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Ruiz-García M, Escobar-Armel P, Martínez-Agüero M, Gaviria M, Álvarez D, Pinedo M, Shostell JM. Are There Barriers Separating the Pink River Dolphin Populations ( Inia boliviensis, Iniidae, Cetacea) within the Mamoré-Iténez River Basins (Bolivia)? An Analysis of Its Genetic Structure by Means of Mitochondrial and Nuclear DNA Markers. Genes (Basel) 2024; 15:1012. [PMID: 39202372 PMCID: PMC11353456 DOI: 10.3390/genes15081012] [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: 07/02/2024] [Revised: 07/27/2024] [Accepted: 07/28/2024] [Indexed: 09/03/2024] Open
Abstract
The pink river dolphin, or bufeo, is one of the dolphins which lives in the rivers of the Orinoco and Amazon basins in South America. The Bolivian bufeo population is considered a differentiated species (Inia boliviensis) from the Amazon and Orinoco species (Inia geoffrensis). Until now, no study has completed an extensive population genetics analysis of the bufeo in Bolivian rivers. We analyzed 82 bufeos from different rivers from the Mamoré and Iténez (Guaporé) river basins for the mt control region (CR), nuclear microsatellites, and DQB-1 gene sequences to determine if the inner rapids of these Bolivian river basins have some influence on the genetic structure of this species. The first relevant result was that the genetic diversity for CR, and the microsatellites were substantially lower in the Bolivian bufeos than in the dolphins studied in other areas of the Amazon and Orinoco. However, the DQB-1 gene sequences yielded similar genetic diversity to those found in other areas. The second relevant result is the existence of some significant genetic heterogeneity among the bufeo populations within Bolivia, although in a small degree, but this differentiation is independent of the inner rapids of the Bolivian rivers we sampled. The third relevant result was the existence of significant isolation by distance for the CR, but not for microsatellites and DQB-1 gene sequences. This was related to differential gene flow capacity of females (philopatric) and males (less philopatric and more migrants) and, possibly, to different selective patterns affecting the molecular markers studied. The fourth relevant result was related to diverse demographic changes of these bufeos. At least two or three bottleneck events and one or two population expansions have occurred in the Bolivian bufeo population. The major part of these events occurred during the Pleistocene.
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Affiliation(s)
- Manuel Ruiz-García
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Unidad de Genética, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Carrera 7A No 43-82, Bogotá 110311, DC, Colombia; (P.E.-A.); (M.G.); (D.Á.); (M.P.)
| | - Pablo Escobar-Armel
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Unidad de Genética, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Carrera 7A No 43-82, Bogotá 110311, DC, Colombia; (P.E.-A.); (M.G.); (D.Á.); (M.P.)
| | - María Martínez-Agüero
- Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá 111321, DC, Colombia;
| | - Magda Gaviria
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Unidad de Genética, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Carrera 7A No 43-82, Bogotá 110311, DC, Colombia; (P.E.-A.); (M.G.); (D.Á.); (M.P.)
| | - Diana Álvarez
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Unidad de Genética, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Carrera 7A No 43-82, Bogotá 110311, DC, Colombia; (P.E.-A.); (M.G.); (D.Á.); (M.P.)
| | - Myreya Pinedo
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Unidad de Genética, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Carrera 7A No 43-82, Bogotá 110311, DC, Colombia; (P.E.-A.); (M.G.); (D.Á.); (M.P.)
| | - Joseph Mark Shostell
- Math, Science and Technology Department, University of Minnesota Crookston, Crookston, MN 56716, USA;
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Morin PA, McCarthy ML, Fung CW, Durban JW, Parsons KM, Perrin WF, Taylor BL, Jefferson TA, Archer FI. Revised taxonomy of eastern North Pacific killer whales ( Orcinus orca): Bigg's and resident ecotypes deserve species status. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231368. [PMID: 38545612 PMCID: PMC10966402 DOI: 10.1098/rsos.231368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/29/2024] [Accepted: 02/10/2024] [Indexed: 04/26/2024]
Abstract
Killer whales (Orcinus orca) are currently recognized as a single ecologically and morphologically diverse, globally distributed species. Multiple morphotypes or ecotypes have been described, often associated with feeding specialization, and several studies have suggested taxonomic revision to include multiple subspecies or species in the genus. We review the ecological, morphological and genetic data for the well-studied 'resident' and Bigg's (aka 'transient') ecotypes in the eastern North Pacific and use quantitative taxonomic guidelines and standards to determine whether the taxonomic status of these killer whale ecotypes should be revised. Our review and new analyses indicate that species-level status is justified in both cases, and we conclude that eastern North Pacific Bigg's killer whales should be recognized as Orcinus rectipinnus (Cope in Scammon, 1869) and resident killer whales should be recognized as Orcinus ater (Cope in Scammon, 1869).
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Affiliation(s)
- Phillip A. Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA92037, USA
| | - Morgan L. McCarthy
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA92037, USA
| | - Charissa W. Fung
- University of British Columbia, Vancouver, British ColumbiaV6T 1Z4, Canada
| | - John W. Durban
- Marine Mammal Institute, Oregon State University, Newport, OR97365, USA
| | - Kim M. Parsons
- Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, WA98112, USA
| | - William F. Perrin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA92037, USA
| | - Barbara L. Taylor
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA92037, USA
| | - Thomas A. Jefferson
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA92037, USA
| | - Frederick I. Archer
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA92037, USA
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3
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Talavera A, Palmada-Flores M, Burriel-Carranza B, Valbuena-Ureña E, Mochales-Riaño G, Adams DC, Tejero-Cicuéndez H, Soler-Membrives A, Amat F, Guinart D, Carbonell F, Obon E, Marquès-Bonet T, Carranza S. Genomic insights into the Montseny brook newt ( Calotriton arnoldi), a Critically Endangered glacial relict. iScience 2024; 27:108665. [PMID: 38226169 PMCID: PMC10788218 DOI: 10.1016/j.isci.2023.108665] [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: 08/14/2023] [Revised: 10/09/2023] [Accepted: 12/05/2023] [Indexed: 01/17/2024] Open
Abstract
The Montseny brook newt (Calotriton arnoldi), considered the most endangered amphibian in Europe, is a relict salamandrid species endemic to a small massif located in northeastern Spain. Although conservation efforts should always be guided by genomic studies, those are yet scarce among urodeles, hampered by the extreme sizes of their genomes. Here, we present the third available genome assembly for the order Caudata, and the first genomic study of the species and its sister taxon, the Pyrenean brook newt (Calotriton asper), combining whole-genome and ddRADseq data. Our results reveal significant demographic oscillations which accurately mirrored Europe's climatic history. Although severe bottlenecks have led to depauperate genomic diversity and long runs of homozygosity along a gigantic genome, inbreeding might have been avoided by assortative mating strategies. Other life history traits, however, seem to have been less advantageous, and the lack of land dispersal has driven to exceptional levels of population fragmentation.
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Affiliation(s)
- Adrián Talavera
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Marc Palmada-Flores
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Bernat Burriel-Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- Museu de Ciències Naturals de Barcelona, Pº Picasso s/n, Parc Ciutadella, 08003 Barcelona, Spain
| | | | | | - Dean C. Adams
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50010, USA
| | - Héctor Tejero-Cicuéndez
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Anna Soler-Membrives
- Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Fèlix Amat
- Àrea d’Herpetologia, BiBIO, Museu de Granollers – Ciències Naturals. Palaudàries 102, Granollers, Barcelona, Spain
| | - Daniel Guinart
- Servei de Gestió de Parcs Naturals, Diputació de Barcelona, Spain
| | - Francesc Carbonell
- Centre de fauna salvatge de Torreferrussa (Forestal Catalana, SA), Santa Perpètua de Mogoda, Spain
| | - Elena Obon
- Centre de fauna salvatge de Torreferrussa (Forestal Catalana, SA), Santa Perpètua de Mogoda, Spain
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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4
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Carvalho PS, Santana DJ, Zaher H, Myers EA. Effects of Environmental Variation in Structuring Population Genetic Variation in the False-Water Cobras (Xenodontinae: Hydrodynastes). Evol Biol 2023. [DOI: 10.1007/s11692-023-09601-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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5
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Suzuki M, Ohno K, Sawayama E, Morinaga SI, Kishida T, Matsumoto T, Kato H. Genomics reveals a genetically isolated population of the Pacific white-sided dolphin (Lagenorhynchus obliquidens) distributed in the Sea of Japan. Mol Ecol 2023; 32:881-891. [PMID: 36440502 DOI: 10.1111/mec.16797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 11/10/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022]
Abstract
The processes by which animals become genetically isolated in an open environment such as the ocean have not yet been fully elucidated. Morphologically different populations of Pacific white-sided dolphin Lagenorhynchus obliquidens are observed sympatrically in the Sea of Japan. However, genetic studies that exclusively used limited mitochondrial loci or microsatellite DNA have failed to demonstrate the existence of genetically distinct populations. Here, to reveal the population structure, we analysed genome-wide population genetic data using single nucleotide polymorphisms (SNPs) gathered in 2018-2021 from all domestic captive individuals in aquaria, the majority of which originated from the wild, as well as from some stranded individuals, together covering a wide area of coastal water around Japan (n = 123). Multiplexed intersimple sequence repeat genotyping-by-sequencing analysis was performed to obtain the SNP data. Principal coordinate analysis and the clustering method structure indicated that two genetically-distinct populations exist, with little interpopulation gene flow revealed. In addition, the genotypic segregation was reflected in differences in external morphotype. Furthermore, a population demographic analysis based on the whole-genome sequences of an individual from each population indicated that sea-level changes during the Last Glacial Period probably led to allopatric divergence of this species in a limited area of the Sea of Japan, with that group subsequently sharing a distribution area with the other population. These findings yield insights into the formation of genetically isolated sympatric populations in the ocean.
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Affiliation(s)
- Miwa Suzuki
- College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | - Kaho Ohno
- College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | - Eitaro Sawayama
- College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | - Shin-Ichi Morinaga
- Department of Natural & Environmental Science, Teikyo University of Science, Tokyo, Japan
| | - Takushi Kishida
- Museum of Natural and Environmental History, Shizuoka, Japan
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6
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de Greef E, Einfeldt AL, Miller PJO, Ferguson SH, Garroway CJ, Lefort KJ, Paterson IG, Bentzen P, Feyrer LJ. Genomics reveal population structure, evolutionary history, and signatures of selection in the northern bottlenose whale, Hyperoodon ampullatus. Mol Ecol 2022; 31:4919-4931. [PMID: 35947506 PMCID: PMC9804413 DOI: 10.1111/mec.16643] [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: 03/17/2022] [Revised: 07/18/2022] [Accepted: 08/03/2022] [Indexed: 01/05/2023]
Abstract
Information on wildlife population structure, demographic history, and adaptations are fundamental to understanding species evolution and informing conservation strategies. To study this ecological context for a cetacean of conservation concern, we conducted the first genomic assessment of the northern bottlenose whale, Hyperoodon ampullatus, using whole-genome resequencing data (n = 37) from five regions across the North Atlantic Ocean. We found a range-wide pattern of isolation-by-distance with a genetic subdivision distinguishing three subgroups: the Scotian Shelf, western North Atlantic, and Jan Mayen regions. Signals of elevated levels of inbreeding in the Endangered Scotian Shelf population indicate this population may be more vulnerable than the other two subgroups. In addition to signatures of inbreeding, evidence of local adaptation in the Scotian Shelf was detected across the genome. We found a long-term decline in effective population size for the species, which poses risks to their genetic diversity and may be exacerbated by the isolating effects of population subdivision. Protecting important habitat and migratory corridors should be prioritized to rebuild population sizes that were diminished by commercial whaling, strengthen gene flow, and ensure animals can move across regions in response to environmental changes.
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Affiliation(s)
- Evelien de Greef
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada,Department of Biological SciencesUniversity of ManitobaWinnipegManitobaCanada
| | | | | | | | - Colin J. Garroway
- Department of Biological SciencesUniversity of ManitobaWinnipegManitobaCanada
| | - Kyle J. Lefort
- Department of Biological SciencesUniversity of ManitobaWinnipegManitobaCanada
| | - Ian G. Paterson
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
| | - Paul Bentzen
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
| | - Laura J. Feyrer
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada,Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNova ScotiaCanada
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7
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Demographic history of two endangered Atlantic eel species, Anguilla anguilla and Anguilla rostrata. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01469-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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8
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Robinson JA, Kyriazis CC, Nigenda-Morales SF, Beichman AC, Rojas-Bracho L, Robertson KM, Fontaine MC, Wayne RK, Lohmueller KE, Taylor BL, Morin PA. The critically endangered vaquita is not doomed to extinction by inbreeding depression. Science 2022; 376:635-639. [PMID: 35511971 PMCID: PMC9881057 DOI: 10.1126/science.abm1742] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
In cases of severe wildlife population decline, a key question is whether recovery efforts will be impeded by genetic factors, such as inbreeding depression. Decades of excess mortality from gillnet fishing have driven Mexico's vaquita porpoise (Phocoena sinus) to ~10 remaining individuals. We analyzed whole-genome sequences from 20 vaquitas and integrated genomic and demographic information into stochastic, individual-based simulations to quantify the species' recovery potential. Our analysis suggests that the vaquita's historical rarity has resulted in a low burden of segregating deleterious variation, reducing the risk of inbreeding depression. Similarly, genome-informed simulations suggest that the vaquita can recover if bycatch mortality is immediately halted. This study provides hope for vaquitas and other naturally rare endangered species and highlights the utility of genomics in predicting extinction risk.
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Affiliation(s)
- Jacqueline A. Robinson
- Institute for Human Genetics, University of California, San Francisco; San Francisco, CA, USA
| | - Christopher C. Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles; Los Angeles, CA, USA
| | - Sergio F. Nigenda-Morales
- Advanced Genomics Unit, National Laboratory of Genomics for Biodiversity (Langebio), Center for Research and Advanced Studies (Cinvestav); Irapuato, Guanajuato, Mexico
| | | | - Lorenzo Rojas-Bracho
- Comisión Nacional de Áreas Naturales Protegidas/SEMARNAT; Ensenada, Mexico
- PNUD-Sinergia en la Comisión Nacional de Áreas Naturales Protegidas, Ensenada, B.C., México
| | - Kelly M. Robertson
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA ; La Jolla, CA, USA
| | - Michael C. Fontaine
- MIVEGEC, Université de Montpellier, CNRS, IRD; Montpellier, France
- Centre de Recherche en Écologie et Évolution de la Santé (CREES); Montpellier, France
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen; Groningen, The Netherlands
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles; Los Angeles, CA, USA
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles; Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, USA
| | - Barbara L. Taylor
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA ; La Jolla, CA, USA
| | - Phillip A. Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA ; La Jolla, CA, USA
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9
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Konstantinidis I, Gkafas GA, Papathanasiou V, Orfanidis S, Küpper FC, Arnaud-Haond S, Exadactylos A. Biogeography pattern of the marine angiosperm Cymodocea nodosa in the eastern Mediterranean Sea related to the quaternary climatic changes. Ecol Evol 2022; 12:e8911. [PMID: 35646317 PMCID: PMC9131598 DOI: 10.1002/ece3.8911] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 04/19/2022] [Accepted: 04/21/2022] [Indexed: 11/07/2022] Open
Abstract
We investigated the population dynamics of a highly clonal marine angiosperm, Cymodocea nodosa, in the eastern Mediterranean Sea, to identify the historical dynamics, demography, and connectivity of the species in the area. Eighteen microsatellite loci were used in conjunction with coalescent methods to investigate the genetic structure and demographic history of C. nodosa meadows. Approximate Bayesian computation (ABC) modeling was used to examine the pattern of divergence over time in the context of environmental change over the course of the Quaternary period. ABC analysis revealed an initial split of the C. nodosa populations between the north-western, northern, and north-eastern Aegean Sea during the Pleistocene epoch, followed by a more recent divergence of the north-western population and the central-western part of the Aegean Sea. According to the results, the most parsimonious historical scenario is that of a pervasive genetic signature of the effects of the drop in sea level during the Pleistocene epoch. This scenario supports the isolation of the north-western, north, and north-eastern area, and the subsequent recolonization after post-glaciation sea level rise that may explain the north-western differentiation as well present-day detected dispersion of C. nodosa.
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Affiliation(s)
- Ioannis Konstantinidis
- Genomics Division Faculty of Biosciences and Aquaculture Nord University Bodø Norway.,Department of Ichthyology and Aquatic Environment School of Agricultural Sciences University of Thessaly Volos Greece
| | - Georgios A Gkafas
- Department of Ichthyology and Aquatic Environment School of Agricultural Sciences University of Thessaly Volos Greece
| | | | | | - Frithjof C Küpper
- School of Biological Sciences University of Aberdeen Aberdeen UK.,Department of Chemistry Marine Biodiscovery Centre University of Aberdeen Aberdeen UK
| | - Sophie Arnaud-Haond
- Ifremer UMR MARBEC (Marine Biodiversity, Exploitation and Conservation) Sète Cedex France
| | - Athanasios Exadactylos
- Department of Ichthyology and Aquatic Environment School of Agricultural Sciences University of Thessaly Volos Greece
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10
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Machado AM, Gomes-dos-Santos A, Fonseca MM, da Fonseca RR, Veríssimo A, Felício M, Capela R, Alves N, Santos M, Salvador-Caramelo F, Domingues M, Ruivo R, Froufe E, Castro LFC. A genome assembly of the Atlantic chub mackerel ( Scomber colias): a valuable teleost fishing resource. GIGABYTE 2022; 2022:gigabyte40. [PMID: 36824513 PMCID: PMC9650269 DOI: 10.46471/gigabyte.40] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/09/2022] [Indexed: 11/09/2022] Open
Abstract
The Atlantic chub mackerel, Scomber colias (Gmelin, 1789), is a medium-sized pelagic fish with substantial importance in the fisheries of the Atlantic Ocean and the Mediterranean Sea. Over the past decade, this species has gained special relevance, being one of the main targets of pelagic fisheries in the NE Atlantic. Here, we sequenced and annotated the first high-quality draft genome assembly of S. colias, produced with PacBio HiFi long reads and Illumina paired-end short reads. The estimated genome size is 814 Mbp, distributed into 2,028 scaffolds and 2,093 contigs with an N50 length of 4.19 and 3.34 Mbp, respectively. We annotated 27,675 protein-coding genes and the BUSCO analyses indicated high completeness, with 97.3% of the single-copy orthologs in the Actinopterygii library profile. The present genome assembly represents a valuable resource to address the biology and management of this relevant fishery. Finally, this genome assembly ranks fourth in high-quality genome assemblies within the order Scombriformes and first in the genus Scomber.
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Affiliation(s)
- André M. Machado
- CIIMAR – Interdisciplinary Centre of Marine and Environmental Research, U. Porto – University of Porto, Porto, Portugal,Department of Biology, Faculty of Sciences, U. Porto - University of Porto, Portugal
| | - André Gomes-dos-Santos
- CIIMAR – Interdisciplinary Centre of Marine and Environmental Research, U. Porto – University of Porto, Porto, Portugal,Department of Biology, Faculty of Sciences, U. Porto - University of Porto, Portugal
| | - Miguel M. Fonseca
- CIIMAR – Interdisciplinary Centre of Marine and Environmental Research, U. Porto – University of Porto, Porto, Portugal
| | - Rute R. da Fonseca
- Center for Global Mountain Biodiversity, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark,Center for Macroecology, Evolution, and Climate, GLOBE Institute, University of Copenhagen, Denmark
| | - Ana Veríssimo
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal,BIOPOLIS - Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Mónica Felício
- Portuguese Institute for the Sea and Atmosphere, I.P. (IPMA), Portugal
| | - Ricardo Capela
- CIIMAR – Interdisciplinary Centre of Marine and Environmental Research, U. Porto – University of Porto, Porto, Portugal,Department of Biology, Faculty of Sciences, U. Porto - University of Porto, Portugal
| | - Nélson Alves
- CIIMAR – Interdisciplinary Centre of Marine and Environmental Research, U. Porto – University of Porto, Porto, Portugal,Department of Biology, Faculty of Sciences, U. Porto - University of Porto, Portugal
| | - Miguel Santos
- CIIMAR – Interdisciplinary Centre of Marine and Environmental Research, U. Porto – University of Porto, Porto, Portugal,Department of Biology, Faculty of Sciences, U. Porto - University of Porto, Portugal
| | - Filipe Salvador-Caramelo
- CIIMAR – Interdisciplinary Centre of Marine and Environmental Research, U. Porto – University of Porto, Porto, Portugal,Department of Biology, Faculty of Sciences, U. Porto - University of Porto, Portugal
| | - Marcos Domingues
- CIIMAR – Interdisciplinary Centre of Marine and Environmental Research, U. Porto – University of Porto, Porto, Portugal
| | - Raquel Ruivo
- CIIMAR – Interdisciplinary Centre of Marine and Environmental Research, U. Porto – University of Porto, Porto, Portugal
| | - Elsa Froufe
- CIIMAR – Interdisciplinary Centre of Marine and Environmental Research, U. Porto – University of Porto, Porto, Portugal
| | - L. Filipe C. Castro
- CIIMAR – Interdisciplinary Centre of Marine and Environmental Research, U. Porto – University of Porto, Porto, Portugal,Department of Biology, Faculty of Sciences, U. Porto - University of Porto, Portugal, Corresponding author. E-mail: ;
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11
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Carroll EL, McGowen MR, McCarthy ML, Marx FG, Aguilar N, Dalebout ML, Dreyer S, Gaggiotti OE, Hansen SS, van Helden A, Onoufriou AB, Baird RW, Baker CS, Berrow S, Cholewiak D, Claridge D, Constantine R, Davison NJ, Eira C, Fordyce RE, Gatesy J, Hofmeyr GJG, Martín V, Mead JG, Mignucci-Giannoni AA, Morin PA, Reyes C, Rogan E, Rosso M, Silva MA, Springer MS, Steel D, Olsen MT. Speciation in the deep: genomics and morphology reveal a new species of beaked whale Mesoplodon eueu. Proc Biol Sci 2021; 288:20211213. [PMID: 34702078 PMCID: PMC8548795 DOI: 10.1098/rspb.2021.1213] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/30/2021] [Indexed: 11/12/2022] Open
Abstract
The deep sea has been described as the last major ecological frontier, as much of its biodiversity is yet to be discovered and described. Beaked whales (ziphiids) are among the most visible inhabitants of the deep sea, due to their large size and worldwide distribution, and their taxonomic diversity and much about their natural history remain poorly understood. We combine genomic and morphometric analyses to reveal a new Southern Hemisphere ziphiid species, Ramari's beaked whale, Mesoplodon eueu, whose name is linked to the Indigenous peoples of the lands from which the species holotype and paratypes were recovered. Mitogenome and ddRAD-derived phylogenies demonstrate reciprocally monophyletic divergence between M. eueu and True's beaked whale (M. mirus) from the North Atlantic, with which it was previously subsumed. Morphometric analyses of skulls also distinguish the two species. A time-calibrated mitogenome phylogeny and analysis of two nuclear genomes indicate divergence began circa 2 million years ago (Ma), with geneflow ceasing 0.35-0.55 Ma. This is an example of how deep sea biodiversity can be unravelled through increasing international collaboration and genome sequencing of archival specimens. Our consultation and involvement with Indigenous peoples offers a model for broadening the cultural scope of the scientific naming process.
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Affiliation(s)
- Emma L. Carroll
- School of Biological Sciences Te Kura Mātauranga Koiora, University of Auckland Waipapa Taumata Rau, Auckland 1010, Aotearoa New Zealand
| | - Michael R. McGowen
- Department of Vertebrate Zoology, Smithsonian National Museum of Natural History, Washington, DC 20560, USA
| | - Morgan L. McCarthy
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, Copenhagen K DK-1353, Denmark
| | - Felix G. Marx
- Museum of New Zealand Te Papa Tongarewa, Wellington, Aotearoa New Zealand
- Department of Geology, University of Otago, Dunedin, Aotearoa New Zealand
| | - Natacha Aguilar
- BIOECOMAC, Department of Animal Biology, Edaphology and Geology, University of La Laguna, San Cristóbal de La Laguna, Tenerife, Canary Islands, Spain
| | - Merel L. Dalebout
- School of Biological, Earth, and Environmental Sciences, University of New South Wales, Kensington 2052, Australia
| | - Sascha Dreyer
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, Copenhagen K DK-1353, Denmark
| | | | - Sabine S. Hansen
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, Copenhagen K DK-1353, Denmark
| | - Anton van Helden
- School of Biological Sciences Te Kura Mātauranga Koiora, University of Auckland Waipapa Taumata Rau, Auckland 1010, Aotearoa New Zealand
- Department of Vertebrate Zoology, Smithsonian National Museum of Natural History, Washington, DC 20560, USA
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, Copenhagen K DK-1353, Denmark
- Museum of New Zealand Te Papa Tongarewa, Wellington, Aotearoa New Zealand
- Department of Geology, University of Otago, Dunedin, Aotearoa New Zealand
- BIOECOMAC, Department of Animal Biology, Edaphology and Geology, University of La Laguna, San Cristóbal de La Laguna, Tenerife, Canary Islands, Spain
- School of Biological, Earth, and Environmental Sciences, University of New South Wales, Kensington 2052, Australia
- School of Biology, University of St Andrews, St Andrews KY16 8LB, UK
- Cascadia Research Collective, 218 1/2 W. 4th Avenue, Olympia, WA 98501, USA
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI 96744, USA
- Marine Mammal Institute and Department of Fisheries and Wildlife, Hatfield Marine Science Center, Oregon State University, Newport, OR 97365, USA
- Irish Whale and Dolphin Group, Merchants Quay, Kilrush, Co Clare, Ireland/Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, Dublin Road, Galway, Ireland
- Northeast Fisheries Science Center, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration (NOAA), 166 Waters Street, Woods Hole, MA 02543, USA
- Bahamas Marine Mammal Research Organisation (BMMRO), Sandy Point, Abaco, Bahamas
- Scottish Marine Animal Stranding Scheme, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
- Departamento de Biologia, CESAM and ECOMARE, Universidade de Aveiro, Campus Universitário de Santiago, Aveiro 3810-193, Portugal
- Sociedade Portuguesa de Vida Selvagem, Estação de Campo de Quiaios, Rua das Matas nacionais, Figueira da Foz 3080-530, Portugal
- Division of Vertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
- Port Elizabeth Museum at Bayworld, Gqeberha 6013, South Africa
- Department of Zoology, Institute for Coastal and Marine Research, Nelson Mandela University, Gqeberha 6031, South Africa
- Study of the Cetaceans in the Canary Archipelago (SECAC) Casa de Los Arroyo, Arrecife de Lanzarote, Canary Islands, Spain
- Caribbean Manatee Conservation Center, Inter American University of Puerto Rico, 500 Carretera Dr John Will Harris, Bayamón 00957, Puerto Rico
- Center for Conservation Medicine and Ecosystem Health, Ross University School of Veterinary Medicine, PO Box 334, Basseterre, St Kitts
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla, CA 92037, USA
- School of Biological, Earth and Environmental Sciences, University College Cork, Ireland
- CIMA Research Foundation, Via Magliotto 2, Savona 17100, Italy
- Okeanos—Instituto de Investigação em Ciências do Mar & IMAR—Instituto do MAR, Universidade dos Açores, Horta, Portugal
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA 92521, USA
| | - Aubrie B. Onoufriou
- BIOECOMAC, Department of Animal Biology, Edaphology and Geology, University of La Laguna, San Cristóbal de La Laguna, Tenerife, Canary Islands, Spain
- School of Biology, University of St Andrews, St Andrews KY16 8LB, UK
| | - Robin W. Baird
- Cascadia Research Collective, 218 1/2 W. 4th Avenue, Olympia, WA 98501, USA
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI 96744, USA
| | - C. Scott Baker
- Marine Mammal Institute and Department of Fisheries and Wildlife, Hatfield Marine Science Center, Oregon State University, Newport, OR 97365, USA
| | - Simon Berrow
- Irish Whale and Dolphin Group, Merchants Quay, Kilrush, Co Clare, Ireland/Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, Dublin Road, Galway, Ireland
| | - Danielle Cholewiak
- Northeast Fisheries Science Center, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration (NOAA), 166 Waters Street, Woods Hole, MA 02543, USA
| | - Diane Claridge
- Bahamas Marine Mammal Research Organisation (BMMRO), Sandy Point, Abaco, Bahamas
| | - Rochelle Constantine
- School of Biological Sciences Te Kura Mātauranga Koiora, University of Auckland Waipapa Taumata Rau, Auckland 1010, Aotearoa New Zealand
| | - Nicholas J. Davison
- Scottish Marine Animal Stranding Scheme, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Catarina Eira
- Departamento de Biologia, CESAM and ECOMARE, Universidade de Aveiro, Campus Universitário de Santiago, Aveiro 3810-193, Portugal
- Sociedade Portuguesa de Vida Selvagem, Estação de Campo de Quiaios, Rua das Matas nacionais, Figueira da Foz 3080-530, Portugal
| | - R. Ewan Fordyce
- Museum of New Zealand Te Papa Tongarewa, Wellington, Aotearoa New Zealand
- Department of Geology, University of Otago, Dunedin, Aotearoa New Zealand
| | - John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - G. J. Greg Hofmeyr
- Port Elizabeth Museum at Bayworld, Gqeberha 6013, South Africa
- Department of Zoology, Institute for Coastal and Marine Research, Nelson Mandela University, Gqeberha 6031, South Africa
| | - Vidal Martín
- Study of the Cetaceans in the Canary Archipelago (SECAC) Casa de Los Arroyo, Arrecife de Lanzarote, Canary Islands, Spain
| | - James G. Mead
- Department of Vertebrate Zoology, Smithsonian National Museum of Natural History, Washington, DC 20560, USA
| | - Antonio A. Mignucci-Giannoni
- Caribbean Manatee Conservation Center, Inter American University of Puerto Rico, 500 Carretera Dr John Will Harris, Bayamón 00957, Puerto Rico
- Center for Conservation Medicine and Ecosystem Health, Ross University School of Veterinary Medicine, PO Box 334, Basseterre, St Kitts
| | - Phillip A. Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla, CA 92037, USA
| | - Cristel Reyes
- School of Biology, University of St Andrews, St Andrews KY16 8LB, UK
| | - Emer Rogan
- School of Biological, Earth and Environmental Sciences, University College Cork, Ireland
| | | | - Mónica A. Silva
- Okeanos—Instituto de Investigação em Ciências do Mar & IMAR—Instituto do MAR, Universidade dos Açores, Horta, Portugal
| | - Mark S. Springer
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA 92521, USA
| | - Debbie Steel
- Marine Mammal Institute and Department of Fisheries and Wildlife, Hatfield Marine Science Center, Oregon State University, Newport, OR 97365, USA
| | - Morten Tange Olsen
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, Copenhagen K DK-1353, Denmark
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12
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Cleary AC, Hoffman JI, Forcada J, Lydersen C, Lowther AD, Kovacs KM. 50,000 years of ice and seals: Impacts of the Last Glacial Maximum on Antarctic fur seals. Ecol Evol 2021; 11:14003-14011. [PMID: 34707834 PMCID: PMC8525082 DOI: 10.1002/ece3.8104] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 08/22/2021] [Accepted: 08/26/2021] [Indexed: 11/11/2022] Open
Abstract
Ice is one of the most important drivers of population dynamics in polar organisms, influencing the locations, sizes, and connectivity of populations. Antarctic fur seals, Arctocephalus gazella, are particularly interesting in this regard, as they are concomitantly reliant on both ice-associated prey and ice-free coastal breeding areas. We reconstructed the history of this species through the Last Glacial Maximum (LGM) using genomic sequence data from seals across their range. Population size trends and divergence events were investigated using continuous-time size estimation analysis and divergence time estimation models. The combined results indicated that a panmictic population present prior to the LGM split into two small refugial populations during peak ice extent. Following ice decline, the western refugial population founded colonies at the South Shetlands, South Georgia, and Bouvetøya, while the eastern refugial population founded the colony on Iles Kerguelen. Postglacial population divergence times closely match geological estimates of when these coastal breeding areas became ice free. Given the predictions regarding continued future warming in polar oceans, these responses of Antarctic fur seals to past climate variation suggest it may be worthwhile giving conservation consideration to potential future breeding locations, such as areas further south along the Antarctic Peninsula, in addition to present colony areas.
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Affiliation(s)
- Alison C. Cleary
- Department of Natural SciencesUniversity of AgderKristiansandNorway
- Norwegian Polar InstituteFram CentreTromsøNorway
| | - Joseph I. Hoffman
- Department of Animal BehaviourUniversity of BielefeldBielefeldGermany
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13
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Foote AD, Hooper R, Alexander A, Baird RW, Baker CS, Ballance L, Barlow J, Brownlow A, Collins T, Constantine R, Dalla Rosa L, Davison NJ, Durban JW, Esteban R, Excoffier L, Martin SLF, Forney KA, Gerrodette T, Gilbert MTP, Guinet C, Hanson MB, Li S, Martin MD, Robertson KM, Samarra FIP, de Stephanis R, Tavares SB, Tixier P, Totterdell JA, Wade P, Wolf JBW, Fan G, Zhang Y, Morin PA. Runs of homozygosity in killer whale genomes provide a global record of demographic histories. Mol Ecol 2021; 30:6162-6177. [PMID: 34416064 DOI: 10.1111/mec.16137] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 08/10/2021] [Accepted: 08/18/2021] [Indexed: 02/06/2023]
Abstract
Runs of homozygosity (ROH) occur when offspring inherit haplotypes that are identical by descent from each parent. Length distributions of ROH are informative about population history; specifically, the probability of inbreeding mediated by mating system and/or population demography. Here, we investigated whether variation in killer whale (Orcinus orca) demographic history is reflected in genome-wide heterozygosity and ROH length distributions, using a global data set of 26 genomes representative of geographic and ecotypic variation in this species, and two F1 admixed individuals with Pacific-Atlantic parentage. We first reconstructed demographic history for each population as changes in effective population size through time using the pairwise sequential Markovian coalescent (PSMC) method. We found a subset of populations declined in effective population size during the Late Pleistocene, while others had more stable demography. Genomes inferred to have undergone ancestral declines in effective population size, were autozygous at hundreds of short ROH (<1 Mb), reflecting high background relatedness due to coalescence of haplotypes deep within the pedigree. In contrast, longer and therefore younger ROH (>1.5 Mb) were found in low latitude populations, and populations of known conservation concern. These include a Scottish killer whale, for which 37.8% of the autosomes were comprised of ROH >1.5 Mb in length. The fate of this population, in which only two adult males have been sighted in the past five years, and zero fecundity over the last two decades, may be inextricably linked to its demographic history and consequential inbreeding depression.
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Affiliation(s)
- Andrew D Foote
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU, Trondheim, Norway.,Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd, UK.,CMPG, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Rebecca Hooper
- University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - Alana Alexander
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | | | - Charles Scott Baker
- Marine Mammal Institute, Oregon State University, Newport, Oregon, USA.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Lisa Ballance
- Marine Mammal Institute, Oregon State University, Newport, Oregon, USA.,Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, La Jolla, California, USA
| | - Jay Barlow
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, La Jolla, California, USA
| | - Andrew Brownlow
- Scottish Marine Animal Stranding Scheme, Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Tim Collins
- Ocean Giants Program, Wildlife Conservation Society, New York City, New York
| | | | - Luciano Dalla Rosa
- Laboratório de Ecologia e Conservação da Megafauna Marinha, Instituto de Oceanografia, Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Nicholas J Davison
- Scottish Marine Animal Stranding Scheme, Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - John W Durban
- Marine Mammal Institute, Oregon State University, Newport, Oregon, USA.,Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, La Jolla, California, USA
| | - Ruth Esteban
- CIRCE, Conservation, Information and Research on Cetaceans, Algeciras, Spain
| | - Laurent Excoffier
- CMPG, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Sarah L Fordyce Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU, Trondheim, Norway
| | - Karin A Forney
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Moss Landing, California, USA.,Moss Landing Marine Laboratories, San Jose State University, Moss Landing, California, USA
| | - Tim Gerrodette
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, La Jolla, California, USA
| | - M Thomas P Gilbert
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU, Trondheim, Norway.,Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Christophe Guinet
- UMR 7372 La Rochelle Université - CNRS, Centre d'Etudes Biologiques de Chizé (CEBC), Villiers-en-Bois, France
| | - M Bradley Hanson
- National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Northwest Fisheries Science Center, Seattle, Washington, USA
| | - Songhai Li
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-Sea Science and Engineering, Chinese Academy of Science, Sanya, China
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU, Trondheim, Norway
| | - Kelly M Robertson
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, La Jolla, California, USA
| | - Filipa I P Samarra
- University of Iceland's Institute of Research Centres, Vestmannaeyjar, Iceland
| | - Renaud de Stephanis
- CIRCE, Conservation, Information and Research on Cetaceans, Algeciras, Spain
| | - Sara B Tavares
- Scottish Oceans Institute, East Sands, University of St. Andrews, St. Andrews, UK.,Cetacean Research Program, Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, Canada
| | - Paul Tixier
- UMR 7372 La Rochelle Université - CNRS, Centre d'Etudes Biologiques de Chizé (CEBC), Villiers-en-Bois, France.,MARBEC Université de Montpellier-CNRS-IFREMER-IRD, Sète, France
| | | | - Paul Wade
- National Marine Mammal Laboratory, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Alaska Fisheries Science Center, Seattle, Washington, USA
| | - Jochen B W Wolf
- Section of Evolutionary Biology, Department of Biology II, Ludwig Maximilian University of Munich, Planegg-Martinsried, Germany
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Yaolei Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,Translational Immunology group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Phillip A Morin
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, La Jolla, California, USA
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14
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Barr K, Beichman AC, Kalhori P, Rajbhandary J, Bay RA, Ruegg K, Smith TB. Persistent panmixia despite extreme habitat loss and population decline in the threatened tricolored blackbird ( Agelaius tricolor). Evol Appl 2021; 14:674-684. [PMID: 33767743 PMCID: PMC7980274 DOI: 10.1111/eva.13147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 09/18/2020] [Accepted: 10/01/2020] [Indexed: 01/25/2023] Open
Abstract
Habitat loss and alteration has driven many species into decline, often to the point of requiring protection and intervention to avert extinction. Genomic data provide the opportunity to inform conservation and recovery efforts with details about vital evolutionary processes with a resolution far beyond that of traditional genetic approaches. The tricolored blackbird (Agelaius tricolor) has suffered severe losses during the previous century largely due to anthropogenic impacts on their habitat. Using a dataset composed of a whole genome paired with reduced representation libraries (RAD-Seq) from samples collected across the species' range, we find evidence for panmixia using multiple methods, including PCA (no geographic clustering), admixture analyses (ADMIXTURE and TESS conclude K = 1), and comparisons of genetic differentiation (average FST = 0.029). Demographic modeling approaches recovered an ancient decline that had a strong impact on genetic diversity but did not detect any effect from the known recent decline. We also did not detect any evidence for selection, and hence adaptive variation, at any site, either geographic or genomic. These results indicate that species continues to have high vagility across its range despite population decline and habitat loss and should be managed as a single unit.
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Affiliation(s)
- Kelly Barr
- Center for Tropical ResearchInstitute of the Environment and SustainabilityUniversity of California, Los AngelesLos AngelesCAUSA
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCAUSA
| | - Annabel C. Beichman
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCAUSA
| | - Pooneh Kalhori
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCAUSA
| | - Jasmine Rajbhandary
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCAUSA
| | - Rachael A. Bay
- Department of Evolution and EcologyUniversity of California, DavisDavisCAUSA
| | - Kristen Ruegg
- Department of BiologyColorado State UniversityFort CollinsCOUSA
| | - Thomas B. Smith
- Center for Tropical ResearchInstitute of the Environment and SustainabilityUniversity of California, Los AngelesLos AngelesCAUSA
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCAUSA
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15
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Moura AE, Shreves K, Pilot M, Andrews KR, Moore DM, Kishida T, Möller L, Natoli A, Gaspari S, McGowen M, Chen I, Gray H, Gore M, Culloch RM, Kiani MS, Willson MS, Bulushi A, Collins T, Baldwin R, Willson A, Minton G, Ponnampalam L, Hoelzel AR. Phylogenomics of the genus Tursiops and closely related Delphininae reveals extensive reticulation among lineages and provides inference about eco-evolutionary drivers. Mol Phylogenet Evol 2020; 146:106756. [DOI: 10.1016/j.ympev.2020.106756] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 01/02/2020] [Accepted: 01/28/2020] [Indexed: 12/30/2022]
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16
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Feyrer LJ, Bentzen P, Whitehead H, Paterson IG, Einfeldt A. Evolutionary impacts differ between two exploited populations of northern bottlenose whale ( Hyperoodon ampullatus). Ecol Evol 2019; 9:13567-13584. [PMID: 31871667 PMCID: PMC6912904 DOI: 10.1002/ece3.5813] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/05/2019] [Accepted: 10/10/2019] [Indexed: 01/10/2023] Open
Abstract
Interpretation of conservation status should be informed by an appreciation of genetic diversity, past demography, and overall trends in population size, which contribute to a species' evolutionary potential and resilience to genetic risks. Low genetic diversity can be symptomatic of rapid demographic declines and impose genetic risks to populations, but can also be maintained by natural processes. The northern bottlenose whale Hyperoodon ampullatus has the lowest known mitochondrial diversity of any cetacean and was intensely whaled in the Northwest Atlantic over the last century, but whether exploitation imposed genetic risks that could limit recovery is unknown. We sequenced full mitogenomes and genotyped 37 novel microsatellites for 128 individuals from known areas of abundance in the Scotian Shelf, Northern and Southern Labrador, Davis Strait, and Iceland, and a newly discovered group off Newfoundland. Despite low diversity and shared haplotypes across all regions, both markers supported the Endangered Scotian Shelf population as distinct from the combined northern regions. The genetic affinity of Newfoundland was uncertain, suggesting an area of mixing with no clear population distinction for the region. Demographic reconstruction using mitogenomes suggests that the northern region underwent population expansion following the last glacial maximum, but for the peripheral Scotian Shelf population, a stable demographic trend was followed by a drastic decline over a temporal scale consistent with increasing human activity in the Northwest Atlantic. Low connectivity between the Scotian Shelf and the rest of the Atlantic likely compounded the impact of intensive whaling for this species, potentially imposing genetic risks affecting recovery of this population. We highlight how the combination of historical environmental conditions and modern exploitation of this species has had very different evolutionary impacts on structured populations of northern bottlenose whales across the western North Atlantic.
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Affiliation(s)
| | - Paul Bentzen
- Biology DepartmentDalhousie UniversityHalifaxNSCanada
| | - Hal Whitehead
- Biology DepartmentDalhousie UniversityHalifaxNSCanada
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17
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Vijay N, Park C, Oh J, Jin S, Kern E, Kim HW, Zhang J, Park JK. Population Genomic Analysis Reveals Contrasting Demographic Changes of Two Closely Related Dolphin Species in the Last Glacial. Mol Biol Evol 2019; 35:2026-2033. [PMID: 29846663 PMCID: PMC6063294 DOI: 10.1093/molbev/msy108] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Population genomic data can be used to infer historical effective population sizes (Ne), which help study the impact of past climate changes on biodiversity. Previous genome sequencing of one individual of the common bottlenose dolphin Tursiops truncatus revealed an unusual, sharp rise in Ne during the last glacial, raising questions about the reliability, generality, underlying cause, and biological implication of this finding. Here we first verify this result by additional sampling of T. truncatus. We then sequence and analyze the genomes of its close relative, the Indo-Pacific bottlenose dolphin T. aduncus. The two species exhibit contrasting demographic changes in the last glacial, likely through actual changes in population size and/or alterations in the level of gene flow among populations. Our findings suggest that even closely related species can have drastically different responses to climatic changes, making predicting the fate of individual species in the ongoing global warming a serious challenge.
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Affiliation(s)
- Nagarjun Vijay
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
| | - Chungoo Park
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, Republic of Korea
| | - Jooseong Oh
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, Republic of Korea
| | - Soyeong Jin
- Division of EcoScience, Ewha Womans University, Seoul, Republic of Korea
| | - Elizabeth Kern
- Division of EcoScience, Ewha Womans University, Seoul, Republic of Korea
| | - Hyun Woo Kim
- Cetacean Research Institute, National Institute of Fisheries Science, Ulsan, Republic of Korea
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
| | - Joong-Ki Park
- Division of EcoScience, Ewha Womans University, Seoul, Republic of Korea
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18
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Voskarides K, Dweep H, Chrysostomou C. Evidence that DNA repair genes, a family of tumor suppressor genes, are associated with evolution rate and size of genomes. Hum Genomics 2019; 13:26. [PMID: 31174607 PMCID: PMC6555970 DOI: 10.1186/s40246-019-0210-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 05/20/2019] [Indexed: 01/05/2023] Open
Abstract
Adaptive radiation and evolutionary stasis are characterized by very different evolution rates. The main aim of this study was to investigate if any genes have a special role to a high or low evolution rate. The availability of animal genomes permitted comparison of gene content of genomes of 24 vertebrate species that evolved through adaptive radiation (representing high evolutionary rate) and of 20 vertebrate species that are considered as living fossils (representing a slow evolutionary rate or evolutionary stasis). Mammals, birds, reptiles, and bony fishes were included in the analysis. Pathway analysis was performed for genes found to be specific in adaptive radiation or evolutionary stasis respectively. Pathway analysis revealed that DNA repair and cellular response to DNA damage are important (false discovery rate = 8.35 × 10−5; 7.15 × 10−6, respectively) for species evolved through adaptive radiation. This was confirmed by further genetic in silico analysis (p = 5.30 × 10−3). Nucleotide excision repair and base excision repair were the most significant pathways. Additionally, the number of DNA repair genes was found to be linearly related to the genome size and the protein number (proteome) of the 44 animals analyzed (p < 1.00 × 10−4), this being compatible with Drake’s rule. This is the first study where radiated and living fossil species have been genetically compared. Evidence has been found that cancer-related genes have a special role in radiated species. Linear association of the number of DNA repair genes with the species genome size has also been revealed. These comparative genetics results can support the idea of punctuated equilibrium evolution.
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Hooper R, Brealey JC, van der Valk T, Alberdi A, Durban JW, Fearnbach H, Robertson KM, Baird RW, Bradley Hanson M, Wade P, Gilbert MTP, Morin PA, Wolf JBW, Foote AD, Guschanski K. Host-derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin. Mol Ecol 2019; 28:484-502. [PMID: 30187987 PMCID: PMC6487819 DOI: 10.1111/mec.14860] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 08/15/2018] [Accepted: 08/27/2018] [Indexed: 12/20/2022]
Abstract
Recent exploration into the interactions and relationship between hosts and their microbiota has revealed a connection between many aspects of the host's biology, health and associated micro-organisms. Whereas amplicon sequencing has traditionally been used to characterize the microbiome, the increasing number of published population genomics data sets offers an underexploited opportunity to study microbial profiles from the host shotgun sequencing data. Here, we use sequence data originally generated from killer whale Orcinus orca skin biopsies for population genomics, to characterize the skin microbiome and investigate how host social and geographical factors influence the microbial community composition. Having identified 845 microbial taxa from 2.4 million reads that did not map to the killer whale reference genome, we found that both ecotypic and geographical factors influence community composition of killer whale skin microbiomes. Furthermore, we uncovered key taxa that drive the microbiome community composition and showed that they are embedded in unique networks, one of which is tentatively linked to diatom presence and poor skin condition. Community composition differed between Antarctic killer whales with and without diatom coverage, suggesting that the previously reported episodic migrations of Antarctic killer whales to warmer waters associated with skin turnover may control the effects of potentially pathogenic bacteria such as Tenacibaculum dicentrarchi. Our work demonstrates the feasibility of microbiome studies from host shotgun sequencing data and highlights the importance of metagenomics in understanding the relationship between host and microbial ecology.
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Affiliation(s)
- Rebecca Hooper
- Animal EcologyDepartment of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Jaelle C. Brealey
- Animal EcologyDepartment of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Tom van der Valk
- Animal EcologyDepartment of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Antton Alberdi
- Centre for GeoGeneticsNatural History Museum of DenmarkUniversity of CopenhagenCopenhagen KDenmark
| | - John W. Durban
- Marine Mammal and Turtle DivisionSouthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationLa JollaCalifornia
| | - Holly Fearnbach
- SR3, SeaLife Response, Rehabilitation, and ResearchSeattleWashington
| | - Kelly M. Robertson
- Marine Mammal and Turtle DivisionSouthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationLa JollaCalifornia
| | | | - M. Bradley Hanson
- Northwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWashington
| | - Paul Wade
- National Marine Mammal LaboratoryAlaska Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWashington
| | - M. Thomas P. Gilbert
- Centre for GeoGeneticsNatural History Museum of DenmarkUniversity of CopenhagenCopenhagen KDenmark
- NTNU University MuseumTrondheimNorway
| | - Phillip A. Morin
- Marine Mammal and Turtle DivisionSouthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationLa JollaCalifornia
| | - Jochen B. W. Wolf
- Science of Life Laboratories and Department of Evolutionary BiologyEvolutionary Biology CentreUppsala UniversityUppsalaSweden
- Section of Evolutionary BiologyFaculty of BiologyLMU MunichMunichGermany
| | - Andrew D. Foote
- Molecular Ecology and Fisheries Genetics LaboratorySchool of Biological SciencesBangor UniversityBangorGwyneddUK
| | - Katerina Guschanski
- Animal EcologyDepartment of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
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20
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Tavares SB, Samarra FIP, Pascoal S, Graves JA, Miller PJO. Killer whales ( Orcinus orca) in Iceland show weak genetic structure among diverse isotopic signatures and observed movement patterns. Ecol Evol 2018; 8:11900-11913. [PMID: 30598785 PMCID: PMC6303705 DOI: 10.1002/ece3.4646] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 09/26/2018] [Accepted: 09/28/2018] [Indexed: 11/07/2022] Open
Abstract
Local adaption through ecological niche specialization can lead to genetic structure between and within populations. In the Northeast Pacific, killer whales (Orcinus orca) of the same population have uniform specialized diets that are non-overlapping with other sympatric, genetically divergent, and socially isolated killer whale ecotypes. However, killer whales in Iceland show intrapopulation variation of isotopic niches and observed movement patterns: some individuals appear to specialize on herring and follow it year-round while others feed upon herring only seasonally or opportunistically. We investigated genetic differentiation among Icelandic killer whales with different isotopic signatures and observed movement patterns. This information is key for management and conservation purposes but also for better understanding how niche specialization drives genetic differentiation. Photo-identified individuals (N = 61) were genotyped for 22 microsatellites and a 611 bp portion of the mitochondrial DNA (mtDNA) control region. Photo-identification of individuals allowed linkage of genetic data to existing data on individual isotopic niche, observed movement patterns, and social associations. Population subdivision into three genetic units was supported by a discriminant analysis of principal components (DAPC). Genetic clustering corresponded to the distribution of isotopic signatures, mtDNA haplotypes, and observed movement patterns, but genetic units were not socially segregated. Genetic differentiation was weak (F ST < 0.1), suggesting ongoing gene flow or recent separation of the genetic units. Our results show that killer whales in Iceland are not as genetically differentiated, ecologically discrete, or socially isolated as the Northeast Pacific prey-specialized killer whales. If any process of ecological divergence and niche specialization is taking place among killer whales in Iceland, it is likely at a very early stage and has not led to the patterns observed in the Northeast Pacific.
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Affiliation(s)
- Sara B. Tavares
- Sea Mammal Research Unit, Scottish Oceans InstituteUniversity of St AndrewsSt Andrews, FifeUK
| | - Filipa I. P. Samarra
- Sea Mammal Research Unit, Scottish Oceans InstituteUniversity of St AndrewsSt Andrews, FifeUK
- Marine and Freshwater Research InstituteReykjavíkIceland
| | - Sonia Pascoal
- Department of ZoologyUniversity of CambridgeCambridgeUK
| | - Jeff A. Graves
- Scottish Oceans InstituteUniversity of St AndrewsSt Andrews, FifeUK
| | - Patrick J. O. Miller
- Sea Mammal Research Unit, Scottish Oceans InstituteUniversity of St AndrewsSt Andrews, FifeUK
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21
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Brüniche-Olsen A, Westerman R, Kazmierczyk Z, Vertyankin VV, Godard-Codding C, Bickham JW, DeWoody JA. The inference of gray whale (Eschrichtius robustus) historical population attributes from whole-genome sequences. BMC Evol Biol 2018; 18:87. [PMID: 29879895 PMCID: PMC5992727 DOI: 10.1186/s12862-018-1204-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Accepted: 05/29/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Commercial whaling caused extensive demographic declines in many great whale species, including gray whales that were extirpated from the Atlantic Ocean and dramatically reduced in the Pacific Ocean. The Eastern Pacific gray whale has recovered since the 1982 ban on commercial whaling, but the Western Pacific gray whale-once considered possibly extinct-consists of only about 200 individuals and is considered critically endangered by some international authorities. Herein, we use whole-genome sequencing to investigate the demographic history of gray whales from the Pacific and use environmental niche modelling to make predictions about future gene flow. RESULTS Our sequencing efforts and habitat niche modelling indicate that: i) western gray whale effective population sizes have declined since the last glacial maximum; ii) contemporary gray whale genomes, both eastern and western, harbor less autosomal nucleotide diversity than most other marine mammals and megafauna; iii) the extent of inbreeding, as measured by autozygosity, is greater in the Western Pacific than in the Eastern Pacific populations; and iv) future climate change is expected to open new migratory routes for gray whales. CONCLUSION Our results indicate that gray whale genomes contain low nucleotide diversity and have been subject to both historical and recent inbreeding. Population sizes over the last million years likely peaked about 25,000 years before present and have declined since then. Our niche modelling suggests that novel migratory routes may develop within the next century and if so this could help retain overall genetic diversity, which is essential for adaption and successful recovery in light of global environmental change and past exploitation.
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Affiliation(s)
- Anna Brüniche-Olsen
- Department of Forestry & Natural Resources, Purdue University, West Lafayette, IN, 47905, USA.
| | - Rick Westerman
- Department of Horticulture & Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
| | - Zuzanna Kazmierczyk
- School of Forensic and Applied Sciences, University of Central Lancashire Preston, Preston, PR1 2HE, UK
| | | | - Celine Godard-Codding
- The Institute of Environmental and Human Health, Department of Environmental Toxicology, Texas Tech University, 1207 Gilbert Drive, Lubbock, TX, 79409, USA
| | - John W Bickham
- Department of Wildlife & Fisheries Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - J Andrew DeWoody
- Department of Forestry & Natural Resources, Purdue University, West Lafayette, IN, 47905, USA
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22
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Cryptic lineage differentiation among Indo-Pacific bottlenose dolphins (Tursiops aduncus) in the northwest Indian Ocean. Mol Phylogenet Evol 2018; 122:1-14. [DOI: 10.1016/j.ympev.2017.12.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 12/15/2017] [Accepted: 12/26/2017] [Indexed: 11/19/2022]
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23
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Ford MJ, Parsons KM, Ward EJ, Hempelmann JA, Emmons CK, Bradley Hanson M, Balcomb KC, Park LK. Inbreeding in an endangered killer whale population. Anim Conserv 2018. [DOI: 10.1111/acv.12413] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- M. J. Ford
- Conservation Biology Division; Northwest Fisheries Science Center; National Marine Fisheries Service; NOAA; Seattle WA USA
| | - K. M. Parsons
- North Gulf Oceanic Society, under contract to Marine Mammal Laboratory; Alaska Fisheries Science Center; National Marine Fisheries Service; NOAA; Seattle WA USA
| | - E. J. Ward
- Conservation Biology Division; Northwest Fisheries Science Center; National Marine Fisheries Service; NOAA; Seattle WA USA
| | - J. A. Hempelmann
- Conservation Biology Division; Northwest Fisheries Science Center; National Marine Fisheries Service; NOAA; Seattle WA USA
| | - C. K. Emmons
- Conservation Biology Division; Northwest Fisheries Science Center; National Marine Fisheries Service; NOAA; Seattle WA USA
| | - M. Bradley Hanson
- Conservation Biology Division; Northwest Fisheries Science Center; National Marine Fisheries Service; NOAA; Seattle WA USA
| | | | - L. K. Park
- Conservation Biology Division; Northwest Fisheries Science Center; National Marine Fisheries Service; NOAA; Seattle WA USA
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24
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Bayas-Rea RDLÁ, Félix F, Montufar R. Genetic divergence and fine scale population structure of the common bottlenose dolphin ( Tursiops truncatus, Montagu) found in the Gulf of Guayaquil, Ecuador. PeerJ 2018; 6:e4589. [PMID: 29707430 PMCID: PMC5916226 DOI: 10.7717/peerj.4589] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 03/19/2018] [Indexed: 11/25/2022] Open
Abstract
The common bottlenose dolphin, Tursiops truncatus, is widely distributed along the western coast of South America. In Ecuador, a resident population of bottlenose dolphins inhabits the inner estuarine area of the Gulf of Guayaquil located in the southwestern part of the country and is under threat from different human activities in the area. Only one genetic study on South American common bottlenose dolphins has been carried out to date, and understanding genetic variation of wildlife populations, especially species that are identified as threatened, is crucial for defining conservation units and developing appropriate conservation strategies. In order to evaluate the evolutionary link of this population, we assessed the phylogenetic relationships, phylogeographic patterns, and population structure using mitochondrial DNA (mtDNA). The sampling comprised: (i) 31 skin samples collected from free-ranging dolphins at three locations in the Gulf of Guayaquil inner estuary, (ii) 38 samples from stranded dolphins available at the collection of the “Museo de Ballenas de Salinas,” (iii) 549 mtDNA control region (mtDNA CR) sequences from GenBank, and (iv) 66 concatenated sequences from 7-mtDNA regions (12S rRNA, 16S rRNA, NADH dehydrogenase subunit I–II, cytochrome oxidase I and II, cytochrome b, and CR) obtained from mitogenomes available in GenBank. Our analyses indicated population structure between both inner and outer estuary dolphin populations as well as with distinct populations of T. truncatus using mtDNA CR. Moreover, the inner estuary bottlenose dolphin (estuarine bottlenose dolphin) population exhibited lower levels of genetic diversity than the outer estuary dolphin population according to the mtDNA CR. Finally, the estuarine bottlenose dolphin population was genetically distinct from other T. truncatus populations based on mtDNA CR and 7-mtDNA regions. From these results, we suggest that the estuarine bottlenose dolphin population should be considered a distinct lineage. This dolphin population faces a variety of anthropogenic threats in this area; thus, we highlight its fragility and urge authorities to issue prompt management and conservation measures.
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Affiliation(s)
| | - Fernando Félix
- Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Quito, Ecuador.,Museo de Ballenas, Salinas, Ecuador
| | - Rommel Montufar
- Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
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25
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Abstract
Whales and dolphins (Cetacea) have excellent social learning skills as well as a long and strong mother-calf bond. These features produce stable cultures, and, in some species, sympatric groups with different cultures. There is evidence and speculation that this cultural transmission of behavior has affected gene distributions. Culture seems to have driven killer whales into distinct ecotypes, which may be incipient species or subspecies. There are ecotype-specific signals of selection in functional genes that correspond to cultural foraging behavior and habitat use by the different ecotypes. The five species of whale with matrilineal social systems have remarkably low diversity of mtDNA. Cultural hitchhiking, the transmission of functionally neutral genes in parallel with selective cultural traits, is a plausible hypothesis for this low diversity, especially in sperm whales. In killer whales the ecotype divisions, together with founding bottlenecks, selection, and cultural hitchhiking, likely explain the low mtDNA diversity. Several cetacean species show habitat-specific distributions of mtDNA haplotypes, probably the result of mother-offspring cultural transmission of migration routes or destinations. In bottlenose dolphins, remarkable small-scale differences in haplotype distribution result from maternal cultural transmission of foraging methods, and large-scale redistributions of sperm whale cultural clans in the Pacific have likely changed mitochondrial genetic geography. With the acceleration of genomics new results should come fast, but understanding gene-culture coevolution will be hampered by the measured pace of research on the socio-cultural side of cetacean biology.
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Affiliation(s)
- Hal Whitehead
- Department of Biology, Dalhousie University, Halifax, NS, Canada B3H 4R2
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26
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Benestan L, Moore JS, Sutherland BJG, Le Luyer J, Maaroufi H, Rougeux C, Normandeau E, Rycroft N, Atema J, Harris LN, Tallman RF, Greenwood SJ, Clark FK, Bernatchez L. Sex matters in massive parallel sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems. Mol Ecol 2017; 26:6767-6783. [DOI: 10.1111/mec.14217] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/23/2017] [Accepted: 03/29/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Laura Benestan
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Jean-Sébastien Moore
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Ben J. G. Sutherland
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Jérémy Le Luyer
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Halim Maaroufi
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Clément Rougeux
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Eric Normandeau
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | | | - Jelle Atema
- Department of Biology; Boston University; Boston MA USA
| | - Les N. Harris
- Fisheries and Oceans Canada; Freshwater Institute; Winnipeg MB Canada
| | - Ross F. Tallman
- Fisheries and Oceans Canada; Freshwater Institute; Winnipeg MB Canada
| | - Spencer J. Greenwood
- Department of Biomedical Sciences & AVC Lobster Science Centre; Atlantic Veterinary College; University of Prince Edward Island; Charlottetown PE Canada
| | - Fraser K. Clark
- Department of Biomedical Sciences & AVC Lobster Science Centre; Atlantic Veterinary College; University of Prince Edward Island; Charlottetown PE Canada
| | - Louis Bernatchez
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
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27
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Chong X, Zhang F, Wu Y, Yang X, Zhao N, Wang H, Guan Z, Fang W, Chen F. A SNP-Enabled Assessment of Genetic Diversity, Evolutionary Relationships and the Identification of Candidate Genes in Chrysanthemum. Genome Biol Evol 2017; 8:3661-3671. [PMID: 28082602 PMCID: PMC5521737 DOI: 10.1093/gbe/evw270] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2016] [Indexed: 12/11/2022] Open
Abstract
Varieties of the economically important ornamental species chrysanthemum have been bred to fit a number of market niches, but the genetic basis and evolutionary relationships among various cultivated types are poorly understood. Here, a DNA marker-based analysis of 199 chrysanthemum entries representing each of the five cultivated types is presented. A set of >90,000 single nucleotide polymorphisms (SNPs) associated with a minor allele frequency of at least 5% was defined, and used to perform a phylogenetic analysis which corresponded well with the phenotypic classification. The analysis revealed that the small-flowered types, spray cut chrysanthemum (SCC) and potted and ground chrysanthemum (PGC), are more closely related to the wild progenitor species (WC) than are the large-flowered ones, disbud cut chrysanthemum (DCC) and traditional chrysanthemum (TC); and the PGC type was closest. Some 550 genetic regions appeared to have experienced selection in the separation of potted and ground-cover types from disbud cut types, and that between potted and ground-cover types from traditional types. A genome-wide association analysis revealed that seven SNPs lying within six genes were predictive of three important traits (ray floret type, cultivated type and flower shape), but no association with flower color was detected. The study has provided a number of novel insights into evolutionary relationships, the population structure and the genetic basis of some key ornamental traits.
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Affiliation(s)
- Xinran Chong
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Fei Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yangyang Wu
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xiaodong Yang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Nan Zhao
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Haibin Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhiyong Guan
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Weimin Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Fadi Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
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28
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Barth JMI, Damerau M, Matschiner M, Jentoft S, Hanel R. Genomic Differentiation and Demographic Histories of Atlantic and Indo-Pacific Yellowfin Tuna (Thunnus albacares) Populations. Genome Biol Evol 2017; 9:1084-1098. [PMID: 28419285 PMCID: PMC5408087 DOI: 10.1093/gbe/evx067] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2017] [Indexed: 12/30/2022] Open
Abstract
Recent developments in the field of genomics have provided new and powerful insights into population structure and dynamics that are essential for the conservation of biological diversity. As a commercially highly valuable species, the yellowfin tuna (Thunnus albacares) is intensely exploited throughout its distribution in tropical oceans around the world, and is currently classified as near threatened. However, conservation efforts for this species have so far been hampered by limited knowledge of its population structure, due to incongruent results of previous investigations. Here, we use whole-genome sequencing in concert with a draft genome assembly to decipher the global population structure of the yellowfin tuna, and to investigate its demographic history. We detect significant differentiation of Atlantic and Indo-Pacific yellowfin tuna populations as well as the possibility of a third diverged yellowfin tuna group in the Arabian Sea. We further observe evidence for past population expansion as well as asymmetric gene flow from the Indo-Pacific to the Atlantic.
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Affiliation(s)
- Julia M I Barth
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Malte Damerau
- Institute of Fisheries Ecology, Johann Heinrich von Thünen Institute, Federal Research Institute for Rural Areas, Forestry and Fisheries, Hamburg, Germany
| | - Michael Matschiner
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.,Centre for Coastal Research, Department of Natural Sciences, University of Agder, Kristiansand, Norway
| | - Reinhold Hanel
- Institute of Fisheries Ecology, Johann Heinrich von Thünen Institute, Federal Research Institute for Rural Areas, Forestry and Fisheries, Hamburg, Germany
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29
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Whitehead H, Vachon F, Frasier TR. Cultural Hitchhiking in the Matrilineal Whales. Behav Genet 2017; 47:324-334. [PMID: 28275880 DOI: 10.1007/s10519-017-9840-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 02/13/2017] [Indexed: 11/25/2022]
Abstract
Five species of whale with matrilineal social systems (daughters remain with mothers) have remarkably low levels of mitochondrial DNA diversity. Non-heritable matriline-level demography could reduce genetic diversity but the required conditions are not consistent with the natural histories of the matrilineal whales. The diversity of nuclear microsatellites is little reduced in the matrilineal whales arguing against bottlenecks. Selective sweeps of the mitochondrial genome are feasible causes but it is not clear why these only occurred in the matrilineal species. Cultural hitchhiking (cultural selection reducing diversity at neutral genetic loci transmitted in parallel to the culture) is supported in sperm whales which possess suitable matrilineal socio-cultural groups (coda clans). Killer whales are delineated into ecotypes which likely originated culturally. Culture, bottlenecks and selection, as well as their interactions, operating between- or within-ecotypes, may have reduced their mitochondrial diversity. The societies, cultures and genetics of false killer and two pilot whale species are insufficiently known to assess drivers of low mitochondrial diversity.
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Affiliation(s)
- Hal Whitehead
- Department of Biology, Dalhousie University, Halifax, NS, B3H 4J1, Canada.
| | - Felicia Vachon
- Department of Biology, Dalhousie University, Halifax, NS, B3H 4J1, Canada
| | - Timothy R Frasier
- Department of Biology & Forensic Sciences Programme, Saint Mary's University, Halifax, Canada
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30
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Killer whales differentiating in geographic sympatry facilitated by divergent behavioural traditions. Heredity (Edinb) 2016; 117:481-482. [PMID: 27804965 DOI: 10.1038/hdy.2016.112] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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31
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Liu S, Hansen MM. PSMC (pairwise sequentially Markovian coalescent) analysis of RAD (restriction site associated DNA) sequencing data. Mol Ecol Resour 2016; 17:631-641. [DOI: 10.1111/1755-0998.12606] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 09/21/2016] [Accepted: 10/04/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Shenglin Liu
- Section for Genetics, Ecology and Evolution; Department of Bioscience; University of Aarhus; Ny Munkegade 114-116 DK-8000 Aarhus C Denmark
| | - Michael M. Hansen
- Section for Genetics, Ecology and Evolution; Department of Bioscience; University of Aarhus; Ny Munkegade 114-116 DK-8000 Aarhus C Denmark
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Liu S, Hansen MM, Jacobsen MW. Region-wide and ecotype-specific differences in demographic histories of threespine stickleback populations, estimated from whole genome sequences. Mol Ecol 2016; 25:5187-5202. [PMID: 27569902 DOI: 10.1111/mec.13827] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 08/18/2016] [Accepted: 08/22/2016] [Indexed: 02/04/2023]
Abstract
We analysed 81 whole genome sequences of threespine sticklebacks from Pacific North America, Greenland and Northern Europe, representing 16 populations. Principal component analysis of nuclear SNPs grouped populations according to geographical location, with Pacific populations being more divergent from each other relative to European and Greenlandic populations. Analysis of mitogenome sequences showed Northern European populations to represent a single phylogeographical lineage, whereas Greenlandic and particularly Pacific populations showed admixture between lineages. We estimated demographic history using a genomewide coalescence with recombination approach. The Pacific populations showed gradual population expansion starting >100 Kya, possibly reflecting persistence in cryptic refuges near the present distributional range, although we do not rule out possible influence of ancient admixture. Sharp population declines ca. 14-15 Kya were suggested to reflect founding of freshwater populations by marine ancestors. In Greenland and Northern Europe, demographic expansion started ca. 20-25 Kya coinciding with the end of the Last Glacial Maximum. In both regions, marine and freshwater populations started to show different demographic trajectories ca. 8-9 Kya, suggesting that this was the time of recolonization. In Northern Europe, this estimate was surprisingly late, but found support in subfossil evidence for presence of several freshwater fish species but not sticklebacks 12 Kya. The results demonstrate distinctly different demographic histories across geographical regions with potential consequences for adaptive processes. They also provide empirical support for previous assumptions about freshwater populations being founded independently from large, coherent marine populations, a key element in the Transporter Hypothesis invoked to explain the widespread occurrence of parallel evolution across freshwater stickleback populations.
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Affiliation(s)
- Shenglin Liu
- Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000, Aarhus C, Denmark
| | - Michael M Hansen
- Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000, Aarhus C, Denmark.
| | - Magnus W Jacobsen
- Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000, Aarhus C, Denmark
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Cammen KM, Andrews KR, Carroll EL, Foote AD, Humble E, Khudyakov JI, Louis M, McGowen MR, Olsen MT, Van Cise AM. Genomic Methods Take the Plunge: Recent Advances in High-Throughput Sequencing of Marine Mammals. J Hered 2016; 107:481-95. [PMID: 27511190 DOI: 10.1093/jhered/esw044] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/12/2016] [Indexed: 12/18/2022] Open
Abstract
The dramatic increase in the application of genomic techniques to non-model organisms (NMOs) over the past decade has yielded numerous valuable contributions to evolutionary biology and ecology, many of which would not have been possible with traditional genetic markers. We review this recent progression with a particular focus on genomic studies of marine mammals, a group of taxa that represent key macroevolutionary transitions from terrestrial to marine environments and for which available genomic resources have recently undergone notable rapid growth. Genomic studies of NMOs utilize an expanding range of approaches, including whole genome sequencing, restriction site-associated DNA sequencing, array-based sequencing of single nucleotide polymorphisms and target sequence probes (e.g., exomes), and transcriptome sequencing. These approaches generate different types and quantities of data, and many can be applied with limited or no prior genomic resources, thus overcoming one traditional limitation of research on NMOs. Within marine mammals, such studies have thus far yielded significant contributions to the fields of phylogenomics and comparative genomics, as well as enabled investigations of fitness, demography, and population structure. Here we review the primary options for generating genomic data, introduce several emerging techniques, and discuss the suitability of each approach for different applications in the study of NMOs.
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Affiliation(s)
- Kristina M Cammen
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise).
| | - Kimberly R Andrews
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Emma L Carroll
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Andrew D Foote
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Emily Humble
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Jane I Khudyakov
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Marie Louis
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Michael R McGowen
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Morten Tange Olsen
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Amy M Van Cise
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
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Genome-culture coevolution promotes rapid divergence of killer whale ecotypes. Nat Commun 2016; 7:11693. [PMID: 27243207 PMCID: PMC4895049 DOI: 10.1038/ncomms11693] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Accepted: 04/18/2016] [Indexed: 12/22/2022] Open
Abstract
Analysing population genomic data from killer whale ecotypes, which we estimate have globally radiated within less than 250,000 years, we show that genetic structuring including the segregation of potentially functional alleles is associated with socially inherited ecological niche. Reconstruction of ancestral demographic history revealed bottlenecks during founder events, likely promoting ecological divergence and genetic drift resulting in a wide range of genome-wide differentiation between pairs of allopatric and sympatric ecotypes. Functional enrichment analyses provided evidence for regional genomic divergence associated with habitat, dietary preferences and post-zygotic reproductive isolation. Our findings are consistent with expansion of small founder groups into novel niches by an initial plastic behavioural response, perpetuated by social learning imposing an altered natural selection regime. The study constitutes an important step towards an understanding of the complex interaction between demographic history, culture, ecological adaptation and evolution at the genomic level. Killer whales have evolved into specialized ecotypes based on hunting strategies and ecological niches. Here, Andrew Foote and colleagues sequenced the whole genome of individual killer whales representing 5 different ecotypes from North Pacific and Antarctic, and show expansion of small founder groups to adapt to specific ecological niches.
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35
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Alexander A, Steel D, Hoekzema K, Mesnick SL, Engelhaupt D, Kerr I, Payne R, Baker CS. What influences the worldwide genetic structure of sperm whales (Physeter macrocephalus)? Mol Ecol 2016; 25:2754-72. [DOI: 10.1111/mec.13638] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 03/06/2016] [Accepted: 03/22/2016] [Indexed: 02/06/2023]
Affiliation(s)
- Alana Alexander
- Marine Mammal Institute; Hatfield Marine Science Center; Oregon State University; 2030 SE Marine Science Drive Newport OR 97365 USA
- Department of Fisheries and Wildlife; Oregon State University; 104 Nash Hall Corvallis OR 97330 USA
- Biodiversity Institute; University of Kansas; 1345 Jayhawk Blvd Lawrence KS 66045 USA
| | - Debbie Steel
- Marine Mammal Institute; Hatfield Marine Science Center; Oregon State University; 2030 SE Marine Science Drive Newport OR 97365 USA
- Department of Fisheries and Wildlife; Oregon State University; 104 Nash Hall Corvallis OR 97330 USA
| | - Kendra Hoekzema
- Department of Fisheries and Wildlife; Oregon State University; 104 Nash Hall Corvallis OR 97330 USA
| | - Sarah L. Mesnick
- Southwest Fisheries Science Center; National Marine Fisheries Service; National Oceanic and Atmospheric Administration; 8901 La Jolla Shores Drive La Jolla CA 92037 USA
| | | | - Iain Kerr
- Ocean Alliance; 32 Horton Street Gloucester MA 01930 USA
| | - Roger Payne
- Ocean Alliance; 32 Horton Street Gloucester MA 01930 USA
| | - C. Scott Baker
- Marine Mammal Institute; Hatfield Marine Science Center; Oregon State University; 2030 SE Marine Science Drive Newport OR 97365 USA
- Department of Fisheries and Wildlife; Oregon State University; 104 Nash Hall Corvallis OR 97330 USA
- School of Biological Sciences; University of Auckland; Private Bag 92019 Auckland 1142 New Zealand
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Szczecińska M, Sramko G, Wołosz K, Sawicki J. Genetic Diversity and Population Structure of the Rare and Endangered Plant Species Pulsatilla patens (L.) Mill in East Central Europe. PLoS One 2016; 11:e0151730. [PMID: 27003296 PMCID: PMC4803199 DOI: 10.1371/journal.pone.0151730] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 03/03/2016] [Indexed: 11/25/2022] Open
Abstract
Pulsatilla patens s.s. is a one of the most endangered plant species in Europe. The present range of this species in Europe is highly fragmented and the size of the populations has been dramatically reduced in the past 50 years. The rapid disappearance of P. patens localities in Europe has prompted the European Commission to initiate active protection of this critically endangered species. The aim of this study was to estimate the degree and distribution of genetic diversity within European populations of this endangered species. We screened 29 populations of P. patens using a set of six microsatellite primers. The results of our study indicate that the analyzed populations are characterized by low levels of genetic diversity (Ho = 0.005) and very high levels of inbreeding (FIS = 0.90). These results suggest that genetic erosion could be partially responsible for the lower fitness in smaller populations of this species. Private allelic richness was very low, being as low as 0.00 for most populations. Average genetic diversity over loci and mean number of alleles in P. patens populations were significantly correlated with population size, suggesting severe genetic drift. The results of AMOVA point to higher levels of variation within populations than between populations.The results of Structure and PCoA analyses suggest that the genetic structure of the studied P. patens populations fall into three clusters corresponding to geographical regions. The most isolated populations (mostly from Romania) formed a separate group with a homogeneous gene pool located at the southern, steppic part of the distribution range. Baltic, mostly Polish, populations fall into two genetic groups which were not fully compatible with their geographic distribution.Our results indicate the serious genetic depauperation of P. patens in the western part of its range, even hinting at an ongoing extinction vortex. Therefore, special conservation attention is required to maintain the populations of this highly endangered species of European Community interest.
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Affiliation(s)
- Monika Szczecińska
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Gabor Sramko
- Department of Botany, University of Debrecen, Debrecen, Hungary
- MTA-ELTE-MTM Ecology Research Group, Budapest, Hungary
| | - Katarzyna Wołosz
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Jakub Sawicki
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
- Department of Biology and Ecology, University of Ostrava, Ostrava, Czech Republic
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37
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Younger JL, van den Hoff J, Wienecke B, Hindell M, Miller KJ. Contrasting responses to a climate regime change by sympatric, ice-dependent predators. BMC Evol Biol 2016; 16:61. [PMID: 26975876 PMCID: PMC5477764 DOI: 10.1186/s12862-016-0630-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 03/01/2016] [Indexed: 02/02/2023] Open
Abstract
Background Models that predict changes in the abundance and distribution of fauna under future climate change scenarios often assume that ecological niche and habitat availability are the major determinants of species’ responses to climate change. However, individual species may have very different capacities to adapt to environmental change, as determined by intrinsic factors such as their dispersal ability, genetic diversity, generation time and rate of evolution. These intrinsic factors are usually excluded from forecasts of species’ abundance and distribution changes. We aimed to determine the importance of these factors by comparing the impact of the most recent climate regime change, the late Pleistocene glacial-interglacial transition, on two sympatric, ice-dependent meso-predators, the emperor penguin (Aptenodytes forsteri) and Weddell seal (Leptonychotes weddellii). Methods We reconstructed the population trend of emperor penguins and Weddell seals in East Antarctica over the past 75,000 years using mitochondrial DNA sequences and an extended Bayesian skyline plot method. We also assessed patterns of contemporary population structure and genetic diversity. Results Despite their overlapping distributions and shared dependence on sea ice, our genetic data revealed very different responses to climate warming between these species. The emperor penguin population grew rapidly following the glacial-interglacial transition, but the size of the Weddell seal population did not change. The expansion of emperor penguin numbers during the warm Holocene may have been facilitated by their higher dispersal ability and gene flow among colonies, and fine-scale differences in preferred foraging locations. Conclusions The vastly different climate change responses of two sympatric ice-dependent predators suggests that differing adaptive capacities and/or fine-scale niche differences can play a major role in species’ climate change responses, and that adaptive capacity should be considered alongside niche and distribution in future species forecasts. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0630-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jane L Younger
- Institute for Marine and Antarctic Studies, University of Tasmania, Private Bag 129, Hobart, 7001, Tasmania, Australia.
| | - John van den Hoff
- Australian Antarctic Division, 203 Channel Highway, Kingston, 7050, Tasmania, Australia
| | - Barbara Wienecke
- Australian Antarctic Division, 203 Channel Highway, Kingston, 7050, Tasmania, Australia
| | - Mark Hindell
- Institute for Marine and Antarctic Studies, University of Tasmania, Private Bag 129, Hobart, 7001, Tasmania, Australia
| | - Karen J Miller
- Australian Institute of Marine Science, The UWA Oceans Institute, 35 Stirling Highway, Crawley, WA, 6009, Australia.,School of Biological Sciences, Private Bag 5, University of Tasmania, Hobart, 7001, Tasmania, Australia
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38
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Kozma R, Melsted P, Magnússon KP, Höglund J. Looking into the past - the reaction of three grouse species to climate change over the last million years using whole genome sequences. Mol Ecol 2016; 25:570-80. [PMID: 26607571 DOI: 10.1111/mec.13496] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 11/19/2015] [Accepted: 11/20/2015] [Indexed: 01/08/2023]
Abstract
Tracking past population fluctuations can give insight into current levels of genetic variation present within species. Analysing population dynamics over larger timescales can be aligned to known climatic changes to determine the response of species to varying environments. Here, we applied the Pairwise Sequentially Markovian Coalescent (psmc) model to infer past population dynamics of three widespread grouse species; black grouse, willow grouse and rock ptarmigan. This allowed the tracking of the effective population size (Ne ) of all three species beyond 1 Mya, revealing that (i) early Pleistocene cooling (~2.5 Mya) caused an increase in the willow grouse and rock ptarmigan populations, (ii) the mid-Brunhes event (~430 kya) and following climatic oscillations decreased the Ne of willow grouse and rock ptarmigan, but increased the Ne of black grouse and (iii) all three species reacted differently to the last glacial maximum (LGM) - black grouse increased prior to it, rock ptarmigan experienced a severe bottleneck and willow grouse was maintained at large population size. We postulate that the varying psmc signal throughout the LGM depicts only the local history of the species. Nevertheless, the large population fluctuations in willow grouse and rock ptarmigan indicate that both species are opportunistic breeders while black grouse tracks the climatic changes more slowly and is maintained at lower Ne . Our results highlight the usefulness of the psmc approach in investigating species' reaction to climate change in the deep past, but also that caution should be taken in drawing general conclusions about the recent past.
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Affiliation(s)
- Radoslav Kozma
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, Uppsala, SE-75236, Sweden
| | - Páll Melsted
- Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, University of Iceland, Reykjavik, 107, Iceland.,deCODE Genetics/Amgen, Reykjavik, Iceland
| | - Kristinn P Magnússon
- The Icelandic Institute of Natural History, Borgir v. Nordurslod, Akureyri, 600, Iceland.,Department of Natural Resource Sciences, University of Akureyri, Borgir vid Nordurslod, Akureyri, 600, Iceland.,Biomedical Center, University of Iceland, Vatnsmýrarvegur 16, Reykjavik, 101, Iceland
| | - Jacob Höglund
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, Uppsala, SE-75236, Sweden
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Dungan SZ, Kosyakov A, Chang BS. Spectral Tuning of Killer Whale (Orcinus orca) Rhodopsin: Evidence for Positive Selection and Functional Adaptation in a Cetacean Visual Pigment. Mol Biol Evol 2015; 33:323-36. [DOI: 10.1093/molbev/msv217] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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Inferring Bottlenecks from Genome-Wide Samples of Short Sequence Blocks. Genetics 2015; 201:1157-69. [PMID: 26341659 PMCID: PMC4649642 DOI: 10.1534/genetics.115.179861] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 09/01/2015] [Indexed: 01/02/2023] Open
Abstract
The advent of the genomic era has necessitated the development of methods capable of analyzing large volumes of genomic data efficiently. Being able to reliably identify bottlenecks—extreme population size changes of short duration—not only is interesting in the context of speciation and extinction but also matters (as a null model) when inferring selection. Bottlenecks can be detected in polymorphism data via their distorting effect on the shape of the underlying genealogy. Here, we use the generating function of genealogies to derive the probability of mutational configurations in short sequence blocks under a simple bottleneck model. Given a large number of nonrecombining blocks, we can compute maximum-likelihood estimates of the time and strength of the bottleneck. Our method relies on a simple summary of the joint distribution of polymorphic sites. We extend the site frequency spectrum by counting mutations in frequency classes in short sequence blocks. Using linkage information over short distances in this way gives greater power to detect bottlenecks than the site frequency spectrum and potentially opens up a wide range of demographic histories to blockwise inference. Finally, we apply our method to genomic data from a species of pig (Sus cebifrons) endemic to islands in the center and west of the Philippines to estimate whether a bottleneck occurred upon island colonization and compare our scheme to Li and Durbin’s pairwise sequentially Markovian coalescent (PSMC) both for the pig data and using simulations.
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Seim I, Ma S, Zhou X, Gerashchenko MV, Lee SG, Suydam R, George JC, Bickham JW, Gladyshev VN. The transcriptome of the bowhead whale Balaena mysticetus reveals adaptations of the longest-lived mammal. Aging (Albany NY) 2015; 6:879-99. [PMID: 25411232 PMCID: PMC4247388 DOI: 10.18632/aging.100699] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mammals vary dramatically in lifespan, by at least two-orders of magnitude, but the molecular basis for this difference remains largely unknown. The bowhead whale Balaena mysticetus is the longest-lived mammal known, with an estimated maximal lifespan in excess of two hundred years. It is also one of the two largest animals and the most cold-adapted baleen whale species. Here, we report the first genome-wide gene expression analyses of the bowhead whale, based on the de novo assembly of its transcriptome. Bowhead whale or cetacean-specific changes in gene expression were identified in the liver, kidney and heart, and complemented with analyses of positively selected genes. Changes associated with altered insulin signaling and other gene expression patterns could help explain the remarkable longevity of bowhead whales as well as their adaptation to a lipid-rich diet. The data also reveal parallels in candidate longevity adaptations of the bowhead whale, naked mole rat and Brandt's bat. The bowhead whale transcriptome is a valuable resource for the study of this remarkable animal, including the evolution of longevity and its important correlates such as resistance to cancer and other diseases.
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Affiliation(s)
- Inge Seim
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Siming Ma
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Xuming Zhou
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Maxim V Gerashchenko
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sang-Goo Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Robert Suydam
- Department of Wildlife Management, North Slope Borough, Barrow, AK 99723, USA
| | - John C George
- Department of Wildlife Management, North Slope Borough, Barrow, AK 99723, USA
| | | | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
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42
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Morin PA, Parsons KM, Archer FI, Ávila-Arcos MC, Barrett-Lennard LG, Dalla Rosa L, Duchêne S, Durban JW, Ellis GM, Ferguson SH, Ford JK, Ford MJ, Garilao C, Gilbert MTP, Kaschner K, Matkin CO, Petersen SD, Robertson KM, Visser IN, Wade PR, Ho SYW, Foote AD. Geographic and temporal dynamics of a global radiation and diversification in the killer whale. Mol Ecol 2015; 24:3964-79. [PMID: 26087773 DOI: 10.1111/mec.13284] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 06/09/2015] [Accepted: 06/17/2015] [Indexed: 02/05/2023]
Abstract
Global climate change during the Late Pleistocene periodically encroached and then released habitat during the glacial cycles, causing range expansions and contractions in some species. These dynamics have played a major role in geographic radiations, diversification and speciation. We investigate these dynamics in the most widely distributed of marine mammals, the killer whale (Orcinus orca), using a global data set of over 450 samples. This marine top predator inhabits coastal and pelagic ecosystems ranging from the ice edge to the tropics, often exhibiting ecological, behavioural and morphological variation suggestive of local adaptation accompanied by reproductive isolation. Results suggest a rapid global radiation occurred over the last 350 000 years. Based on habitat models, we estimated there was only a 15% global contraction of core suitable habitat during the last glacial maximum, and the resources appeared to sustain a constant global effective female population size throughout the Late Pleistocene. Reconstruction of the ancestral phylogeography highlighted the high mobility of this species, identifying 22 strongly supported long-range dispersal events including interoceanic and interhemispheric movement. Despite this propensity for geographic dispersal, the increased sampling of this study uncovered very few potential examples of ancestral dispersal among ecotypes. Concordance of nuclear and mitochondrial data further confirms genetic cohesiveness, with little or no current gene flow among sympatric ecotypes. Taken as a whole, our data suggest that the glacial cycles influenced local populations in different ways, with no clear global pattern, but with secondary contact among lineages following long-range dispersal as a potential mechanism driving ecological diversification.
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Affiliation(s)
- Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla, CA, 92037, USA
| | - Kim M Parsons
- Alaska Fisheries Science Center, National Marine Fisheries Service, NOAA, 7600 Sand Point Way NE, Seattle, WA, 98115, USA
| | - Frederick I Archer
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla, CA, 92037, USA
| | - María C Ávila-Arcos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Lance G Barrett-Lennard
- Vancouver Aquarium Marine Science Centre, 845 Avison Way, Vancouver, British Columbia, V6G 3E2, Canada
| | - Luciano Dalla Rosa
- Laboratório de Ecologia e Conservação da Megafauna Marinha, Instituto de Oceanografia, Universidade Federal do Rio Grande, Av. Itália km. 8 s/n, Campus Carreiros, Rio Grande, RS, 96201-900, Brazil
| | - Sebastián Duchêne
- School of Biological Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - John W Durban
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla, CA, 92037, USA.,Alaska Fisheries Science Center, National Marine Fisheries Service, NOAA, 7600 Sand Point Way NE, Seattle, WA, 98115, USA
| | - Graeme M Ellis
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Rd, Nanaimo, British Columbia, Canada
| | - Steven H Ferguson
- Fisheries & Oceans Canada, 501 University Crescent, Winnipeg, Manitoba, R3T 2N6, Canada
| | - John K Ford
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Rd, Nanaimo, British Columbia, Canada
| | - Michael J Ford
- Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA 2725 Montlake Blvd E, Seattle, WA, USA
| | - Cristina Garilao
- GEOMAR Helmholtz-Zentrum für Ozeanforschung Kiel Düsternbrooker Weg 2, 24105, Kiel, Germany
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark.,Trace and Environmental DNA laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia, 6845, Australia
| | - Kristin Kaschner
- Department of Biometry and Environmental System Analysis, Albert-Ludwigs-University of Freiburg, Tennenbacher Strasse 4, 79106, Freiburg, Germany
| | - Craig O Matkin
- North Gulf Oceanic Society, 3430 Main St. Ste. B1, Homer, AK, 99603, USA
| | - Stephen D Petersen
- Assiniboine Park Zoo, 2595 Roblin Blvd, Winnipeg, Manitoba, R3P 2N7, Canada
| | - Kelly M Robertson
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla, CA, 92037, USA
| | - Ingrid N Visser
- Orca Research Trust, P.O. Box 402043, Tutukaka, Northland, 0153, New Zealand
| | - Paul R Wade
- Alaska Fisheries Science Center, National Marine Fisheries Service, NOAA, 7600 Sand Point Way NE, Seattle, WA, 98115, USA
| | - Simon Y W Ho
- School of Biological Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Andrew D Foote
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark.,Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
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43
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Resource specialisation and the divergence of killer whale populations. Heredity (Edinb) 2015; 115:93-5. [PMID: 25990875 DOI: 10.1038/hdy.2015.45] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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44
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Drivers of Population Structure of the Bottlenose Dolphin (Tursiops truncatus) in the Eastern Mediterranean Sea. Evol Biol 2015. [DOI: 10.1007/s11692-015-9309-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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45
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Moura AE, Kenny JG, Chaudhuri RR, Hughes MA, Reisinger RR, de Bruyn PJN, Dahlheim ME, Hall N, Hoelzel AR. Phylogenomics of the killer whale indicates ecotype divergence in sympatry. Heredity (Edinb) 2015; 114:48-55. [PMID: 25052415 PMCID: PMC4815593 DOI: 10.1038/hdy.2014.67] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2013] [Revised: 03/28/2014] [Accepted: 05/30/2014] [Indexed: 12/26/2022] Open
Abstract
For many highly mobile species, the marine environment presents few obvious barriers to gene flow. Even so, there is considerable diversity within and among species, referred to by some as the 'marine speciation paradox'. The recent and diverse radiation of delphinid cetaceans (dolphins) represents a good example of this. Delphinids are capable of extensive dispersion and yet many show fine-scale genetic differentiation among populations. Proposed mechanisms include the division and isolation of populations based on habitat dependence and resource specializations, and habitat release or changing dispersal corridors during glacial cycles. Here we use a phylogenomic approach to investigate the origin of differentiated sympatric populations of killer whales (Orcinus orca). Killer whales show strong specialization on prey choice in populations of stable matrifocal social groups (ecotypes), associated with genetic and phenotypic differentiation. Our data suggest evolution in sympatry among populations of resource specialists.
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Affiliation(s)
- A E Moura
- School of Biological and Biomedical Sciences, Durham University, Durham, UK
| | - J G Kenny
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - R R Chaudhuri
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - M A Hughes
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - R R Reisinger
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - P J N de Bruyn
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - M E Dahlheim
- National Marine Mammal Laboratory, National Marine Fisheries Service, Seattle, WA, USA
| | - N Hall
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - A R Hoelzel
- School of Biological and Biomedical Sciences, Durham University, Durham, UK
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46
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Moura AE, Kenny JG, Chaudhuri R, Hughes MA, J Welch A, Reisinger RR, de Bruyn PJN, Dahlheim ME, Hall N, Hoelzel AR. Population genomics of the killer whale indicates ecotype evolution in sympatry involving both selection and drift. Mol Ecol 2014; 23:5179-92. [PMID: 25244680 PMCID: PMC4237148 DOI: 10.1111/mec.12929] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 09/09/2014] [Accepted: 09/15/2014] [Indexed: 12/30/2022]
Abstract
The evolution of diversity in the marine ecosystem is poorly understood, given the relatively high potential for connectivity, especially for highly mobile species such as whales and dolphins. The killer whale (Orcinus orca) has a worldwide distribution, and individual social groups travel over a wide geographic range. Even so, regional populations have been shown to be genetically differentiated, including among different foraging specialists (ecotypes) in sympatry. Given the strong matrifocal social structure of this species together with strong resource specializations, understanding the process of differentiation will require an understanding of the relative importance of both genetic drift and local adaptation. Here we provide a high-resolution analysis based on nuclear single-nucleotide polymorphic markers and inference about differentiation at both neutral loci and those potentially under selection. We find that all population comparisons, within or among foraging ecotypes, show significant differentiation, including populations in parapatry and sympatry. Loci putatively under selection show a different pattern of structure compared to neutral loci and are associated with gene ontology terms reflecting physiologically relevant functions (e.g. related to digestion). The pattern of differentiation for one ecotype in the North Pacific suggests local adaptation and shows some fixed differences among sympatric ecotypes. We suggest that differential habitat use and resource specializations have promoted sufficient isolation to allow differential evolution at neutral and functional loci, but that the process is recent and dependent on both selection and drift.
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Affiliation(s)
- Andre E Moura
- School of Biological and Biomedical Sciences, Durham University, South Road, Durham, DH1 3LE, UK
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47
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Ferchaud AL, Pedersen SH, Bekkevold D, Jian J, Niu Y, Hansen MM. A low-density SNP array for analyzing differential selection in freshwater and marine populations of threespine stickleback (Gasterosteus aculeatus). BMC Genomics 2014; 15:867. [PMID: 25286752 PMCID: PMC4196021 DOI: 10.1186/1471-2164-15-867] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 09/29/2014] [Indexed: 11/23/2022] Open
Abstract
Background The threespine stickleback (Gasterosteus aculeatus) has become an important model species for studying both contemporary and parallel evolution. In particular, differential adaptation to freshwater and marine environments has led to high differentiation between freshwater and marine stickleback populations at the phenotypic trait of lateral plate morphology and the underlying candidate gene Ectodysplacin (EDA). Many studies have focused on this trait and candidate gene, although other genes involved in marine-freshwater adaptation may be equally important. In order to develop a resource for rapid and cost efficient analysis of genetic divergence between freshwater and marine sticklebacks, we generated a low-density SNP (Single Nucleotide Polymorphism) array encompassing markers of chromosome regions under putative directional selection, along with neutral markers for background. Results RAD (Restriction site Associated DNA) sequencing of sixty individuals representing two freshwater and one marine population led to the identification of 33,993 SNP markers. Ninety-six of these were chosen for the low-density SNP array, among which 70 represented SNPs under putatively directional selection in freshwater vs. marine environments, whereas 26 SNPs were assumed to be neutral. Annotation of these regions revealed several genes that are candidates for affecting stickleback phenotypic variation, some of which have been observed in previous studies whereas others are new. Conclusions We have developed a cost-efficient low-density SNP array that allows for rapid screening of polymorphisms in threespine stickleback. The array provides a valuable tool for analyzing adaptive divergence between freshwater and marine stickleback populations beyond the well-established candidate gene Ectodysplacin (EDA). Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-867) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Michael M Hansen
- Department of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark.
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48
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Caspermeyer J. Orca's Survival during the Ice Age. Mol Biol Evol 2014; 31:1325. [DOI: 10.1093/molbev/msu066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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