena Essel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Cesare de Filippo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Isabelle Glocke
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Steffi Grote
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Fabrizio Mafessoni
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Sarah Nagel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Janet Kelso
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Kay Prüfer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Benjamin Vernot
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Ian Barnes
- Centre for Human Evolution Research, Department of Earth Sciences, The Natural History Museum, London SW7 5BD, United Kingdom
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany;
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Chris Stringer
- Centre for Human Evolution Research, Department of Earth Sciences, The Natural History Museum, London SW7 5BD, United Kingdom
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20
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Brace S, Diekmann Y, Booth TJ, van Dorp L, Faltyskova Z, Rohland N, Mallick S, Olalde I, Ferry M, Michel M, Oppenheimer J, Broomandkhoshbacht N, Stewardson K, Martiniano R, Walsh S, Kayser M, Charlton S, Hellenthal G, Armit I, Schulting R, Craig OE, Sheridan A, Pearson MP, Stringer C, Reich D, Thomas MG, Barnes I. Author Correction: Ancient genomes indicate population replacement in Early Neolithic Britain. Nat Ecol Evol 2019; 3:986-987. [PMID: 31068681 DOI: 10.1038/s41559-019-0912-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the version of this Article originally published, there were errors in the colour ordering of the legend in Fig. 5b, and in the positions of the target and surrogate populations in Fig. 5c. This has now been corrected. The conclusions of the study are in no way affected. The errors have been corrected in the HTML and PDF versions of the article.
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Affiliation(s)
- Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Yoan Diekmann
- Research Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Thomas J Booth
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, London, UK
| | - Zuzana Faltyskova
- Research Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Swapan Mallick
- UCL Genetics Institute, University College London, London, UK.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Rui Martiniano
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Susan Walsh
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - Sophy Charlton
- Department of Earth Sciences, Natural History Museum, London, UK.,Bioarch, University of York, York, UK
| | | | - Ian Armit
- School of Archaeological and Forensic Sciences, University of Bradford, Bradford, UK
| | - Rick Schulting
- Institute of Archaeology, University of Oxford, Oxford, UK
| | | | | | | | - Chris Stringer
- Department of Earth Sciences, Natural History Museum, London, UK
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Mark G Thomas
- Research Department of Genetics, Evolution and Environment, University College London, London, UK. .,UCL Genetics Institute, University College London, London, UK.
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London, UK.
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21
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Brace S, Diekmann Y, Booth TJ, van Dorp L, Faltyskova Z, Rohland N, Mallick S, Olalde I, Ferry M, Michel M, Oppenheimer J, Broomandkhoshbacht N, Stewardson K, Martiniano R, Walsh S, Kayser M, Charlton S, Hellenthal G, Armit I, Schulting R, Craig OE, Sheridan A, Parker Pearson M, Stringer C, Reich D, Thomas MG, Barnes I. Ancient genomes indicate population replacement in Early Neolithic Britain. Nat Ecol Evol 2019; 3:765-771. [PMID: 30988490 DOI: 10.1038/s41559-019-0871-9] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 03/06/2019] [Indexed: 11/09/2022]
Abstract
The roles of migration, admixture and acculturation in the European transition to farming have been debated for over 100 years. Genome-wide ancient DNA studies indicate predominantly Aegean ancestry for continental Neolithic farmers, but also variable admixture with local Mesolithic hunter-gatherers. Neolithic cultures first appear in Britain circa 4000 BC, a millennium after they appeared in adjacent areas of continental Europe. The pattern and process of this delayed British Neolithic transition remain unclear. We assembled genome-wide data from 6 Mesolithic and 67 Neolithic individuals found in Britain, dating 8500-2500 BC. Our analyses reveal persistent genetic affinities between Mesolithic British and Western European hunter-gatherers. We find overwhelming support for agriculture being introduced to Britain by incoming continental farmers, with small, geographically structured levels of hunter-gatherer ancestry. Unlike other European Neolithic populations, we detect no resurgence of hunter-gatherer ancestry at any time during the Neolithic in Britain. Genetic affinities with Iberian Neolithic individuals indicate that British Neolithic people were mostly descended from Aegean farmers who followed the Mediterranean route of dispersal. We also infer considerable variation in pigmentation levels in Europe by circa 6000 BC.
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Affiliation(s)
- Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Yoan Diekmann
- Research Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Thomas J Booth
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, London, UK
| | - Zuzana Faltyskova
- Research Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Swapan Mallick
- UCL Genetics Institute, University College London, London, UK.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Rui Martiniano
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Susan Walsh
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - Sophy Charlton
- Department of Earth Sciences, Natural History Museum, London, UK.,Bioarch, University of York, York, UK
| | | | - Ian Armit
- School of Archaeological and Forensic Sciences, University of Bradford, Bradford, UK
| | - Rick Schulting
- Institute of Archaeology, University of Oxford, Oxford, UK
| | | | | | | | - Chris Stringer
- Department of Earth Sciences, Natural History Museum, London, UK
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Mark G Thomas
- Research Department of Genetics, Evolution and Environment, University College London, London, UK. .,UCL Genetics Institute, University College London, London, UK.
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London, UK.
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22
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Travouillon KJ, Simões BF, Miguez RP, Brace S, Brewer P, Stemmer D, Price GJ, Cramb J, Louys J. Hidden in plain sight: reassessment of the pig-footed bandicoot, Chaeropus ecaudatus (Peramelemorphia, Chaeropodidae), with a description of a new species from central australia, and use of the fossil record to trace its past distribution. Zootaxa 2019; 4566:zootaxa.4566.1.1. [PMID: 31716448 DOI: 10.11646/zootaxa.4566.1.1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Indexed: 11/04/2022]
Abstract
The Pig-footed Bandicoot, Chaeropus ecaudatus, an extinct arid-adapted bandicoot, was named in 1838 based on a specimen without a tail from the Murray River in New South Wales. Two additional species were later named, C. castanotis and C. occidentalis, which have since been synonymised with C. ecaudatus. Taxonomic research on the genus is rather difficult because of the limited material available for study. Aside from the types of C. castanotis and C. occidentalis housed at the Natural History Museum in London, and the type of C. ecaudatus at the Australian Museum in Sydney, there are fewer than 30 other modern specimens in other collections scattered around the world. Examining skeletal and dental characters for several specimens, and using a combination of traditional morphology, morphometrics, palaeontology and molecular phylogenetics, we have identified two distinct species, C. ecaudatus and C. yirratji sp. nov., with C. ecaudatus having two distinct subspecies, C. e. ecaudatus and C. e. occidentalis. We use palaeontological data to reconstruct the pre-European distribution of the two species, and review the ecological information known about these extinct taxa.
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23
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Woods R, Turvey ST, Brace S, MacPhee RDE, Barnes I. Ancient DNA of the extinct Jamaican monkey Xenothrix reveals extreme insular change within a morphologically conservative radiation. Proc Natl Acad Sci U S A 2018; 115:12769-12774. [PMID: 30420497 PMCID: PMC6294883 DOI: 10.1073/pnas.1808603115] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The insular Caribbean until recently contained a diverse mammal fauna including four endemic platyrrhine primate species, all of which died out during the Holocene. Previous morphological studies have attempted to establish how these primates are related to fossil and extant platyrrhines, whether they represent ancient or recent colonists, and whether they constitute a monophyletic group. These efforts have generated multiple conflicting hypotheses, from close sister-taxon relationships with several different extant platyrrhines to derivation from a stem platyrrhine lineage outside the extant Neotropical radiation. This diversity of opinion reflects the fact that Caribbean primates were morphologically extremely unusual, displaying numerous autapomorphies and apparently derived conditions present across different platyrrhine clades. Here we report ancient DNA data for an extinct Caribbean primate: a limited-coverage entire mitochondrial genome and seven regions of nuclear genome for the most morphologically derived taxon, the Jamaican monkey Xenothrix mcgregori We demonstrate that Xenothrix is part of the existing platyrrhine radiation rather than a late-surviving stem platyrrhine, despite its unusual adaptations, and falls within the species-rich but morphologically conservative titi monkey clade (Callicebinae) as sister to the newly recognized genus Cheracebus These results are not congruent with previous morphology-based hypotheses and suggest that even morphologically conservative lineages can exhibit phenetic plasticity in novel environments like those found on islands. Xenothrix and Cheracebus diverged ca. 11 Ma, but primates have been present in the Caribbean since 17.5-18.5 Ma, indicating that Caribbean primate diversity was generated by multiple over-water colonizations.
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Affiliation(s)
- Roseina Woods
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, United Kingdom
- School of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, United Kingdom
| | - Samuel T Turvey
- Institute of Zoology, Zoological Society of London, London NW1 4RY, United Kingdom;
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, United Kingdom
| | - Ross D E MacPhee
- Department of Mammalogy, American Museum of Natural History, New York, NY 10024
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, United Kingdom
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24
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Ní Leathlobhair M, Perri AR, Irving-Pease EK, Witt KE, Linderholm A, Haile J, Lebrasseur O, Ameen C, Blick J, Boyko AR, Brace S, Cortes YN, Crockford SJ, Devault A, Dimopoulos EA, Eldridge M, Enk J, Gopalakrishnan S, Gori K, Grimes V, Guiry E, Hansen AJ, Hulme-Beaman A, Johnson J, Kitchen A, Kasparov AK, Kwon YM, Nikolskiy PA, Lope CP, Manin A, Martin T, Meyer M, Myers KN, Omura M, Rouillard JM, Pavlova EY, Sciulli P, Sinding MHS, Strakova A, Ivanova VV, Widga C, Willerslev E, Pitulko VV, Barnes I, Gilbert MTP, Dobney KM, Malhi RS, Murchison EP, Larson G, Frantz LAF. The evolutionary history of dogs in the Americas. Science 2018; 361:81-85. [PMID: 29976825 PMCID: PMC7116273 DOI: 10.1126/science.aao4776] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 12/26/2017] [Accepted: 05/10/2018] [Indexed: 01/01/2023]
Abstract
Dogs were present in the Americas before the arrival of European colonists, but the origin and fate of these precontact dogs are largely unknown. We sequenced 71 mitochondrial and 7 nuclear genomes from ancient North American and Siberian dogs from time frames spanning ~9000 years. Our analysis indicates that American dogs were not derived from North American wolves. Instead, American dogs form a monophyletic lineage that likely originated in Siberia and dispersed into the Americas alongside people. After the arrival of Europeans, native American dogs almost completely disappeared, leaving a minimal genetic legacy in modern dog populations. The closest detectable extant lineage to precontact American dogs is the canine transmissible venereal tumor, a contagious cancer clone derived from an individual dog that lived up to 8000 years ago.
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Affiliation(s)
- Máire Ní Leathlobhair
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Angela R Perri
- Department of Archaeology, Durham University, Durham, UK
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Evan K Irving-Pease
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Kelsey E Witt
- School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana-Champaign, IL, USA
| | - Anna Linderholm
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
- Department of Anthropology, Texas A&M University, College Station, TX, USA
| | - James Haile
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ophelie Lebrasseur
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Carly Ameen
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK
| | - Jeffrey Blick
- Department of Government and Sociology, Georgia College and State University, Milledgeville, GA, USA
| | - Adam R Boyko
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | | | | | | | - Evangelos A Dimopoulos
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | | | - Jacob Enk
- Arbor Biosciences, Ann Arbor, MI, USA
| | - Shyam Gopalakrishnan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Kevin Gori
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Vaughan Grimes
- Department of Archaeology, Memorial University, Queen's College, St. John's, Canada
| | - Eric Guiry
- Department of Anthropology, University of British Columbia, Vancouver, Canada
| | - Anders J Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- The Qimmeq Project, University of Greenland, Nuussuaq, Greenland
| | - Ardern Hulme-Beaman
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK
| | - John Johnson
- Department of Anthropology, Santa Barbara Museum of Natural History, Santa Barbara, CA, USA
| | - Andrew Kitchen
- Department of Anthropology, University of Iowa, Iowa City, IA, USA
| | - Aleksei K Kasparov
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
| | - Young-Mi Kwon
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Pavel A Nikolskiy
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
- Geological Institute, Russian Academy of Sciences, Moscow, Russia
| | | | - Aurélie Manin
- Department of Archaeology, BioArCh, University of York, York, UK
- UMR 7209, Archéozoologie, Archéobotanique, Muséum National d'Histoire Naturelle, Paris, France
| | - Terrance Martin
- Research and Collections Center, Illinois State Museum, Springfield, IL, USA
| | - Michael Meyer
- Touray & Meyer Veterinary Clinic, Serrekunda, Gambia
| | - Kelsey Noack Myers
- Glenn A. Black Laboratory of Anthropology, Indiana University Bloomington, Bloomington, IN, USA
| | - Mark Omura
- Department of Mammalogy, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Jean-Marie Rouillard
- Arbor Biosciences, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Elena Y Pavlova
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
- Arctic & Antarctic Research Institute, St. Petersburg, Russia
| | - Paul Sciulli
- Department of Anthropology, Ohio State University, Columbus, OH, USA
| | - Mikkel-Holger S Sinding
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- The Qimmeq Project, University of Greenland, Nuussuaq, Greenland
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Andrea Strakova
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Christopher Widga
- Center of Excellence in Paleontology, East Tennessee State University, Gray, TN, USA
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Vladimir V Pitulko
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London, UK
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Norwegian University of Science and Technology, University Museum, Trondheim, Norway
| | - Keith M Dobney
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK
- Department of Archaeology, University of Aberdeen, Aberdeen, UK
| | - Ripan S Malhi
- Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana-Champaign, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana-Champaign, IL, USA
| | - Elizabeth P Murchison
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.
| | - Laurent A F Frantz
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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25
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Olalde I, Brace S, Allentoft ME, Armit I, Kristiansen K, Booth T, Rohland N, Mallick S, Szécsényi-Nagy A, Mittnik A, Altena E, Lipson M, Lazaridis I, Harper TK, Patterson N, Broomandkhoshbacht N, Diekmann Y, Faltyskova Z, Fernandes D, Ferry M, Harney E, de Knijff P, Michel M, Oppenheimer J, Stewardson K, Barclay A, Alt KW, Liesau C, Ríos P, Blasco C, Miguel JV, García RM, Fernández AA, Bánffy E, Bernabò-Brea M, Billoin D, Bonsall C, Bonsall L, Allen T, Büster L, Carver S, Navarro LC, Craig OE, Cook GT, Cunliffe B, Denaire A, Dinwiddy KE, Dodwell N, Ernée M, Evans C, Kuchařík M, Farré JF, Fowler C, Gazenbeek M, Pena RG, Haber-Uriarte M, Haduch E, Hey G, Jowett N, Knowles T, Massy K, Pfrengle S, Lefranc P, Lemercier O, Lefebvre A, Martínez CH, Olmo VG, Ramírez AB, Maurandi JL, Majó T, McKinley JI, McSweeney K, Mende BG, Modi A, Kulcsár G, Kiss V, Czene A, Patay R, Endrődi A, Köhler K, Hajdu T, Szeniczey T, Dani J, Bernert Z, Hoole M, Cheronet O, Keating D, Velemínský P, Dobeš M, Candilio F, Brown F, Fernández RF, Herrero-Corral AM, Tusa S, Carnieri E, Lentini L, Valenti A, Zanini A, Waddington C, Delibes G, Guerra-Doce E, Neil B, Brittain M, Luke M, Mortimer R, Desideri J, Besse M, Brücken G, Furmanek M, Hałuszko A, Mackiewicz M, Rapiński A, Leach S, Soriano I, Lillios KT, Cardoso JL, Pearson MP, Włodarczak P, Price TD, Prieto P, Rey PJ, Risch R, Guerra MAR, Schmitt A, Serralongue J, Silva AM, Smrčka V, Vergnaud L, Zilhão J, Caramelli D, Higham T, Thomas MG, Kennett DJ, Fokkens H, Heyd V, Sheridan A, Sjögren KG, Stockhammer PW, Krause J, Pinhasi R, Haak W, Barnes I, Lalueza-Fox C, Reich D. Erratum: The Beaker phenomenon and the genomic transformation of northwest Europe. Nature 2018; 555:543. [PMID: 29565364 DOI: 10.1038/nature26164] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This corrects the article DOI: 10.1038/nature25738.
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26
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Olalde I, Brace S, Allentoft ME, Armit I, Kristiansen K, Booth T, Rohland N, Mallick S, Szécsényi-Nagy A, Mittnik A, Altena E, Lipson M, Lazaridis I, Harper TK, Patterson N, Broomandkhoshbacht N, Diekmann Y, Faltyskova Z, Fernandes D, Ferry M, Harney E, de Knijff P, Michel M, Oppenheimer J, Stewardson K, Barclay A, Alt KW, Liesau C, Ríos P, Blasco C, Miguel JV, García RM, Fernández AA, Bánffy E, Bernabò-Brea M, Billoin D, Bonsall C, Bonsall L, Allen T, Büster L, Carver S, Navarro LC, Craig OE, Cook GT, Cunliffe B, Denaire A, Dinwiddy KE, Dodwell N, Ernée M, Evans C, Kuchařík M, Farré JF, Fowler C, Gazenbeek M, Pena RG, Haber-Uriarte M, Haduch E, Hey G, Jowett N, Knowles T, Massy K, Pfrengle S, Lefranc P, Lemercier O, Lefebvre A, Martínez CH, Olmo VG, Ramírez AB, Maurandi JL, Majó T, McKinley JI, McSweeney K, Mende BG, Modi A, Kulcsár G, Kiss V, Czene A, Patay R, Endrődi A, Köhler K, Hajdu T, Szeniczey T, Dani J, Bernert Z, Hoole M, Cheronet O, Keating D, Velemínský P, Dobeš M, Candilio F, Brown F, Fernández RF, Herrero-Corral AM, Tusa S, Carnieri E, Lentini L, Valenti A, Zanini A, Waddington C, Delibes G, Guerra-Doce E, Neil B, Brittain M, Luke M, Mortimer R, Desideri J, Besse M, Brücken G, Furmanek M, Hałuszko A, Mackiewicz M, Rapiński A, Leach S, Soriano I, Lillios KT, Cardoso JL, Pearson MP, Włodarczak P, Price TD, Prieto P, Rey PJ, Risch R, Rojo Guerra MA, Schmitt A, Serralongue J, Silva AM, Smrčka V, Vergnaud L, Zilhão J, Caramelli D, Higham T, Thomas MG, Kennett DJ, Fokkens H, Heyd V, Sheridan A, Sjögren KG, Stockhammer PW, Krause J, Pinhasi R, Haak W, Barnes I, Lalueza-Fox C, Reich D. The Beaker phenomenon and the genomic transformation of northwest Europe. Nature 2018; 555:190-196. [PMID: 29466337 PMCID: PMC5973796 DOI: 10.1038/nature25738] [Citation(s) in RCA: 248] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 01/04/2018] [Indexed: 12/19/2022]
Abstract
From around 2750 to 2500 bc, Bell Beaker pottery became widespread across western and central Europe, before it disappeared between 2200 and 1800 bc. The forces that propelled its expansion are a matter of long-standing debate, and there is support for both cultural diffusion and migration having a role in this process. Here we present genome-wide data from 400 Neolithic, Copper Age and Bronze Age Europeans, including 226 individuals associated with Beaker-complex artefacts. We detected limited genetic affinity between Beaker-complex-associated individuals from Iberia and central Europe, and thus exclude migration as an important mechanism of spread between these two regions. However, migration had a key role in the further dissemination of the Beaker complex. We document this phenomenon most clearly in Britain, where the spread of the Beaker complex introduced high levels of steppe-related ancestry and was associated with the replacement of approximately 90% of Britain's gene pool within a few hundred years, continuing the east-to-west expansion that had brought steppe-related ancestry into central and northern Europe over the previous centuries.
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Affiliation(s)
- Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - Morten E Allentoft
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen 1350, Denmark
| | - Ian Armit
- School of Archaeological and Forensic Sciences, University of Bradford, Bradford BD7 1DP, UK
| | | | - Thomas Booth
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Anna Szécsényi-Nagy
- Laboratory of Archaeogenetics, Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary
| | - Alissa Mittnik
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72070, Germany
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Eveline Altena
- Department of Human Genetics, Leiden University Medical Center, Leiden 2333 ZC, The Netherlands
| | - Mark Lipson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Iosif Lazaridis
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Thomas K Harper
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yoan Diekmann
- Research Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Zuzana Faltyskova
- Research Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Daniel Fernandes
- Earth Institute, University College Dublin, Dublin 4, Ireland
- Department of Anthropology, University of Vienna, Vienna 1090, Austria
- Research Center for Anthropology and Health, Department of Life Science, University of Coimbra, Coimbra 3000-456, Portugal
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Eadaoin Harney
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Center, Leiden 2333 ZC, The Netherlands
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | - Kurt Werner Alt
- Center of Natural and Cultural History of Man, Danube Private University, Krems 3500, Austria
- Department of Biomedical Engineering, Basel University, Basel 4123, Switzerland
- Integrative Prehistory and Archaeological Science, Basel University, Basel, Switzerland
| | - Corina Liesau
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Patricia Ríos
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Concepción Blasco
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | | | | | | | - Eszter Bánffy
- Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary
- Romano-Germanic Commission, German Archaeological Institute, Frankfurt am Main 60325, Germany
| | | | - David Billoin
- INRAP, Institut National de Recherches Archéologiques Préventives, Buffard 25440, France
| | - Clive Bonsall
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, UK
| | | | - Tim Allen
- Oxford Archaeology, Oxford OX2 0ES, UK
| | - Lindsey Büster
- School of Archaeological and Forensic Sciences, University of Bradford, Bradford BD7 1DP, UK
| | - Sophie Carver
- Department of Archaeology and Anthropology, University of Bristol, Bristol BS8 1UU, UK
| | - Laura Castells Navarro
- School of Archaeological and Forensic Sciences, University of Bradford, Bradford BD7 1DP, UK
| | - Oliver E Craig
- BioArCh, Department of Archaeology, University of York, York YO10 5DD, UK
| | - Gordon T Cook
- Scottish Universities Environmental Research Centre, East Kilbride G75 0QF, UK
| | - Barry Cunliffe
- Institute of Archaeology, University of Oxford, Oxford OX1 2PG, UK
| | | | | | | | - Michal Ernée
- Institute of Archaeology, Czech Academy of Sciences, Prague 118 01, Czech Republic
| | - Christopher Evans
- Cambridge Archaeological Unit, Department of Archaeology, University of Cambridge, Cambridge CB3 0DT, UK
| | | | - Joan Francès Farré
- Museu i Poblat Ibèric de Ca n'Oliver, Cerdanyola del Vallès 08290, Spain
| | - Chris Fowler
- School of History, Classics & Archaeology, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Michiel Gazenbeek
- INRAP, Institut National de Recherches Archéologiques Préventives, Nice 06300, France
| | - Rafael Garrido Pena
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | | | - Elżbieta Haduch
- Institute of Zoology and Biomedical Research, Jagiellonian University, Kraków 31-007, Poland
| | - Gill Hey
- Oxford Archaeology, Oxford OX2 0ES, UK
| | - Nick Jowett
- Great Orme Mines, Great Orme, Llandudno LL30 2XG, UK
| | - Timothy Knowles
- Bristol Radiocarbon Accelerator Mass Spectrometry Facility, University of Bristol, Bristol BS8 1UU, UK
| | - Ken Massy
- Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, Munich 80539, Germany
| | - Saskia Pfrengle
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72070, Germany
| | - Philippe Lefranc
- INRAP, Institut National de Recherches Archéologiques Préventives, Strasbourg 67100, France
| | - Olivier Lemercier
- Université Paul-Valéry - Montpellier 3, UMR 5140 ASM, Montpellier 34199, France
| | - Arnaud Lefebvre
- INRAP, Institut National de Recherches Archéologiques Préventives, Metz 57063, France
- UMR 5199, Pacea, équipe A3P, Université de Bordeaux, Talence 33400, France
| | - César Heras Martínez
- TRÉBEDE, Patrimonio y Cultura SL, Torres de la Alameda 28813, Spain
- Departamento de Ciencias de la Vida, Universidad de Alcalá, Alcalá de Henares 28801, Spain
- Instituto Universitario de Investigación en Ciencias Policiales (IUICP), Alcalá de Henares 28801, Spain
| | - Virginia Galera Olmo
- Departamento de Ciencias de la Vida, Universidad de Alcalá, Alcalá de Henares 28801, Spain
- Instituto Universitario de Investigación en Ciencias Policiales (IUICP), Alcalá de Henares 28801, Spain
| | | | | | - Tona Majó
- Archaeom, Departament de Prehistòria, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | | | - Kathleen McSweeney
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Balázs Gusztáv Mende
- Laboratory of Archaeogenetics, Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary
| | - Alessandra Modi
- Department of Biology, University of Florence, Florence 50121, Italy
| | - Gabriella Kulcsár
- Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary
| | - Viktória Kiss
- Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary
| | | | - Róbert Patay
- Ferenczy Museum Center, Szentendre 2100, Hungary
| | | | - Kitti Köhler
- Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary
| | - Tamás Hajdu
- Department of Biological Anthropology, Eötvös Loránd University, Budapest 1117, Hungary
- Hungarian Natural History Museum, Budapest 1083, Hungary
| | - Tamás Szeniczey
- Department of Biological Anthropology, Eötvös Loránd University, Budapest 1117, Hungary
| | | | - Zsolt Bernert
- Hungarian Natural History Museum, Budapest 1083, Hungary
| | - Maya Hoole
- Historic Environment Scotland, Edinburgh EH9 1SH, UK
| | - Olivia Cheronet
- Earth Institute, University College Dublin, Dublin 4, Ireland
- Department of Anthropology, University of Vienna, Vienna 1090, Austria
| | - Denise Keating
- Humanities Institute, University College Dublin, Dublin 4, Ireland
| | - Petr Velemínský
- Department of Anthropology, National Museum, Prague 115 79, Czech Republic
| | - Miroslav Dobeš
- Institute of Archaeology, Czech Academy of Sciences, Prague 118 01, Czech Republic
| | - Francesca Candilio
- Soprintendenza Archeologia belle arti e paesaggio per la città metropolitana di Cagliari e per le province di Oristano e Sud Sardegna, Cagliari 9124, Italy
- Physical Anthropology Section, University of Philadelphia Museum of Archaeology and Anthropology, Philadelphia, Pennsylvania 19104, USA
- Department of Environmental Biology, Sapienza University of Rome, Rome 00185, Italy
| | | | | | | | | | - Emiliano Carnieri
- Facoltà di Lettere e Filosofia, Università di Palermo, Palermo 90133, Italy
| | - Luigi Lentini
- Soprintendenza per i beni culturali e ambientali di Trapani, Trapani 91100, Italy
| | | | | | | | - Germán Delibes
- Departamento de Prehistoria, Facultad de Filosofía y Letras, Universidad de Valladolid, Valladolid 47011, Spain
| | - Elisa Guerra-Doce
- Departamento de Prehistoria, Facultad de Filosofía y Letras, Universidad de Valladolid, Valladolid 47011, Spain
| | - Benjamin Neil
- Cambridge Archaeological Unit, Department of Archaeology, University of Cambridge, Cambridge CB3 0DT, UK
| | - Marcus Brittain
- Cambridge Archaeological Unit, Department of Archaeology, University of Cambridge, Cambridge CB3 0DT, UK
| | - Mike Luke
- Albion Archaeology, Bedford MK42 0AS, UK
| | | | - Jocelyne Desideri
- Laboratory of Prehistoric Archaeology and Anthropology, Department F.-A. Forel for Environmental and Aquatic Sciences, University of Geneva, Geneva 4, Switzerland
| | - Marie Besse
- Laboratory of Prehistoric Archaeology and Anthropology, Department F.-A. Forel for Environmental and Aquatic Sciences, University of Geneva, Geneva 4, Switzerland
| | - Günter Brücken
- General Department of Cultural Heritage Rhineland Palatinate, Department of Archaeology, Mainz 55116, Germany
| | - Mirosław Furmanek
- Institute of Archaeology, University of Wroclaw, Wrocław 50-137, Poland
| | - Agata Hałuszko
- Institute of Archaeology, University of Wroclaw, Wrocław 50-137, Poland
| | - Maksym Mackiewicz
- Institute of Archaeology, University of Wroclaw, Wrocław 50-137, Poland
| | - Artur Rapiński
- Institute of Archaeology, Silesian University in Opava, Opava 746 01, Czech Republic
| | - Stephany Leach
- Department of Archaeology, University of Exeter, Exeter EX4 4QE, UK
| | - Ignacio Soriano
- Departament de Prehistòria, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Katina T Lillios
- Department of Anthropology, University of Iowa, Iowa City, Iowa 52240, USA
| | - João Luís Cardoso
- Centro de Arqueologia, Universidade de Lisboa, Lisboa 1600-214, Portugal
- Universidade Aberta, Lisboa 1269-001, Portugal
| | | | - Piotr Włodarczak
- Institute of Archaeology and Ethnology, Polish Academy of Sciences, Kraków 31-016, Poland
| | - T Douglas Price
- Laboratory for Archaeological Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Pilar Prieto
- University of Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Pierre-Jérôme Rey
- UMR 5204 Laboratoire Edytem, Université Savoie Mont Blanc, Chambéry 73376, France
| | - Roberto Risch
- Departament de Prehistòria, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Manuel A Rojo Guerra
- Department of Prehistory and Archaeology, Faculty of Philosophy and Letters, Valladolid University, Valladolid 47011, Spain
| | - Aurore Schmitt
- UMR 7268 ADES, CNRS, Aix-Marseille Univ, EFS, Faculté de médecine Nord, Marseille 13015, France
| | - Joël Serralongue
- Service archéologique, Conseil Général de la Haute-Savoie, Annecy 74000, France
| | - Ana Maria Silva
- Laboratory of Prehistory, Research Center for Anthropology and Health, Department of Life Science, University of Coimbra, Coimbra 3000-456, Portugal
| | - Václav Smrčka
- Institute for History of Medicine and Foreign Languages, First Faculty of Medicine, Charles University, Prague 121 08, Czech Republic
| | - Luc Vergnaud
- ANTEA Bureau d'étude en Archéologie, Habsheim 68440, France
| | - João Zilhão
- Centro de Arqueologia, Universidade de Lisboa, Lisboa 1600-214, Portugal
- Institució Catalana de Recerca i Estudis Avançats, Barcelona 08010, Spain
- Departament d'Història i Arqueologia, Universitat de Barcelona, Barcelona 08001, Spain
| | - David Caramelli
- Department of Biology, University of Florence, Florence 50121, Italy
| | - Thomas Higham
- Oxford Radiocarbon Accelerator Unit, RLAHA, University of Oxford, Oxford OX1 3QY, UK
| | - Mark G Thomas
- Research Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Douglas J Kennett
- Department of Anthropology & Institute for Energy and the Environment, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Harry Fokkens
- Faculty of Archaeology, Leiden University, 2333 CC Leiden, The Netherlands
| | - Volker Heyd
- Department of Archaeology and Anthropology, University of Bristol, Bristol BS8 1UU, UK
- Department of Philosophy, History, Culture and Art Studies, Section of Archaeology, University of Helsinki, Helsinki 00014, Finland
| | | | | | - Philipp W Stockhammer
- Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, Munich 80539, Germany
- Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Ron Pinhasi
- Earth Institute, University College Dublin, Dublin 4, Ireland
- Department of Anthropology, University of Vienna, Vienna 1090, Austria
| | - Wolfgang Haak
- Max Planck Institute for the Science of Human History, Jena 07745, Germany
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide 5005, South Australia, Australia
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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Marr MM, Brace S, Schreve DC, Barnes I. Identifying source populations for the reintroduction of the Eurasian beaver, Castor fiber L. 1758, into Britain: evidence from ancient DNA. Sci Rep 2018; 8:2708. [PMID: 29426903 PMCID: PMC5807398 DOI: 10.1038/s41598-018-21173-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/17/2018] [Indexed: 11/09/2022] Open
Abstract
Establishing true phylogenetic relationships between populations is a critical consideration when sourcing individuals for translocation. This presents huge difficulties with threatened and endangered species that have become extirpated from large areas of their former range. We utilise ancient DNA (aDNA) to reconstruct the phylogenetic relationships of a keystone species which has become extinct in Britain, the Eurasian beaver Castor fiber. We sequenced seventeen 492 bp partial tRNAPro and control region sequences from Late Pleistocene and Holocene age beavers and included these in network, demographic and genealogy analyses. The mode of postglacial population expansion from refugia was investigated by employing tests of neutrality and a pairwise mismatch distribution analysis. We found evidence of a pre-Late Glacial Maximum ancestor for the Western C. fiber clade which experienced a rapid demographic expansion during the terminal Pleistocene to early Holocene period. Ancient British beavers were found to originate from the Western phylogroup but showed no phylogenetic affinity to any one modern relict population over another. Instead, we find that they formed part of a large, continuous, pan-Western European clade that harbored little internal substructure. Our study highlights the utility of aDNA in reconstructing population histories of extirpated species which has real-world implications for conservation planning.
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Affiliation(s)
- Melissa M Marr
- Department of Geography, Royal Holloway University of London, Egham Hill, Egham, Surrey, TW20 0EX, UK.
- Department of Earth Sciences, Natural History Museum London, Cromwell Road, South Kensington, London, SW7 5BD, UK.
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum London, Cromwell Road, South Kensington, London, SW7 5BD, UK
| | - Danielle C Schreve
- Department of Geography, Royal Holloway University of London, Egham Hill, Egham, Surrey, TW20 0EX, UK
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum London, Cromwell Road, South Kensington, London, SW7 5BD, UK
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Woods R, Marr MM, Brace S, Barnes I. The Small and the Dead: A Review of Ancient DNA Studies Analysing Micromammal Species. Genes (Basel) 2017; 8:E312. [PMID: 29117125 PMCID: PMC5704225 DOI: 10.3390/genes8110312] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/13/2017] [Accepted: 10/13/2017] [Indexed: 02/06/2023] Open
Abstract
The field of ancient DNA (aDNA) has recently been in a state of exponential growth, largely driven by the uptake of Next Generation Sequencing (NGS) techniques. Much of this work has focused on the mammalian megafauna and ancient humans, with comparatively less studies looking at micromammal fauna, despite the potential of these species in testing evolutionary, environmental and taxonomic theories. Several factors make micromammal fauna ideally suited for aDNA extraction and sequencing. Micromammal subfossil assemblages often include the large number of individuals appropriate for population level analyses, and, furthermore, the assemblages are frequently found in cave sites where the constant temperature and sheltered environment provide favourable conditions for DNA preservation. This review looks at studies that include the use of aDNA in molecular analysis of micromammal fauna, in order to examine the wide array of questions that can be answered in the study of small mammals using new palaeogenetic techniques. This study highlights the bias in current aDNA studies and assesses the future use of aDNA as a tool for the study of micromammal fauna.
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Affiliation(s)
- Roseina Woods
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
| | - Melissa M Marr
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
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Turvey ST, Barnes I, Marr M, Brace S. Imperial trophy or island relict? A new extinction paradigm for Père David's deer: a Chinese conservation icon. R Soc Open Sci 2017; 4:171096. [PMID: 29134102 PMCID: PMC5666285 DOI: 10.1098/rsos.171096] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 09/25/2017] [Indexed: 06/07/2023]
Abstract
Determining the 'dynamic biogeography' of range collapse in threatened species is essential for effective conservation, but reconstruction of spatio-temporal patterns of population vulnerability and resilience can require use of non-standard ecological data such as historical archives. Père David's deer or milu, one of the few living mammal species that has become extinct in the wild, is historically known only from a small captive herd of unknown provenance that survived until 1900 in the Imperial Hunting Park near Beijing, from which all living individuals are descended. Using ancient DNA analysis, we demonstrate that two fawns collected in 1868 from Hainan Island, off the southern Chinese mainland, represent the only known wild milu specimens and were sampled from probably the last wild population. The Hainan milu population shows extremely low genetic differentiation from descendants of the Beijing herd, suggesting that this now-extinct population may have been the source of the captive herd. This revised extinction model refutes the supposed long-term survival of a captive milu herd for centuries or millennia after final extinction of wild populations, highlighting the vulnerability of remnant mammal populations in the absence of proactive management and the importance of historical museum collections for providing unique new insights on evolution, biogeography and conservation. Milu experienced a pattern of final population persistence on an island at the periphery of their former range, consistent with the 'range eclipse' or 'contagion' model of range collapse, and matching the spatial extinction dynamics of other extinct mammals such as the thylacine and woolly mammoth.
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Affiliation(s)
- Samuel T. Turvey
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK
| | - Ian Barnes
- Earth Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Melissa Marr
- Earth Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK
- School of Geography, Royal Holloway University of London, Egham TW20 0EX, UK
| | - Selina Brace
- Earth Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK
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Brace S, Ruddy M, Miller R, Schreve DC, Stewart JR, Barnes I. The colonization history of British water vole (Arvicola amphibius (Linnaeus, 1758)): origins and development of the Celtic fringe. Proc Biol Sci 2017; 283:rspb.2016.0130. [PMID: 27122559 DOI: 10.1098/rspb.2016.0130] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 04/06/2016] [Indexed: 12/13/2022] Open
Abstract
The terminal Pleistocene and Early Holocene, a period from 15 000 to 18 000 Before Present (BP), was critical in establishing the current Holarctic fauna, with temperate-climate species largely replacing cold-adapted ones at mid-latitudes. However, the timing and nature of this process remain unclear for many taxa, a point that impacts on current and future management strategies. Here, we use an ancient DNA dataset to test more directly postglacial histories of the water vole (Arvicola amphibius, formerly A terrestris), a species that is both a conservation priority and a pest in different parts of its range. We specifically examine colonization of Britain, where a complex genetic structure can be observed today. Although we focus on population history at the limits of the species' range, the inclusion of additional European samples allows insights into European postglacial colonization events and provides a molecular perspective on water vole taxonomy.
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Affiliation(s)
- Selina Brace
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | | | - Rebecca Miller
- Service of Prehistory, University of Liège, Liège 4000, Belgium
| | - Danielle C Schreve
- Department of Geography, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| | - John R Stewart
- School of Applied Sciences, Bournemouth University, Poole, Dorset BH12 5BB, UK
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
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Brace S, Thomas JA, Dalén L, Burger J, MacPhee RDE, Barnes I, Turvey ST. Evolutionary History of the Nesophontidae, the Last Unplaced Recent Mammal Family. Mol Biol Evol 2016; 33:3095-3103. [PMID: 27624716 DOI: 10.1093/molbev/msw186] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The mammalian evolutionary tree has lost several major clades through recent human-caused extinctions. This process of historical biodiversity loss has particularly affected tropical island regions such as the Caribbean, an area of great evolutionary diversification but poor molecular preservation. The most enigmatic of the recently extinct endemic Caribbean mammals are the Nesophontidae, a family of morphologically plesiomorphic lipotyphlan insectivores with no consensus on their evolutionary affinities, and which constitute the only major recent mammal clade to lack any molecular information on their phylogenetic placement. Here, we use a palaeogenomic approach to place Nesophontidae within the phylogeny of recent Lipotyphla. We recovered the near-complete mitochondrial genome and sequences for 17 nuclear genes from a ∼750-year-old Hispaniolan Nesophontes specimen, and identify a divergence from their closest living relatives, the Solenodontidae, more than 40 million years ago. Nesophontidae is thus an older distinct lineage than many extant mammalian orders, highlighting not only the role of island systems as "museums" of diversity that preserve ancient lineages, but also the major human-caused loss of evolutionary history.
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Affiliation(s)
- Selina Brace
- Department of Earth Sciences, Natural History Museum, London, United Kingdom
| | | | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Joachim Burger
- Institute of Anthropology Johannes Gutenberg-University, Anselm-Franz-von-Bentzel-Weg 7, Mainz, Germany
| | - Ross D E MacPhee
- Department of Mammalogy, American Museum of Natural History, New York, NY
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London, United Kingdom
| | - Samuel T Turvey
- Zoological Society of London, Institute of Zoology, London, United Kingdom
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Abstract
Identifying general patterns of colonization and radiation in island faunas is often hindered by past human-caused extinctions. The insular Caribbean is one of the only complex oceanic-type island systems colonized by land mammals, but has witnessed the globally highest level of mammalian extinction during the Holocene. Using ancient DNA analysis, we reconstruct the evolutionary history of one of the Caribbean's now-extinct major mammal groups, the insular radiation of oryzomyine rice rats. Despite the significant problems of recovering DNA from prehistoric tropical archaeological material, it was possible to identify two discrete Late Miocene colonizations of the main Lesser Antillean island chain from mainland South America by oryzomyine lineages that were only distantly related. A high level of phylogenetic diversification was observed within oryzomyines across the Lesser Antilles, even between allopatric populations on the same island bank. The timing of oryzomyine colonization is closely similar to the age of several other Caribbean vertebrate taxa, suggesting that geomorphological conditions during the Late Miocene facilitated broadly simultaneous overwater waif dispersal of many South American lineages to the Lesser Antilles. These data provide an important baseline by which to further develop the Caribbean as a unique workshop for studying island evolution.
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Affiliation(s)
- Selina Brace
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| | - Samuel T Turvey
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK
| | - Marcelo Weksler
- Laboratório de Ecoepidemiologia da Doença de Chagas, Instituto Oswaldo Cruz, Fiocruz, Avenida Brasil 4365, 21045-900 Rio de Janeiro, Brazil Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, São Cristóvão, 20940-040 Rio de Janeiro, Brazil
| | - Menno L P Hoogland
- Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333CC Leiden, The Netherlands
| | - Ian Barnes
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
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Turvey ST, Peters S, Brace S, Young RP, Crumpton N, Hansford J, Nuñez-Miño JM, King G, Tsalikidis K, Ottenwalder JA, Timpson A, Funk SM, Brocca JL, Thomas MG, Barnes I. Independent evolutionary histories in allopatric populations of a threatened Caribbean land mammal. DIVERS DISTRIB 2016. [DOI: 10.1111/ddi.12420] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Samuel T. Turvey
- Institute of Zoology; Zoological Society of London; Regent's Park London NW1 4RY UK
| | - Stuart Peters
- Research Department of Genetics, Evolution and Environment; University College London; Gower Street London WC1E 6BT UK
| | - Selina Brace
- Natural History Museum; Cromwell Road London SW7 5BD UK
| | - Richard P. Young
- Durrell Wildlife Conservation Trust; Les Augrès Manor Trinity Jersey JE3 5BP Channel Islands
| | - Nick Crumpton
- Natural History Museum; Cromwell Road London SW7 5BD UK
- Research Department of Cell and Developmental Biology; University College London; Gower Street London WC1E 6BT UK
| | - James Hansford
- Institute of Zoology; Zoological Society of London; Regent's Park London NW1 4RY UK
- Ocean and Earth Science, National Oceanography Centre Southampton; University of Southampton Waterfront Campus; European Way Southampton UK
| | - Jose M. Nuñez-Miño
- Durrell Wildlife Conservation Trust; Les Augrès Manor Trinity Jersey JE3 5BP Channel Islands
| | - Gemma King
- School of Biological Sciences; Royal Holloway University of London; Egham Hill Egham TW20 OEX UK
| | - Katrina Tsalikidis
- School of Biological Sciences; Royal Holloway University of London; Egham Hill Egham TW20 OEX UK
| | | | - Adrian Timpson
- Institute of Archaeology; University College London; Gordon Square London WC1H 0PY UK
| | | | - Jorge L. Brocca
- Sociedad Ornitológica de la Hispaniola; Parque Zoologico Nacional; Avenida de la Vega Real Arroyo Hondo Santo Domingo Dominican Republic
| | - Mark G. Thomas
- Research Department of Genetics, Evolution and Environment; University College London; Gower Street London WC1E 6BT UK
| | - Ian Barnes
- Natural History Museum; Cromwell Road London SW7 5BD UK
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Field J, Shreeves G, Kennedy M, Brace S, Gilbert JDJ. Sex-biased parental care and sexual size dimorphism in a provisioning arthropod. Behav Ecol Sociobiol 2015. [DOI: 10.1007/s00265-015-2002-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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35
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Ludtmann MHR, Otto GP, Schilde C, Chen ZH, Allan CY, Brace S, Beesley PW, Kimmel AR, Fisher P, Killick R, Williams RSB. An ancestral non-proteolytic role for presenilin proteins in multicellular development of the social amoeba Dictyostelium discoideum. J Cell Sci 2014; 127:1576-84. [PMID: 24463814 PMCID: PMC3970561 DOI: 10.1242/jcs.140939] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 12/29/2013] [Indexed: 11/20/2022] Open
Abstract
Mutations in either of two presenilin genes can cause familial Alzheimer's disease. Presenilins have both proteolysis-dependent functions, as components of the γ-secretase complex, and proteolysis-independent functions in signalling. In this study, we investigate a conserved function of human presenilins in the development of the simple model organism Dictyostelium discoideum. We show that the block in Dictyostelium development caused by the ablation of both Dictyostelium presenilins is rescued by the expression of human presenilin 1, restoring the terminal differentiation of multiple cell types. This developmental role is independent of proteolytic activity, because the mutation of both catalytic aspartates does not affect presenilin ability to rescue development, and the ablation of nicastrin, a γ-secretase component that is crucial for proteolytic activity, does not block development. The role of presenilins during Dictyostelium development is therefore independent of their proteolytic activity. However, presenilin loss in Dictyostelium results in elevated cyclic AMP (cAMP) levels and enhanced stimulation-induced calcium release, suggesting that presenilins regulate these intracellular signalling pathways. Our data suggest that presenilin proteins perform an ancient non-proteolytic role in regulating intracellular signalling and development, and that Dictyostelium is a useful model for analysing human presenilin function.
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Affiliation(s)
- Marthe H. R. Ludtmann
- Centre for Biomedical Sciences, School of Biological Sciences, Royal Holloway University of London TW20 0EX, UK
| | - Grant P. Otto
- Centre for Biomedical Sciences, School of Biological Sciences, Royal Holloway University of London TW20 0EX, UK
| | | | - Zhi-Hui Chen
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Claire Y. Allan
- Faculty of Science, Technology and Engineering, La Trobe University, Bundoora VIC 3086, Australia
| | - Selina Brace
- Centre for Ecology and Evolution, School of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| | - Philip W. Beesley
- Centre for Biomedical Sciences, School of Biological Sciences, Royal Holloway University of London TW20 0EX, UK
| | - Alan R. Kimmel
- NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul Fisher
- Faculty of Science, Technology and Engineering, La Trobe University, Bundoora VIC 3086, Australia
| | - Richard Killick
- Institute of Psychiatry, King's College London, London SE5 8AF, UK
| | - Robin S. B. Williams
- Centre for Biomedical Sciences, School of Biological Sciences, Royal Holloway University of London TW20 0EX, UK
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36
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Martínková N, Barnett R, Cucchi T, Struchen R, Pascal M, Pascal M, Fischer MC, Higham T, Brace S, Ho SYW, Quéré JP, O'Higgins P, Excoffier L, Heckel G, Hoelzel AR, Dobney KM, Searle JB. Divergent evolutionary processes associated with colonization of offshore islands. Mol Ecol 2013; 22:5205-20. [PMID: 23998800 PMCID: PMC4159590 DOI: 10.1111/mec.12462] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2013] [Revised: 07/02/2013] [Accepted: 07/09/2013] [Indexed: 11/25/2022]
Abstract
Oceanic islands have been a test ground for evolutionary theory, but here, we focus on the possibilities for evolutionary study created by offshore islands. These can be colonized through various means and by a wide range of species, including those with low dispersal capabilities. We use morphology, modern and ancient sequences of cytochrome b (cytb) and microsatellite genotypes to examine colonization history and evolutionary change associated with occupation of the Orkney archipelago by the common vole (Microtus arvalis), a species found in continental Europe but not in Britain. Among possible colonization scenarios, our results are most consistent with human introduction at least 5100 bp (confirmed by radiocarbon dating). We used approximate Bayesian computation of population history to infer the coast of Belgium as the possible source and estimated the evolutionary timescale using a Bayesian coalescent approach. We showed substantial morphological divergence of the island populations, including a size increase presumably driven by selection and reduced microsatellite variation likely reflecting founder events and genetic drift. More surprisingly, our results suggest that a recent and widespread cytb replacement event in the continental source area purged cytb variation there, whereas the ancestral diversity is largely retained in the colonized islands as a genetic ‘ark’. The replacement event in the continental M. arvalis was probably triggered by anthropogenic causes (land‐use change). Our studies illustrate that small offshore islands can act as field laboratories for studying various evolutionary processes over relatively short timescales, informing about the mainland source area as well as the island.
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Affiliation(s)
- Natália Martínková
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK; Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Květná 8, Brno, 603 65, Czech Republic
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37
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Hansford J, Nuñez-Miño JM, Young RP, Brace S, Brocca JL, Turvey ST. Taxonomy-testing and the ‘Goldilocks Hypothesis’: morphometric analysis of species diversity in living and extinct Hispaniolan hutias. SYST BIODIVERS 2012. [DOI: 10.1080/14772000.2012.748697] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- James Hansford
- a Department of Biology , University of York, Wentworth Way , York YO10 5DD , UK
- b Institute of Zoology, Zoological Society of London, Regent's Park , London , NW1 4RY , UK
| | - José M. Nuñez-Miño
- c Durrell Wildlife Conservation Trust, Les Augrès Manor, Trinity , Jersey JE3 5BP, Channel Islands
| | - Richard P. Young
- c Durrell Wildlife Conservation Trust, Les Augrès Manor, Trinity , Jersey JE3 5BP, Channel Islands
- d Department of Biology and Biochemistry , University of Bath , Bath BA2 7AY, UK
| | - Selina Brace
- e School of Biological Sciences , Royal Holloway University of London, Egham TW20 0EX , UK
| | - Jorge L. Brocca
- f Sociedad Ornitológica de la Hispaniola , Parque Zoologico Nacional, Avenida de la Vega Real, Arroyo Hondo , Santo Domingo , Dominican Republic
| | - Samuel T. Turvey
- b Institute of Zoology, Zoological Society of London, Regent's Park , London , NW1 4RY , UK
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38
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Brace S, Barnes I, Powell A, Pearson R, Woolaver LG, Thomas MG, Turvey ST. Population history of the Hispaniolan hutia Plagiodontia aedium (Rodentia: Capromyidae): testing the model of ancient differentiation on a geotectonically complex Caribbean island. Mol Ecol 2012; 21:2239-53. [PMID: 22404699 DOI: 10.1111/j.1365-294x.2012.05514.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Hispaniola is a geotectonically complex island consisting of two palaeo-islands that docked c. 10 Ma, with a further geological boundary subdividing the southern palaeo-island into eastern and western regions. All three regions have been isolated by marine barriers during the late Cenozoic and possess biogeographically distinct terrestrial biotas. However, there is currently little evidence to indicate whether Hispaniolan mammals show distributional patterns reflecting this geotectonic history, as the island's endemic land mammal fauna is now almost entirely extinct. We obtained samples of Hispaniolan hutia (Plagiodontia aedium), one of the two surviving Hispaniolan land mammal species, through fieldwork and historical museum collections from seven localities distributed across all three of the island's biogeographic regions. Phylogenetic analysis using mitochondrial DNA (cytochrome b) reveals a pattern of historical allopatric lineage divergence in this species, with the spatial distribution of three distinct hutia lineages biogeographically consistent with the island's geotectonic history. Coalescent modelling, approximate Bayesian computation and approximate Bayes factor analyses support our phylogenetic inferences, indicating near-complete genetic isolation of these biogeographically separate populations and differing estimates of their effective population sizes. Spatial congruence of hutia lineage divergence is not however matched by temporal congruence with divergences in other Hispaniolan taxa or major events in Hispaniola's geotectonic history; divergence between northern and southern hutia lineages dates to c. 0.6 Ma, significantly later than the unification of the palaeo-islands. The three allopatric Plagiodontia populations should all be treated as distinct management units for conservation, with particular attention required for the northern population (low haplotype diversity) and the south-western population (high haplotype diversity but highly threatened).
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Affiliation(s)
- Selina Brace
- School of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK
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39
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O'Connor A, Brace S, Gould S, Dewell R, Engelken T. A Randomized Clinical Trial Evaluating a Farm-of-Origin Autogenous Moraxella bovis Vaccine to Control Infectious Bovine Keratoconjunctivis (Pinkeye) in Beef Cattle. J Vet Intern Med 2011; 25:1447-53. [DOI: 10.1111/j.1939-1676.2011.00803.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 06/24/2011] [Accepted: 08/09/2011] [Indexed: 11/28/2022] Open
Affiliation(s)
- A.M. O'Connor
- Department of Veterinary Diagnostics and Production Animal Medicine; Iowa State University College of Veterinary Medicine; Ames; IA
| | - S. Brace
- Department of Veterinary Diagnostics and Production Animal Medicine; Iowa State University College of Veterinary Medicine; Ames; IA
| | - S. Gould
- Department of Veterinary Diagnostics and Production Animal Medicine; Iowa State University College of Veterinary Medicine; Ames; IA
| | - R. Dewell
- Department of Veterinary Diagnostics and Production Animal Medicine; Iowa State University College of Veterinary Medicine; Ames; IA
| | - T. Engelken
- Department of Veterinary Diagnostics and Production Animal Medicine; Iowa State University College of Veterinary Medicine; Ames; IA
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Abstract
The evolution of helping, in which some individuals forfeit their own reproduction and help others to reproduce, is a central problem in evolutionary biology. Recently proposed insurance-based mechanisms rely on a pre-existing life history with a long period of offspring dependency relative to the short life expectancies of adult carers: a lone mother's offspring are doomed if she dies young, whereas after a helper dies, other group members can finish rearing the offspring. A critical question, however, is how this life history could evolve in ancestral non-social populations, as offspring survival would then depend on a single, short-lived carer. Here, we resolve this paradox by focusing on the extended parental care inherent in prolonged dependency. We show experimentally that in non-social wasps, extended care can significantly reduce the impact of interspecific parasites. Under extended care, offspring are less vulnerable by the time they are exposed to parasites, and costs of parasitism are reduced because mothers have the option to terminate investment in failing offspring. By experimentally simulating aspects of extended care in a species where it is lacking, we demonstrate that neither benefit requires specialized behaviour. Such benefits could therefore offset the disadvantage of prolonged dependency in non-social species, thereby facilitating the evolution of helping.
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Affiliation(s)
- Jeremy Field
- Department of Biology, University College London, Wolfson House, 4 Stephenson Way, London NW1 2HE, UK.
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41
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Abstract
Intracellular injections of Neurobiotin were used to determine whether the major ganglion cell classes of the macaque monkey retina, the magnocellular-projecting parasol, and the parvocellular-projecting midget cells showed evidence of cellular coupling similar to that recently described for cat retinal ganglion cells. Ganglion cells were labeled with the fluorescent dye acridine orange in an in vitro, isolated retina preparation and were selectively targeted for intracellular injection under direct microscopic control. The macaque midget cells, like the beta cells of the cat's retina, showed no evidence of tracer coupling when injected with Neurobiotin. By contrast, Neurobiotin-filled parasol cells, like cat alpha cells, showed a distinct pattern of tracer coupling to each other (homotypic coupling) and to amacrine cells (heterotypic coupling). In instances of homotypic coupling, the injected parasol cell was surrounded by a regular array of 3-6 neighboring parasol cells. The somata and proximal dendrites of these tracer-coupled cells were lightly labeled and appeared to costratify with the injected cell. Analysis of the nearest-neighbor distances for the parasol cell clusters showed that dendritic-field overlap remained constant as dendritic-field size increased from 100-400 microns in diameter. At least two amacrine cell types showed tracer coupling to parasol cells. One amacrine type had a small soma and thin, sparsely branching dendrites that extended for 1-2 mm in the inner plexiform layer. A second amacrine type had a relatively large soma, thick main dendrites, and distinct, axon-like processes that extended for at least 2-3 mm in the inner plexiform layer. The main dendrites of the large amacrine cells were closely apposed to the dendrites of parasol cells and may be the site of Neurobiotin transfer between the two cell types. We suggest that the tracer coupling between neighboring parasol cells takes place indirectly via the dendrites of the large amacrine cells and provides a mechanism, absent in midget cells, for increasing parasol cell receptive-field size and luminance contrast sensitivity.
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Affiliation(s)
- D M Dacey
- Department of Biological Structure, University of Washington, Seattle 98195
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42
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Aebischer P, Guénard V, Brace S. Peripheral nerve regeneration through blind-ended semipermeable guidance channels: effect of the molecular weight cutoff. J Neurosci 1989; 9:3590-5. [PMID: 2795143 PMCID: PMC6569902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Synthetic nerve guidance channels are used to better understand the cellular and molecular events controlling peripheral nerve regeneration. In the present study, the contribution of wound-healing molecules to peripheral nerve regeneration was assessed by varying the molecular weight cutoff of the tubular membrane. Nerve regeneration through polysulfone tubular membranes with molecular weight (Mw) cutoffs of 10(5) and 10(6) Da was analyzed in a transected hamster sciatic nerve model. Cohorts of 6 animals received tubes of either type for 4 or 8 weeks with the distal end of the polymer tube capped. Other cohorts of 6 animals received tubes of either type for 4 weeks with the distal nerve stump secured within the guidance channel so as to create a 4 or 8 mm gap between both nerve stumps. Both types of channels contained regenerated tissue cables extending to the distal end of the guidance channel at both 4 and 8 weeks in the absence of a distal nerve stump. The cables regenerated in the 10(5) Da channels were composed of nerve fascicles surrounded by a loose epineurial sheath, whereas those regenerated in the 10(6) Da channels were composed mainly of granulation tissue. The numbers of myelinated and unmyelinated axons were significantly greater in the 10(5) Da than in the 10(6) Da channels at both 4 and 8 weeks. Both types of channel contained regenerated tissue cables with numerous nerve fascicles when the distal nerve stump was present with either gap length. However, when the gap distance was 8 mm, the 10(6) Da channels contained significantly fewer myelinated axons than the 10(5) Da channels. The present study reveals that the Mw cutoff of a semipermeable guidance channel strongly influences the outcome of peripheral nerve regeneration, possibly by controlling the exchange of molecules between the channel's lumen and the external wound-healing environment. These results suggest that the wound-healing environment secretes humoral factors that can either promote or inhibit the nerve-regeneration process.
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Affiliation(s)
- P Aebischer
- Artificial Organ Laboratory, Brown University, Providence, Rhode Island 02912
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