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Larsson MNA, Morell Miranda P, Pan L, Başak Vural K, Kaptan D, Rodrigues Soares AE, Kivikero H, Kantanen J, Somel M, Özer F, Johansson AM, Storå J, Günther T. Ancient Sheep Genomes Reveal Four Millennia of North European Short-Tailed Sheep in the Baltic Sea Region. Genome Biol Evol 2024; 16:evae114. [PMID: 38795367 PMCID: PMC11162877 DOI: 10.1093/gbe/evae114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 04/24/2024] [Accepted: 05/21/2024] [Indexed: 05/27/2024] Open
Abstract
Sheep are among the earliest domesticated livestock species, with a wide variety of breeds present today. However, it remains unclear how far back this diversity goes, with formal documentation only dating back a few centuries. North European short-tailed (NEST) breeds are often assumed to be among the oldest domestic sheep populations, even thought to represent relicts of the earliest sheep expansions during the Neolithic period reaching Scandinavia <6,000 years ago. This study sequenced the genomes (up to 11.6X) of five sheep remains from the Baltic islands of Gotland and Åland, dating from the Late Neolithic (∼4,100 cal BP) to historical times (∼1,600 CE). Our findings indicate that these ancient sheep largely possessed the genetic characteristics of modern NEST breeds, suggesting a substantial degree of long-term continuity of this sheep type in the Baltic Sea region. Despite the wide temporal spread, population genetic analyses show high levels of affinity between the ancient genomes and they also exhibit relatively high genetic diversity when compared to modern NEST breeds, implying a loss of diversity in most breeds during the last centuries associated with breed formation and recent bottlenecks. Our results shed light on the development of breeds in Northern Europe specifically as well as the development of genetic diversity in sheep breeds, and their expansion from the domestication center in general.
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Affiliation(s)
- Martin N A Larsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Pedro Morell Miranda
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Li Pan
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Kıvılcım Başak Vural
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Damla Kaptan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | | | - Hanna Kivikero
- Department of Culture, University of Helsinki, Helsinki, Finland
| | - Juha Kantanen
- Natural Resources Institute Finland, Jokioinen, Finland
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Füsun Özer
- Department of Anthropology, Hacettepe University, Ankara, Turkey
| | - Anna M Johansson
- Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jan Storå
- Osteoarchaeological Research Laboratory, Stockholm University, Stockholm, Sweden
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
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2
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Childebayeva A, Zavala EI. Review: Computational analysis of human skeletal remains in ancient DNA and forensic genetics. iScience 2023; 26:108066. [PMID: 37927550 PMCID: PMC10622734 DOI: 10.1016/j.isci.2023.108066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023] Open
Abstract
Degraded DNA is used to answer questions in the fields of ancient DNA (aDNA) and forensic genetics. While aDNA studies typically center around human evolution and past history, and forensic genetics is often more concerned with identifying a specific individual, scientists in both fields face similar challenges. The overlap in source material has prompted periodic discussions and studies on the advantages of collaboration between fields toward mutually beneficial methodological advancements. However, most have been centered around wet laboratory methods (sampling, DNA extraction, library preparation, etc.). In this review, we focus on the computational side of the analytical workflow. We discuss limitations and considerations to consider when working with degraded DNA. We hope this review provides a framework to researchers new to computational workflows for how to think about analyzing highly degraded DNA and prompts an increase of collaboration between the forensic genetics and aDNA fields.
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Affiliation(s)
- Ainash Childebayeva
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anthropology, University of Kansas, Lawrence, KS, USA
| | - Elena I. Zavala
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Biology, University of Oregon, Eugene, OR, USA
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3
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Doan K, Schnitzler A, Preston F, Griggo C, Lang G, Belhaoues F, Blaise E, Crégut-Bonnoure E, Frère S, Foucras S, Gardeisen A, Laurent A, Müller W, Picavet R, Puissant S, Yvinec JH, Pilot M. Evolutionary history of the extinct wolf population from France in the context of global phylogeographic changes throughout the Holocene. Mol Ecol 2023; 32:4627-4647. [PMID: 37337956 DOI: 10.1111/mec.17054] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 05/20/2023] [Accepted: 06/05/2023] [Indexed: 06/21/2023]
Abstract
Phylogeographic patterns in large mammals result from natural environmental factors and anthropogenic effects, which in some cases include domestication. The grey wolf was once widely distributed across the Holarctic, but experienced phylogeographic shifts and demographic declines during the Holocene. In the 19th-20th centuries, the species became extirpated from large parts of Europe due to direct extermination and habitat loss. We reconstructed the evolutionary history of the extinct Western European wolves based on the mitogenomic composition of 78 samples from France (Neolithic-20th century) in the context of other populations of wolves and dogs worldwide. We found a close genetic similarity of French wolves from ancient, medieval and recent populations, which suggests the long-term continuity of maternal lineages. MtDNA haplotypes of the French wolves showed large diversity and fell into two main haplogroups of modern Holarctic wolves. Our worldwide phylogeographic analysis indicated that haplogroup W1, which includes wolves from Eurasia and North America, originated in Northern Siberia. Haplogroup W2, which includes only European wolves, originated in Europe ~35 kya and its frequency was reduced during the Holocene due to an expansion of haplogroup W1 from the east. Moreover, we found that dog haplogroup D, currently restricted to Europe and the Middle East, was nested within the wolf haplogroup W2. This suggests European origin of haplogroup D, probably as a result of an ancient introgression from European wolves. Our results highlight the dynamic evolutionary history of European wolves during the Holocene, with a partial lineage replacement and introgressive hybridization with local dog populations.
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Affiliation(s)
- Karolina Doan
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland
| | - Annik Schnitzler
- UMR 7194 HNHP CNRS/MNHN/UPVD, Equipe NOMADE, Muséum national d'histoire naturelle, Paris, France
| | | | - Christophe Griggo
- Université Grenoble Alpes, Laboratoire EDYTEM, URM 5204 Bâtiment "Pôle Montagne", 5 bd de la mer Caspienne, France
| | - Gérard Lang
- Espace Chasse et Nature Chemin de Strasbourg, France
| | - Fabien Belhaoues
- ASM - Archéologie des Sociétés Méditerranéennes, UMR 5140, Université Paul-Valéry, CNRS, MCC, Montpellier, France
- Labex ARCHIMEDE programme IA-ANR-11-LABX-0032-01, Montpellier, France
| | - Emilie Blaise
- ASM - Archéologie des Sociétés Méditerranéennes, UMR 5140, Université Paul-Valéry, CNRS, MCC, Montpellier, France
- Labex ARCHIMEDE programme IA-ANR-11-LABX-0032-01, Montpellier, France
| | - Evelyne Crégut-Bonnoure
- Muséum Requien, Avignon; Laboratoire TRACES-UMR 5608, Université Toulouse-Jean Jaurès, Toulouse, France
| | - Stéphane Frère
- Inrap, UMR 7209 AASPE, Muséum National d'Histoire Naturelle, La Courneuve, France
| | | | - Armelle Gardeisen
- ASM - Archéologie des Sociétés Méditerranéennes, UMR 5140, Université Paul-Valéry, CNRS, MCC, Montpellier, France
- Labex ARCHIMEDE programme IA-ANR-11-LABX-0032-01, Montpellier, France
| | | | - Werner Müller
- Laboratoire d'archéozoologie, Université de Neuchâtel, Avenue de Bellevaux 51, Neuchâtel, Switzerland
| | | | - Stéphane Puissant
- Muséum d'Histoire naturelle - Jardin de l'Arquebuse CS 73310 F-21033 Dijon Cedex, France
| | - Jean-Hervé Yvinec
- INRAP, UMR 7209 AASPE, Laboratoire d'archéozoologie de Compiègne, CRAVO, Compiègne, France
| | - Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland
- School of Life Sciences, University of Lincoln, Lincoln, UK
- Faculty of Biology, University of Gdańsk, Gdańsk, Poland
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4
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Brüniche-Olsen A, Bickham JW, Godard-Codding CA, Brykov VA, Kellner KF, Urban J, DeWoody JA. Influence of Holocene habitat availability on Pacific gray whale ( Eschrichtius robustus) population dynamics as inferred from whole mitochondrial genome sequences and environmental niche modeling. J Mammal 2021. [DOI: 10.1093/jmammal/gyab032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Environmental changes since the Pleistocene and commercial whaling in the last few centuries have drastically reduced many whale populations, including gray whales in the North Pacific. Herein we use complete mitogenome sequences from 74 individuals to evaluate gray whale phylogeography and historical demography, then use environmental niche modeling to assess how habitat availability has changed through time for Pacific gray whales. We identify a large degree of haplotype sharing between gray whales sampled in Russian and Mexican waters, coupled with very limited matrilineal population structure. Confirming previous studies, our environmental niche models showed a decrease in available habitat during the Last Glacial Maximum, but we find no genetic signals of recent population declines in mitochondrial genomes despite both sustained habitat loss and a commercial whaling bottleneck. Our results illustrate the complex dynamics of baleen whale biogeography since the Holocene as well as the difficulty in detecting recent demographic bottlenecks from mitochondrial DNA sequences.
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Affiliation(s)
- Anna Brüniche-Olsen
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, USA
| | - John W Bickham
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, USA
| | - Celine A Godard-Codding
- Institute of Environmental and Human Health, Texas Tech University (TTU) and TTU Health Sciences Center, Lubbock, TX, USA
| | - Vladimir A Brykov
- National Scientific Center for Marine Biology, Russian Academy of Sciences, Far Eastern Branch, Vladivostok, Russia
| | - Kenneth F Kellner
- Global Wildlife Conservation Center, State University of New York College of Environmental Science and Forestry, Syracuse, NY, USA
| | - Jorge Urban
- Departamento Academico de Ciencias Marinas y Costeras, Universidad Autonoma de Baja California Sur, Km 5.5 Carretera al Sur, Mezquitito, La Paz, BCS, Mexico
| | - J Andrew DeWoody
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
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5
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Ewers-Saucedo C, Allspach A, Barilaro C, Bick A, Brandt A, Fiege D, Füting S, Hausdorf B, Hayer S, Husemann M, Joger U, Kamcke C, Küster M, Lohrmann V, Martin I, Michalik P, Reinicke GB, Schwentner M, Stiller M, Brandis D. Natural history collections recapitulate 200 years of faunal change. ROYAL SOCIETY OPEN SCIENCE 2021; 8:201983. [PMID: 33996123 PMCID: PMC8059531 DOI: 10.1098/rsos.201983] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 03/15/2021] [Indexed: 06/12/2023]
Abstract
Changing species assemblages represent major challenges to ecosystems around the world. Retracing these changes is limited by our knowledge of past biodiversity. Natural history collections represent archives of biodiversity and are therefore an unparalleled source to study biodiversity changes. In the present study, we tested the value of natural history collections for reconstructing changes in the abundance and presence of species over time. In total, we scrutinized 17 080 quality-checked records for 242 epibenthic invertebrate species from the North and Baltic Seas collected throughout the last 200 years. Our approaches identified eight previously reported species introductions, 10 range expansions, six of which are new to science, as well as the long-term decline of 51 marine invertebrate species. The cross-validation of our results with published accounts of endangered species and neozoa of the area confirmed the results for two of the approaches for 49 to 55% of the identified species, and contradicted our results for 9 to 10%. The results based on relative record trends were less validated. We conclude that, with the proper approaches, natural history collections are an unmatched resource for recovering early species introductions and declines.
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Affiliation(s)
- Christine Ewers-Saucedo
- Zoologisches Museum, Christian-Albrechts-Universität zu Kiel, Hegewischstraße 3, 24105 Kiel, Germany
| | - Andreas Allspach
- Senckenberg Research Institute and Natural History Museum, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Christina Barilaro
- Landesmuseum Natur und Mensch Oldenburg, Damm 38-44, 26135 Oldenburg, Germany
| | - Andreas Bick
- Zoological Collections of the University of Rostock, Institute for Biological Sciences, General and Systematic Zoology, Universitätsplatz 2, 18055 Rostock, Germany
| | - Angelika Brandt
- Senckenberg Research Institute and Natural History Museum, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Goethe-University of Frankfurt, FB 15, Institute for Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, 60439 Frankfurt am Main, Germany
| | - Dieter Fiege
- Senckenberg Research Institute and Natural History Museum, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Susanne Füting
- Museum für Natur und Umwelt Lübeck, Musterbahn 8, 23552 Lübeck, Germany
| | - Bernhard Hausdorf
- Centrum für Naturkunde (CeNak), Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Sarah Hayer
- Zoologisches Museum, Christian-Albrechts-Universität zu Kiel, Hegewischstraße 3, 24105 Kiel, Germany
| | - Martin Husemann
- Centrum für Naturkunde (CeNak), Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Ulrich Joger
- Staatliches Naturhistorisches Museum, Pockelsstraße 10, 38106 Braunschweig, Germany
| | - Claudia Kamcke
- Staatliches Naturhistorisches Museum, Pockelsstraße 10, 38106 Braunschweig, Germany
| | - Mathias Küster
- Müritzeum, Zur Steinmole 1, 17192 Waren (Müritz), Germany
| | - Volker Lohrmann
- Übersee-Museum Bremen, Bahnhofsplatz 13, 28195 Bremen, Germany
| | - Ines Martin
- Deutsches Meeresmuseum, Katharinenberg 14-20, 18439 Stralsund, Germany
| | - Peter Michalik
- Zoologisches Museum der Universität Greifswald, Loitzer Straße 26, 17489 Greifswald, Germany
| | | | - Martin Schwentner
- Centrum für Naturkunde (CeNak), Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
- Naturhistorisches Museum Wien, Burgring 7, 1140 Wien, Austria
| | - Michael Stiller
- Übersee-Museum Bremen, Bahnhofsplatz 13, 28195 Bremen, Germany
| | - Dirk Brandis
- Zoologisches Museum, Christian-Albrechts-Universität zu Kiel, Hegewischstraße 3, 24105 Kiel, Germany
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6
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Davidson R, Fehren-Schmitz L, Llamas B. A Multidisciplinary Review of the Inka Imperial Resettlement Policy and Implications for Future Investigations. Genes (Basel) 2021; 12:215. [PMID: 33540755 PMCID: PMC7913103 DOI: 10.3390/genes12020215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 01/10/2023] Open
Abstract
The rulers of the Inka empire conquered approximately 2 million km2 of the South American Andes in just under 100 years from 1438-1533 CE. Inside the empire, the elite conducted a systematic resettlement of the many Indigenous peoples in the Andes that had been rapidly colonised. The nature of this resettlement phenomenon is recorded within the Spanish colonial ethnohistorical record. Here we have broadly characterised the resettlement policy, despite the often incomplete and conflicting details in the descriptions. We then review research from multiple disciplines that investigate the empirical reality of the Inka resettlement policy, including stable isotope analysis, intentional cranial deformation morphology, ceramic artefact chemical analyses and genetics. Further, we discuss the benefits and limitations of each discipline for investigating the resettlement policy and emphasise their collective value in an interdisciplinary characterisation of the resettlement policy.
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Affiliation(s)
- Roberta Davidson
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia
| | - Lars Fehren-Schmitz
- UCSC Paleogenomics, University of California Santa Cruz, Santa Cruz, CA 95064, USA;
- UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Adelaide, Adelaide, SA 5005, Australia
- National Centre for Indigenous Genomics (NCIG), Australian National University, Canberra, ACT 0200, Australia
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7
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Pont C, Wagner S, Kremer A, Orlando L, Plomion C, Salse J. Paleogenomics: reconstruction of plant evolutionary trajectories from modern and ancient DNA. Genome Biol 2019; 20:29. [PMID: 30744646 PMCID: PMC6369560 DOI: 10.1186/s13059-019-1627-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
How contemporary plant genomes originated and evolved is a fascinating question. One approach uses reference genomes from extant species to reconstruct the sequence and structure of their common ancestors over deep timescales. A second approach focuses on the direct identification of genomic changes at a shorter timescale by sequencing ancient DNA preserved in subfossil remains. Merged within the nascent field of paleogenomics, these complementary approaches provide insights into the evolutionary forces that shaped the organization and regulation of modern genomes and open novel perspectives in fostering genetic gain in breeding programs and establishing tools to predict future population changes in response to anthropogenic pressure and global warming.
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Affiliation(s)
- Caroline Pont
- INRA-UCA UMR 1095 Génétique Diversité et Ecophysiologie des Céréales, 63100, Clermont-Ferrand, France
| | - Stefanie Wagner
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, allées Jules Guesde, Bâtiment A, 31000, Toulouse, France.,INRA-Université Bordeaux UMR1202, Biodiversité Gènes et Communautés, 33610, Cestas, France
| | - Antoine Kremer
- INRA-Université Bordeaux UMR1202, Biodiversité Gènes et Communautés, 33610, Cestas, France
| | - Ludovic Orlando
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, allées Jules Guesde, Bâtiment A, 31000, Toulouse, France.,Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade, 1350K, Copenhagen, Denmark
| | - Christophe Plomion
- INRA-Université Bordeaux UMR1202, Biodiversité Gènes et Communautés, 33610, Cestas, France
| | - Jerome Salse
- INRA-UCA UMR 1095 Génétique Diversité et Ecophysiologie des Céréales, 63100, Clermont-Ferrand, France.
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8
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Leonardi M, Librado P, Der Sarkissian C, Schubert M, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Gamba C, Willerslev E, Orlando L. Evolutionary Patterns and Processes: Lessons from Ancient DNA. Syst Biol 2018; 66:e1-e29. [PMID: 28173586 PMCID: PMC5410953 DOI: 10.1093/sysbio/syw059] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 06/04/2016] [Accepted: 06/06/2016] [Indexed: 12/02/2022] Open
Abstract
Ever since its emergence in 1984, the field of ancient DNA has struggled to overcome the challenges related to the decay of DNA molecules in the fossil record. With the recent development of high-throughput DNA sequencing technologies and molecular techniques tailored to ultra-damaged templates, it has now come of age, merging together approaches in phylogenomics, population genomics, epigenomics, and metagenomics. Leveraging on complete temporal sample series, ancient DNA provides direct access to the most important dimension in evolution—time, allowing a wealth of fundamental evolutionary processes to be addressed at unprecedented resolution. This review taps into the most recent findings in ancient DNA research to present analyses of ancient genomic and metagenomic data.
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Affiliation(s)
- Michela Leonardi
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Pablo Librado
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Clio Der Sarkissian
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Ahmed H Alfarhan
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Saleh A Alquraishi
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | - Cristina Gamba
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark.,Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark.,Université de Toulouse, University Paul Sabatier (UPS), Laboratoire AMIS, Toulouse, France
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9
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Genetic diversity through time and space: diversity and demographic history from natural history specimens and serially sampled contemporary populations of the threatened Gouldian finch (Erythrura gouldiae). CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1051-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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10
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Llamas B, Willerslev E, Orlando L. Human evolution: a tale from ancient genomes. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2015.0484. [PMID: 27994125 DOI: 10.1098/rstb.2015.0484] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2016] [Indexed: 12/21/2022] Open
Abstract
The field of human ancient DNA (aDNA) has moved from mitochondrial sequencing that suffered from contamination and provided limited biological insights, to become a fully genomic discipline that is changing our conception of human history. Recent successes include the sequencing of extinct hominins, and true population genomic studies of Bronze Age populations. Among the emerging areas of aDNA research, the analysis of past epigenomes is set to provide more new insights into human adaptation and disease susceptibility through time. Starting as a mere curiosity, ancient human genetics has become a major player in the understanding of our evolutionary history.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
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Affiliation(s)
- Bastien Llamas
- Australian Centre for ADNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 K Copenhagen, Denmark.,Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.,Wellcome Genome Campus Hinxton, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 K Copenhagen, Denmark .,Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, Université de Toulouse, University Paul Sabatier, CNRS UMR 5288, 31000 Toulouse, France
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11
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MacHugh DE, Larson G, Orlando L. Taming the Past: Ancient DNA and the Study of Animal Domestication. Annu Rev Anim Biosci 2016; 5:329-351. [PMID: 27813680 DOI: 10.1146/annurev-animal-022516-022747] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
During the last decade, ancient DNA research has been revolutionized by the availability of increasingly powerful DNA sequencing and ancillary genomics technologies, giving rise to the new field of paleogenomics. In this review, we show how our understanding of the genetic basis of animal domestication and the origins and dispersal of livestock and companion animals during the Upper Paleolithic and Neolithic periods is being rapidly transformed through new scientific knowledge generated with paleogenomic methods. These techniques have been particularly informative in revealing high-resolution patterns of artificial and natural selection and evidence for significant admixture between early domestic animal populations and their wild congeners.
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Affiliation(s)
- David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland; .,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Greger Larson
- Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, United Kingdom;
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark; .,Université de Toulouse, University Paul Sabatier, Laboratoire AMIS, CNRS UMR 5288, 31000 Toulouse, France
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12
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Bolnick DA, Raff JA, Springs LC, Reynolds AW, Miró-Herrans AT. Native American Genomics and Population Histories. ANNUAL REVIEW OF ANTHROPOLOGY 2016. [DOI: 10.1146/annurev-anthro-102215-100036] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Studies of Native American genetic diversity and population history have been transformed over the last decade by important developments in anthropological genetics. During this time, researchers have adopted new DNA technologies and computational approaches for analyzing genomic data, and they have become increasingly sensitive to the views of research participants and communities. As new methods are applied to long-standing questions, and as more research is conducted in collaboration with indigenous communities, we are gaining new insights into the history and diversity of indigenous populations. This review discusses the recent methodological advances and genetic studies that have improved our understanding of Native American genomics and population histories. We synthesize current knowledge about Native American genomic variation and build a model of population history in the Americas. We also discuss the broader implications of this research for anthropology and related disciplines, and we highlight challenges and other considerations for future research.
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Affiliation(s)
- Deborah A. Bolnick
- Department of Anthropology, University of Texas at Austin, Austin, Texas 78712;, , ,
- Population Research Center, University of Texas at Austin, Austin, Texas 78712
| | - Jennifer A. Raff
- Department of Anthropology, University of Kansas, Lawrence, Kansas 66045-7556
| | - Lauren C. Springs
- Department of Anthropology, University of Texas at Austin, Austin, Texas 78712;, , ,
| | - Austin W. Reynolds
- Department of Anthropology, University of Texas at Austin, Austin, Texas 78712;, , ,
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712
| | - Aida T. Miró-Herrans
- Department of Anthropology, University of Texas at Austin, Austin, Texas 78712;, , ,
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13
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Cooper A, Turney C, Hughen KA, Brook BW, McDonald HG, Bradshaw CJA. Abrupt warming events drove Late Pleistocene Holarctic megafaunal turnover. Science 2015; 349:602-6. [DOI: 10.1126/science.aac4315] [Citation(s) in RCA: 236] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 07/03/2015] [Indexed: 01/02/2023]
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14
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Conservation archaeogenomics: ancient DNA and biodiversity in the Anthropocene. Trends Ecol Evol 2015; 30:540-9. [PMID: 26169594 DOI: 10.1016/j.tree.2015.06.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 06/11/2015] [Accepted: 06/15/2015] [Indexed: 11/22/2022]
Abstract
There is growing consensus that we have entered the Anthropocene, a geologic epoch characterized by human domination of the ecosystems of the Earth. With the future uncertain, we are faced with understanding how global biodiversity will respond to anthropogenic perturbations. The archaeological record provides perspective on human-environment relations through time and across space. Ancient DNA (aDNA) analyses of plant and animal remains from archaeological sites are particularly useful for understanding past human-environment interactions, which can help guide conservation decisions during the environmental changes of the Anthropocene. Here, we define the emerging field of conservation archaeogenomics, which integrates archaeological and genomic data to generate baselines or benchmarks for scientists, managers, and policy-makers by evaluating climatic and human impacts on past, present, and future biodiversity.
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15
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Der Sarkissian C, Allentoft ME, Ávila-Arcos MC, Barnett R, Campos PF, Cappellini E, Ermini L, Fernández R, da Fonseca R, Ginolhac A, Hansen AJ, Jónsson H, Korneliussen T, Margaryan A, Martin MD, Moreno-Mayar JV, Raghavan M, Rasmussen M, Velasco MS, Schroeder H, Schubert M, Seguin-Orlando A, Wales N, Gilbert MTP, Willerslev E, Orlando L. Ancient genomics. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130387. [PMID: 25487338 PMCID: PMC4275894 DOI: 10.1098/rstb.2013.0387] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past.
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Affiliation(s)
- Clio Der Sarkissian
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Morten E Allentoft
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - María C Ávila-Arcos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ross Barnett
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Paula F Campos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Enrico Cappellini
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Luca Ermini
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ruth Fernández
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Rute da Fonseca
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Aurélien Ginolhac
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Anders J Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Hákon Jónsson
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Thorfinn Korneliussen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ashot Margaryan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Michael D Martin
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - J Víctor Moreno-Mayar
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Maanasa Raghavan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Morten Rasmussen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Marcela Sandoval Velasco
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Hannes Schroeder
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Nathan Wales
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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16
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Peacock E, Sonsthagen SA, Obbard ME, Boltunov A, Regehr EV, Ovsyanikov N, Aars J, Atkinson SN, Sage GK, Hope AG, Zeyl E, Bachmann L, Ehrich D, Scribner KT, Amstrup SC, Belikov S, Born EW, Derocher AE, Stirling I, Taylor MK, Wiig Ø, Paetkau D, Talbot SL. Implications of the circumpolar genetic structure of polar bears for their conservation in a rapidly warming Arctic. PLoS One 2015; 10:e112021. [PMID: 25562525 PMCID: PMC4285400 DOI: 10.1371/journal.pone.0112021] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 09/19/2014] [Indexed: 11/18/2022] Open
Abstract
We provide an expansive analysis of polar bear (Ursus maritimus) circumpolar genetic variation during the last two decades of decline in their sea-ice habitat. We sought to evaluate whether their genetic diversity and structure have changed over this period of habitat decline, how their current genetic patterns compare with past patterns, and how genetic demography changed with ancient fluctuations in climate. Characterizing their circumpolar genetic structure using microsatellite data, we defined four clusters that largely correspond to current ecological and oceanographic factors: Eastern Polar Basin, Western Polar Basin, Canadian Archipelago and Southern Canada. We document evidence for recent (ca. last 1–3 generations) directional gene flow from Southern Canada and the Eastern Polar Basin towards the Canadian Archipelago, an area hypothesized to be a future refugium for polar bears as climate-induced habitat decline continues. Our data provide empirical evidence in support of this hypothesis. The direction of current gene flow differs from earlier patterns of gene flow in the Holocene. From analyses of mitochondrial DNA, the Canadian Archipelago cluster and the Barents Sea subpopulation within the Eastern Polar Basin cluster did not show signals of population expansion, suggesting these areas may have served also as past interglacial refugia. Mismatch analyses of mitochondrial DNA data from polar and the paraphyletic brown bear (U. arctos) uncovered offset signals in timing of population expansion between the two species, that are attributed to differential demographic responses to past climate cycling. Mitogenomic structure of polar bears was shallow and developed recently, in contrast to the multiple clades of brown bears. We found no genetic signatures of recent hybridization between the species in our large, circumpolar sample, suggesting that recently observed hybrids represent localized events. Documenting changes in subpopulation connectivity will allow polar nations to proactively adjust conservation actions to continuing decline in sea-ice habitat.
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Affiliation(s)
- Elizabeth Peacock
- Alaska Science Center, US Geological Survey, Anchorage, Alaska, United States of America
- Department of Environment, Government of Nunavut, Igloolik, Nunavut, Canada
- * E-mail:
| | - Sarah A. Sonsthagen
- Alaska Science Center, US Geological Survey, Anchorage, Alaska, United States of America
| | - Martyn E. Obbard
- Ontario Ministry of Natural Resources and Forestry, Peterborough, Ontario, Canada
| | - Andrei Boltunov
- All-Russian Research Institute for Nature Protection, Moscow, Russian Federation
| | - Eric V. Regehr
- US Fish and Wildlife Service, Marine Mammals Management, Anchorage, Alaska, United States of America
| | | | - Jon Aars
- Norwegian Polar Institute, Tromsø, Norway
| | | | - George K. Sage
- Alaska Science Center, US Geological Survey, Anchorage, Alaska, United States of America
| | - Andrew G. Hope
- Alaska Science Center, US Geological Survey, Anchorage, Alaska, United States of America
| | - Eve Zeyl
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Lutz Bachmann
- Natural History Museum, University of Oslo, Oslo, Norway
| | | | - Kim T. Scribner
- Department of Zoology, Michigan State University, East Lansing, Michigan, United States of America
| | - Steven C. Amstrup
- Polar Bears International, Bozeman, Montana, United States of America
| | - Stanislav Belikov
- All-Russian Research Institute for Nature Protection, Moscow, Russian Federation
| | - Erik W. Born
- Greenland Institute of Natural Resources, Copenhagen, Denmark
| | - Andrew E. Derocher
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Ian Stirling
- Science & Technology Branch, Environment Canada, Edmonton, Alberta, Canada
| | - Mitchell K. Taylor
- Faculty of Science and Environmental Studies, Lakehead University, Thunder Bay, Ontario, Canada
| | - Øystein Wiig
- Natural History Museum, University of Oslo, Oslo, Norway
| | - David Paetkau
- Wildlife Genetics International, Nelson, British Columbia, Canada
| | - Sandra L. Talbot
- Alaska Science Center, US Geological Survey, Anchorage, Alaska, United States of America
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17
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Major transitions in human evolution revisited: a tribute to ancient DNA. J Hum Evol 2014; 79:4-20. [PMID: 25532800 DOI: 10.1016/j.jhevol.2014.06.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 06/06/2014] [Accepted: 06/19/2014] [Indexed: 11/23/2022]
Abstract
The origin and diversification of modern humans have been characterized by major evolutionary transitions and demographic changes. Patterns of genetic variation within modern populations can help with reconstructing this ∼200 thousand year-long population history. However, by combining this information with genomic data from ancient remains, one can now directly access our evolutionary past and reveal our population history in much greater detail. This review outlines the main recent achievements in ancient DNA research and illustrates how the field recently moved from the polymerase chain reaction (PCR) amplification of short mitochondrial fragments to whole-genome sequencing and thereby revisited our own history. Ancient DNA research has revealed the routes that our ancestors took when colonizing the planet, whom they admixed with, how they domesticated plant and animal species, how they genetically responded to changes in lifestyle, and also, which pathogens decimated their populations. These approaches promise to soon solve many pending controversies about our own origins that are indecipherable from modern patterns of genetic variation alone, and therefore provide an extremely powerful toolkit for a new generation of molecular anthropologists.
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18
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Orlando L, Cooper A. Using Ancient DNA to Understand Evolutionary and Ecological Processes. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2014. [DOI: 10.1146/annurev-ecolsys-120213-091712] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ancient DNA provides a unique means to record genetic change through time and directly observe evolutionary and ecological processes. Although mostly based on mitochondrial DNA, the increasing availability of genomic sequences is leading to unprecedented levels of resolution. Temporal studies of population genetics have revealed dynamic patterns of change in many large vertebrates, featuring localized extinctions, migrations, and population bottlenecks. The pronounced climate cycles of the Late Pleistocene have played a key role, reducing the taxonomic and genetic diversity of many taxa and shaping modern populations. Importantly, the complex series of events revealed by ancient DNA data is seldom reflected in current biogeographic patterns. DNA preserved in ancient sediments and coprolites has been used to characterize a range of paleoenvironments and reconstruct functional relationships in paleoecological systems. In the near future, genome-level surveys of ancient populations will play an increasingly important role in revealing, calibrating, and testing evolutionary processes.
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Affiliation(s)
- Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350K Copenhagen, Denmark;,
| | - Alan Cooper
- Australian Center for Ancient DNA, University of Adelaide, Adelaide, South Australia
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19
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Skoglund P, Sjödin P, Skoglund T, Lascoux M, Jakobsson M. Investigating population history using temporal genetic differentiation. Mol Biol Evol 2014; 31:2516-27. [PMID: 24939468 PMCID: PMC4137715 DOI: 10.1093/molbev/msu192] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The rapid advance of sequencing technology, coupled with improvements in molecular methods for obtaining genetic data from ancient sources, holds the promise of producing a wealth of genomic data from time-separated individuals. However, the population-genetic properties of time-structured samples have not been extensively explored. Here, we consider the implications of temporal sampling for analyses of genetic differentiation and use a temporal coalescent framework to show that complex historical events such as size reductions, population replacements, and transient genetic barriers between populations leave a footprint of genetic differentiation that can be traced through history using temporal samples. Our results emphasize explicit consideration of the temporal structure when making inferences and indicate that genomic data from ancient individuals will greatly increase our ability to reconstruct population history.
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Affiliation(s)
- Pontus Skoglund
- Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden
| | - Per Sjödin
- Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden
| | - Tobias Skoglund
- Department of Evolutionary Biology, Uppsala University, Uppsala, SwedenDepartment of Information Technology, Uppsala University, Uppsala, Sweden
| | - Martin Lascoux
- Department of Ecology and Genetics, Program in Plant Ecology and Evolution, Uppsala University, Uppsala, SwedenScience for Life Laboratory, Uppsala, Sweden
| | - Mattias Jakobsson
- Department of Evolutionary Biology, Uppsala University, Uppsala, SwedenScience for Life Laboratory, Uppsala, Sweden
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20
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Fordham DA, Brook BW, Moritz C, Nogués-Bravo D. Better forecasts of range dynamics using genetic data. Trends Ecol Evol 2014; 29:436-43. [DOI: 10.1016/j.tree.2014.05.007] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2013] [Revised: 05/17/2014] [Accepted: 05/19/2014] [Indexed: 10/25/2022]
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21
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Hope AG, Ho SYW, Malaney JL, Cook JA, Talbot SL. ACCOUNTING FOR RATE VARIATION AMONG LINEAGES IN COMPARATIVE DEMOGRAPHIC ANALYSES. Evolution 2014; 68:2689-700. [DOI: 10.1111/evo.12469] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2013] [Accepted: 05/22/2014] [Indexed: 01/16/2023]
Affiliation(s)
- Andrew G. Hope
- U.S. Geological Survey; Alaska Science Center; 4210 University Drive Anchorage Alaska 99508
| | - Simon Y. W. Ho
- School of Biological Sciences; Edgeworth David Building A11; The University of Sydney; Sydney New South Wales 2006 Australia
| | - Jason L. Malaney
- Department of Natural Resources and Environmental Science; University of Nevada-Reno; Reno Nevada 89557
| | - Joseph A. Cook
- Department of Biology; University of New Mexico; Museum of Southwestern Biology MSC03 2020; Albuquerque New Mexico 87131
| | - Sandra L. Talbot
- U.S. Geological Survey; Alaska Science Center; 4210 University Drive Anchorage Alaska 99508
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22
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Lounsberry ZT, Almeida JB, Lanctot RB, Liebezeit JR, Sandercock BK, Strum KM, Zack S, Wisely SM. Museum collections reveal that Buff-breasted Sandpipers (Calidris subruficollis) maintained mtDNA variability despite large population declines during the past 135 years. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0611-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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Gray MM, Wegmann D, Haasl RJ, White MA, Gabriel SI, Searle JB, Cuthbert RJ, Ryan PG, Payseur BA. Demographic history of a recent invasion of house mice on the isolated Island of Gough. Mol Ecol 2014; 23:1923-39. [PMID: 24617968 PMCID: PMC4086876 DOI: 10.1111/mec.12715] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 02/24/2014] [Accepted: 02/26/2014] [Indexed: 02/05/2023]
Abstract
Island populations provide natural laboratories for studying key contributors to evolutionary change, including natural selection, population size and the colonization of new environments. The demographic histories of island populations can be reconstructed from patterns of genetic diversity. House mice (Mus musculus) inhabit islands throughout the globe, making them an attractive system for studying island colonization from a genetic perspective. Gough Island, in the central South Atlantic Ocean, is one of the remotest islands in the world. House mice were introduced to Gough Island by sealers during the 19th century and display unusual phenotypes, including exceptionally large body size and carnivorous feeding behaviour. We describe genetic variation in Gough Island mice using mitochondrial sequences, nuclear sequences and microsatellites. Phylogenetic analysis of mitochondrial sequences suggested that Gough Island mice belong to Mus musculus domesticus, with the maternal lineage possibly originating in England or France. Cluster analyses of microsatellites revealed genetic membership for Gough Island mice in multiple coastal populations in Western Europe, suggesting admixed ancestry. Gough Island mice showed substantial reductions in mitochondrial and nuclear sequence variation and weak reductions in microsatellite diversity compared with Western European populations, consistent with a population bottleneck. Approximate Bayesian computation (ABC) estimated that mice recently colonized Gough Island (~100 years ago) and experienced a 98% reduction in population size followed by a rapid expansion. Our results indicate that the unusual phenotypes of Gough Island mice evolved rapidly, positioning these mice as useful models for understanding rapid phenotypic evolution.
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Affiliation(s)
- Melissa M. Gray
- Laboratory of Genetics, University of Wisconsin, Madison, WI 53706 USA
| | - Daniel Wegmann
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Ryan J. Haasl
- Laboratory of Genetics, University of Wisconsin, Madison, WI 53706 USA
| | - Michael A. White
- Laboratory of Genetics, University of Wisconsin, Madison, WI 53706 USA
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
| | - Sofia I. Gabriel
- Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, 1749–016 Lisbon, Portugal
| | - Jeremy B. Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853-2701 USA
| | - Richard J. Cuthbert
- Royal Society for the Protection of Birds, The Lodge, Sandy, Bedfordshire, UK
| | - Peter G. Ryan
- Percy FitzPatrick Institute of African Ornithology, University of Cape Town, DST/NRF Centre of Excellence, Rondebosch 7701 South Africa
| | - Bret A. Payseur
- Laboratory of Genetics, University of Wisconsin, Madison, WI 53706 USA
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24
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Ólafsdóttir GÁ, Westfall KM, Edvardsson R, Pálsson S. Historical DNA reveals the demographic history of Atlantic cod (Gadus morhua) in medieval and early modern Iceland. Proc Biol Sci 2014; 281:20132976. [PMID: 24403343 DOI: 10.1098/rspb.2013.2976] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Atlantic cod (Gadus morhua) vertebrae from archaeological sites were used to study the history of the Icelandic Atlantic cod population in the time period of 1500-1990. Specifically, we used coalescence modelling to estimate population size and fluctuations from the sequence diversity at the cytochrome b (cytb) and Pantophysin I (PanI) loci. The models are consistent with an expanding population during the warm medieval period, large historical effective population size (NE), a marked bottleneck event at 1400-1500 and a decrease in NE in early modern times. The model results are corroborated by the reduction of haplotype and nucleotide variation over time and pairwise population distance as a significant portion of nucleotide variation partitioned across the 1550 time mark. The mean age of the historical fished stock is high in medieval times with a truncation in age in early modern times. The population size crash coincides with a period of known cooling in the North Atlantic, and we conclude that the collapse may be related to climate or climate-induced ecosystem change.
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Affiliation(s)
- Guðbjörg Ásta Ólafsdóttir
- Research Centre of the Westfjords, University of Iceland, , Adalstraeti 21, IS415 Bolungarvik, Iceland, VÖR Marine Research Centre, , Nordurtangi, IS355 Snæfellsbær, Iceland, Department of Environmental and Life Science, University of Iceland, , Sturlugata 7, IS101 Reykjavík, Iceland
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25
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Gattepaille LM, Jakobsson M, Blum MGB. Inferring population size changes with sequence and SNP data: lessons from human bottlenecks. Heredity (Edinb) 2013; 110:409-19. [PMID: 23423148 PMCID: PMC3630807 DOI: 10.1038/hdy.2012.120] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Reconstructing historical variation of population size from sequence and single-nucleotide polymorphism (SNP) data is valuable for understanding the evolutionary history of species. Changes in the population size of humans have been thoroughly investigated, and we review different methodologies of demographic reconstruction, specifically focusing on human bottlenecks. In addition to the classical approaches based on the site-frequency spectrum (SFS) or based on linkage disequilibrium, we also review more recent approaches that utilize atypical shared genomic fragments, such as identical by descent or homozygous segments between or within individuals. Compared with methods based on the SFS, these methods are well suited for detecting recent bottlenecks. In general, all these various methods suffer from bias and dependencies on confounding factors such as population structure or poor specification of the mutational and recombination processes, which can affect the demographic reconstruction. With the exception of SFS-based methods, the effects of confounding factors on the inference methods remain poorly investigated. We conclude that an important step when investigating population size changes rests on validating the demographic model by investigating to what extent the fitted demographic model can reproduce the main features of the polymorphism data.
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Affiliation(s)
- L M Gattepaille
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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26
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Palsbøll PJ, Zachariah Peery M, Olsen MT, Beissinger SR, Bérubé M. Inferring recent historic abundance from current genetic diversity. Mol Ecol 2012. [PMID: 23181682 DOI: 10.1111/mec.12094] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Recent historic abundance is an elusive parameter of great importance for conserving endangered species and understanding the pre-anthropogenic state of the biosphere. The number of studies that have used population genetic theory to estimate recent historic abundance from contemporary levels of genetic diversity has grown rapidly over the last two decades. Such assessments often yield unexpectedly large estimates of historic abundance. We review the underlying theory and common practices of estimating recent historic abundance from contemporary genetic diversity, and critically evaluate the potential issues at various estimation steps. A general issue of mismatched spatio-temporal scales between the estimation itself and the objective of the estimation emerged from our assessment; genetic diversity-based estimates of recent historic abundance represent long-term averages, whereas the objective typically is an estimate of recent abundance for a specific population. Currently, the most promising approach to estimate the difference between recent historic and contemporary abundance requires that genetic data be collected from samples of similar spatial and temporal duration. Novel genome-enabled inference methods may be able to utilize additional information of dense genome-wide distributions of markers, such as of identity-by-descent tracts, to infer recent historic abundance from contemporary samples only.
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Affiliation(s)
- Per J Palsbøll
- Marine Evolution and Conservation, Centre of Evolutionary and Ecological Studies, University of Groningen, PO Box 11103 CC, Groningen, The Netherlands.
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27
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Mata-Míguez J, Overholtzer L, Rodríguez-Alegría E, Kemp BM, Bolnick DA. The genetic impact of aztec imperialism: Ancient mitochondrial DNA evidence from Xaltocan, Mexico. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2012; 149:504-16. [DOI: 10.1002/ajpa.22152] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 08/28/2012] [Indexed: 11/11/2022]
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28
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Welch AJ, Wiley AE, James HF, Ostrom PH, Stafford TW, Fleischer RC. Ancient DNA reveals genetic stability despite demographic decline: 3,000 years of population history in the endemic Hawaiian petrel. Mol Biol Evol 2012; 29:3729-40. [PMID: 22844071 DOI: 10.1093/molbev/mss185] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In the Hawaiian Islands, human colonization, which began approximately 1,200 to 800 years ago, marks the beginning of a period in which nearly 75% of the endemic avifauna became extinct and the population size and range of many additional species declined. It remains unclear why some species persisted whereas others did not. The endemic Hawaiian petrel (Pterodroma sandwichensis) has escaped extinction, but colonies on two islands have been extirpated and populations on remaining islands have contracted. We obtained mitochondrial DNA sequences from 100 subfossil bones, 28 museum specimens, and 289 modern samples to investigate patterns of gene flow and temporal changes in the genetic diversity of this endangered species over the last 3,000 years, as Polynesians and then Europeans colonized the Hawaiian Islands. Genetic differentiation was found to be high between both modern and ancient petrel populations. However, gene flow was substantial between the extirpated colonies on Oahu and Molokai and modern birds from the island of Lanai. No significant reductions in genetic diversity occurred over this period, despite fears in the mid-1900s that this species may have been extinct. Simulations show that even a decline to a stable effective population size of 100 individuals would result in the loss of only 5% of the expected heterozygosity. Simulations also show that high levels of genetic diversity may be retained due to the long generation time of this species. Such decoupling between population size and genetic diversity in long-lived species can have important conservation implications. It appears that a pattern of dispersal from declining colonies, in addition to long generation time, may have allowed the Hawaiian petrel to escape a severe genetic bottleneck, and the associated extinction vortex, and persist despite a large population decline after human colonization.
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Affiliation(s)
- Andreanna J Welch
- Smithsonian Conservation Biology Institute, Center for Conservation and Evolutionary Genetics, National Zoological Park, Washington, DC, USA.
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