1
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Lin AT, Hammond-Kaarremaa L, Liu HL, Stantis C, McKechnie I, Pavel M, Pavel SSM, Wyss SSÁ, Sparrow DQ, Carr K, Aninta SG, Perri A, Hartt J, Bergström A, Carmagnini A, Charlton S, Dalén L, Feuerborn TR, France CAM, Gopalakrishnan S, Grimes V, Harris A, Kavich G, Sacks BN, Sinding MHS, Skoglund P, Stanton DWG, Ostrander EA, Larson G, Armstrong CG, Frantz LAF, Hawkins MTR, Kistler L. The history of Coast Salish "woolly dogs" revealed by ancient genomics and Indigenous Knowledge. Science 2023; 382:1303-1308. [PMID: 38096292 PMCID: PMC7615573 DOI: 10.1126/science.adi6549] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 10/25/2023] [Indexed: 12/18/2023]
Abstract
Ancestral Coast Salish societies in the Pacific Northwest kept long-haired "woolly dogs" that were bred and cared for over millennia. However, the dog wool-weaving tradition declined during the 19th century, and the population was lost. In this study, we analyzed genomic and isotopic data from a preserved woolly dog pelt from "Mutton," collected in 1859. Mutton is the only known example of an Indigenous North American dog with dominant precolonial ancestry postdating the onset of settler colonialism. We identified candidate genetic variants potentially linked with their distinct woolly phenotype. We integrated these data with interviews from Coast Salish Elders, Knowledge Keepers, and weavers about shared traditional knowledge and memories surrounding woolly dogs, their importance within Coast Salish societies, and how colonial policies led directly to their disappearance.
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Affiliation(s)
- Audrey T Lin
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Richard Gilder Graduate School, American Museum of Natural History, New York, NY, USA
| | - Liz Hammond-Kaarremaa
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Vancouver Island University, Nanaimo, BC, Canada
| | - Hsiao-Lei Liu
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Chris Stantis
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Department of Geology and Geophysics, University of Utah, Salt Lake City, UT, USA
| | - Iain McKechnie
- Department of Anthropology, University of Victoria, Victoria, BC, Canada
| | - Michael Pavel
- Twana/Skokomish Indian Tribe, Skokomish Nation, WA, USA
| | - Susan sa'hLa mitSa Pavel
- Twana/Skokomish Indian Tribe, Skokomish Nation, WA, USA
- Coast Salish Wool Weaving Center, Skokomish Nation, WA, USA
- The Evergreen State College, Olympia, WA, USA
| | | | | | | | - Sabhrina Gita Aninta
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Angela Perri
- Department of Anthropology, Texas A&M University, College Station, TX, USA
- Chronicle Heritage, Phoenix, AZ, USA
| | - Jonathan Hartt
- Department of Indigenous Studies, Simon Fraser University, Burnaby, BC, Canada
| | - Anders Bergström
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Alberto Carmagnini
- Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universität, Munich, Germany
| | - Sophy Charlton
- PalaeoBARN, School of Archaeology, University of Oxford, Oxford, UK
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Tatiana R Feuerborn
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Shyam Gopalakrishnan
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Vaughan Grimes
- Department of Archaeology, Memorial University of Newfoundland, St. Johns, NL, Canada
| | - Alex Harris
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gwénaëlle Kavich
- Museum Conservation Institute, Smithsonian Institution, Suitland, MD, USA
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | | | - Pontus Skoglund
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
| | - David W G Stanton
- Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universität, Munich, Germany
- Cardiff School of Biosciences, Cardiff University, Cardiff, UK
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Greger Larson
- PalaeoBARN, School of Archaeology, University of Oxford, Oxford, UK
| | - Chelsey G Armstrong
- Department of Indigenous Studies, Simon Fraser University, Burnaby, BC, Canada
| | - Laurent A F Frantz
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
- Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universität, Munich, Germany
| | - Melissa T R Hawkins
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Logan Kistler
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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2
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Conrado AC, Demetrio WC, Stanton DWG, Bartz MLC, James SW, Santos A, da Silva E, Ferreira T, Acioli ANS, Ferreira AC, Maia LS, Silva TAC, Lavelle P, Velasquez E, Tapia-Coral SC, Muniz AW, Segalla RF, Decaëns T, Nadolny HS, Peña-Venegas CP, Pasini A, de Oliveira Júnior RC, Kille P, Brown GG, Cunha L. Amazonian earthworm biodiversity is heavily impacted by ancient and recent human disturbance. Sci Total Environ 2023; 895:165087. [PMID: 37379924 DOI: 10.1016/j.scitotenv.2023.165087] [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] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 06/30/2023]
Abstract
Despite the importance of earthworms for soil formation, more is needed to know about how Pre-Columbian modifications to soils and the landscape. Gaining a deeper understanding is essential for comprehending the historical drivers of earthworm communities and the development of effective conservation strategies in the Amazon rainforest. Human disturbance can significantly impact earthworm diversity, especially in rainforest soils, and in the particular case of the Amazonian rainforest, both recent and ancient anthropic practices may be important. Amazonian Dark Earths (ADEs) are fertile soils found throughout the Amazon Basin, created by sedentary habits and intensification patterns of pre-Colombian societies primarily developed in the second part of the Holocene period. We have sampled earthworm communities in three Brazilian Amazonian (ADEs) and adjacent reference soils (REF) under old and young forests and monocultures. To better assess taxonomic richness, we used morphology and the barcode region of the COI gene to identify juveniles and cocoons and delimit Molecular Operational Taxonomic Units (MOTUs). Here we suggest using Integrated Operational Taxonomical units (IOTUs) which combine both morphological and molecular data and provide a more comprehensive assessment of diversity, while MOTUs only rely on molecular data. A total of 970 individuals were collected, resulting in 51 taxonomic units (IOTUs, MOTUs, and morphospecies combined). From this total, 24 taxonomic units were unique to REF soils, 17 to ADEs, and ten were shared between both soils. The highest richness was found in old forest sites for ADEs (12 taxonomic units) and REFs (21 taxonomic units). The beta-diversity calculations reveal a high species turnover between ADEs and REF soils, providing evidence that ADEs and REFs possess distinct soil biota. Furthermore, results suggest that ADE sites, formed by Pre-Columbian human activities, conserve a high number of native species in the landscape and maintain a high abundance, despite their long-term nature.
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Affiliation(s)
- Ana C Conrado
- Biochemistry Department, Federal University of Paraná, Curitiba, PR 81531-980, Brazil
| | - Wilian C Demetrio
- Department of Soil Science, Federal University of Paraná, Curitiba, PR 80035-050, Brazil
| | | | - Marie L C Bartz
- Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Samuel W James
- Maharishi International University, Fairfield, IA 52557, United States
| | - Alessandra Santos
- Department of Soil Science, Federal University of Paraná, Curitiba, PR 80035-050, Brazil
| | | | - Talita Ferreira
- Department of Soil Science, Federal University of Paraná, Curitiba, PR 80035-050, Brazil
| | - Agno N S Acioli
- Federal University of Amazonas, Manaus, AM 69067-005, Brazil
| | - Alexandre C Ferreira
- Entomology Department, Federal University of Paraná, 81530-900 Curitiba, PR, Brazil
| | - Lilianne S Maia
- Department of Soil Science, Federal University of Paraná, Curitiba, PR 80035-050, Brazil
| | - Telma A C Silva
- Instituto Nacional de Pesquisas da Amazônia, Manaus, AM 69067-375, Brazil
| | - Patrick Lavelle
- Institut de Recherche pour le Développement, Cali 763537, Colombia
| | - Elena Velasquez
- Universidad Nacional de Colombia, Palmira 32 #12-00, Colombia
| | | | - Aleksander W Muniz
- Entomology Department, Federal University of Paraná, 81530-900 Curitiba, PR, Brazil; Embrapa Amazônia Ocidental, Manaus, AM 69010-970, Brazil
| | - Rodrigo F Segalla
- Department of Soil Science, Federal University of Paraná, Curitiba, PR 80035-050, Brazil
| | - Thibaud Decaëns
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Herlon S Nadolny
- Department of Soil Science, Federal University of Paraná, Curitiba, PR 80035-050, Brazil
| | | | - Amarildo Pasini
- Universidade Estadual de Londrina, Londrina, PR 86057-970, Brazil
| | | | - Peter Kille
- Cardiff University, Cardiff CF103AT, United Kingdom
| | - George G Brown
- Department of Soil Science, Federal University of Paraná, Curitiba, PR 80035-050, Brazil; Embrapa Florestas, Colombo, PR 83411-000, Brazil
| | - Luís Cunha
- Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal; School of Applied Sciences, University of South Wales, Pontypridd CF374BD, United Kingdom.
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3
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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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4
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Kutschera VE, Kierczak M, van der Valk T, von Seth J, Dussex N, Lord E, Dehasque M, Stanton DWG, Khoonsari PE, Nystedt B, Dalén L, Díez-Del-Molino D. GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species. BMC Bioinformatics 2022; 23:228. [PMID: 35698034 PMCID: PMC9195343 DOI: 10.1186/s12859-022-04757-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 03/08/2022] [Accepted: 05/30/2022] [Indexed: 11/25/2022] Open
Abstract
Background Many wild species have suffered drastic population size declines over the past centuries, which have led to ‘genomic erosion’ processes characterized by reduced genetic diversity, increased inbreeding, and accumulation of harmful mutations. Yet, genomic erosion estimates of modern-day populations often lack concordance with dwindling population sizes and conservation status of threatened species. One way to directly quantify the genomic consequences of population declines is to compare genome-wide data from pre-decline museum samples and modern samples. However, doing so requires computational data processing and analysis tools specifically adapted to comparative analyses of degraded, ancient or historical, DNA data with modern DNA data as well as personnel trained to perform such analyses. Results Here, we present a highly flexible, scalable, and modular pipeline to compare patterns of genomic erosion using samples from disparate time periods. The GenErode pipeline uses state-of-the-art bioinformatics tools to simultaneously process whole-genome re-sequencing data from ancient/historical and modern samples, and to produce comparable estimates of several genomic erosion indices. No programming knowledge is required to run the pipeline and all bioinformatic steps are well-documented, making the pipeline accessible to users with different backgrounds. GenErode is written in Snakemake and Python3 and uses Conda and Singularity containers to achieve reproducibility on high-performance compute clusters. The source code is freely available on GitHub (https://github.com/NBISweden/GenErode). Conclusions GenErode is a user-friendly and reproducible pipeline that enables the standardization of genomic erosion indices from temporally sampled whole genome re-sequencing data. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04757-0.
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Affiliation(s)
- 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
| | - Tom van der Valk
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johanna von Seth
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 106 91, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, 106 91, Stockholm, Sweden
| | - Nicolas Dussex
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 106 91, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, 106 91, Stockholm, Sweden
| | - Edana Lord
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 106 91, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, 106 91, Stockholm, Sweden
| | - Marianne Dehasque
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 106 91, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, 106 91, Stockholm, Sweden
| | - David W G Stanton
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 106 91, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Payam Emami Khoonsari
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Björn Nystedt
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 106 91, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, 106 91, Stockholm, Sweden
| | - David Díez-Del-Molino
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 106 91, Stockholm, Sweden. .,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden. .,Department of Zoology, Stockholm University, 106 91, Stockholm, Sweden.
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5
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Moorhouse‐Gann RJ, Vaughan IP, Cole NC, Goder M, Tatayah V, Jones CG, Mike D, Young RP, Bruford MW, Rivers MC, Hipperson H, Russo IM, Stanton DWG, Symondson WOC. Impacts of herbivory by ecological replacements on an island ecosystem. J Appl Ecol 2021. [DOI: 10.1111/1365-2664.14096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Rosemary J. Moorhouse‐Gann
- Durrell Wildlife Conservation Trust Les Augrès Manor Trinity Jersey
- Cardiff University Cardiff UK
- NERC Biomolecular Analysis FacilityDepartment of Animal & Plant Sciences Sheffield UK
| | | | - Nik C. Cole
- Durrell Wildlife Conservation Trust Les Augrès Manor Trinity Jersey
- Mauritian Wildlife Foundation Vacoas Mauritius
| | | | | | - Carl G. Jones
- Durrell Wildlife Conservation Trust Les Augrès Manor Trinity Jersey
- Mauritian Wildlife Foundation Vacoas Mauritius
| | | | - Richard P. Young
- Durrell Wildlife Conservation Trust Les Augrès Manor Trinity Jersey
| | | | | | - Helen Hipperson
- NERC Biomolecular Analysis FacilityDepartment of Animal & Plant Sciences Sheffield UK
| | | | - David W. G. Stanton
- Cardiff University Cardiff UK
- Queen Mary University of London School of Biological and Chemical Sciences London UK
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6
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Demetrio WC, Conrado AC, Acioli ANS, Ferreira AC, Bartz MLC, James SW, da Silva E, Maia LS, Martins GC, Macedo RS, Stanton DWG, Lavelle P, Velasquez E, Zangerlé A, Barbosa R, Tapia‐Coral SC, Muniz AW, Santos A, Ferreira T, Segalla RF, Decaëns T, Nadolny HS, Peña‐Venegas CP, Maia CMBF, Pasini A, Mota AF, Taube Júnior PS, Silva TAC, Rebellato L, de Oliveira Júnior RC, Neves EG, Lima HP, Feitosa RM, Vidal Torrado P, McKey D, Clement CR, Shock MP, Teixeira WG, Motta ACV, Melo VF, Dieckow J, Garrastazu MC, Chubatsu LS, Kille P, Brown GG, Cunha L. A "Dirty" Footprint: Macroinvertebrate diversity in Amazonian Anthropic Soils. Glob Chang Biol 2021; 27:4575-4591. [PMID: 34118093 PMCID: PMC9292437 DOI: 10.1111/gcb.15752] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 05/25/2021] [Indexed: 06/12/2023]
Abstract
Amazonian rainforests, once thought to be pristine wilderness, are increasingly known to have been widely inhabited, modified, and managed prior to European arrival, by human populations with diverse cultural backgrounds. Amazonian Dark Earths (ADEs) are fertile soils found throughout the Amazon Basin, created by pre-Columbian societies with sedentary habits. Much is known about the chemistry of these soils, yet their zoology has been neglected. Hence, we characterized soil fertility, macroinvertebrate communities, and their activity at nine archeological sites in three Amazonian regions in ADEs and adjacent reference soils under native forest (young and old) and agricultural systems. We found 673 morphospecies and, despite similar richness in ADEs (385 spp.) and reference soils (399 spp.), we identified a tenacious pre-Columbian footprint, with 49% of morphospecies found exclusively in ADEs. Termite and total macroinvertebrate abundance were higher in reference soils, while soil fertility and macroinvertebrate activity were higher in the ADEs, and associated with larger earthworm quantities and biomass. We show that ADE habitats have a unique pool of species, but that modern land use of ADEs decreases their populations, diversity, and contributions to soil functioning. These findings support the idea that humans created and sustained high-fertility ecosystems that persist today, altering biodiversity patterns in Amazonia.
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Affiliation(s)
- Wilian C. Demetrio
- Department of Soil ScienceFederal University of ParanáCuritibaPRBrazil
- Present address:
INPE – National Institute for Space ResearchSão José dos CamposSP12227‐010Brazil
| | - Ana C. Conrado
- Biochemistry DepartmentFederal University of ParanáCuritibaPRBrazil
| | | | | | - Marie L. C. Bartz
- Centre for Functional EcologyDepartment of Life SciencesUniversity of CoimbraCoimbraPortugal
| | | | | | - Lilianne S. Maia
- Department of Soil ScienceFederal University of ParanáCuritibaPRBrazil
| | | | | | - David W. G. Stanton
- Department of Bioinformatics and GeneticsSwedish Museum of Natural HistoryStockholmSweden
| | | | | | - Anne Zangerlé
- Ministère de l’Agriculture, de la Viticulture et de la Protection des consommateursLuxembourgLuxembourg
| | | | | | | | - Alessandra Santos
- Department of Soil ScienceFederal University of ParanáCuritibaPRBrazil
| | - Talita Ferreira
- Department of Soil ScienceFederal University of ParanáCuritibaPRBrazil
| | | | - Thibaud Decaëns
- CEFEUniv MontpellierCNRSEPHEIRDUniv Paul‐Valéry MontpellierMontpellierFrance
| | - Herlon S. Nadolny
- Department of Soil ScienceFederal University of ParanáCuritibaPRBrazil
| | | | | | | | - André F. Mota
- Biochemistry DepartmentFederal University of ParanáCuritibaPRBrazil
| | | | | | | | | | - Eduardo G. Neves
- Museu de Arqueologia e EtnologiaUniversidade de São PauloSão PauloSPBrazil
| | | | | | - Pablo Vidal Torrado
- Soil Science DepartmentEscola Superior de Agricultura Luís de QueirozUniversidade de São PauloPiracicabaSPBrazil
| | - Doyle McKey
- CEFEUniv MontpellierCNRSEPHEIRDUniv Paul‐Valéry MontpellierMontpellierFrance
| | | | | | | | | | - Vander F. Melo
- Department of Soil ScienceFederal University of ParanáCuritibaPRBrazil
| | - Jeferson Dieckow
- Department of Soil ScienceFederal University of ParanáCuritibaPRBrazil
| | | | - Leda S. Chubatsu
- Biochemistry DepartmentFederal University of ParanáCuritibaPRBrazil
| | | | - Peter Kille
- School of BiosciencesCardiff UniversityCardiffCFUK
| | - George G. Brown
- Department of Soil ScienceFederal University of ParanáCuritibaPRBrazil
- Embrapa FlorestasColomboPRBrazil
| | - Luís Cunha
- Centre for Functional EcologyDepartment of Life SciencesUniversity of CoimbraCoimbraPortugal
- School of Applied SciencesUniversity of South WalesPontypriddCFUK
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7
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Larsson P, von Seth J, Hagen IJ, Götherström A, Androsov S, Germonpré M, Bergfeldt N, Fedorov S, Eide NE, Sokolova N, Berteaux D, Angerbjörn A, Flagstad Ø, Plotnikov V, Norén K, Díez-Del-Molino D, Dussex N, Stanton DWG, Dalén L. Consequences of past climate change and recent human persecution on mitogenomic diversity in the arctic fox. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190212. [PMID: 31679495 PMCID: PMC6863501 DOI: 10.1098/rstb.2019.0212] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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] [Indexed: 01/12/2023] Open
Abstract
Ancient DNA provides a powerful means to investigate the timing, rate and extent of population declines caused by extrinsic factors, such as past climate change and human activities. One species probably affected by both these factors is the arctic fox, which had a large distribution during the last glaciation that subsequently contracted at the start of the Holocene. More recently, the arctic fox population in Scandinavia went through a demographic bottleneck owing to human persecution. To investigate the consequences of these processes, we generated mitogenome sequences from a temporal dataset comprising Pleistocene, historical and modern arctic fox samples. We found no evidence that Pleistocene populations in mid-latitude Europe or Russia contributed to the present-day gene pool of the Scandinavian population, suggesting that postglacial climate warming led to local population extinctions. Furthermore, during the twentieth-century bottleneck in Scandinavia, at least half of the mitogenome haplotypes were lost, consistent with a 20-fold reduction in female effective population size. In conclusion, these results suggest that the arctic fox in mainland Western Europe has lost genetic diversity as a result of both past climate change and human persecution. Consequently, it might be particularly vulnerable to the future challenges posed by climate change. This article is part of a discussion meeting issue 'The past is a foreign country: how much can the fossil record actually inform conservation?'
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Affiliation(s)
- Petter Larsson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Johanna von Seth
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | | | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | | | - Mietje Germonpré
- Operational Direction 'Earth and History of Life', Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Nora Bergfeldt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Sergey Fedorov
- Mammoth Museum of Institute of Applied Ecology of the North, North-Eastern Federal University, Yakutsk, Republic Sakha (Yakutia), Russia
| | - Nina E Eide
- Norwegian Institute for Nature Research, Trondheim, Norway
| | - Natalia Sokolova
- Arctic Research Station of Institute of Plant and Animal Ecology, Ural Branch of Russian Academy of Sciences, Yamal-Nenets Autonomous District, Russia.,Arctic Research Center of Yamal-Nenets Autonomous District, Salekhard, Russia
| | - Dominique Berteaux
- Canada Research Chair on Northern Biodiversity and Centre for Northern Studies, Université du Québec à Rimouski, Rimouski, Canada
| | | | | | - Valeri Plotnikov
- Academy of Sciences of Sakha Republic, Lenin Avenue 33, Republic of Sakha, Yakutia, Russia
| | - Karin Norén
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - David Díez-Del-Molino
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Nicolas Dussex
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - David W G Stanton
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
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8
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Stanton DWG, Frandsen P, Waples RK, Heller R, Russo IRM, Orozco-terWengel PA, Pedersen CET, Siegismund HR, Bruford MW. More grist for the mill? Species delimitation in the genomic era and its implications for conservation. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01149-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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9
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Conrado AC, Arruda H, Stanton DWG, James SW, Peter Kille, Brown G, Silva E, Dupont L, Taheri S, Morgan AJ, Simões N, Rodrigues A, Montiel R, Cunha L. The complete mitochondrial DNA sequence of the pantropical earthworm Pontoscolex corethrurus (Rhinodrilidae, Clitellata): Mitogenome characterization and phylogenetic positioning. Zookeys 2017:1-13. [PMID: 29118589 PMCID: PMC5672579 DOI: 10.3897/zookeys.688.13721] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 05/16/2017] [Accepted: 07/17/2017] [Indexed: 11/21/2022] Open
Abstract
Pontoscolexcorethrurus (Müller, 1857) plays an important role in tropical soil ecosystems and has been widely used as an animal model for a large variety of ecological studies in particular due to its common presence and generally high abundance in human-disturbed tropical soils. In this study we describe the complete mitochondrial genome of the peregrine earthworm P.corethrurus. This is the first record of a mitochondrial genome within the Rhinodrilidae family. Its mitochondrial genome is 14 835 bp in length containing 37 genes (13 protein-coding genes (PCG) 2 rRNA genes and 22 tRNA genes). It has the same gene content and structure as in other sequenced earthworms but unusual among invertebrates it hasseveral overlapping open reading frames. All genes are encoded on the same strand. Most of the PCGs use ATG as the start codon except for ND3 which uses GTG as the start codon. The A+T content of the mitochondrial genome is 59.9% (31.8% A 28.1% T 14.6% G and 25.6% for C). The annotated genome sequence has been deposited in GenBank under the accession number KT988053.
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Affiliation(s)
- Ana C Conrado
- Universidade Federal do Paraná, Departamento de Ciências do Solo, Curitiba, Paraná, Brazil
| | - Hugo Arruda
- CIRN/Departamento de Biologia, Universidade dos Açores, Ponta Delgada, Portugal
| | - David W G Stanton
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, UK CF10 3AX
| | - Samuel W James
- Maharishi University of Management, Sustainable Living Dept., Fairfield,IA, USA
| | - Peter Kille
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, UK CF10 3AX
| | - George Brown
- EMBRAPA-Florestas, Empresa Brasileira de Pesquisa Agropecuária (Embrapa), Colombo, PR, Brazil
| | - Elodie Silva
- EMBRAPA-Florestas, Empresa Brasileira de Pesquisa Agropecuária (Embrapa), Colombo, PR, Brazil
| | - Lise Dupont
- Université Paris Est Créteil, Institut d'écologie et des sciences de l'environnement de Paris (IEES), Créteil, France
| | - Shabnam Taheri
- Université Paris Est Créteil, Institut d'écologie et des sciences de l'environnement de Paris (IEES), Créteil, France
| | - Andrew J Morgan
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, UK CF10 3AX
| | - Nelson Simões
- CIRN/Departamento de Biologia, Universidade dos Açores, Ponta Delgada, Portugal
| | - Armindo Rodrigues
- Centro de Vulcanologia e Avaliação de Riscos Geológicos (CVARG), Universidade dos Açores, Ponta Delgada, Portugal
| | - Rafael Montiel
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, México
| | - Luis Cunha
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, UK CF10 3AX.,EMBRAPA-Florestas, Empresa Brasileira de Pesquisa Agropecuária (Embrapa), Colombo, PR, Brazil
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10
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Stanton DWG, Mulville JA, Bruford MW. Colonization of the Scottish islands via long-distance Neolithic transport of red deer (Cervus elaphus). Proc Biol Sci 2016; 283:rspb.2016.0095. [PMID: 27053752 PMCID: PMC4843653 DOI: 10.1098/rspb.2016.0095] [Citation(s) in RCA: 16] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 03/07/2016] [Indexed: 02/01/2023] Open
Abstract
Red deer (Cervus elaphus) have played a key role in human societies throughout history, with important cultural significance and as a source of food and materials. This relationship can be traced back to the earliest human cultures and continues to the present day. Humans are thought to be responsible for the movement of a considerable number of deer throughout history, although the majority of these movements are poorly described or understood. Studying such translocations allows us to better understand ancient human-wildlife interactions, and in the case of island colonizations, informs us about ancient human maritime practices. This study uses DNA sequences to characterise red deer genetic diversity across the Scottish islands (Inner and Outer Hebrides and Orkney) and mainland using ancient deer samples, and attempts to infer historical colonization events. We show that deer from the Outer Hebrides and Orkney are unlikely to have originated from mainland Scotland, implying that humans introduced red deer from a greater distance. Our results are also inconsistent with an origin from Ireland or Norway, suggesting long-distance maritime travel by Neolithic people to the outer Scottish Isles from an unknown source. Common haplotypes and low genetic differentiation between the Outer Hebrides and Orkney imply common ancestry and/or gene flow across these islands. Close genetic proximity between the Inner Hebrides and Ireland, however, corroborates previous studies identifying mainland Britain as a source for red deer introductions into Ireland. This study provides important information on the processes that led to the current distribution of the largest surviving indigenous land mammal in the British Isles.
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Affiliation(s)
- David W G Stanton
- School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK
| | - Jacqueline A Mulville
- School of History, Archaeology and Religion, Cardiff University, Humanities Building, Column Drive, Cardiff CF10 3EU, UK
| | - Michael W Bruford
- School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK
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11
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Sitko J, Bizos J, Sherrard-Smith E, Stanton DWG, Komorová P, Heneberg P. Integrative taxonomy of European parasitic flatworms of the genus Metorchis Looss, 1899 (Trematoda: Opisthorchiidae). Parasitol Int 2016; 65:258-67. [PMID: 26794684 DOI: 10.1016/j.parint.2016.01.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [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: 10/13/2015] [Revised: 01/05/2016] [Accepted: 01/15/2016] [Indexed: 11/17/2022]
Abstract
Metorchis spp. are flukes (Platyhelminthes: Digenea) that infect vertebrates, including humans, dogs, cats, poultry and wild game, with cyprinid freshwater fish serving as typical second intermediate hosts. In their definitive hosts, the Metorchis spp. are difficult to identify to species. We provide and analyze sequences of two nuclear (18S rDNA and ITS2) and two mitochondrial (CO1 and ND1) DNA loci of four morphologically identified European species of the Metorchis, namely Metorchis albidus, Metorchis bilis, Metorchis crassiusculus and Metorchis xanthosomus, and of another opisthorchiid, Euamphimerus pancreaticus. DNA analysis suggests that the Metorchis specimens identified morphologically as M. albidus (from Lutra lutra), M. bilis (from Phalacrocorax carbo) and M. crassiusculus (from Aquila heliaca and Buteo rufinus) represent a single species. Thus, M. albidus (Braun, 1893) Loos, 1899 and M. crassiusculus (Rudolphi, 1809) Looss, 1899 are recognized as junior subjective synonyms of M. bilis (Braun, 1790) Odening, 1962. We also provide comparative measurements of the Central European Metorchis spp., and address their tissue specificity and prevalence based on the examination of extensive bird cohort from 1962 to 2015. M. bilis and M. xanthosomus can be morphologically diagnosed by measuring the extent of genitalia relative to body length and by the size ratio of their suckers. They also differ in their core definitive hosts, with ducks (Anas, Aythya) and coots (Fulica) hosting M. xanthosomus, and cormorants (Phalacrocorax), the birds of prey (Buteo, Aquila, etc.), piscivorous mammals (Lutra, Vulpes, Ursus, etc.) and humans hosting M. bilis. Previous reports on the Metorchis spp. contain numerous suspected misidentifications.
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Affiliation(s)
- Jiljí Sitko
- Comenius Museum, Moravian Ornithological Station, Přerov, Czech Republic
| | - Jiří Bizos
- Charles University in Prague, Third Faculty of Medicine, Prague, Czech Republic
| | - Eleanor Sherrard-Smith
- Cardiff University, School of Biosciences, Cardiff, United Kingdom; Imperial College London, Department of Infectious Disease Epidemiology, London, United Kingdom
| | | | | | - Petr Heneberg
- Charles University in Prague, Third Faculty of Medicine, Prague, Czech Republic.
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12
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Stanton DWG, Hobbs GI, McCafferty DJ, Chadwick EA, Philbey AW, Saccheri IJ, Slater FM, Bruford MW. Contrasting genetic structure of the Eurasian otter (Lutra lutra) across a latitudinal divide. J Mammal 2014. [DOI: 10.1644/13-mamm-a-201] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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13
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Stanton DWG, Hart J, Galbusera P, Helsen P, Shephard J, Kümpel NF, Wang J, Ewen JG, Bruford MW. Distinct and diverse: range-wide phylogeography reveals ancient lineages and high genetic variation in the endangered okapi (Okapia johnstoni). PLoS One 2014; 9:e101081. [PMID: 25007188 PMCID: PMC4090074 DOI: 10.1371/journal.pone.0101081] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [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: 03/07/2014] [Accepted: 06/02/2014] [Indexed: 11/22/2022] Open
Abstract
The okapi is an endangered, evolutionarily distinctive even-toed ungulate classified within the giraffidae family that is endemic to the Democratic Republic of Congo. The okapi is currently under major anthropogenic threat, yet to date nothing is known about its genetic structure and evolutionary history, information important for conservation management given the species' current plight. The distribution of the okapi, being confined to the Congo Basin and yet spanning the Congo River, also makes it an important species for testing general biogeographic hypotheses for Congo Basin fauna, a currently understudied area of research. Here we describe the evolutionary history and genetic structure of okapi, in the context of other African ungulates including the giraffe, and use this information to shed light on the biogeographic history of Congo Basin fauna in general. Using nuclear and mitochondrial DNA sequence analysis of mainly non-invasively collected samples, we show that the okapi is both highly genetically distinct and highly genetically diverse, an unusual combination of genetic traits for an endangered species, and feature a complex evolutionary history. Genetic data are consistent with repeated climatic cycles leading to multiple Plio-Pleistocene refugia in isolated forests in the Congo catchment but also imply historic gene flow across the Congo River.
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Affiliation(s)
| | - John Hart
- Lukuru Foundation, Projet Tshuapa-Lomami-Lualaba (TL2), Kinshasa, Democratic Republic of Congo
| | - Peter Galbusera
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | - Philippe Helsen
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | - Jill Shephard
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | - Noëlle F. Kümpel
- Conservation Programmes, Zoological Society of London, London, United Kingdom
| | - Jinliang Wang
- Institute of Zoology, Zoological Society of London, London, United Kingdom
| | - John G. Ewen
- Institute of Zoology, Zoological Society of London, London, United Kingdom
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14
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Morrissey CA, Stanton DWG, Tyler CR, Pereira MG, Newton J, Durance I, Ormerod SJ. Developmental impairment in eurasian dipper nestlings exposed to urban stream pollutants. Environ Toxicol Chem 2014; 33:1315-23. [PMID: 24648128 DOI: 10.1002/etc.2555] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 02/05/2014] [Accepted: 02/10/2014] [Indexed: 05/09/2023]
Abstract
Avian studies of endocrine disruption traditionally have focused on reproductive impairment, given that many environmental contaminants affect sex steroid hormones. There is also increasing interest in altered thyroid function, and associated early development, particularly in altricial species with extended developmental windows. Both types of effect are relevant under the complex pollutant conditions created in streams draining urban areas, but case studies are scarce. Therefore, the authors measured breeding performance, as well as nestling growth, condition, and plasma thyroid hormones, in 87 Eurasian dipper (Cinclus cinclus) nests on 36 urban and rural streams in south and mid-Wales (UK); invertebrate prey data were also collected. The objective of the present study was to evaluate whether urban stream pollution or food scarcity might affect reproduction or development in this specialized aquatic songbird. Clutch sizes and egg fertility were similar on rural and urban streams, whereas nest success was actually higher at urban sites and food abundance was not significantly reduced. However, subtle but important differences were apparent. Urban nestlings were significantly lighter than rural nestlings for their body size (condition index), and brood sex ratios were increasingly male biased with increasing urbanization. The nestling thyroid hormone profile closely reflected urban land use, whereas depressed triiodothyronine (T3) hormones and poorer body condition were associated with higher exposure to polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs) at urbanized sites. These data suggest that PCBs, PBDEs, and/or accompanying contaminants in urban streams could be affecting dipper nestling development, with potential consequences for the birds' fitness.
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Affiliation(s)
- Christy A Morrissey
- Department of Biology and School of Environment and Sustainability, University of Saskatchewan, Saskatoon, Saskatchewan, Canada; Catchment Research Group, School of Biosciences, Cardiff University, Cardiff, United Kingdom
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Crowther TW, Stanton DWG, Thomas SM, A'Bear AD, Hiscox J, Jones TH, Voříšková J, Baldrian P, Boddy L. Top-down control of soil fungal community composition by a globally distributed keystone consumer. Ecology 2013; 94:2518-28. [DOI: 10.1890/13-0197.1] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Morrissey CA, Stanton DWG, Pereira MG, Newton J, Durance I, Tyler CR, Ormerod SJ. Eurasian dipper eggs indicate elevated organohalogenated contaminants in urban rivers. Environ Sci Technol 2013; 47:8931-8939. [PMID: 23819781 DOI: 10.1021/es402124z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Many urban European streams are recovering from industrial, mining, and sewage pollution during the 20th century. However, associated recolonization by clean water organisms can potentially result in exposure to legacy or novel toxic pollutants that persist in the environment. Between 2008 and 2010, we sampled eggs of a river passerine, the Eurasian dipper (Cinclus cinclus), from 33 rivers in South Wales and the English borders (UK) which varied in catchment land use from rural to highly urbanized. Dipper egg δ(15)N and δ(13)C stable isotopes were enriched from urban rivers while δ(34)S was strongly depleted, effectively discriminating their urban or rural origins at thresholds of 10% urban land cover or 1000 people/km(2). Concentrations of total polychlorinated biphenyls (PCBs) and polybrominated biphenyl ethers (PBDEs) were positively related to urban land cover and human population density while legacy organochlorine pesticides such as p,p'-DDE, lindane, and hexachlorobenzene were found in higher concentrations at rural sites. Levels of PBDEs in urban dipper eggs (range of 136-9299 ng/g lw) were among the highest ever reported in passerines, and some egg contaminants were at or approaching levels sufficient for adverse effects on avian development. With the exception of dieldrin, our data shows PCBs and other organochlorine pesticides have remained stable or increased in the past 20 years in dipper eggs, despite discontinued use.
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Affiliation(s)
- Christy A Morrissey
- Department of Biology and School of Environment and Sustainability, University of Saskatchewan, 112 Science Place, Saskatoon, Saskatchewan S7N 5E2, Canada.
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