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Bredemeyer KR, vonHoldt BM, Foley NM, Childers IR, Brzeski KE, Murphy WJ. The value of hybrid genomes: Building two highly contiguous reference genome assemblies to advance Canis genomic studies. J Hered 2024; 115:480-486. [PMID: 38416051 DOI: 10.1093/jhered/esae013] [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: 01/02/2024] [Revised: 02/21/2024] [Accepted: 02/27/2024] [Indexed: 02/29/2024] Open
Abstract
Previous studies of canid population and evolutionary genetics have relied on high-quality domestic dog reference genomes that have been produced primarily for biomedical and trait mapping studies in dog breeds. However, the absence of highly contiguous genomes from other Canis species like the gray wolf and coyote, that represent additional distinct demographic histories, may bias inferences regarding interspecific genetic diversity and phylogenetic relationships. Here, we present single haplotype de novo genome assemblies for the gray wolf and coyote, generated by applying the trio-binning approach to long sequence reads generated from the genome of a female first-generation hybrid produced from a gray wolf and coyote mating. The assemblies were highly contiguous, with contig N50 sizes of 44.6 and 42.0 Mb for the wolf and coyote, respectively. Genome scaffolding and alignments between the two Canis assemblies and published dog reference genomes showed near complete collinearity, with one exception: a coyote-specific chromosome fission of chromosome 13 and fusion of the proximal portion of that chromosome with chromosome 8, retaining the Canis-typical haploid chromosome number of 2n = 78. We evaluated mapping quality for previous RADseq data from 334 canids and found nearly identical mapping quality and patterns among canid species and regional populations regardless of the genome used for alignment (dog, coyote, or gray wolf). These novel wolf and coyote genome reference assemblies will be important resources for proper and accurate inference of Canis demography, taxonomic evaluation, and conservation genetics.
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Affiliation(s)
- Kevin R Bredemeyer
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, United States
| | - Bridgett M vonHoldt
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ, United States
| | - Nicole M Foley
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
| | - Isabella R Childers
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, United States
| | - Kristin E Brzeski
- College of Forest Resources and Environment Science, Michigan Technological University, Houghton, MI, United States
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, United States
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2
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Musiani M, Randi E. Conservation genomics of wolves: The global impact of RK Wayne's research. J Hered 2024; 115:458-469. [PMID: 38381553 DOI: 10.1093/jhered/esae007] [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: 07/20/2023] [Revised: 01/31/2024] [Accepted: 02/20/2024] [Indexed: 02/23/2024] Open
Abstract
RK Wayne has arguably been the most influential geneticist of canids, famously promoting the conservation of wolves in his homeland, the United States. His influence has been felt in other countries and regions outside the contiguous United States, where he inspired others, also including former graduate students and research fellows of his, to use modern molecular techniques to examine the evolutionary biology of canids to inform the conservation and management of wolves. In this review, we focus on the implications of Wayne's work on wolves outside the United States. He envisioned a clear future for wolf conservation research, involving the study of wolves' ecological and genetic diversity, and the description of ecotypes requiring conservation. He also documented widespread hybridization among canids and introgression of DNA from domestic dogs to wolves, a process that started dozens of thousands of years ago. His work therefore calls for innovative studies, such as examining the potential fitness benefits of introgression. Inspired by his results, for example, on the purging of deleterious alleles in small populations, wolf researchers should use novel molecular tools to challenge other conservation genetics paradigms. Overall, RK Wayne's work constitutes a call for answers, which as scientists or citizens concerned with conservation matters, we are obliged to address, as we contribute to monitoring and maintaining biodiversity during our period of dramatic transformations of the biosphere.
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Affiliation(s)
- Marco Musiani
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), University of Bologna, Bologna, Italy
| | - Ettore Randi
- Department of Chemistry and Bioscience, Aalborg University, Aalborg Øst, Denmark
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3
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vonHoldt BM, Stahler DR, Brzeski KE, Musiani M, Peterson R, Phillips M, Stephenson J, Laudon K, Meredith E, Vucetich JA, Leonard JA, Wayne RK. Demographic history shapes North American gray wolf genomic diversity and informs species' conservation. Mol Ecol 2024; 33:e17231. [PMID: 38054561 DOI: 10.1111/mec.17231] [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: 06/05/2023] [Revised: 11/19/2023] [Accepted: 11/21/2023] [Indexed: 12/07/2023]
Abstract
Effective population size estimates are critical information needed for evolutionary predictions and conservation decisions. This is particularly true for species with social factors that restrict access to breeding or experience repeated fluctuations in population size across generations. We investigated the genomic estimates of effective population size along with diversity, subdivision, and inbreeding from 162,109 minimally filtered and 81,595 statistically neutral and unlinked SNPs genotyped in 437 grey wolf samples from North America collected between 1986 and 2021. We found genetic structure across North America, represented by three distinct demographic histories of western, central, and eastern regions of the continent. Further, grey wolves in the northern Rocky Mountains have lower genomic diversity than wolves of the western Great Lakes and have declined over time. Effective population size estimates revealed the historical signatures of continental efforts of predator extermination, despite a quarter century of recovery efforts. We are the first to provide molecular estimates of effective population size across distinct grey wolf populations in North America, which ranged between Ne ~ 275 and 3050 since early 1980s. We provide data that inform managers regarding the status and importance of effective population size estimates for grey wolf conservation, which are on average 5.2-9.3% of census estimates for this species. We show that while grey wolves fall above minimum effective population sizes needed to avoid extinction due to inbreeding depression in the short term, they are below sizes predicted to be necessary to avoid long-term risk of extinction.
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Affiliation(s)
- Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Daniel R Stahler
- Yellowstone Center for Resources, Yellowstone National Park, Wyoming, USA
| | - Kristin E Brzeski
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | - Marco Musiani
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), Università di Bologna, Bologna, Italy
| | - Rolf Peterson
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | | | | | - Kent Laudon
- California Department of Fish and Wildlife, Northern Region, Redding, California, USA
| | - Erin Meredith
- California Department of Fish and Wildlife, Wildlife Forensic Laboratory, Sacramento, California, USA
| | - John A Vucetich
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, USA
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4
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Fibi-Smetana S, Inglis C, Schuster D, Eberle N, Granados-Soler JL, Liu W, Krohn S, Junghanss C, Nolte I, Taher L, Murua Escobar H. The TiHoCL panel for canine lymphoma: a feasibility study integrating functional genomics and network biology approaches for comparative oncology targeted NGS panel design. Front Vet Sci 2023; 10:1301536. [PMID: 38144469 PMCID: PMC10748409 DOI: 10.3389/fvets.2023.1301536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/20/2023] [Indexed: 12/26/2023] Open
Abstract
Targeted next-generation sequencing (NGS) enables the identification of genomic variants in cancer patients with high sensitivity at relatively low costs, and has thus opened the era to personalized human oncology. Veterinary medicine tends to adopt new technologies at a slower pace compared to human medicine due to lower funding, nonetheless it embraces technological advancements over time. Hence, it is reasonable to assume that targeted NGS will be incorporated into routine veterinary practice in the foreseeable future. Many animal diseases have well-researched human counterparts and hence, insights gained from the latter might, in principle, be harnessed to elucidate the former. Here, we present the TiHoCL targeted NGS panel as a proof of concept, exemplifying how functional genomics and network approaches can be effectively used to leverage the wealth of information available for human diseases in the development of targeted sequencing panels for veterinary medicine. Specifically, the TiHoCL targeted NGS panel is a molecular tool for characterizing and stratifying canine lymphoma (CL) patients designed based on human non-Hodgkin lymphoma (NHL) research outputs. While various single nucleotide polymorphisms (SNPs) have been associated with high risk of developing NHL, poor prognosis and resistance to treatment in NHL patients, little is known about the genetics of CL. Thus, the ~100 SNPs featured in the TiHoCL targeted NGS panel were selected using functional genomics and network approaches following a literature and database search that shielded ~500 SNPs associated with, in nearly all cases, human hematologic malignancies. The TiHoCL targeted NGS panel underwent technical validation and preliminary functional assessment by sequencing DNA samples isolated from blood of 29 lymphoma dogs using an Ion Torrent™ PGM System achieving good sequencing run metrics. Our design framework holds new possibilities for the design of similar molecular tools applied to other diseases for which limited knowledge is available and will improve drug target discovery and patient care.
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Affiliation(s)
- Silvia Fibi-Smetana
- Institute of Biomedical Informatics, Graz University of Technology, Graz, Austria
| | - Camila Inglis
- Small Animal Clinic, University of Veterinary Medicine Hannover Foundation, Hannover, Germany
- Clinic for Hematology, Oncology and Palliative Care, Rostock University Medical Center, University of Rostock, Rostock, Germany
| | - Daniela Schuster
- Division of Bioinformatics, Department of Biology, Friedrich-Alexander-University, Erlangen, Germany
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, University of Rostock, Rostock, Germany
| | - Nina Eberle
- Small Animal Clinic, University of Veterinary Medicine Hannover Foundation, Hannover, Germany
| | - José Luis Granados-Soler
- Small Animal Clinic, University of Veterinary Medicine Hannover Foundation, Hannover, Germany
- UQVETS Small Animal Hospital, School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia
| | - Wen Liu
- Clinic for Hematology, Oncology and Palliative Care, Rostock University Medical Center, University of Rostock, Rostock, Germany
| | - Saskia Krohn
- Clinic for Hematology, Oncology and Palliative Care, Rostock University Medical Center, University of Rostock, Rostock, Germany
| | - Christian Junghanss
- Clinic for Hematology, Oncology and Palliative Care, Rostock University Medical Center, University of Rostock, Rostock, Germany
| | - Ingo Nolte
- Small Animal Clinic, University of Veterinary Medicine Hannover Foundation, Hannover, Germany
| | - Leila Taher
- Institute of Biomedical Informatics, Graz University of Technology, Graz, Austria
- Clinic for Hematology, Oncology and Palliative Care, Rostock University Medical Center, University of Rostock, Rostock, Germany
- Division of Bioinformatics, Department of Biology, Friedrich-Alexander-University, Erlangen, Germany
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, University of Rostock, Rostock, Germany
| | - Hugo Murua Escobar
- Clinic for Hematology, Oncology and Palliative Care, Rostock University Medical Center, University of Rostock, Rostock, Germany
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5
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Jan M, Stronen AV, Boljte B, Černe R, Huber Đ, Iosif R, Kljun F, Konec M, Kos I, Krofel M, Kusak J, Luštrik R, Majić Skrbinšek A, Promberger-Füerpass B, Potočnik H, Rigg R, Trontelj P, Skrbinšek T. Wolf genetic diversity compared across Europe using the yardstick method. Sci Rep 2023; 13:13727. [PMID: 37608038 PMCID: PMC10444868 DOI: 10.1038/s41598-023-40834-x] [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: 01/19/2023] [Accepted: 08/17/2023] [Indexed: 08/24/2023] Open
Abstract
Integrating data across studies with traditional microsatellite genetic markers requires careful calibration and represents an obstacle for investigation of wide-ranging species where populations require transboundary management. We used the "yardstick" method to compare results published across Europe since 2002 and new wolf (Canis lupus) genetic profiles from the Carpathian Mountains in Central Europe and the Dinaric Mountains in Southeastern Europe, with the latter as our reference population. We compared each population with Dinaric wolves, considering only shared markers (range 4-17). For each population, we calculated standard genetic diversity indices plus calibrated heterozygosity (Hec) and allelic richness (Ac). Hec and Ac in Dinaric (0.704 and 9.394) and Carpathian wolves (0.695 and 7.023) were comparable to those observed in other large and mid-sized European populations, but smaller than those of northeastern Europe. Major discrepancies in marker choices among some studies made comparisons more difficult. However, the yardstick method, including the new measures of Hec and Ac, provided a direct comparison of genetic diversity values among wolf populations and an intuitive interpretation of the results. The yardstick method thus permitted the integration of diverse sources of publicly available microsatellite data for spatiotemporal genetic monitoring of evolutionary potential.
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Affiliation(s)
- Maja Jan
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia.
| | - Astrid Vik Stronen
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
- DivjaLabs d.o.o., Aljaževa ulica 35a, 1000, Ljubljana, Slovenia
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Barbara Boljte
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
- DivjaLabs d.o.o., Aljaževa ulica 35a, 1000, Ljubljana, Slovenia
| | - Rok Černe
- Slovenia Forest Service, Večna pot 2, 1000, Ljubljana, Slovenia
| | - Đuro Huber
- Faculty of Veterinary Medicine, University of Zagreb, Vjekoslava Heinzelova 55, 10000, Zagreb, Croatia
| | - Ruben Iosif
- Foundation Conservation Carpathia, 27 Calea Feldioarei, 500471, Brașov, Romania
| | - Franc Kljun
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
| | - Marjeta Konec
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
- DivjaLabs d.o.o., Aljaževa ulica 35a, 1000, Ljubljana, Slovenia
| | - Ivan Kos
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
| | - Miha Krofel
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
| | - Josip Kusak
- Faculty of Veterinary Medicine, University of Zagreb, Vjekoslava Heinzelova 55, 10000, Zagreb, Croatia
| | - Roman Luštrik
- Genialis Inc, Vojkova cesta 63, 1000, Ljubljana, Slovenia
| | - Aleksandra Majić Skrbinšek
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
- DivjaLabs d.o.o., Aljaževa ulica 35a, 1000, Ljubljana, Slovenia
| | | | - Hubert Potočnik
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
| | - Robin Rigg
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
- Slovak Wildlife Society, Belanská 574/6, P.O. Box 72, Liptovský Hrádok, 033 01, Slovakia
| | - Peter Trontelj
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
| | - Tomaž Skrbinšek
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
- DivjaLabs d.o.o., Aljaževa ulica 35a, 1000, Ljubljana, Slovenia
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Ciucani MM, Ramos-Madrigal J, Hernández-Alonso G, Carmagnini A, Aninta SG, Sun X, Scharff-Olsen CH, Lanigan LT, Fracasso I, Clausen CG, Aspi J, Kojola I, Baltrūnaitė L, Balčiauskas L, Moore J, Åkesson M, Saarma U, Hindrikson M, Hulva P, Bolfíková BČ, Nowak C, Godinho R, Smith S, Paule L, Nowak S, Mysłajek RW, Lo Brutto S, Ciucci P, Boitani L, Vernesi C, Stenøien HK, Smith O, Frantz L, Rossi L, Angelici FM, Cilli E, Sinding MHS, Gilbert MTP, Gopalakrishnan S. The extinct Sicilian wolf shows a complex history of isolation and admixture with ancient dogs. iScience 2023; 26:107307. [PMID: 37559898 PMCID: PMC10407145 DOI: 10.1016/j.isci.2023.107307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 11/04/2022] [Accepted: 07/04/2023] [Indexed: 08/11/2023] Open
Abstract
The Sicilian wolf remained isolated in Sicily from the end of the Pleistocene until its extermination in the 1930s-1960s. Given its long-term isolation on the island and distinctive morphology, the genetic origin of the Sicilian wolf remains debated. We sequenced four nuclear genomes and five mitogenomes from the seven existing museum specimens to investigate the Sicilian wolf ancestry, relationships with extant and extinct wolves and dogs, and diversity. Our results show that the Sicilian wolf is most closely related to the Italian wolf but carries ancestry from a lineage related to European Eneolithic and Bronze Age dogs. The average nucleotide diversity of the Sicilian wolf was half of the Italian wolf, with 37-50% of its genome contained in runs of homozygosity. Overall, we show that, by the time it went extinct, the Sicilian wolf had high inbreeding and low-genetic diversity, consistent with a population in an insular environment.
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Affiliation(s)
- Marta Maria Ciucani
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jazmín Ramos-Madrigal
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Germán Hernández-Alonso
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Alberto Carmagnini
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Sabhrina Gita Aninta
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Xin Sun
- Center for Evolutionary Hologenomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Liam Thomas Lanigan
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ilaria Fracasso
- Forest Ecology Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige (TN), Italy
| | - Cecilie G. Clausen
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jouni Aspi
- Ecology and Genetics Research Unit, University of Oulu, Finland
| | - Ilpo Kojola
- Natural Resources Institute Finland, Rovaniemi, Finland
| | | | | | - Jane Moore
- Società Amatori Cirneco dell’Etna, Modica (RG), Italy
| | - Mikael Åkesson
- Swedish University of Agricultural Sciences, Grimsö Wildlife Research Station, Department of Ecology, Riddarhyttan, Sweden
| | - Urmas Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Maris Hindrikson
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Pavel Hulva
- Charles University, Department of Zoology, Faculty of Science, Prague 2, Czech Republic
| | | | - Carsten Nowak
- Center for Wildlife Genetics, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany
| | - Raquel Godinho
- CIBIO/InBIO, University of Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Steve Smith
- Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, Vienna, Austria
| | - Ladislav Paule
- Faculty of Forestry, Technical University, Zvolen, Slovakia
| | - Sabina Nowak
- Department of Ecology, Institute of Functional Biology and Ecology, Faculty of Biology, University of Warsaw, Biological and Chemical Research Centre, Warszawa, Poland
| | - Robert W. Mysłajek
- Department of Ecology, Institute of Functional Biology and Ecology, Faculty of Biology, University of Warsaw, Biological and Chemical Research Centre, Warszawa, Poland
| | - Sabrina Lo Brutto
- Department of Biological, Chemical, and Pharmaceutical Sciences and Technology (STEBICEF), University of Palermo, Palermo, Italy
- Museum of Zoology "P. Doderlein", SIMUA, University of Palermo, Palermo, Italy
| | - Paolo Ciucci
- Università di Roma La Sapienza, Department Biology and Biotechnologies "Charles Darwin", Roma, Italy
| | - Luigi Boitani
- Università di Roma La Sapienza, Department Biology and Biotechnologies "Charles Darwin", Roma, Italy
| | - Cristiano Vernesi
- Forest Ecology Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige (TN), Italy
| | - Hans K. Stenøien
- NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Oliver Smith
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Laurent Frantz
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | | | - Francesco Maria Angelici
- FIZV, Via Marco Aurelio 2, Roma, Italy
- National Center for Wildlife, Al Imam Faisal Ibn Turki Ibn Abdullah, Ulaishah, Saudi Arabia
| | - Elisabetta Cilli
- Laboratory of Ancient DNA, Department of Cultural Heritage (DBC), University of Bologna, Bologna, Italy
| | - Mikkel-Holger S. Sinding
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - M. Thomas P. Gilbert
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
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7
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Tancredi D, Cardinali I. Being a Dog: A Review of the Domestication Process. Genes (Basel) 2023; 14:genes14050992. [PMID: 37239352 DOI: 10.3390/genes14050992] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/19/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
The process of canine domestication represents certainly one of the most interesting questions that evolutionary biology aims to address. A "multiphase" view of this process is now accepted, with a first phase during which different groups of wolves were attracted by the anthropogenic niche and a second phase characterized by the gradual establishment of mutual relationships between wolves and humans. Here, we provide a review of dog (Canis familiaris) domestication, highlighting the ecological differences between dogs and wolves, analyzing the molecular mechanisms which seem to have influenced the affiliative behaviors first observed in Belyaev's foxes, and describing the genetics of ancient European dogs. Then, we focus on three Mediterranean peninsulas (Balkan, Iberian and Italian), which together represent the main geographic area for studying canine domestication dynamics, as it has shaped the current genetic variability of dog populations, and where a well-defined European genetic structure was pinpointed through the analysis of uniparental genetic markers and their phylogeny.
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Affiliation(s)
- Domenico Tancredi
- Department of Chemistry, Biology and Biotechnology, Università degli Studi di Perugia, 06123 Perugia, Italy
| | - Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, Università degli Studi di Perugia, 06123 Perugia, Italy
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8
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Vilaça ST, Donaldson ME, Benazzo A, Wheeldon TJ, Vizzari MT, Bertorelle G, Patterson BR, Kyle CJ. Tracing Eastern Wolf Origins From Whole-Genome Data in Context of Extensive Hybridization. Mol Biol Evol 2023; 40:msad055. [PMID: 37046402 PMCID: PMC10098045 DOI: 10.1093/molbev/msad055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Abstract
Southeastern Canada is inhabited by an amalgam of hybridizing wolf-like canids, raising fundamental questions regarding their taxonomy, origins, and timing of hybridization events. Eastern wolves (Canis lycaon), specifically, have been the subject of significant controversy, being viewed as either a distinct taxonomic entity of conservation concern or a recent hybrid of coyotes (C. latrans) and grey wolves (C. lupus). Mitochondrial DNA analyses show some evidence of eastern wolves being North American evolved canids. In contrast, nuclear genome studies indicate eastern wolves are best described as a hybrid entity, but with unclear timing of hybridization events. To test hypotheses related to these competing findings we sequenced whole genomes of 25 individuals, representative of extant Canadian wolf-like canid types of known origin and levels of contemporary hybridization. Here we present data describing eastern wolves as a distinct taxonomic entity that evolved separately from grey wolves for the past ∼67,000 years with an admixture event with coyotes ∼37,000 years ago. We show that Great Lakes wolves originated as a product of admixture between grey wolves and eastern wolves after the last glaciation (∼8,000 years ago) while eastern coyotes originated as a product of admixture between "western" coyotes and eastern wolves during the last century. Eastern wolf nuclear genomes appear shaped by historical and contemporary gene flow with grey wolves and coyotes, yet evolutionary uniqueness remains among eastern wolves currently inhabiting a restricted range in southeastern Canada.
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Affiliation(s)
- Sibelle T Vilaça
- Environmental and Life Sciences Graduate Program, Trent University, Ontario, Canada
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Michael E Donaldson
- Environmental and Life Sciences Graduate Program, Trent University, Ontario, Canada
| | - Andrea Benazzo
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Tyler J Wheeldon
- Ontario Ministry of Natural Resources and Forestry, Wildlife Research and Monitoring Section, Trent University, Ontario, Canada
| | - Maria Teresa Vizzari
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Giorgio Bertorelle
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Brent R Patterson
- Ontario Ministry of Natural Resources and Forestry, Wildlife Research and Monitoring Section, Trent University, Ontario, Canada
| | - Christopher J Kyle
- Environmental and Life Sciences Graduate Program, Trent University, Ontario, Canada
- Forensic Science Department, Trent University, Ontario, Canada
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9
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Mech LD, Nowak RM. A Plea for Red Wolf Conservation throughout Its Recent Distribution. SOUTHEAST NAT 2023. [DOI: 10.1656/058.022.0111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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10
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Penning LC, van den Boom R. Companion animal organoid technology to advance veterinary regenerative medicine. Front Vet Sci 2023; 10:1032835. [PMID: 37008367 PMCID: PMC10063859 DOI: 10.3389/fvets.2023.1032835] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 02/28/2023] [Indexed: 03/19/2023] Open
Abstract
First year medical and veterinary students are made very aware that drugs can have very different effects in various species or even in breeds of one specific species. On the other hand, the “One Medicine” concept implies that therapeutic and technical approaches are exchangeable between man and animals. These opposing views on the (dis)similarities between human and veterinary medicine are magnified in regenerative medicine. Regenerative medicine promises to stimulate the body's own regenerative capacity via activation of stem cells and/or the application of instructive biomaterials. Although the potential is enormous, so are the hurdles that need to be overcome before large scale clinical implementation is realistic. It is in the advancement of regenerative medicine that veterinary regenerative medicine can play an instrumental and crucial role. This review describes the discovery of (adult) stem cells in domesticated animals, mainly cats and dogs. The promise of cell-mediated regenerative veterinary medicine is compared to the actual achievements, and this will lead to a set of unanswered questions (controversies, research gaps, potential developments in relation to fundamental, pre-clinical, and clinical research). For veterinary regenerative medicine to have impact, either for human medicine and/or for domesticated animals, answering these questions is pivotal.
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11
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Balog K, Mizeranschi AE, Wanjala G, Sipos B, Kusza S, Bagi Z. Application potential of chicken DNA chip in domestic pigeon species - Preliminary results. Saudi J Biol Sci 2023; 30:103594. [PMID: 36874200 PMCID: PMC9975693 DOI: 10.1016/j.sjbs.2023.103594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/12/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
Introducing the SNP technology to pigeon breeding will enhance the competitiveness of a sector that produces one of the healthiest and best quality meats. The present study aimed to test the applicability of the Illumina Chicken_50K_CobbCons array on 24 domestic pigeon individuals from the Mirthys hybrids and Racing pigeon breeds. A total of 53,313 SNPs were genotyped. Principal component analysis shows a significant overlap between the two groups. The chip performed poorly in this data set, with a call rate per sample of 0.474 (49%). The low call rate was likely due to an increase in the evolutionary distance. A total of 356 SNPs were retained after a relatively strict quality control. We have demonstrated that it is technically feasible to use a chicken microarray chip on pigeon samples. Presumably, with a larger sample size and by assigning phenotypic data, efficiency would be improved, allowing more thorough analyses, such as genome-wide association studies.
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Affiliation(s)
- Katalin Balog
- University of Debrecen, Doctoral School of Animal Science, Böszörményi út 138, 4032, Debrecen, Hungary.,Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4002 Debrecen, Hungary
| | | | - George Wanjala
- University of Debrecen, Doctoral School of Animal Science, Böszörményi út 138, 4032, Debrecen, Hungary.,Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4002 Debrecen, Hungary
| | - Bíborka Sipos
- University of Debrecen, Faculty of Agricultural and Food Sciences and Environmental Management, Böszörményi út 138, 4032, Debrecen, Hungary
| | - Szilvia Kusza
- Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4002 Debrecen, Hungary
| | - Zoltán Bagi
- Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4002 Debrecen, Hungary
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12
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Mooney JA, Marsden CD, Yohannes A, Wayne RK, Lohmueller KE. Long-term Small Population Size, Deleterious Variation, and Altitude Adaptation in the Ethiopian Wolf, a Severely Endangered Canid. Mol Biol Evol 2023; 40:msac277. [PMID: 36585842 PMCID: PMC9847632 DOI: 10.1093/molbev/msac277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/07/2022] [Accepted: 12/22/2022] [Indexed: 01/01/2023] Open
Abstract
Ethiopian wolves, a canid species endemic to the Ethiopian Highlands, have been steadily declining in numbers for decades. Currently, out of 35 extant species, it is now one of the world's most endangered canids. Most conservation efforts have focused on preventing disease, monitoring movements and behavior, and assessing the geographic ranges of sub-populations. Here, we add an essential layer by determining the Ethiopian wolf's demographic and evolutionary history using high-coverage (∼40×) whole-genome sequencing from 10 Ethiopian wolves from the Bale Mountains. We observe exceptionally low diversity and enrichment of weakly deleterious variants in the Ethiopian wolves in comparison with two North American gray wolf populations and four dog breeds. These patterns are consequences of long-term small population size, rather than recent inbreeding. We infer the demographic history of the Ethiopian wolf and find it to be concordant with historic records and previous genetic analyses, suggesting Ethiopian wolves experienced a series of both ancient and recent bottlenecks, resulting in a census population size of fewer than 500 individuals and an estimated effective population size of approximately 100 individuals. Additionally, long-term small population size may have limited the accumulation of strongly deleterious recessive mutations. Finally, as the Ethiopian wolves have inhabited high-altitude areas for thousands of years, we searched for evidence of high-altitude adaptation, finding evidence of positive selection at a transcription factor in a hypoxia-response pathway [CREB-binding protein (CREBBP)]. Our findings are pertinent to continuing conservation efforts and understanding how demography influences the persistence of deleterious variation in small populations.
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Affiliation(s)
- Jazlyn A Mooney
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biology, Stanford University, Stanford, CA, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Clare D Marsden
- Department of Ecology & Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Abigail Yohannes
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Robert K Wayne
- Department of Ecology & Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Kirk E Lohmueller
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Ecology & Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA
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13
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Russo BM, Jones AS, Clement MJ, Fyffe N, Mesler JI, Rubin ES. Camera trapping as a method for estimating abundance of Mexican wolves. WILDLIFE SOC B 2022. [DOI: 10.1002/wsb.1416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Brianna M. Russo
- Arizona Game and Fish Department, Research Branch 5000 W. Carefree Highway Phoenix AZ 85086 USA
| | - Andrew S. Jones
- Arizona Game and Fish Department, Research Branch 5000 W. Carefree Highway Phoenix AZ 85086 USA
| | - Matthew J. Clement
- Arizona Game and Fish Department, Research Branch 5000 W. Carefree Highway Phoenix AZ 85086 USA
| | - Nathan Fyffe
- Arizona Game and Fish Department, Research Branch 5000 W. Carefree Highway Phoenix AZ 85086 USA
| | - Jacob I. Mesler
- Arizona Game and Fish Department, Research Branch 5000 W. Carefree Highway Phoenix AZ 85086 USA
| | - Esther S. Rubin
- Arizona Game and Fish Department, Research Branch 5000 W. Carefree Highway Phoenix AZ 85086 USA
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14
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Barnes TM, Karlin M, vonHoldt BM, Adams JR, Waits LP, Hinton JW, Henderson J, Brzeski KE. Genetic diversity and family groups detected in a coyote population with red wolf ancestry on Galveston Island, Texas. BMC Ecol Evol 2022; 22:134. [PMID: 36376792 PMCID: PMC9664737 DOI: 10.1186/s12862-022-02084-9] [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: 05/18/2022] [Accepted: 10/20/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Hybridization can be a conservation concern if genomic introgression leads to the loss of an endangered species' unique genome, or when hybrid offspring are sterile or less fit than their parental species. Yet hybridization can also be an adaptive management tool if rare populations are inbred and have reduced genetic variation, and there is the opportunity to enhance genetic variation through hybridization. The red wolf (Canis rufus) is a critically endangered wolf endemic to the eastern United States, where all extant red wolves are descended from 14 founders which has led to elevated levels of inbreeding over time. Red wolves were considered extirpated from the wild by 1980, but before they disappeared, they interbred with encroaching coyotes creating a genetically admixed population of canids along coastal Texas and Louisiana. In 2018, a genetic study identified individuals on Galveston Island, Texas with significant amounts of red wolf ancestry. We collected 203 fecal samples from Galveston for a more in-depth analysis of this population to identify the amount of red wolf ancestry present and potential mechanisms that support retention of red wolf ancestry on the landscape. RESULTS We identified 24 individual coyotes from Galveston Island and 8 from mainland Texas with greater than 10% red wolf ancestry. Two of those individuals from mainland Texas had greater than 50% red wolf ancestry estimates. Additionally, this population had 5 private alleles that were absent in the North American reference canid populations used in this study, which included 107 southeastern coyotes, 19 captive red wolves, and 38 gray wolves, possibly representing lost red wolf genetic variation. We also identified several individuals on Galveston Island and the mainland of Texas that retained a unique red wolf mitochondrial haplotype present in the red wolf founding population. On Galveston Island, we identified a minimum of four family groups and found coyotes on the island to be highly related, but not genetically depauperate. We did not find clear associations between red wolf ancestry estimates and landscape features, such as open green space or developed areas. CONCLUSION Our results confirm the presence of substantial red wolf ancestry persisting on Galveston Island and adjacent mainland Texas. This population has the potential to benefit future red wolf conservation efforts through novel reproductive techniques and possibly through de-introgression strategies, with the goals of recovering extinct red wolf genetic variation and reducing inbreeding within the species.
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Affiliation(s)
- Tanner M Barnes
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, USA
| | - Melissa Karlin
- Department of Physics and Environmental Science, St. Mary's University, San Antonio, TX, USA
| | - Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Jennifer R Adams
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA
| | - Lisette P Waits
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA
| | | | | | - Kristin E Brzeski
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, USA.
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15
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vonHoldt BM, Brzeski KE, Aardema ML, Schell CJ, Rutledge LY, Fain SR, Shutt AC, Linderholm A, Murphy WJ. Persistence and expansion of cryptic endangered red wolf genomic ancestry along the American Gulf coast. Mol Ecol 2022; 31:5440-5454. [PMID: 34585803 DOI: 10.1111/mec.16200] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 09/03/2021] [Accepted: 09/22/2021] [Indexed: 12/24/2022]
Abstract
Admixture and introgression play a critical role in adaptation and genetic rescue that has only recently gained a deeper appreciation. Here, we explored the geographical and genomic landscape of cryptic ancestry of the endangered red wolf that persists within the genome of a ubiquitous sister taxon, the coyote, all while the red wolf has been extinct in the wild since the early 1980s. We assessed admixture across 120,621 single nucleotiode polymorphism (SNP) loci genotyped in 293 canid genomes. We found support for increased red wolf ancestry along a west-to-east gradient across the southern United States associated with historical admixture in the past 100 years. Southwestern Louisiana and southeastern Texas, the geographical zone where the last red wolves were known prior to extinction in the wild, contained the highest and oldest levels of red wolf ancestry. Further, given the paucity of inferences based on chromosome types, we compared patterns of ancestry on the X chromosome and autosomes. We additionally aimed to explore the relationship between admixture timing and recombination rate variation to investigate gene flow events. We found that X-linked regions of low recombination rates were depleted of introgression, relative to the autosomes, consistent with the large X effect and enrichment with loci involved in maintaining reproductive isolation. Recombination rate was positively correlated with red wolf ancestry across coyote genomes, consistent with theoretical predictions. The geographical and genomic extent of cryptic red wolf ancestry can provide novel genomic resources for recovery plans targeting the conservation of the endangered red wolf.
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Affiliation(s)
- Bridgett M vonHoldt
- Ecology & Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Kristin E Brzeski
- College of Forest Resources and Environment Science, Michigan Technological University, Houghton, Michigan, USA
| | - Matthew L Aardema
- Department of Biology, Montclair State University, Montclair, New Jersey, USA.,Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
| | - Christopher J Schell
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, USA
| | - Linda Y Rutledge
- Biology Department, Trent University, Peterborough, Ontario, Canada
| | - Steven R Fain
- USFWS, Clark R. Bavin National Forensics Laboratory, Ashland, Oregon, USA
| | | | - Anna Linderholm
- Department of Anthropology, Texas A&M University, College Station, Texas, USA
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, USA
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16
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Kazimirov PA, Leontyev SV, Nechaeva AV, Belokon MM, Belokon YS, Bondarev AY, Davydov AV, Politov DV. Population Genetic Structure of the Steppe Wolf of Russia and Kazakhstan by Microsatellite Loci. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422110047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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17
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Caragiulo A, Gaughran SJ, Duncan N, Nagy C, Weckel M, vonHoldt BM. Coyotes in New York City Carry Variable Genomic Dog Ancestry and Influence Their Interactions with Humans. Genes (Basel) 2022; 13:1661. [PMID: 36140828 PMCID: PMC9498729 DOI: 10.3390/genes13091661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/03/2022] [Accepted: 09/08/2022] [Indexed: 11/23/2022] Open
Abstract
Coyotes are ubiquitous on the North American landscape as a result of their recent expansion across the continent. They have been documented in the heart of some of the most urbanized cities, such as Chicago, Los Angeles, and New York City. Here, we explored the genomic composition of 16 coyotes in the New York metropolitan area to investigate genomic demography and admixture for urban-dwelling canids in Queens County, New York. We identified moderate-to-high estimates of relatedness among coyotes living in Queens (r = 0.0-0.5) and adjacent neighborhoods, suggestive of a relatively small population. Although we found low background levels of domestic-dog ancestry across most coyotes in our sample (5%), we identified a male suspected to be a first-generation coyote-dog hybrid with 46% dog ancestry, as well as his two putative backcrossed offspring that carried approximately 25% dog ancestry. The male coyote-dog hybrid and one backcrossed offspring each carried two transposable element insertions that are associated with human-directed hypersociability in dogs and gray wolves. An additional, unrelated coyote with little dog ancestry also carried two of these insertions. These genetic patterns suggest that gene flow from domestic dogs may become an increasingly important consideration as coyotes continue to inhabit metropolitan regions.
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Affiliation(s)
| | - Stephen J. Gaughran
- American Museum of Natural History, New York, NY 10024, USA
- Ecology & Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Neil Duncan
- American Museum of Natural History, New York, NY 10024, USA
| | | | - Mark Weckel
- American Museum of Natural History, New York, NY 10024, USA
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18
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Hendricks SA, King JL, Duncan CL, Vickers W, Hohenlohe PA, Davis BW. Genomic Assessment of Cancer Susceptibility in the Threatened Catalina Island Fox ( Urocyon littoralis catalinae). Genes (Basel) 2022; 13:1496. [PMID: 36011407 PMCID: PMC9408614 DOI: 10.3390/genes13081496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/12/2022] [Accepted: 08/12/2022] [Indexed: 12/12/2022] Open
Abstract
Small effective population sizes raise the probability of extinction by increasing the frequency of potentially deleterious alleles and reducing fitness. However, the extent to which cancers play a role in the fitness reduction of genetically depauperate wildlife populations is unknown. Santa Catalina island foxes (Urocyon littoralis catalinae) sampled in 2007-2008 have a high prevalence of ceruminous gland tumors, which was not detected in the population prior to a recent bottleneck caused by a canine distemper epidemic. The disease appears to be associated with inflammation from chronic ear mite (Otodectes) infections and secondary elevated levels of Staphyloccus pseudointermedius bacterial infections. However, no other environmental factors to date have been found to be associated with elevated cancer risk in this population. Here, we used whole genome sequencing of the case and control individuals from two islands to identify candidate loci associated with cancer based on genetic divergence, nucleotide diversity, allele frequency spectrum, and runs of homozygosity. We identified several candidate loci based on genomic signatures and putative gene functions, suggesting that cancer susceptibility in this population may be polygenic. Due to the efforts of a recovery program and weak fitness effects of late-onset disease, the population size has increased, which may allow selection to be more effective in removing these presumably slightly deleterious alleles. Long-term monitoring of the disease alleles, as well as overall genetic diversity, will provide crucial information for the long-term persistence of this threatened population.
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Affiliation(s)
- Sarah A. Hendricks
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Julie L. King
- Catalina Island Conservancy, P.O. Box 2739, Avalon, CA 90704, USA
| | - Calvin L. Duncan
- Catalina Island Conservancy, P.O. Box 2739, Avalon, CA 90704, USA
| | - Winston Vickers
- Institute for Wildlife Studies, Arcata, CA 95521, USA
- Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Paul A. Hohenlohe
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID 83844, USA
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Brian W. Davis
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Science, Texas A&M University, College Station, TX 77840, USA
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Science, Texas A&M University, College Station, TX 77840, USA
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19
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Pacheco C, Stronen AV, Jędrzejewska B, Plis K, Okhlopkov IM, Mamaev NV, Drovetski SV, Godinho R. Demography and evolutionary history of grey wolf populations around the Bering Strait. Mol Ecol 2022; 31:4851-4865. [PMID: 35822863 PMCID: PMC9545117 DOI: 10.1111/mec.16613] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 06/16/2022] [Accepted: 07/04/2022] [Indexed: 11/28/2022]
Abstract
Glacial and interglacial periods throughout the Pleistocene have been substantial drivers of change in species distributions. Earlier analyses suggested that modern grey wolves (Canis lupus) trace their origin to a single Late Pleistocene Beringian population that expanded east and westwards, starting c. 25,000 years ago (ya). Here, we examined the demographic and phylogeographic histories of extant populations around the Bering Strait with wolves from two inland regions of the Russian Far East (RFE) and one coastal and two inland regions of North‐western North America (NNA), genotyped for 91,327 single nucleotide polymorphisms. Our results indicated that RFE and NNA wolves had a common ancestry until c. 34,400 ya, suggesting that these populations started to diverge before the previously proposed expansion out of Beringia. Coastal and inland NNA populations diverged c. 16,000 ya, concordant with the minimum proposed date for the ecological viability of the migration route along the Pacific Northwest coast. Demographic reconstructions for inland RFE and NNA populations reveal spatial and temporal synchrony, with large historical effective population sizes that declined throughout the Pleistocene, possibly reflecting the influence of broadscale climatic changes across continents. In contrast, coastal NNA wolves displayed a consistently lower effective population size than the inland populations. Differences between the demographic history of inland and coastal wolves may have been driven by multiple ecological factors, including historical gene flow patterns, natural landscape fragmentation, and more recent anthropogenic disturbance.
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Affiliation(s)
- Carolina Pacheco
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Astrid Vik Stronen
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.,Department of Biotechnology and Life Sciences, Insubria University, Varese, Italy.,Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | - Kamila Plis
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Innokentiy M Okhlopkov
- Institute of Biological Problems of Cryolithozone, Siberian Branch of Russian Academy of Sciences, Yakutsk, Russia
| | - Nikolay V Mamaev
- Institute of Biological Problems of Cryolithozone, Siberian Branch of Russian Academy of Sciences, Yakutsk, Russia
| | - Sergei V Drovetski
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Raquel Godinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
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20
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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: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [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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21
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vonHoldt BM, Hinton JW, Shutt AC, Murphy SM, Karlin ML, Adams JR, Waits LP, Brzeski KE. Reviving ghost alleles: Genetically admixed coyotes along the American Gulf Coast are critical for saving the endangered red wolf. SCIENCE ADVANCES 2022; 8:eabn7731. [PMID: 35767623 PMCID: PMC9242586 DOI: 10.1126/sciadv.abn7731] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
The last known red wolves were captured in southwestern Louisiana and eastern Texas in 1980 to establish a captive breeding population. Before their extirpation, gene flow with coyotes resulted in the persistence of endangered red wolf genetic variation in local coyote populations. We assessed genomic ancestry and morphology of coyotes in southwestern Louisiana. We detected that 38 to 62% of the coyote genomes contained red wolf ancestry acquired in the past 30 years and have an admixture profile similar to that of the canids captured before the extirpation of red wolves. We further documented a positive correlation between ancestry and weight. Our findings highlight the importance of hybrids and admixed genomes as a reservoir of endangered species ancestry for innovative conservation efforts. Together, this work presents an unprecedented system that conservation can leverage to enrich the recovery program of an endangered species.
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Affiliation(s)
- Bridgett M. vonHoldt
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | | | | | - Sean M. Murphy
- Forestry and Natural Resources, University of Kentucky, Lexington, KY, USA
| | - Melissa L. Karlin
- Department of Physics and Environmental Science, St. Mary’s University, San Antonio, TX, USA
| | - Jennifer R. Adams
- Laboratory for Ecological, Evolutionary and Conservation Genetics, Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA
| | - Lisette P. Waits
- Laboratory for Ecological, Evolutionary and Conservation Genetics, Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA
| | - Kristin E. Brzeski
- College of Forest Resources and Environment Science, Michigan Technological University, Houghton, MI, USA
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22
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Jensen AJ, Marneweck CJ, Kilgo JC, Jachowski DS. Coyote diet in North America: geographic and ecological patterns during range expansion. Mamm Rev 2022. [DOI: 10.1111/mam.12299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Alex J. Jensen
- Department of Forestry and Environmental Conservation Clemson University Clemson South Carolina 29631 USA
| | - Courtney J. Marneweck
- Department of Forestry and Environmental Conservation Clemson University Clemson South Carolina 29631 USA
| | - John C. Kilgo
- USDA Forest Service, Southern Research Station New Ellenton South Carolina 29809 USA
| | - David S. Jachowski
- Department of Forestry and Environmental Conservation Clemson University Clemson South Carolina 29631 USA
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23
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A reduced SNP panel to trace gene flow across southern European wolf populations and detect hybridization with other Canis taxa. Sci Rep 2022; 12:4195. [PMID: 35264717 PMCID: PMC8907317 DOI: 10.1038/s41598-022-08132-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 03/01/2022] [Indexed: 12/18/2022] Open
Abstract
Intra- and inter-specific gene flow are natural evolutionary processes. However, human-induced hybridization is a global conservation concern across taxa, and the development of discriminant genetic markers to differentiate among gene flow processes is essential. Wolves (Canis lupus) are affected by hybridization, particularly in southern Europe, where ongoing recolonization of historic ranges is augmenting gene flow among divergent populations. Our aim was to provide diagnostic canid markers focused on the long-divergent Iberian, Italian and Dinaric wolf populations, based on existing genomic resources. We used 158 canid samples to select a panel of highly informative single nucleotide polymorphisms (SNPs) to (i) distinguish wolves in the three regions from domestic dogs (C. l. familiaris) and golden jackals (C. aureus), and (ii) identify their first two hybrid generations. The resulting 192 SNPs correctly identified the five canid groups, all simulated first-generation (F1) hybrids (0.482 ≤ Qi ≤ 0.512 between their respective parental groups) and all first backcross (BC1) individuals (0.723 ≤ Qi ≤ 0.827 to parental groups). An assay design and test with invasive and non-invasive canid samples performed successfully for 178 SNPs. By separating natural population admixture from inter-specific hybridization, our reduced panel can help advance evolutionary research, monitoring, and timely conservation management.
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24
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Cairns KM, Crowther MS, Nesbitt B, Letnic M. The myth of wild dogs in Australia: are there any out there? AUSTRALIAN MAMMALOGY 2022. [DOI: 10.1071/am20055] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Hybridisation between wild and domestic canids is a global conservation and management issue. In Australia, dingoes are a distinct lineage of wild-living canid with a controversial domestication status. They are mainland Australia’s apex terrestrial predator. There is ongoing concern that the identity of dingoes has been threatened from breeding with domestic dogs, and that feral dogs have established populations in rural Australia. We collate the results of microsatellite DNA testing from 5039 wild canids to explore patterns of domestic dog ancestry in dingoes and observations of feral domestic dogs across the continent. Only 31 feral dogs were detected, challenging the perception that feral dogs are widespread in Australia. First generation dingo × dog hybrids were similarly rare, with only 27 individuals identified. Spatial patterns of genetic ancestry across Australia identified that dingo populations in northern, western and central Australia were largely free from domestic dog introgression. Our findings challenge the perception that dingoes are virtually extinct in the wild and that feral dogs are common. A shift in terminology from wild dog to dingo would better reflect the identity of these wild canids and allow more nuanced debate about the balance between conservation and management of dingoes in Australia.
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25
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Parker LD, Campana MG, Quinta JD, Cypher B, Rivera I, Fleischer RC, Ralls K, Wilbert TR, Boarman R, Boarman WI, Maldonado JE. An efficient method for simultaneous species, individual, and sex identification via in-solution single nucleotide polymorphism capture from low-quality scat samples. Mol Ecol Resour 2021; 22:1345-1361. [PMID: 34779133 DOI: 10.1111/1755-0998.13552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/24/2021] [Accepted: 10/27/2021] [Indexed: 12/01/2022]
Abstract
Understanding predator population dynamics is important for conservation management because of the critical roles predators play within ecosystems. Noninvasive genetic sampling methods are useful for the study of predators like canids that can be difficult to capture or directly observe. Here, we introduce the FAECES* method (Fast and Accurate Enrichment of Canid Excrement for Species* and other analyses) which expands the toolbox for canid researchers and conservationists by using in-solution hybridization sequence capture to produce single nucleotide polymorphism (SNP) genotypes for multiple canid species from scat-derived DNA using a single enrichment. We designed a set of hybridization probes to genotype both coyotes (Canis latrans) and kit foxes (Vulpes macrotis) at hundreds of polymorphic SNP loci and we tested the probes on both tissues and field-collected scat samples. We enriched and genotyped by sequencing 52 coyote and 70 kit fox scats collected in and around a conservation easement in the Nevada Mojave Desert. We demonstrate that the FAECES* method produces genotypes capable of differentiating coyotes and kit foxes, identifying individuals and their sex, and estimating genetic diversity and effective population sizes, even using highly degraded, low-quantity DNA extracted from scat. We found that the study area harbours a large and diverse population of kit foxes and a relatively smaller population of coyotes. By replicating our methods in the future, conservationists can assess the impacts of management decisions on canid populations. The method can also be adapted and applied more broadly to enrich and sequence multiple loci from any species of interest using scat or other noninvasive genetic samples.
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Affiliation(s)
- Lillian D Parker
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA.,School of Systems Biology, George Mason University, Fairfax, Virginia, USA
| | - Michael G Campana
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA.,School of Systems Biology, George Mason University, Fairfax, Virginia, USA.,Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA
| | - Jessica D Quinta
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA
| | - Brian Cypher
- Endangered Species Recovery Program, California State University, Turlock, California, USA
| | - Isabel Rivera
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA
| | - Katherine Ralls
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA
| | - Tammy R Wilbert
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA
| | - Ryan Boarman
- Conservation Science Research and Consultation, Spring Valley, California, USA
| | - William I Boarman
- Conservation Science Research and Consultation, Spring Valley, California, USA
| | - Jesús E Maldonado
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA.,School of Systems Biology, George Mason University, Fairfax, Virginia, USA.,Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA
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26
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Zdjelar N, Nagendran L, Kendall C, Ackermann RR, Schroeder L. The hybrid skull of the eastern coyote (Canis latrans var.): Nonmetric traits and craniomandibular shape. J Morphol 2021; 282:1745-1764. [PMID: 34609013 DOI: 10.1002/jmor.21417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 09/14/2021] [Accepted: 10/05/2021] [Indexed: 12/24/2022]
Abstract
The increasing awareness that hybridization, and resultant gene flow, plays a major role in animal diversification has led to a growing number of studies that have focused on assessing the morphological consequences of this process. Analyses of mammalian hybrids have identified skeletal effects of hybridization, including a suite of anomalous dental and sutural traits on the skull that are present at high frequencies in hybrid populations. These studies have also detected consistent patterns of morphological shape and size differences between hybrids and parental taxa across a wide variety of organisms. However, more research is required to understand the universality of these traits and shape/size differences. Building on these previous studies, a sample of genetically determined canid hybrids was examined, specifically the eastern coyote (Canis latrans var.), a hybrid between coyotes, wolves, and dogs, to test whether this group exhibits a comparable pattern of anomalous nonmetric characters, and to assess differences in craniomandibular shape and size. First, specimens of C. latrans var., C. latrans, and C. lupus were scored for anomalous traits, including supernumerary and rotated teeth, dental crowding, and sutural anomalies. Geometric morphometric analyses were then conducted on a subset of these individuals to explore craniomandibular size and shape variation, as well as allometry. The results are largely consistent with other studies, indicating that the incidence of dental anomalies, dental crowding, and sutural anomalies is significantly higher in hybrids. However, differences are not significant for supernumerary teeth. The exploration of morphometric variation identifies intermediate morphology in the hybrids, and some indication of greater morphological variability in the mandible. When these results are combined with previous studies, they suggest that skeletal signatures of hybridization are common to different mammalian taxa across multiple generations; however, some traits such as supernumerary teeth may be lost after a few generations.
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Affiliation(s)
- Natasa Zdjelar
- Department of Anthropology, University of Toronto, Toronto, Ontario, Canada
| | - Lavania Nagendran
- Department of Anthropology, University of Toronto, Toronto, Ontario, Canada
| | | | - Rebecca Rogers Ackermann
- Human Evolution Research Institute, University of Cape Town, Rondebosch, South Africa.,Department of Archaeology, University of Cape Town, Rondebosch, South Africa
| | - Lauren Schroeder
- Human Evolution Research Institute, University of Cape Town, Rondebosch, South Africa.,Department of Anthropology, University of Toronto Mississauga, Mississauga, Ontario, Canada.,Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
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27
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Hogg CJ, Morrison C, Dudley JS, Alquezar‐Planas DE, Beasley‐Hall PG, Magrath MJL, Ho SYW, Lo N, Johnson RN, Grueber CE. Using phylogenetics to explore interspecies genetic rescue options for a critically endangered parrot. CONSERVATION SCIENCE AND PRACTICE 2021. [DOI: 10.1111/csp2.483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Carolyn J. Hogg
- School of Life and Environmental Sciences The University of Sydney Sydney New South Wales Australia
| | - Caitlin Morrison
- School of Life and Environmental Sciences The University of Sydney Sydney New South Wales Australia
- Australian Museum Research Institute Sydney New South Wales Australia
| | - Jessica S. Dudley
- School of Life and Environmental Sciences The University of Sydney Sydney New South Wales Australia
| | | | - Perry G. Beasley‐Hall
- School of Life and Environmental Sciences The University of Sydney Sydney New South Wales Australia
- School of Biological Sciences The University of Adelaide Adelaide South Australia Australia
| | - Michael J. L. Magrath
- Wildlife Conservation and Science, Zoos Victoria Melbourne Victoria Australia
- School of BioSciences University of Melbourne Victoria Australia
| | - Simon Y. W. Ho
- School of Life and Environmental Sciences The University of Sydney Sydney New South Wales Australia
| | - Nathan Lo
- School of Life and Environmental Sciences The University of Sydney Sydney New South Wales Australia
| | - Rebecca N. Johnson
- Australian Museum Research Institute Sydney New South Wales Australia
- National Museum of Natural History, Smithsonian Institution Washington District of Columbia USA
| | - Catherine E. Grueber
- School of Life and Environmental Sciences The University of Sydney Sydney New South Wales Australia
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28
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Interface of Human/Wildlife Interactions: An Example of a Bold Coyote (Canis latrans) in Atlanta, GA, USA. DIVERSITY 2021. [DOI: 10.3390/d13080372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
There is arguably no other North American species that better illustrates the complexities of the human-wildlife interface than the coyote. In this study, a melanistic coyote in metropolitan Atlanta, Georgia was exhibiting unusually bold behaviors that included encounters with humans, domestic dogs, and attempts to enter homes. After tracking this coyote (nicknamed Carmine) across a highly urbanized landscape with participatory science, including at least 80 publicly reported sightings, he was captured and relocated to a wildlife sanctuary. Genome-wide analyses revealed 92.8% coyote ancestry, 1.7% gray wolf ancestry, and 5.5% domestic dog ancestry. The dog alleles in Carmine’s genome were estimated to have been acquired by his ancestors 14–29 years ago. Despite his bold behavior, Carmine did not carry any mutations known to shape hypersociability in canines. He did, however, carry a single copy of the dominant mutation responsible for his melanistic coat color. This detailed study of Carmine dispels common assumptions about the reticent coyote personality and the origins of behavior. His unusual bold behavior created a higher level of human-coyote interaction. He now serves as a public ambassador for human-wildlife coexistence, urging the global community to reconsider mythologies about wildlife and promote coexistence with them in landscapes significantly altered by human activity in our rapidly changing world.
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29
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Suvorov A, Scornavacca C, Fujimoto MS, Bodily P, Clement M, Crandall KA, Whiting MF, Schrider DR, Bybee SM. Deep ancestral introgression shapes evolutionary history of dragonflies and damselflies. Syst Biol 2021; 71:526-546. [PMID: 34324671 PMCID: PMC9017697 DOI: 10.1093/sysbio/syab063] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 07/20/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022] Open
Abstract
Introgression is an important biological process affecting at least 10% of the extant species in the animal kingdom. Introgression significantly impacts inference of phylogenetic species relationships where a strictly binary tree model cannot adequately explain reticulate net-like species relationships. Here we use phylogenomic approaches to understand patterns of introgression along the evolutionary history of a unique, non-model insect system: dragonflies and damselflies (Odonata). We demonstrate that introgression is a pervasive evolutionary force across various taxonomic levels within Odonata. In particular, we show that the morphologically "intermediate" species of Anisozygoptera (one of the three primary suborders within Odonata besides Zygoptera and Anisoptera), which retain phenotypic characteristics of the other two suborders, experienced high levels of introgression likely coming from zygopteran genomes. Additionally, we find evidence for multiple cases of deep inter-superfamilial ancestral introgression.
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Affiliation(s)
- Anton Suvorov
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Celine Scornavacca
- Institut des Sciences de l'Evolution Université de Montpellier, CNRS, IRD, EPHE CC 064, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
| | - M Stanley Fujimoto
- Department of Computer Science, Brigham Young University, Provo, UT, United States
| | - Paul Bodily
- Department of Computer Science, Idaho State University, Pocatello, ID, United States
| | - Mark Clement
- Department of Computer Science, Brigham Young University, Provo, UT, United States
| | - Keith A Crandall
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, United States
| | - Michael F Whiting
- Department of Biology, Brigham Young University, Provo, UT, United States.,M.L. Bean Museum, Brigham Young University, Provo, UT, United States
| | - Daniel R Schrider
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Seth M Bybee
- Department of Biology, Brigham Young University, Provo, UT, United States.,M.L. Bean Museum, Brigham Young University, Provo, UT, United States
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30
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Wilson PJ, Rutledge LY. Considering Pleistocene North American wolves and coyotes in the eastern Canis origin story. Ecol Evol 2021; 11:9137-9147. [PMID: 34257949 PMCID: PMC8258226 DOI: 10.1002/ece3.7757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 05/14/2021] [Accepted: 05/18/2021] [Indexed: 01/22/2023] Open
Abstract
The evolutionary origins and hybridization patterns of Canis species in North America have been hotly debated for the past 30 years. Disentangling ancestry and timing of hybridization in Great Lakes wolves, eastern Canadian wolves, red wolves, and eastern coyotes are most often partitioned into a 2-species model that assigns all ancestry to gray wolves and/or coyotes, and a 3-species model that includes a third, North American evolved eastern wolf genome. The proposed models address recent or sometimes late Holocene hybridization events but have largely ignored potential Pleistocene era progenitors and opportunities for hybridization that may have impacted the current mixed genomes in eastern Canada and the United States. Here, we re-analyze contemporary and ancient mitochondrial DNA genomes with Bayesian phylogenetic analyses to more accurately estimate divergence dates among lineages. We combine that with a review of the literature on Late Pleistocene Canis distributions to: (a) identify potential Pleistocene progenitors to southern North American gray wolves and eastern wolves; and (b) illuminate opportunities for ancient hybridization events. Specifically, we propose that Beringian gray wolves (C. lupus) and extinct large wolf-like coyotes (C. latrans orcutti) are likely progenitors to Mexican and Plains gray wolves and eastern wolves, respectively, and may represent a potentially unrecognized source of introgressed genomic variation within contemporary Canis genomes. These events speak to the potential origins of contemporary genomes and provide a new perspective on Canis ancestry, but do not negate current conservation priorities of dwindling wolf populations with unique genomic signatures and key ecologically critical roles.
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31
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Mikkelsen EK, Irwin D. Ongoing production of low-fitness hybrids limits range overlap between divergent cryptic species. Mol Ecol 2021; 30:4090-4102. [PMID: 34101940 DOI: 10.1111/mec.16015] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 05/13/2021] [Accepted: 05/26/2021] [Indexed: 01/23/2023]
Abstract
Contact zones between recently diverged taxa provide opportunities to examine the causes of reproductive isolation and the processes that determine whether two species can coexist over a broad region. The Pacific wren (Troglodytes pacificus) and winter wren (Troglodytes hiemalis) are two morphologically similar songbirds that started diverging about 4 million years ago, older than most sister species pairs of temperate songbirds. The ranges of these species come into narrow contact in western Canada, where the two species remain distinct. To assess evidence for differentiation, hybridization and introgression in this system, we examined variation in over 250,000 single nucleotide polymorphism markers distributed across the genome. The two species formed highly divergent genetic clusters, consistent with long-term differentiation. In a set of 75 individuals, two first-generation hybrids (i.e., F1 's) were detected, indicating only moderate levels of assortative mating between these taxa. We found no recent backcrosses or other evidence of recent breeding success of F1 's, indicating very low or zero fitness of F1 hybrids. Examination of genomic variation shows evidence for only a single backcrossing event many generations ago. The moderate rate of hybridization combined with very low F1 hybrid fitness is expected to result in a population sink in the contact zone, largely explaining the narrow overlap of the two species. If such dynamics are common in nature, they could explain the narrow range overlap often observed between pairs of closely related species.
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Affiliation(s)
- Else K Mikkelsen
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Darren Irwin
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
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32
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Taron UH, Salado I, Escobar-Rodríguez M, Westbury MV, Butschkau S, Paijmans JLA, vonHoldt BM, Hofreiter M, Leonard JA. A sliver of the past: The decimation of the genetic diversity of the Mexican wolf. Mol Ecol 2021; 30:6340-6354. [PMID: 34161633 DOI: 10.1111/mec.16037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 06/21/2021] [Indexed: 01/07/2023]
Abstract
The endangered Mexican wolf (Canis lupus baileyi) is known to carry exceedingly low levels of genetic diversity. This could be (i) the result of long-term evolutionary patterns as they exist at the southernmost limit of the species distribution at a relatively reduced effective size, or (ii) due to rapid population decline caused by human persecution over the last century. If the former, purifying selection is expected to have minimized the impact of inbreeding. If the latter, rapid and recent declines in genetic diversity may have resulted in severe fitness consequences. To differentiate these hypotheses, we conducted comparative whole-genome analyses of five historical Mexican wolves (1907-1917) and 18 contemporary Mexican and grey wolves from North America and Eurasia. Based on whole-genome data, historical and modern Mexican wolves together form a discrete unit. Moreover, we found that modern Mexican wolves have reduced genetic diversity and increased inbreeding relative to the historical population, which was widespread across the southwestern United States and not restricted to Mexico as previously assumed. Finally, although Mexican wolves have evolved in sympatry with coyotes (C. latrans), we observed lower introgression between historical Mexican wolves and coyotes than with modern Mexican wolves, despite similarities in body size. Taken together, our data show that recent population declines probably caused the reduced level of genetic diversity, but not the observed differentiation of the Mexican wolves from other North American wolves.
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Affiliation(s)
- Ulrike H Taron
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Isabel Salado
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | | | - Michael V Westbury
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Susanne Butschkau
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | - Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
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33
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vonHoldt BM, Aardema ML. Updating the Bibliography of Interbreeding among Canis in North America. J Hered 2021; 111:249-262. [PMID: 32034410 DOI: 10.1093/jhered/esaa004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 02/05/2020] [Indexed: 01/29/2023] Open
Abstract
This bibliography provides a collection of references that documents the evolution of studies evidencing interbreeding among Canis species in North America. Over the past several decades, advances in biology and genomic technology greatly improved our ability to detect and characterize species interbreeding, which has significance for understanding species in a changing landscape as well as for endangered species management. This bibliography includes a discussion within each category of interbreeding, the timeline of developing evidence, and includes a review of past research conducted on experimental crosses. Research conducted in the early 20th century is rich with detailed records and photographs of hybrid offspring development and behavior. With the progression of molecular methods, studies can estimate historical demographic parameters and detect chromosomal patterns of ancestry. As these methods continue to increase in accessibility, the field will gain a deeper and richer understanding of the evolutionary history of North American Canis.
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Affiliation(s)
- Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ
| | - Matthew L Aardema
- Department of Biology, Montclair State University, Montclair, NJ.,Sackler Institute for Comparative Genomics, American Museum of Natural History, New York City, NY
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34
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Valenciano A, Morales J, Govender R. Eucyon khoikhoi sp. nov. (Carnivora: Canidae) from Langebaanweg ‘E’ Quarry (early Pliocene, South Africa): the most complete African canini from the Mio-Pliocene. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
A new medium-sized canid, Eucyon khoikhoi sp. nov., is described from the early Pliocene site of Langebaanweg ‘E’ Quarry (South Africa). It possesses a robust dentition with large upper- and lower-second molars, an m1 talonid without a transverse cristid between the entoconid and the hypoconid, and a well-developed hypoconulid shelf. Our cladistic analysis of the earliest better-known African canini, places E. khoikhoi as the most basal taxon of an African clade composed of E. wokari, ?Nyctereutes barryi, ?Schaeffia mohibi and Schaeffia adusta (living side-striped jackal). We suggest an alternative arrangement for the poorly known East African E. intrepidus from the Late Miocene and E. kuta from the Middle Pliocene. Eucyon intrepidus could belong to the same clade as E. khoikhoi, unlike E. kuta, whose dentition suggests a closer relation with the Lupulella group. Thus, these results support the paraphyly of Eucyon, demonstrating the need for an in-depth review of the genus. Eucyon khoikhoi has a body mass comparable to E. kuta and the European E. debonisi and E. monticinensis. We conclude that E. khoikhoi may have had a comparable role in the ecosystem to the extant hypocarnivorous S. adusta.
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Affiliation(s)
- Alberto Valenciano
- Research and Exhibitions Department, Iziko Museums of South Africa, Cape Town, South Africa
- Department of Biological Sciences, University of Cape Town, Palaeobiological Research Group, Cape Town, South Africa
- Departamento de Ciencias de la Tierra and Instituto Universitario de Investigación en Ciencias Ambientales de Aragón (IUCA), Universidad de Zaragoza, Zaragoza, Spain
| | - Jorge Morales
- Departamento de Paleobiología, Museo Nacional de Ciencias Naturales-CSIC, Madrid, Spain
| | - Romala Govender
- Research and Exhibitions Department, Iziko Museums of South Africa, Cape Town, South Africa
- Department of Biological Sciences, University of Cape Town, Palaeobiological Research Group, Cape Town, South Africa
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35
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Carroll C, Rohlf DJ, vonHoldt BM, Treves A, Hendricks SA. Wolf Delisting Challenges Demonstrate Need for an Improved Framework for Conserving Intraspecific Variation under the Endangered Species Act. Bioscience 2021; 71:73-84. [PMID: 33442329 PMCID: PMC7791361 DOI: 10.1093/biosci/biaa125] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Recent advances in genomics have increased our understanding of geographic patterns of intraspecific variation and the importance of this variation in enhancing species’ potential to adapt to novel threats. However, as part of an effort to limit the scope of the Endangered Species Act (ESA), the US government has proposed the removal of the gray wolf from the list of protected species on the basis of a claim that the statute permits a species to be declared recovered given the existence of a single presently secure population. We rebut this interpretation and propose a framework for the conservation of adaptive potential that builds on current agency practice in delineating subspecific recovery units and reconciles the definition of significance in the statute's “distinct population segment” and “significant portion of range” clauses. Such a coordinated policy would enhance the ESA's effectiveness in stemming loss of biodiversity in the face of climate change and other factors altering Earth's ecosystems.
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Affiliation(s)
- Carlos Carroll
- Klamath Center for Conservation Research, Orleans, California
| | - Daniel J Rohlf
- Earthrise Law Center, in the Lewis and Clark Law School, Portland, Oregon
| | - Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey
| | - Adrian Treves
- Nelson Institute for Environmental Studies, University of Wisconsin, Madison, Wisconsin
| | - Sarah A Hendricks
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho
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36
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Perri AR, Mitchell KJ, Mouton A, Álvarez-Carretero S, Hulme-Beaman A, Haile J, Jamieson A, Meachen J, Lin AT, Schubert BW, Ameen C, Antipina EE, Bover P, Brace S, Carmagnini A, Carøe C, Samaniego Castruita JA, Chatters JC, Dobney K, Dos Reis M, Evin A, Gaubert P, Gopalakrishnan S, Gower G, Heiniger H, Helgen KM, Kapp J, Kosintsev PA, Linderholm A, Ozga AT, Presslee S, Salis AT, Saremi NF, Shew C, Skerry K, Taranenko DE, Thompson M, Sablin MV, Kuzmin YV, Collins MJ, Sinding MHS, Gilbert MTP, Stone AC, Shapiro B, Van Valkenburgh B, Wayne RK, Larson G, Cooper A, Frantz LAF. Dire wolves were the last of an ancient New World canid lineage. Nature 2021; 591:87-91. [PMID: 33442059 DOI: 10.1038/s41586-020-03082-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 11/12/2020] [Indexed: 11/09/2022]
Abstract
Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America1, yet relatively little is known about their evolution or extinction. Here, to reconstruct the evolutionary history of dire wolves, we sequenced five genomes from sub-fossil remains dating from 13,000 to more than 50,000 years ago. Our results indicate that although they were similar morphologically to the extant grey wolf, dire wolves were a highly divergent lineage that split from living canids around 5.7 million years ago. In contrast to numerous examples of hybridization across Canidae2,3, there is no evidence for gene flow between dire wolves and either North American grey wolves or coyotes. This suggests that dire wolves evolved in isolation from the Pleistocene ancestors of these species. Our results also support an early New World origin of dire wolves, while the ancestors of grey wolves, coyotes and dholes evolved in Eurasia and colonized North America only relatively recently.
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Affiliation(s)
- Angela R Perri
- Department of Archaeology, Durham University, Durham, UK.
| | - Kieren J Mitchell
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.
| | - Alice Mouton
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | | | - Ardern Hulme-Beaman
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK.,School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK
| | - James Haile
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, Oxford, UK
| | - Alexandra Jamieson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, Oxford, UK
| | - Julie Meachen
- Department of Anatomy, Des Moines University, Des Moines, IA, USA
| | - Audrey T Lin
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, Oxford, UK.,Department of Zoology, University of Oxford, Oxford, UK.,Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Blaine W Schubert
- Center of Excellence in Paleontology & Department of Geosciences, East Tennessee State University, Johnson City, TN, USA
| | - Carly Ameen
- Department of Archaeology, University of Exeter, Exeter, UK
| | | | - Pere Bover
- ARAID Foundation, Instituto Universitario de Investigación en Ciencias Ambientales (IUCA) - Aragosaurus Group, Universidad de Zaragoza, Zaragoza, Spain
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Alberto Carmagnini
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Christian Carøe
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Keith Dobney
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK.,Department of Archaeology, University of Sydney, Sydney, New South Wales, Australia.,Department of Archaeology, University of Aberdeen, Aberdeen, UK.,Department of Archaeology, Simon Fraser University, Burnaby, Canada
| | - Mario Dos Reis
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Allowen Evin
- Institut des Sciences de l'Evolution - Montpellier, CNRS, Université de Montpellier, IRD, EPHE, Montpellier, France
| | - Philippe Gaubert
- Laboratoire Evolution & Diversité Biologique, UPS/CNRS/IRD, Université Paul Sabatier, Toulouse, France
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Graham Gower
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Holly Heiniger
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Kristofer M Helgen
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Josh Kapp
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Pavel A Kosintsev
- Institute of Plant and Animal Ecology, Urals Branch of the Russian Academy of Sciences, Yekaterinburg, Russia.,Ural Federal University, Yekaterinburg, Russia
| | - Anna Linderholm
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, Oxford, UK.,Department of Anthropology, Texas A&M University, College Station, TX, USA
| | - Andrew T Ozga
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.,School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Halmos College of Arts and Sciences, Nova Southeastern University, Fort Lauderdale, FL, USA
| | | | - Alexander T Salis
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Nedda F Saremi
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Colin Shew
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Katherine Skerry
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Dmitry E Taranenko
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Mary Thompson
- Idaho Museum of Natural History, Idaho State University, Pocatello, ID, USA
| | - Mikhail V Sablin
- Zoological Institute of the Russian Academy of Sciences, St Petersburg, Russia
| | - Yaroslav V Kuzmin
- Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Tomsk State University, Tomsk, Russia
| | - Matthew J Collins
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
| | - Mikkel-Holger S Sinding
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Greenland Institute of Natural Resources, Nuuk, Greenland
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,NTNU University Museum, Trondheim, Norway
| | - Anne C Stone
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.,School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Institute of Human Origins, Arizona State University, Tempe, AZ, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Blaire Van Valkenburgh
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Greger Larson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, Oxford, UK
| | - Alan Cooper
- South Australian Museum, Adelaide, South Australia, Australia
| | - Laurent A F Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK. .,Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany.
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Ramos-Madrigal J, Sinding MHS, Carøe C, Mak SST, Niemann J, Samaniego Castruita JA, Fedorov S, Kandyba A, Germonpré M, Bocherens H, Feuerborn TR, Pitulko VV, Pavlova EY, Nikolskiy PA, Kasparov AK, Ivanova VV, Larson G, Frantz LAF, Willerslev E, Meldgaard M, Petersen B, Sicheritz-Ponten T, Bachmann L, Wiig Ø, Hansen AJ, Gilbert MTP, Gopalakrishnan S. Genomes of Pleistocene Siberian Wolves Uncover Multiple Extinct Wolf Lineages. Curr Biol 2021; 31:198-206.e8. [PMID: 33125870 PMCID: PMC7809626 DOI: 10.1016/j.cub.2020.10.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/28/2020] [Accepted: 10/01/2020] [Indexed: 12/30/2022]
Abstract
Extant Canis lupus genetic diversity can be grouped into three phylogenetically distinct clades: Eurasian and American wolves and domestic dogs.1 Genetic studies have suggested these groups trace their origins to a wolf population that expanded during the last glacial maximum (LGM)1-3 and replaced local wolf populations.4 Moreover, ancient genomes from the Yana basin and the Taimyr peninsula provided evidence of at least one extinct wolf lineage that dwelled in Siberia during the Pleistocene.35 Previous studies have suggested that Pleistocene Siberian canids can be classified into two groups based on cranial morphology. Wolves in the first group are most similar to present-day populations, although those in the second group possess intermediate features between dogs and wolves.67 However, whether this morphological classification represents distinct genetic groups remains unknown. To investigate this question and the relationships between Pleistocene canids, present-day wolves, and dogs, we resequenced the genomes of four Pleistocene canids from Northeast Siberia dated between >50 and 14 ka old, including samples from the two morphological categories. We found these specimens cluster with the two previously sequenced Pleistocene wolves, which are genetically more similar to Eurasian wolves. Our results show that, though the four specimens represent extinct wolf lineages, they do not form a monophyletic group. Instead, each Pleistocene Siberian canid branched off the lineage that gave rise to present-day wolves and dogs. Finally, our results suggest the two previously described morphological groups could represent independent lineages similarly related to present-day wolves and dogs.
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Affiliation(s)
- Jazmín Ramos-Madrigal
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel-Holger S Sinding
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Natural History Museum, University of Oslo, Oslo, Norway; The Qimmeq Project, University of Greenland, Nuussuaq, Greenland; Greenland Institute of Natural Resources, Nuuk, Greenland; Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Christian Carøe
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Sarah S T Mak
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Niemann
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Sergey Fedorov
- Mammoth Museum of North-Eastern Federal University, Yakutsk, Russia
| | - Alexander Kandyba
- Department of Stone Age Archeology, Institute of Archaeology and Ethnography of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Mietje Germonpré
- Directorate Earth and History of Life, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Hervé Bocherens
- Department of Geosciences, Biogeology, University of Tübingen, Tübingen, Germany; Senckenberg Centre for Human Evolution and Palaeoenvironment, Tübingen, Germany
| | - Tatiana R Feuerborn
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; The Qimmeq Project, University of Greenland, Nuussuaq, Greenland; Section for GeoGenetics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Vladimir V Pitulko
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
| | - Elena Y Pavlova
- Arctic and Antarctic Research Institute, St. Petersburg, Russia
| | | | - Aleksei K Kasparov
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
| | - Varvara V Ivanova
- VNIIOkeangeologia Research Institute (The All-Russian Research Institute of Geology and Mineral Resources of the World Ocean), St. Petersburg, Russia
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Laurent A F Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK; Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
| | - Eske Willerslev
- Section for GeoGenetics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Danish Institute for Advanced Study (D-IAS), University of Southern Denmark, Odense, Denmark; Department of Zoology, University of Cambridge, Cambridge, UK; Wellcome Trust Sanger Institute, University of Cambridge, Cambridge, UK
| | - Morten Meldgaard
- The Qimmeq Project, University of Greenland, Nuussuaq, Greenland; Section for GeoGenetics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Bent Petersen
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Thomas Sicheritz-Ponten
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Lutz Bachmann
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Øystein Wiig
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Anders J Hansen
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; The Qimmeq Project, University of Greenland, Nuussuaq, Greenland; Section for GeoGenetics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark.
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38
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Dog colour patterns explained by modular promoters of ancient canid origin. Nat Ecol Evol 2021; 5:1415-1423. [PMID: 34385618 PMCID: PMC8484016 DOI: 10.1038/s41559-021-01524-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 07/01/2021] [Indexed: 02/06/2023]
Abstract
Distinctive colour patterns in dogs are an integral component of canine diversity. Colour pattern differences are thought to have arisen from mutation and artificial selection during and after domestication from wolves but important gaps remain in understanding how these patterns evolved and are genetically controlled. In other mammals, variation at the ASIP gene controls both the temporal and spatial distribution of yellow and black pigments. Here, we identify independent regulatory modules for ventral and hair cycle ASIP expression, and we characterize their action and evolutionary origin. Structural variants define multiple alleles for each regulatory module and are combined in different ways to explain five distinctive dog colour patterns. Phylogenetic analysis reveals that the haplotype combination for one of these patterns is shared with Arctic white wolves and that its hair cycle-specific module probably originated from an extinct canid that diverged from grey wolves more than 2 million years ago. Natural selection for a lighter coat during the Pleistocene provided the genetic framework for widespread colour variation in dogs and wolves.
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39
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Sadanandan KR, Low GW, Sridharan S, Gwee CY, Ng EYX, Yuda P, Prawiradilaga DM, Lee JGH, Tritto A, Rheindt FE. The conservation value of admixed phenotypes in a critically endangered species complex. Sci Rep 2020; 10:15549. [PMID: 32968132 PMCID: PMC7511927 DOI: 10.1038/s41598-020-72428-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/17/2020] [Indexed: 11/19/2022] Open
Abstract
In today's environmental crisis, conservationists are increasingly confronted with terminally endangered species whose last few surviving populations may be affected by allelic introgression from closely related species. Yet there is a worrying lack of evidence-based recommendations and solutions for this emerging problem. We analyzed genome-wide DNA markers and plumage variability in a critically endangered insular songbird, the Black-winged Myna (BWM, Acridotheres melanopterus). This species is highly threatened by the illegal wildlife trade, with its wild population numbering in the low hundreds, and its continued survival urgently depending on ex-situ breeding. Its three subspecies occur along a geographic gradient of melanism and are variably interpreted as three species. However, our integrative approach revealed that melanism poorly reflects the pattern of limited genomic differentiation across BWM subspecies. We also uncovered allelic introgression into the most melanistic subspecies, tertius, from the all-black congeneric Javan Myna (A. javanicus), which is native to the same islands. Based on our results, we recommend the establishment of three separate breeding programs to maintain subspecific traits that may confer local adaptation, but with the option of occasional cross-breeding between insurance populations in order to boost genetic diversity and increase overall viability prospects of each breeding program. Our results underscore the importance of evidence-based integrative approaches when determining appropriate conservation units. Given the rapid increase of terminally endangered organisms in need of ex-situ conservation, this study provides an important blueprint for similar programs dealing with phenotypically variable species.
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Affiliation(s)
- Keren R Sadanandan
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
- Max Planck Institute for Ornithology, 82319, Seewiesen, Germany
| | - Gabriel W Low
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Sheeraja Sridharan
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
- Department of Biological Sciences, University of Alberta, 116 St & 85 Ave, Edmonton, AB, T6G 2R3, Canada
| | - Chyi Yin Gwee
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
| | - Elize Y X Ng
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
| | - Pramana Yuda
- Universitas Atma Jaya, Jl. Babarsari 44, Janti, Caturtunggal, Kec. Depok, Kabupaten Sleman, Daerah Istimewa Yogyakarta, 55281, Indonesia
| | - Dewi M Prawiradilaga
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor KM 46, Cibinong Science Center, Cibinong, 16911, Indonesia
| | - Jessica G H Lee
- Wildlife Reserves Singapore, 80 Mandai Lake Road, Singapore, 729826, Singapore
| | - Anaïs Tritto
- Wildlife Reserves Singapore, 80 Mandai Lake Road, Singapore, 729826, Singapore
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore.
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40
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Lutgen D, Ritter R, Olsen R, Schielzeth H, Gruselius J, Ewels P, García JT, Shirihai H, Schweizer M, Suh A, Burri R. Linked‐read sequencing enables haplotype‐resolved resequencing at population scale. Mol Ecol Resour 2020; 20:1311-1322. [DOI: 10.1111/1755-0998.13192] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 04/25/2020] [Accepted: 05/06/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Dave Lutgen
- Department of Population Ecology Institute of Ecology and Evolution Friedrich Schiller University Jena Jena Germany
| | - Raphael Ritter
- Department of Population Ecology Institute of Ecology and Evolution Friedrich Schiller University Jena Jena Germany
| | - Remi‐André Olsen
- Science for Life Laboratory Department of Biochemistry and Biophysics Stockholm University Solna Sweden
| | - Holger Schielzeth
- Department of Population Ecology Institute of Ecology and Evolution Friedrich Schiller University Jena Jena Germany
| | - Joel Gruselius
- Science for Life Laboratory Department of Biosciences and Nutrition Karolinska Institutet Stockholm Sweden
| | - Philip Ewels
- Science for Life Laboratory Department of Biochemistry and Biophysics Stockholm University Solna Sweden
| | - Jesús T. García
- Instituto de Investigación en Recursos Cinegéticos (IREC) CSIC‐UCLM‐JCCM Ciudad Real Spain
| | | | - Manuel Schweizer
- Natural History Museum Bern Bern Switzerland
- Institute of Ecology and Evolution University of Bern Bern Switzerland
| | - Alexander Suh
- Department of Organismal Biology – Systematic Biology Evolutionary Biology Centre (EBC) Uppsala University Uppsala Sweden
| | - Reto Burri
- Department of Population Ecology Institute of Ecology and Evolution Friedrich Schiller University Jena Jena Germany
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41
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Phung TN, Wayne RK, Wilson MA, Lohmueller KE. Complex patterns of sex-biased demography in canines. Proc Biol Sci 2020; 286:20181976. [PMID: 31113325 DOI: 10.1098/rspb.2018.1976] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The demographic history of dogs is complex, involving multiple bottlenecks, admixture events and artificial selection. However, existing genetic studies have not explored variance in the number of reproducing males and females, and whether it has changed across evolutionary time. While male-biased mating practices, such as male-biased migration and multiple paternity, have been observed in wolves, recent breeding practices could have led to female-biased mating patterns in breed dogs. For example, breed dogs are thought to have experienced a popular sire effect, where a small number of males father many offspring with a large number of females. Here we use genetic variation data to test how widespread sex-biased mating practices in canines are during different evolutionary time points. Using whole-genome sequence data from 33 dogs and wolves, we show that patterns of diversity on the X chromosome and autosomes are consistent with a higher number of reproducing males than females over ancient evolutionary history in both dogs and wolves, suggesting that mating practices did not change during early dog domestication. By contrast, since breed formation, we found evidence for a larger number of reproducing females than males in breed dogs, consistent with the popular sire effect. Our results confirm that canine demography has been complex, with opposing sex-biased processes occurring throughout their history. The signatures observed in genetic data are consistent with documented sex-biased mating practices in both the wild and domesticated populations, suggesting that these mating practices are pervasive.
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Affiliation(s)
- Tanya N Phung
- 1 Interdepartmental Program in Bioinformatics, University of California , Los Angeles, CA 90095 , USA
| | - Robert K Wayne
- 2 Department of Ecology and Evolutionary Biology, University of California , Los Angeles, CA 90095 , USA
| | - Melissa A Wilson
- 4 School of Life Sciences and Center for Evolution and Medicine, The Biodesign Institute, Arizona State University , Tempe, AZ 85281 , USA
| | - Kirk E Lohmueller
- 1 Interdepartmental Program in Bioinformatics, University of California , Los Angeles, CA 90095 , USA.,2 Department of Ecology and Evolutionary Biology, University of California , Los Angeles, CA 90095 , USA.,3 Department of Human Genetics, David Geffen School of Medicine, University of California , Los Angeles, CA 90095 , USA
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Abstract
Introgressive hybridization can affect the evolution of populations in several important ways. It may retard or reverse divergence of species, enable the development of novel traits, enhance the potential for future evolution by elevating levels of standing variation, create new species, and alleviate inbreeding depression in small populations. Most of what is known of contemporary hybridization in nature comes from the study of pairs of species, either coexisting in the same habitat or distributed parapatrically and separated by a hybrid zone. More rarely, three species form an interbreeding complex (triad), reported in vertebrates, insects, and plants. Often, one species acts as a genetic link or conduit for the passage of genes (alleles) between two others that rarely, if ever, hybridize. Demographic and genetic consequences are unknown. Here we report results of a long-term study of interbreeding Darwin's finches on Daphne Major island, Galápagos. Geospiza fortis acted as a conduit for the passage of genes between two others that have never been observed to interbreed on Daphne: Geospiza fuliginosa, a rare immigrant, and Geospiza scandens, a resident. Microsatellite gene flow from G. fortis into G. scandens increased in frequency during 30 y of favorable ecological conditions, resulting in genetic and morphological convergence. G. fortis, G. scandens, and the derived dihybrids and trihybrids experienced approximately equal fitness. Especially relevant to young adaptive radiations, where species differ principally in ecology and behavior, these findings illustrate how new combinations of genes created by hybridization among three species can enhance the potential for evolutionary change.
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43
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Caniglia R, Galaverni M, Velli E, Mattucci F, Canu A, Apollonio M, Mucci N, Scandura M, Fabbri E. A standardized approach to empirically define reliable assignment thresholds and appropriate management categories in deeply introgressed populations. Sci Rep 2020; 10:2862. [PMID: 32071323 PMCID: PMC7028925 DOI: 10.1038/s41598-020-59521-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 01/28/2020] [Indexed: 11/09/2022] Open
Abstract
Anthropogenic hybridization is recognized as a major threat to the long-term survival of natural populations. While identifying F1 hybrids might be simple, the detection of older admixed individuals is far from trivial and it is still debated whether they should be targets of management. Examples of anthropogenic hybridization have been described between wolves and domestic dogs, with numerous cases detected in the Italian wolf population. After selecting appropriate wild and domestic reference populations, we used empirical and simulated 39-autosomal microsatellite genotypes, Bayesian assignment and performance analyses to develop a workflow to detect different levels of wolf x dog admixture. Membership proportions to the wild cluster (qiw) and performance indexes identified two q-thresholds which allowed to efficiently classify the analysed genotypes into three assignment classes: pure (with no or negligible domestic ancestry), older admixed (with a marginal domestic ancestry) and recent admixed (with a clearly detectable domestic ancestry) animals. Based on their potential to spread domestic variants, such classes were used to define three corresponding management categories: operational pure, introgressed and operational hybrid individuals. Our multiple-criteria approach can help wildlife managers and decision makers in more efficiently targeting the available resources for the long-term conservation of species threatened by anthropogenic hybridization.
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Affiliation(s)
- Romolo Caniglia
- Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell' Emilia, Bologna, Italy.
| | | | - Edoardo Velli
- Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell' Emilia, Bologna, Italy
| | - Federica Mattucci
- Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell' Emilia, Bologna, Italy
| | - Antonio Canu
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Marco Apollonio
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Nadia Mucci
- Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell' Emilia, Bologna, Italy
| | - Massimo Scandura
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Elena Fabbri
- Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell' Emilia, Bologna, Italy
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44
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Barbato M, Hailer F, Upadhyay M, Del Corvo M, Colli L, Negrini R, Kim ES, Crooijmans RPMA, Sonstegard T, Ajmone-Marsan P. Adaptive introgression from indicine cattle into white cattle breeds from Central Italy. Sci Rep 2020; 10:1279. [PMID: 31992729 PMCID: PMC6987186 DOI: 10.1038/s41598-020-57880-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/26/2019] [Indexed: 11/19/2022] Open
Abstract
Cattle domestication occurred at least twice independently and gave rise to the modern taurine and indicine cattle breeds. European cattle diversity is generally dominated by taurine cattle, although elevated levels of indicine ancestry have been recorded in several breeds from southern Europe. Here we use genome-wide high-density SNP genotyping data to investigate the taurine and indicine ancestry in southern European cattle, based on a dataset comprising 508 individuals from 23 cattle breeds of taurine, indicine and mixed ancestry, including three breeds from Central Italy known to exhibit the highest levels of indicine introgression among southern European breeds. Based on local genomic ancestry analyses, we reconstruct taurine and indicine ancestry genome-wide and along chromosomes. We scrutinise local genomic introgression signals and identify genomic regions that have introgressed from indicine into taurine cattle under positive selection, harbouring genes with functions related to body size and feed efficiency. These findings suggest that indicine-derived traits helped enhance Central Italian cattle through adaptive introgression. The identified genes could provide genomic targets for selection for improved cattle performance. Our findings elucidate the key role of adaptive introgression in shaping the phenotypic features of modern cattle, aided by cultural and livestock exchange among historic human societies.
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Affiliation(s)
- Mario Barbato
- Università Cattolica del Sacro Cuore, Department of Animal Science Food and Nutrition - DIANA, Nutrigenomics and Proteomics Research Centre - PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy.
| | - Frank Hailer
- School of Biosciences, Cardiff University, Cardiff, Wales, UK
| | - Maulik Upadhyay
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Marcello Del Corvo
- Università Cattolica del Sacro Cuore, Department of Animal Science Food and Nutrition - DIANA, Nutrigenomics and Proteomics Research Centre - PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Licia Colli
- Università Cattolica del Sacro Cuore, Department of Animal Science Food and Nutrition - DIANA, Nutrigenomics and Proteomics Research Centre - PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Riccardo Negrini
- Università Cattolica del Sacro Cuore, Department of Animal Science Food and Nutrition - DIANA, Nutrigenomics and Proteomics Research Centre - PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | | | | | | | - Paolo Ajmone-Marsan
- Università Cattolica del Sacro Cuore, Department of Animal Science Food and Nutrition - DIANA, Nutrigenomics and Proteomics Research Centre - PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy.
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45
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Ericson HS, Fedorca A, Toderas I, Hegyeli Z, Plis K, Dykyy I, Jędrzejewska B, Ionescu G, Fedorca M, Iacolina L, Stronen AV. Genome-wide profiles indicate wolf population connectivity within the eastern Carpathian Mountains. Genetica 2019; 148:33-39. [PMID: 31873826 DOI: 10.1007/s10709-019-00083-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 12/17/2019] [Indexed: 11/26/2022]
Abstract
The Carpathian Mountains provide critical wildlife habitat in central Europe, and previous genome-wide studies have found western Carpathian Mountain wolves (Canis lupus) to be a separate population. Whereas differentiation to the north may be explained by a lowland-mountain transition and habitat fragmentation, the eastern Carpathian Mountains extending through Romania appear to offer continuous wildlife habitat southward. Our objective was to assess gene flow patterns and population connectivity among wolves in Romania, western Ukraine, and the Republic of Moldova. We sought to determine if the Carpathian Mountain region is best described by a north-south gradient in genetic profiles, or whether Romanian wolves show population structure with northern individuals clustering with western Ukraine. We genotyped 48 individuals with 170 000 single nucleotide polymorphism markers, and successful profiles from Romania (n = 27) and Moldova (n = 2) were merged with existing data from western Ukraine (n = 10). Expected heterozygosity was 0.234 (SE 0.001) for Romania and 0.229 (SE 0.001) for western Ukraine, whereas observed heterozygosity values were 0.230 (SE 0.001) versus 0.231 (SE 0.001). Population structure analyses with a maximum likelihood method supported K = 1 population, followed by K = 2 where Romania formed one cluster, and western Ukraine and Moldova formed another. Principal component analysis results were broadly consistent with K = 2. Pairwise FST between western Ukraine and Romania was 0.042 (p = 0.001). Our findings indicated weak population differentiation, and future research may clarify whether the spatial distribution of genetic diversity in the region is associated with environmental and ecological factors such as terrain ruggedness and the distribution of prey species.
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Affiliation(s)
- H S Ericson
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - A Fedorca
- National Institute for Research and Development in Forestry "Marin Dracea", Brasov, Romania
- Transilvania University of Brasov, Brasov, Romania
| | - I Toderas
- Institute of Zoology, Moldova Academy of Sciences, Chisinau, Republic of Moldova
| | - Z Hegyeli
- "Milvus Group" Bird and Nature Protection Association, Târgu Mureș, Romania
| | - K Plis
- Mammal Research Institute Polish Academy of Sciences, Białowieża, Poland
| | - I Dykyy
- Department of Zoology, Biological Faculty, Ivan Franko National University of Lviv, Lviv, Ukraine
| | - B Jędrzejewska
- Mammal Research Institute Polish Academy of Sciences, Białowieża, Poland
| | - G Ionescu
- National Institute for Research and Development in Forestry "Marin Dracea", Brasov, Romania
- Transilvania University of Brasov, Brasov, Romania
| | - M Fedorca
- National Institute for Research and Development in Forestry "Marin Dracea", Brasov, Romania
- Transilvania University of Brasov, Brasov, Romania
| | - L Iacolina
- Department of Fisheries, Apiculture, Wildlife Management and Special Zoology, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000, Zagreb, Croatia
| | - A V Stronen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
- Department of Biotechnology and Life Sciences, Insubria University, Varese, Italy.
- Biology Department, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000, Ljubljana, Slovenia.
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46
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Pilot M, Moura AE, Okhlopkov IM, Mamaev NV, Alagaili AN, Mohammed OB, Yavruyan EG, Manaseryan NH, Hayrapetyan V, Kopaliani N, Tsingarska E, Krofel M, Skoglund P, Bogdanowicz W. Global Phylogeographic and Admixture Patterns in Grey Wolves and Genetic Legacy of An Ancient Siberian Lineage. Sci Rep 2019; 9:17328. [PMID: 31757998 PMCID: PMC6874602 DOI: 10.1038/s41598-019-53492-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 11/01/2019] [Indexed: 12/12/2022] Open
Abstract
The evolutionary relationships between extinct and extant lineages provide important insight into species' response to environmental change. The grey wolf is among the few Holarctic large carnivores that survived the Late Pleistocene megafaunal extinctions, responding to that period's profound environmental changes with loss of distinct lineages and phylogeographic shifts, and undergoing domestication. We reconstructed global genome-wide phylogeographic patterns in modern wolves, including previously underrepresented Siberian wolves, and assessed their evolutionary relationships with a previously genotyped wolf from Taimyr, Siberia, dated at 35 Kya. The inferred phylogeographic structure was affected by admixture with dogs, coyotes and golden jackals, stressing the importance of accounting for this process in phylogeographic studies. The Taimyr lineage was distinct from modern Siberian wolves and constituted a sister lineage of modern Eurasian wolves and domestic dogs, with an ambiguous position relative to North American wolves. We detected gene flow from the Taimyr lineage to Arctic dog breeds, but population clustering methods indicated closer similarity of the Taimyr wolf to modern wolves than dogs, implying complex post-divergence relationships among these lineages. Our study shows that introgression from ecologically diverse con-specific and con-generic populations was common in wolves' evolutionary history, and could have facilitated their adaptation to environmental change.
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Affiliation(s)
- Małgorzata Pilot
- School of Life Sciences, University of Lincoln, Lincoln, United Kingdom
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland
| | - Andre E Moura
- School of Life Sciences, University of Lincoln, Lincoln, United Kingdom
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland
| | - Innokentiy M Okhlopkov
- Institute of Biological Problems of Cryolithozone, Siberian Branch of Russian Academy of Sciences, Yakutsk, Russia
| | - Nikolay V Mamaev
- Institute of Biological Problems of Cryolithozone, Siberian Branch of Russian Academy of Sciences, Yakutsk, Russia
| | - Abdulaziz N Alagaili
- KSU Mammals Research Chair, Department of Zoology, King Saud University, Riyadh, Saudi Arabia
| | - Osama B Mohammed
- KSU Mammals Research Chair, Department of Zoology, King Saud University, Riyadh, Saudi Arabia
| | - Eduard G Yavruyan
- Scientific Center of Zoology and Hydroecology, National Academy of Sciences, Yerevan, Armenia
| | - Ninna H Manaseryan
- Scientific Center of Zoology and Hydroecology, National Academy of Sciences, Yerevan, Armenia
| | | | - Natia Kopaliani
- Institute of Ecology, Ilia State University, Tbilisi, Georgia
| | | | - Miha Krofel
- Department of Forestry, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | | | - Wiesław Bogdanowicz
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland.
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47
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Fitak RR, Rinkevich SE, Culver M. Genome-Wide Analysis of SNPs Is Consistent with No Domestic Dog Ancestry in the Endangered Mexican Wolf (Canis lupus baileyi). J Hered 2019; 109:372-383. [PMID: 29757430 DOI: 10.1093/jhered/esy009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 02/28/2018] [Indexed: 11/13/2022] Open
Abstract
The Mexican gray wolf (Canis lupus baileyi) was historically distributed throughout the southwestern United States and northern Mexico. Extensive predator removal campaigns during the early 20th century, however, resulted in its eventual extirpation by the mid 1980s. At this time, the Mexican wolf existed only in 3 separate captive lineages (McBride, Ghost Ranch, and Aragón) descended from 3, 2, and 2 founders, respectively. These lineages were merged in 1995 to increase the available genetic variation, and Mexican wolves were reintroduced into Arizona and New Mexico in 1998. Despite the ongoing management of the Mexican wolf population, it has been suggested that a proportion of the Mexican wolf ancestry may be recently derived from hybridization with domestic dogs. In this study, we genotyped 87 Mexican wolves, including individuals from all 3 captive lineages and cross-lineage wolves, for more than 172000 single nucleotide polymorphisms. We identified levels of genetic variation consistent with the pedigree record and effects of genetic rescue. To identify the potential to detect hybridization with domestic dogs, we compared our Mexican wolf genotypes with those from studies of domestic dogs and other gray wolves. The proportion of Mexican wolf ancestry assigned to domestic dogs was only between 0.06% (SD 0.23%) and 7.8% (SD 1.0%) for global and local ancestry estimates, respectively; and was consistent with simulated levels of incomplete lineage sorting. Overall, our results suggested that Mexican wolves lack biologically significant ancestry with dogs and have useful implications for the conservation and management of this endangered wolf subspecies.
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Affiliation(s)
| | | | - Melanie Culver
- US Geological Survey Arizona Cooperative Fish and Wildlife Research Unit, School of Natural Resources and the Environment, University of Arizona, Tucson, AZ
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48
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Wang GD, Zhang M, Wang X, Yang MA, Cao P, Liu F, Lu H, Feng X, Skoglund P, Wang L, Fu Q, Zhang YP. Genomic Approaches Reveal an Endemic Subpopulation of Gray Wolves in Southern China. iScience 2019; 20:110-118. [PMID: 31563851 PMCID: PMC6817678 DOI: 10.1016/j.isci.2019.09.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 06/21/2019] [Accepted: 09/05/2019] [Indexed: 12/30/2022] Open
Abstract
Although gray wolves (Canis lupus) are one of the most widely distributed terrestrial mammals, their origins in China are not well understood. We sequenced six specimens from wolf skins, showing that gray wolves from Southern China (SC) derive from a single lineage, distinct from gray wolves from the Tibetan Plateau and Northern China, suggesting that SC gray wolves may form a distinct subpopulation. Of SC gray wolves, one wolf from Zhejiang carries a genetic component from a canid and had gene flow from a population related to or further diverged from wolves than the dhole. This may indicate that interspecific gene flow likely played an important role in shaping the speciation patterns and population structure in the genus Canis. Our study is the first to survey museum gray wolves' genomes from Southern China, highlighting how sequencing the paleogenome from museum specimens can help us to study extinct species.
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Affiliation(s)
- Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Ming Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuan Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Melinda A Yang
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China
| | - Feng Liu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China
| | - Heng Lu
- Department of Molecular and Cell Biology, School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China
| | | | - Lu Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
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49
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Molecular and morphological evidence for hybrid origin and matroclinal inheritance of an endangered wild rose, Rosa × pseudobanksiae (Rosaceae) from China. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01227-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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50
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Szpiech ZA, Mak ACY, White MJ, Hu D, Eng C, Burchard EG, Hernandez RD. Ancestry-Dependent Enrichment of Deleterious Homozygotes in Runs of Homozygosity. Am J Hum Genet 2019; 105:747-762. [PMID: 31543216 PMCID: PMC6817522 DOI: 10.1016/j.ajhg.2019.08.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 08/27/2019] [Indexed: 12/20/2022] Open
Abstract
Runs of homozygosity (ROH) are important genomic features that manifest when an individual inherits two haplotypes that are identical by descent. Their length distributions are informative about population history, and their genomic locations are useful for mapping recessive loci contributing to both Mendelian and complex disease risk. We have previously shown that ROH, and especially long ROH that are likely the result of recent parental relatedness, are enriched for homozygous deleterious coding variation in a worldwide sample of outbred individuals. However, the distribution of ROH in admixed populations and their relationship to deleterious homozygous genotypes is understudied. Here we analyze whole-genome sequencing data from 1,441 unrelated individuals from self-identified African American, Puerto Rican, and Mexican American populations. These populations are three-way admixed between European, African, and Native American ancestries and provide an opportunity to study the distribution of deleterious alleles partitioned by local ancestry and ROH. We re-capitulate previous findings that long ROH are enriched for deleterious variation genome-wide. We then partition by local ancestry and show that deleterious homozygotes arise at a higher rate when ROH overlap African ancestry segments than when they overlap European or Native American ancestry segments of the genome. These results suggest that, while ROH on any haplotype background are associated with an inflation of deleterious homozygous variation, African haplotype backgrounds may play a particularly important role in the genetic architecture of complex diseases for admixed individuals, highlighting the need for further study of these populations.
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Affiliation(s)
- Zachary A Szpiech
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Department of Biological Sciences, Auburn University, Auburn, AL 36842, USA.
| | - Angel C Y Mak
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Marquitta J White
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Donglei Hu
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Celeste Eng
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Esteban G Burchard
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Ryan D Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA; Department of Human Genetics, McGill University, Montreal, QC H3A 0G1, Canada; Genome Quebec Innovation Center, McGill University, Montreal, QC H3A 0G1, Canada.
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