1
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Strøm JF, Bøhn T, Skjaeraasen JE, Gjelland KØ, Karlsen Ø, Johansen T, Hanebrekke T, Bjørn PA, Olsen EM. Movement diversity and partial sympatry of coastal and Northeast Arctic cod ecotypes at high latitudes. J Anim Ecol 2023; 92:1966-1978. [PMID: 37485731 DOI: 10.1111/1365-2656.13989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/04/2023] [Indexed: 07/25/2023]
Abstract
Movement diversity within species represent an important but often neglected, component of biodiversity that affects ecological and genetic interactions, as well as the productivity of exploited systems. By combining individual tracking data from acoustic telemetry with novel genetic analyses, we describe the movement diversity of two Atlantic cod Gadus morhua ecotypes in two high-latitude fjord systems: the highly migratory Northeast Arctic cod (NEA cod) that supports the largest cod fishery in the world, and the more sedentary Norwegian coastal cod, which is currently in a depleted state. As predicted, coastal cod displayed a higher level of fjord residency than NEA cod. Of the cod tagged during the spawning season, NEA cod left the fjords permanently to a greater extent and earlier compared to coastal cod, which to a greater extent remained resident and left the fjords temporarily. Despite this overall pattern, horizontal movements atypical for the ecotypes were common with some NEA cod remaining within the fjords year-round and some coastal cod displaying a low fjord fidelity. Fjord residency and exit timing also differed with spawning status and body size, with spawning cod and large individuals tagged during the feeding season more prone to leave the fjords and earlier than non-spawning and smaller individuals. While our results confirm a lower fjord dependency for NEA cod, they highlight a movement diversity within each ecotype and sympatric residency between ecotypes, previously undetected by population-level monitoring. This new knowledge is relevant for the management, which should base their fisheries advice for these interacting ecotypes on their habitat use and seasonal movements.
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Affiliation(s)
| | - Thomas Bøhn
- Institute of Marine Research, Tromsø, Norway
| | | | - Karl Øystein Gjelland
- Department of Arctic Ecology, Norwegian Institute of Nature Research (NINA), Tromsø, Norway
| | | | | | | | | | - Esben Moland Olsen
- Institute of Marine Research, His, Norway
- Department of Natural Sciences, Centre for Coastal Research, University of Agder, Kristiansand, Norway
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2
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Buss DL, Atmore LM, Zicos MH, Goodall-Copestake WP, Brace S, Archer FI, Baker CS, Barnes I, Carroll EL, Hart T, Kitchener AC, Sabin R, Sremba AL, Weir CR, Jackson JA. Historical Mitogenomic Diversity and Population Structuring of Southern Hemisphere Fin Whales. Genes (Basel) 2023; 14:1038. [PMID: 37239398 PMCID: PMC10218396 DOI: 10.3390/genes14051038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
Fin whales Balaenoptera physalus were hunted unsustainably across the globe in the 19th and 20th centuries, leading to vast reductions in population size. Whaling catch records indicate the importance of the Southern Ocean for this species; approximately 730,000 fin whales were harvested during the 20th century in the Southern Hemisphere (SH) alone, 94% of which were at high latitudes. Genetic samples from contemporary whales can provide a window to past population size changes, but the challenges of sampling in remote Antarctic waters limit the availability of data. Here, we take advantage of historical samples in the form of bones and baleen available from ex-whaling stations and museums to assess the pre-whaling diversity of this once abundant species. We sequenced 27 historical mitogenomes and 50 historical mitochondrial control region sequences of fin whales to gain insight into the population structure and genetic diversity of Southern Hemisphere fin whales (SHFWs) before and after the whaling. Our data, both independently and when combined with mitogenomes from the literature, suggest SHFWs are highly diverse and may represent a single panmictic population that is genetically differentiated from Northern Hemisphere populations. These are the first historic mitogenomes available for SHFWs, providing a unique time series of genetic data for this species.
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Affiliation(s)
- Danielle L. Buss
- British Antarctic Survey, National Environment Research Council, Cambridge CB3 0ET, UK
- Department of Archaeology, University of Cambridge, Downing Street, Cambridge CB2 3DZ, UK
| | - Lane M. Atmore
- Department of Archaeology, University of Cambridge, Downing Street, Cambridge CB2 3DZ, UK
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Maria H. Zicos
- The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - William P. Goodall-Copestake
- British Antarctic Survey, National Environment Research Council, Cambridge CB3 0ET, UK
- Scottish Association for Marine Science, Oban PA37 1QA, UK
| | - Selina Brace
- The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Frederick I. Archer
- National Oceanic and Atmospheric Administration, Southwest Fisheries Science Center, La Jolla, CA 92037, USA
| | - C. Scott Baker
- Marine Mammal Institute and Department of Fisheries and Wildlife, Hatfield Marine Science Center, Oregon State University, Newport, OR 97365, USA
| | - Ian Barnes
- The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Emma L. Carroll
- Te Kura Mātauranga Koiora—School of Biological Sciences, University of Auckland Waipapa Taumata Rau, Auckland 1010, New Zealand
| | - Tom Hart
- Department of Zoology, University of Oxford, Mansfield Road, Oxford OX1 3SZ, UK
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK
- School of Geosciences, University of Edinburgh, Drummond Street, Edinburgh EH8 9XP, UK
| | - Richard Sabin
- The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Angela L. Sremba
- Marine Mammal Institute and Department of Fisheries and Wildlife, Hatfield Marine Science Center, Oregon State University, Newport, OR 97365, USA
| | - Caroline R. Weir
- Falklands Conservation, Ross Road, Stanley F1QQ 1ZZ, Falkland Islands
| | - Jennifer A. Jackson
- British Antarctic Survey, National Environment Research Council, Cambridge CB3 0ET, UK
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3
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Hersh TA, Gero S, Rendell L, Whitehead H. Using identity calls to detect structure in acoustic datasets. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Taylor A. Hersh
- Department of Biology Dalhousie University Halifax Nova Scotia Canada
| | - Shane Gero
- Department of Biology Dalhousie University Halifax Nova Scotia Canada
- Zoophysiology Department of Bioscience Aarhus University Aarhus Denmark
| | - Luke Rendell
- Centre for Social Learning and Cognitive Evolution School of Biology University of St. Andrews St. Andrews UK
| | - Hal Whitehead
- Department of Biology Dalhousie University Halifax Nova Scotia Canada
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4
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Sarano F, Girardet J, Sarano V, Vitry H, Preud'homme A, Heuzey R, Garcia-Cegarra AM, Madon B, Delfour F, Glotin H, Adam O, Jung JL. Kin relationships in cultural species of the marine realm: case study of a matrilineal social group of sperm whales off Mauritius island, Indian Ocean. ROYAL SOCIETY OPEN SCIENCE 2021; 8:201794. [PMID: 33972866 PMCID: PMC8074673 DOI: 10.1098/rsos.201794] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/11/2021] [Indexed: 05/14/2023]
Abstract
Understanding the organization and dynamics of social groups of marine mammals through the study of kin relationships is particularly challenging. Here, we studied a stable social group of sperm whales off Mauritius, using underwater observations, individual-specific identification, non-invasive sampling and genetic analyses based on mitochondrial sequencing and microsatellite profiling. Twenty-four sperm whales were sampled between 2017 and 2019. All individuals except one adult female shared the same mitochondrial DNA (mtDNA) haplotype-one that is rare in the western Indian Ocean-thus confirming with near certainty the matrilineality of the group. All probable first- and second-degree kin relationships were depicted in the sperm whale social group: 13 first-degree and 27 second-degree relationships were identified. Notably, we highlight the likely case of an unrelated female having been integrated into a social unit, in that she presented a distinct mtDNA haplotype and no close relationships with any members of the group. Investigating the possible matrilineality of sperm whale cultural units (i.e. vocal clans) is the next step in our research programme to elucidate and better apprehend the complex organization of sperm whale social groups.
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Affiliation(s)
| | - Justine Girardet
- Université de Brest, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, ISYEB, Brest, France
| | | | - Hugues Vitry
- Marine Megafauna Conservation Organisation, Mauritius
| | | | | | - Ana M. Garcia-Cegarra
- Centro de Investigación de Fauna Marina y Avistamiento de Cetáceos, CIFAMAC, Mejillones, Chile
- Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad Santo Tomás, Antofagasta, Chile
| | - Bénédicte Madon
- Université de Brest, AMURE - Aménagement des Usages des Ressources et des Espaces marins et littoraux - Centre de droit et d'économie de la mer, Plouzané, France
| | - Fabienne Delfour
- Laboratoire d'Ethologie Expérimentale et Comparée EA 4443, Université Paris 13, Sorbonne Paris Cité, Villetaneuse, France
| | - Hervé Glotin
- Toulon University, Aix Marseille Université, CNRS, LIS, DYNI Team, Marseille, France
| | - Olivier Adam
- Sorbonne Université, CNRS, Institut Jean Le Rond d'Alembert, UMR 7190, Paris, France
- Institute of Neurosciences Paris-Saclay, Bioacoustics Team, CNRS UMR 9197, Université Paris Sud, Orsay, France
| | - Jean-Luc Jung
- Université de Brest, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, ISYEB, Brest, France
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5
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Gravena W, Hrbek T, da Silva VMF, Farias IP. Boto ( Inia geoffrensis-Cetacea: Iniidae) aggregations in two provisioning sites in the lower Negro River-Amazonas, Brazil: are they related? PeerJ 2019; 7:e6692. [PMID: 31024759 PMCID: PMC6475133 DOI: 10.7717/peerj.6692] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 02/28/2019] [Indexed: 11/20/2022] Open
Abstract
The Negro River currently has seven floating houses where tourists can feed and interact with botos, each with its own history of how these aggregations were formed. Some keepers say these groups are familial, even reporting individuals being born into the group. However, behavioral studies have shown that botos are solitary, only forming groups at feeding areas and during the mating season. In the present study we used 12 microsatellite and molecular sex markers to characterize relationships within and between two boto aggregations (ten and seven botos each) in the lower Negro River. Molecular sexing revealed that all botos sampled from both aggregations were males. This may be explained by habitat preference, as male botos are primarily found in the main channels of large rivers, whereas females prefer more protected areas, such as flooded forests and its channels and lakes. Most of the animals were unrelated within each aggregation, demonstrating that these aggregations are not normally formed due to kinship bonds, but are exclusively for feeding, as botos learn that these places provide easy access to food. This study provides important information that helps us understand how human interaction is affecting the social structure and behavior of these animals.
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Affiliation(s)
- Waleska Gravena
- Instituto de Saúde e Biotecnologia (ISB), Universidade Federal do Amazonas (UFAM), Coari, Amazonas, Brazil
- Laboratório de Evolução e Genética Animal (LEGAL), Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brazil
- Laboratório de Mamíferos Aquáticos (LMA), Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Amazonas, Brazil
| | - Tomas Hrbek
- Laboratório de Evolução e Genética Animal (LEGAL), Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brazil
| | - Vera Maria Ferreira da Silva
- Laboratório de Mamíferos Aquáticos (LMA), Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Amazonas, Brazil
| | - Izeni Pires Farias
- Laboratório de Evolução e Genética Animal (LEGAL), Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brazil
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6
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Chua MAH, Lane DJW, Ooi SK, Tay SHX, Kubodera T. Diet and mitochondrial DNA haplotype of a sperm whale ( Physeter macrocephalus) found dead off Jurong Island, Singapore. PeerJ 2019; 7:e6705. [PMID: 30984481 PMCID: PMC6452849 DOI: 10.7717/peerj.6705] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 03/03/2019] [Indexed: 11/20/2022] Open
Abstract
Despite numerous studies across the large geographic range of the sperm whale (Physeter macrocephalus), little is known about the diet and mitochondrial DNA haplotypes of this strongly female philopatric species in waters off Southeast Asia. A female sperm whale found dead in Singapore waters provided the opportunity to study her diet and mitochondrial DNA haplotype. Here we report on the identification of stomach contents and mitochondrial DNA haplotype of this individual, and we include coastal hydrodynamic modelling to determine the possible geographic origin of the whale. At least 28 species of prey were eaten by this adult female whale, most of which were cephalopods. The mesopelagic squids Taonius pavo, Histioteuthis pacifica, Chiroteuthis imperator,and Ancistrocheirus lesueurii made up over 65% of the whale's stomach contents. Plastic debris was also found in the whale's stomach. Based on the diet, genetics, and coastal hydrodynamic modelling that suggest an easterly drift of the whale carcass over several days, the dead sperm whale in Singapore probably originated from a pod in the Southern Indian Ocean. This study provides an increase in the understanding the diet and natural history of the sperm whale in Southeast Asia. The combined analyses of stomach contents, DNA, and hydrodynamic modeling could provide a context to future studies on the sperm whale strandings, and have broader applicability for other marine mammals in the region.
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Affiliation(s)
- Marcus A H Chua
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore, Singapore.,Department of Environmental Science and Policy, George Mason University, Fairfax, VA, United States of America
| | - David J W Lane
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore, Singapore
| | - Seng Keat Ooi
- Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | - Serene H X Tay
- Civil and Environmental Engineering, National University of Singapore, Singapore, Singapore
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7
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Konrad CM, Frasier TR, Rendell L, Whitehead H, Gero S. Kinship and association do not explain vocal repertoire variation among individual sperm whales or social units. Anim Behav 2018. [DOI: 10.1016/j.anbehav.2018.09.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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8
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Eberle J, Bazzato E, Fabrizi S, Rossini M, Colomba M, Cillo D, Uliana M, Sparacio I, Sabatinelli G, Warnock RCM, Carpaneto G, Ahrens D. Sex-Biased Dispersal Obscures Species Boundaries in Integrative Species Delimitation Approaches. Syst Biol 2018; 68:441-459. [DOI: 10.1093/sysbio/syy072] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 10/22/2018] [Accepted: 10/23/2018] [Indexed: 01/05/2023] Open
Affiliation(s)
- Jonas Eberle
- Zoological Research Museum Alexander Koenig, Centre of Taxonomy and Evolutionary Research, Adenauerallee 160, 53113 Bonn, Germany
| | - Erika Bazzato
- Zoological Research Museum Alexander Koenig, Centre of Taxonomy and Evolutionary Research, Adenauerallee 160, 53113 Bonn, Germany
- Department of Life and Environmental Sciences, Botany Division, University of Cagliari, viale Sant’Ignazio da Laconi 13, 09123, Cagliari (CA), Italy
| | - Silvia Fabrizi
- Zoological Research Museum Alexander Koenig, Centre of Taxonomy and Evolutionary Research, Adenauerallee 160, 53113 Bonn, Germany
| | - Michele Rossini
- Zoological Research Museum Alexander Koenig, Centre of Taxonomy and Evolutionary Research, Adenauerallee 160, 53113 Bonn, Germany
- Strada dei Guazzi, 1/3, 61122 Pesaro (PU), Italy
| | - Mariastella Colomba
- Università di Urbino, Dipartimento di Scienze Biomolecolari (DiSB), Via maggetti 22, 61029 Urbino (PU), Italy
| | | | - Marco Uliana
- Museo di Storia Naturale, Santa Croce 1730, 30135 Venezia, Italy
| | | | - Guido Sabatinelli
- Muséum d’Histoire Naturelle, Route de Malagnou 1, 1208 Geneva, Switzerland
| | | | - Giuseppe Carpaneto
- Dipartimento di Scienze, Università Roma Tre, Viale Marconi 446, 00146 Roma, Italy
| | - Dirk Ahrens
- Zoological Research Museum Alexander Koenig, Centre of Taxonomy and Evolutionary Research, Adenauerallee 160, 53113 Bonn, Germany
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Morin PA, Foote AD, Baker CS, Hancock‐Hanser BL, Kaschner K, Mate BR, Mesnick SL, Pease VL, Rosel PE, Alexander A. Demography or selection on linked cultural traits or genes? Investigating the driver of low mtDNA diversity in the sperm whale using complementary mitochondrial and nuclear genome analyses. Mol Ecol 2018; 27:2604-2619. [DOI: 10.1111/mec.14698] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 03/26/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Phillip A. Morin
- Southwest Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration La Jolla California
| | - Andrew D. Foote
- Molecular Ecology and Fisheries Genetics Laboratory School of Biological Sciences Bangor University Bangor Gwynedd UK
| | - Charles Scott Baker
- Marine Mammal Institute Hatfield Marine Science Center Oregon State University Newport Oregon
- Department of Fisheries and Wildlife College of Agricultural Sciences Corvallis Oregon
| | - Brittany L. Hancock‐Hanser
- Southwest Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration La Jolla California
| | - Kristin Kaschner
- Department of Biometry and Environmental System Analysis Albert‐Ludwigs‐University of Freiburg Freiburg Germany
| | - Bruce R. Mate
- Marine Mammal Institute Hatfield Marine Science Center Oregon State University Newport Oregon
- Department of Fisheries and Wildlife College of Agricultural Sciences Corvallis Oregon
| | - Sarah L. Mesnick
- Southwest Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration La Jolla California
| | - Victoria L. Pease
- Southwest Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration La Jolla California
| | - Patricia E. Rosel
- Southeast Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration Lafayette Louisiana
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10
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Pace DS, Arcangeli A, Mussi B, Vivaldi C, Ledon C, Lagorio S, Giacomini G, Pavan G, Ardizzone G. Habitat suitability modeling in different sperm whale social groups. J Wildl Manage 2018. [DOI: 10.1002/jwmg.21453] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Daniela Silvia Pace
- Department of Environmental Biology; Sapienza University of Rome, Italy; Oceanomare Delphis Onlus, Viale delle Rimembranze 14; Rimini 47924 Italy
| | | | - Barbara Mussi
- Oceanomare Delphis Onlus; Viale delle Rimembranze 14; Rimini 47924 Italy
| | - Carlotta Vivaldi
- Oceanomare Delphis Onlus; Viale delle Rimembranze 14; Rimini 47924 Italy
| | - Cristina Ledon
- Halmos College of Natural Sciences and Oceanography; Nova Southeastern University; FL USA
| | - Serena Lagorio
- Department of Life and Environmental Sciences; Marche Polytechnic University; Ancona Italy
| | | | - Gianni Pavan
- Department of Earth and Environmental Sciences; CIBRA, University of Pavia; Italy
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11
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Vachon F, Whitehead H, Frasier TR. What factors shape genetic diversity in cetaceans? Ecol Evol 2018; 8:1554-1572. [PMID: 29435232 PMCID: PMC5792597 DOI: 10.1002/ece3.3727] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 11/07/2017] [Accepted: 11/20/2017] [Indexed: 01/01/2023] Open
Abstract
Understanding what factors drive patterns of genetic diversity is a central aspect of many biological questions, ranging from the inference of historical demography to assessing the evolutionary potential of a species. However, as a larger number of datasets have become available, it is becoming clear that the relationship between the characteristics of a species and its genetic diversity is more complex than previously assumed. This may be particularly true for cetaceans, due to their relatively long lifespans, long generation times, complex social structures, and extensive ranges. In this study, we used microsatellite and mitochondrial DNA data from a systematic literature review to produce estimates of diversity for both markers across 42 cetacean species. Factors relating to demography, distribution, classification, biology, and behavior were then tested using phylogenetic methods and linear models to assess their relative influence on the genetic diversity of both marker types. The results show that while relative nuclear diversity is correlated with population size, mitochondrial diversity is not. This is particularly relevant given the widespread use of mitochondrial DNA to infer historical demography. Instead, mitochondrial diversity was mostly influenced by the range and social structure of the species. In addition to population size, habitat type (neritic vs. oceanic) had a significant correlation with relative nuclear diversity. Combined, these results show that many often-unconsidered factors are likely influencing patterns of genetic diversity in cetaceans, with implications regarding how to interpret, and what can be inferred from, existing patterns of diversity.
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Affiliation(s)
- Felicia Vachon
- Department of BiologyDalhousie UniversityHalifaxNSCanada
| | - Hal Whitehead
- Department of BiologyDalhousie UniversityHalifaxNSCanada
| | - Timothy R. Frasier
- Department of Biology and Forensic Sciences ProgrammeSaint Mary's UniversityHalifaxNSCanada
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12
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Autenrieth M, Ernst A, Deaville R, Demaret F, IJsseldijk LL, Siebert U, Tiedemann R. Putative origin and maternal relatedness of male sperm whales (Physeter macrocephalus) recently stranded in the North Sea. Mamm Biol 2018. [DOI: 10.1016/j.mambio.2017.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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13
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Gariboldi MC, Túnez JI, Failla M, Hevia M, Panebianco MV, Paso Viola MN, Vitullo AD, Cappozzo HL. Patterns of population structure at microsatellite and mitochondrial DNA markers in the franciscana dolphin ( Pontoporia blainvillei). Ecol Evol 2016; 6:8764-8776. [PMID: 28035267 PMCID: PMC5192793 DOI: 10.1002/ece3.2596] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 10/07/2016] [Accepted: 10/19/2016] [Indexed: 12/25/2022] Open
Abstract
The franciscana dolphin, Pontorporia blainvillei, is an endemic cetacean of the Atlantic coast of South America. Its coastal distribution and restricted movement patterns make this species vulnerable to anthropogenic factors, particularly to incidental bycatch. We used mitochondrial DNA control region sequences, 10 microsatellites, and sex data to investigate the population structure of the franciscana dolphin from a previously established management area, which includes the southern edge of its geographic range. F‐statistics and Bayesian cluster analyses revealed the existence of three genetically distinct populations. Based on the microsatellite loci, similar levels of genetic variability were found in the area; 13 private alleles were found in Monte Hermoso, but none in Claromecó. When considering the mitochondrial DNA control region sequences, lower levels of genetic diversity were found in Monte Hermoso, when compared to the other localities. Low levels of gene flow were found between most localities. Additionally, no evidence of isolation by distance nor sex‐biased dispersal was detected in the study area. In view of these results showing that populations from Necochea/Claromecó, Monte Hermoso, and Río Negro were found to be genetically distinct and the available genetic information for the species previously published, Argentina would comprise five distinct populations: Samborombón West/Samborombón South, Cabo San Antonio/Buenos Aires East, Necochea/Claromecó/Buenos Aires Southwest, Monte Hermoso, and Río Negro. In order to ensure the long‐term survival of the franciscana dolphin, management and conservation strategies should be developed considering each of these populations as different management units.
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Affiliation(s)
- María Constanza Gariboldi
- Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnóstico (CEBBAD) Universidad MaimónidesCiudad Autónoma de Buenos Aires Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Ciudad Autónoma de Buenos Aires Argentina
| | - Juan Ignacio Túnez
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Ciudad Autónoma de Buenos Aires Argentina; Grupo de Estudios en Ecología de Mamíferos Departamento de Ciencias Básicas Universidad Nacional de Luján Luján Argentina
| | | | | | - María Victoria Panebianco
- Laboratorio de Ecología Comportamiento y Mamíferos Marinos Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" Ciudad Autónoma de Buenos Aires Argentina
| | - María Natalia Paso Viola
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Ciudad Autónoma de Buenos Aires Argentina; Laboratorio de Ecología Comportamiento y Mamíferos Marinos Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" Ciudad Autónoma de Buenos Aires Argentina; Laboratorio de Ecología y Conservación de Vida Silvestre Centro Austral de Investigaciones Científicas (CADIC) Ushuaia Argentina
| | - Alfredo Daniel Vitullo
- Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnóstico (CEBBAD) Universidad MaimónidesCiudad Autónoma de Buenos Aires Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Ciudad Autónoma de Buenos Aires Argentina
| | - Humberto Luis Cappozzo
- Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnóstico (CEBBAD) Universidad Maimónides Ciudad Autónoma de Buenos Aires Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Ciudad Autónoma de Buenos Aires Argentina; Laboratorio de Ecología Comportamiento y Mamíferos Marinos Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" Ciudad Autónoma de Buenos Aires Argentina; Fundación de Historia Natural Félix de Azara Universidad Maimónides Ciudad Autónoma de Buenos Aires Argentina
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14
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Baltazar-Soares M, Eizaguirre C. Does asymmetric gene flow among matrilines maintain the evolutionary potential of the European eel? Ecol Evol 2016; 6:5305-20. [PMID: 27551384 PMCID: PMC4984505 DOI: 10.1002/ece3.2098] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 03/02/2016] [Accepted: 03/03/2016] [Indexed: 01/14/2023] Open
Abstract
Using evolutionary theory to predict the dynamics of populations is one of the aims of evolutionary conservation. In endangered species, with geographic range extending over continuous areas, the predictive capacity of evolutionary-based conservation measures greatly depends on the accurate identification of reproductive units. The endangered European eel (Anguilla anguilla) is a highly migratory fish species with declining population due to a steep recruitment collapse in the beginning of the 1980s. Despite punctual observations of genetic structure, the population is viewed as a single panmictic reproductive unit. To understand the possible origin of the detected structure in this species, we used a combination of mitochondrial and nuclear loci to indirectly evaluate the possible existence of cryptic demes. For that, 403 glass eels from three successive cohorts arriving at a single location were screened for phenotypic and genetic diversity, while controlling for possible geographic variation. Over the 3 years of sampling, we consistently identified three major matrilines which we hypothesized to represent demes. Interestingly, not only we found that population genetic models support the existence of those matriline-driven demes over a completely panmictic mode of reproduction, but also we found evidence for asymmetric gene flow amongst those demes. We uphold the suggestion that the detection of demes related to those matrilines reflect a fragmented spawning ground, a conceptually plausible consequence of the low abundance that the European eel has been experiencing for three decades. Furthermore, we suggest that this cryptic organization may contribute to the maintenance of the adaptive potential of the species.
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Affiliation(s)
- Miguel Baltazar-Soares
- GEOMAR Helmholtz Centre for Ocean Research Kiel Düsternbrooker Weg 20 24105 Kiel Germany
| | - Christophe Eizaguirre
- GEOMAR Helmholtz Centre for Ocean Research Kiel Düsternbrooker Weg 20 24105 Kiel Germany; School of Biological and Chemical Sciences Queen Mary University of London Mile End Road LondonE1 4NS UK
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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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Fais A, Lewis TP, Zitterbart DP, Álvarez O, Tejedor A, Aguilar Soto N. Abundance and Distribution of Sperm Whales in the Canary Islands: Can Sperm Whales in the Archipelago Sustain the Current Level of Ship-Strike Mortalities? PLoS One 2016; 11:e0150660. [PMID: 26999791 PMCID: PMC4801403 DOI: 10.1371/journal.pone.0150660] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 02/16/2016] [Indexed: 12/02/2022] Open
Abstract
Sperm whales are present in the Canary Islands year-round, suggesting that the archipelago is an important area for this species in the North Atlantic. However, the area experiences one of the highest reported rates of sperm whale ship-strike in the world. Here we investigate if the number of sperm whales found in the archipelago can sustain the current rate of ship-strike mortality. The results of this study may also have implications for offshore areas where concentrations of sperm whales may coincide with high densities of ship traffic, but where ship-strikes may be undocumented. The absolute abundance of sperm whales in an area of 52933 km2, covering the territorial waters of the Canary Islands, was estimated from 2668 km of acoustic line-transect survey using Distance sampling analysis. Data on sperm whale diving and acoustic behaviour, obtained from bio-logging, were used to calculate g(0) = 0.92, this is less than one because of occasional extended periods when whales do not echolocate. This resulted in an absolute abundance estimate of 224 sperm whales (95% log-normal CI 120–418) within the survey area. The recruitment capability of this number of whales, some 2.5 whales per year, is likely to be exceeded by the current ship-strike mortality rate. Furthermore, we found areas of higher whale density within the archipelago, many coincident with those previously described, suggesting that these are important habitats for females and immature animals inhabiting the archipelago. Some of these areas are crossed by active shipping lanes increasing the risk of ship-strikes. Given the philopatry in female sperm whales, replacement of impacted whales might be limited. Therefore, the application of mitigation measures to reduce the ship-strike mortality rate seems essential for the conservation of sperm whales in the Canary Islands.
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Affiliation(s)
- Andrea Fais
- Biodiversidad, Ecología Marina y Conservación (BIOECOMAC), Dept. Animal Biology, Geology and Edaphology, La Laguna University, Tenerife, Canary Islands, Spain
- * E-mail:
| | - Tim P. Lewis
- Biodiversidad, Ecología Marina y Conservación (BIOECOMAC), Dept. Animal Biology, Geology and Edaphology, La Laguna University, Tenerife, Canary Islands, Spain
| | - Daniel P. Zitterbart
- Ocean Acoustics Lab, Alfred-Wegener-Institut Helmholtz-Zentrum für Polar-und Meeresforschung, Bremerhaven, Germany
- Applied Ocean Physics and Engineering, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United States of America
| | - Omar Álvarez
- Biodiversidad, Ecología Marina y Conservación (BIOECOMAC), Dept. Animal Biology, Geology and Edaphology, La Laguna University, Tenerife, Canary Islands, Spain
- CIMA Canarias, Avda. Los Majuelos 115, 38107 Santa Cruz de Tenerife, Tenerife, Canary Islands, Spain
| | - Ana Tejedor
- KAI Marine Services, Nalon 16, 28240, Hoyo de Manzanares, Madrid, Spain
| | - Natacha Aguilar Soto
- Biodiversidad, Ecología Marina y Conservación (BIOECOMAC), Dept. Animal Biology, Geology and Edaphology, La Laguna University, Tenerife, Canary Islands, Spain
- CREEM, Centre for Research into Ecological and Environmental Modelling, Scottish Oceans Institute, University of St. Andrews, St Andrews, Scotland
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Driller C, Merker S, Perwitasari-Farajallah D, Sinaga W, Anggraeni N, Zischler H. Stop and Go - Waves of Tarsier Dispersal Mirror the Genesis of Sulawesi Island. PLoS One 2015; 10:e0141212. [PMID: 26559527 PMCID: PMC4641617 DOI: 10.1371/journal.pone.0141212] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 10/05/2015] [Indexed: 11/18/2022] Open
Abstract
The Indonesian island of Sulawesi harbors a highly endemic and diverse fauna sparking fascination since long before Wallace’s contemplation of biogeographical patterns in the region. Allopatric diversification driven by geological or climatic processes has been identified as the main mechanism shaping present faunal distribution on the island. There is both consensus and conflict among range patterns of terrestrial species pointing to the different effects of vicariant events on once co-distributed taxa. Tarsiers, small nocturnal primates with possible evidence of an Eocene fossil record on the Asian mainland, are at present exclusively found in insular Southeast Asia. Sulawesi is hotspot of tarsier diversity, whereby island colonization and subsequent radiation of this old endemic primate lineage remained largely enigmatic. To resolve the phylogeographic history of Sulawesi tarsiers we analyzed an island-wide sample for a set of five approved autosomal phylogenetic markers (ABCA1, ADORA3, AXIN1, RAG1, and TTR) and the paternally inherited SRY gene. We constructed ML and Bayesian phylogenetic trees and estimated divergence times between tarsier populations. We found that their arrival at the Proto-Sulawesi archipelago coincided with initial Miocene tectonic uplift and hypothesize that tarsiers dispersed over the region in distinct waves. Intra-island diversification was spurred by land emergence and a rapid succession of glacial cycles during the Plio-Pleistocene. Some tarsier range boundaries concur with spatial limits in other taxa backing the notion of centers of faunal endemism on Sulawesi. This congruence, however, has partially been superimposed by taxon-specific dispersal patterns.
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Affiliation(s)
- Christine Driller
- Institute of Anthropology, Johannes-Gutenberg University Mainz, Mainz, Germany
- * E-mail:
| | - Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart, Stuttgart, Germany
| | - Dyah Perwitasari-Farajallah
- Primate Research Center, Bogor Agricultural University, Bogor, Indonesia
- Department of Biology, Bogor Agricultural University, Bogor, Indonesia
| | - Walberto Sinaga
- Primate Research Center, Bogor Agricultural University, Bogor, Indonesia
| | - Novita Anggraeni
- School of Graduate Studies, Bogor Agricultural University, Bogor, Indonesia
| | - Hans Zischler
- Institute of Anthropology, Johannes-Gutenberg University Mainz, Mainz, Germany
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Andrews KR, Norton EL, Fernandez-Silva I, Portner E, Goetze E. Multilocus evidence for globally distributed cryptic species and distinct populations across ocean gyres in a mesopelagic copepod. Mol Ecol 2015; 23:5462-79. [PMID: 25283587 DOI: 10.1111/mec.12950] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 09/17/2014] [Accepted: 09/23/2014] [Indexed: 11/29/2022]
Abstract
Zooplanktonic taxa have a greater number of distinct populations and species than might be predicted based on their large population sizes and open-ocean habitat, which lacks obvious physical barriers to dispersal and gene flow. To gain insight into the evolutionary mechanisms driving genetic diversification in zooplankton, we developed eight microsatellite markers to examine the population structure of an abundant, globally distributed mesopelagic copepod, Haloptilus longicornis, at 18 sample sites across the Atlantic and Pacific Oceans (n = 761). When comparing our microsatellite results with those of a prior study that used a mtDNA marker (mtCOII, n = 1059, 43 sample sites), we unexpectedly found evidence for the presence of a cryptic species pair. These species were globally distributed and apparently sympatric, and were separated by relatively weak genetic divergence (reciprocally monophyletic mtCOII lineages 1.6% divergent; microsatellite FST ranging from 0.28 to 0.88 across loci, P < 0.00001). Using both mtDNA and microsatellite data for the most common of the two species (n = 669 for microsatellites, n = 572 for mtDNA), we also found evidence for allopatric barriers to gene flow within species, with distinct populations separated by continental landmasses and equatorial waters in both the Atlantic and Pacific Ocean basins. Our study shows that oceanic barriers to gene flow can act as a mechanism promoting allopatric diversification in holoplanktonic taxa, despite the high potential dispersal abilities and pelagic habitat for these species.
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Affiliation(s)
- Kimberly R Andrews
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA; School of Biological and Biomedical Sciences, Durham University, South Road, Durham, DH1 3LE, UK
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20
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Torres-Florez JP, Hucke-Gaete R, LeDuc R, Lang A, Taylor B, Pimper LE, Bedriñana-Romano L, Rosenbaum HC, Figueroa CC. Blue whale population structure along the eastern South Pacific Ocean: evidence of more than one population. Mol Ecol 2014; 23:5998-6010. [DOI: 10.1111/mec.12990] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 10/24/2014] [Accepted: 10/24/2014] [Indexed: 11/29/2022]
Affiliation(s)
- J. P. Torres-Florez
- Instituto de Ciencias Ambientales y Evolutivas; Universidad Austral de Chile; Casilla 567 Valdivia Chile
- Centro Ballena Azul/Blue Whale Center; Pamplona 58 Silos de Torobayo Valdivia Chile
| | - R. Hucke-Gaete
- Centro Ballena Azul/Blue Whale Center; Pamplona 58 Silos de Torobayo Valdivia Chile
- Instituto de Ciencias Marinas y Limnológicas; Universidad Austral de Chile; Casilla 567 Valdivia Chile
| | - R. LeDuc
- Marine Mammal and Turtle Division; Southwest Fisheries Science Center; National Marine Fisheries Service; NOAA; 8901 La Jolla Shores Drive La Jolla CA USA
| | - A. Lang
- Marine Mammal and Turtle Division; Southwest Fisheries Science Center; National Marine Fisheries Service; NOAA; 8901 La Jolla Shores Drive La Jolla CA USA
| | - B. Taylor
- Marine Mammal and Turtle Division; Southwest Fisheries Science Center; National Marine Fisheries Service; NOAA; 8901 La Jolla Shores Drive La Jolla CA USA
| | - L. E. Pimper
- Lab. de Genética de la Estructura Poblacional; Depto. de Ecología; Genética y Evolución; Ciudad Universitaria, Pabellón II, 4to. piso; FCEN; Universidad de Buenos Aires; Buenos Aires Argentina
| | - L. Bedriñana-Romano
- Centro Ballena Azul/Blue Whale Center; Pamplona 58 Silos de Torobayo Valdivia Chile
- Instituto de Ciencias Marinas y Limnológicas; Universidad Austral de Chile; Casilla 567 Valdivia Chile
| | - H. C. Rosenbaum
- Ocean Giants Program; Wildlife Conservation Society; 2300 Southern Blvd Bronx NY 10460 USA
- Sackler Institute for Comparative Genomics; American Museum of Natural History; Central Park West at 79th Street New York NY 10024-5192 USA
| | - C. C. Figueroa
- Instituto de Ciencias Biológicas; Universidad de Talca; 2 Norte 685 Talca Chile
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Burns LE, Frasier TR, Broders HG. Genetic connectivity among swarming sites in the wide ranging and recently declining little brown bat (Myotis lucifugus). Ecol Evol 2014; 4:4130-49. [PMID: 25505539 PMCID: PMC4242565 DOI: 10.1002/ece3.1266] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 08/29/2014] [Accepted: 09/03/2014] [Indexed: 01/29/2023] Open
Abstract
Characterizing movement dynamics and spatial aspects of gene flow within a species permits inference on population structuring. As patterns of structuring are products of historical and current demographics and gene flow, assessment of structure through time can yield an understanding of evolutionary dynamics acting on populations that are necessary to inform management. Recent dramatic population declines in hibernating bats in eastern North America from white-nose syndrome have prompted the need for information on movement dynamics for multiple bat species. We characterized population genetic structure of the little brown bat, Myotis lucifugus, at swarming sites in southeastern Canada using 9 nuclear microsatellites and a 292-bp region of the mitochondrial genome. Analyses of F ST, ΦST, and Bayesian clustering (STRUCTURE) found weak levels of genetic structure among swarming sites for the nuclear and mitochondrial genome (Global F ST = 0.001, P < 0.05, Global ΦST = 0.045, P < 0.01, STRUCTURE K = 1) suggesting high contemporary gene flow. Hierarchical AMOVA also suggests little structuring at a regional (provincial) level. Metrics of nuclear genetic structure were not found to differ between males and females suggesting weak asymmetries in gene flow between the sexes. However, a greater degree of mitochondrial structuring does support male-biased dispersal long term. Demographic analyses were consistent with past population growth and suggest a population expansion occurred from approximately 1250 to 12,500 BP, following Pleistocene deglaciation in the region. Our study suggests high gene flow and thus a high degree of connectivity among bats that visit swarming sites whereby mainland areas of the region may be best considered as one large gene pool for management and conservation.
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Affiliation(s)
- Lynne E Burns
- Department of Biology, Dalhousie University, Life Sciences Centre 1355 Oxford Street, Halifax, Nova Scotia, B3H 4J1, Canada
| | - Timothy R Frasier
- Department of Biology, Saint Mary's University 923 Robie Street, Halifax, Nova Scotia, B3H 3C3, Canada
| | - Hugh G Broders
- Department of Biology, Saint Mary's University 923 Robie Street, Halifax, Nova Scotia, B3H 3C3, Canada
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Investigating population genetic structure in a highly mobile marine organism: the minke whale Balaenoptera acutorostrata acutorostrata in the North East Atlantic. PLoS One 2014; 9:e108640. [PMID: 25268591 PMCID: PMC4182549 DOI: 10.1371/journal.pone.0108640] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 08/04/2014] [Indexed: 11/19/2022] Open
Abstract
Inferring the number of genetically distinct populations and their levels of connectivity is of key importance for the sustainable management and conservation of wildlife. This represents an extra challenge in the marine environment where there are few physical barriers to gene-flow, and populations may overlap in time and space. Several studies have investigated the population genetic structure within the North Atlantic minke whale with contrasting results. In order to address this issue, we analyzed ten microsatellite loci and 331 bp of the mitochondrial D-loop on 2990 whales sampled in the North East Atlantic in the period 2004 and 2007-2011. The primary findings were: (1) No spatial or temporal genetic differentiations were observed for either class of genetic marker. (2) mtDNA identified three distinct mitochondrial lineages without any underlying geographical pattern. (3) Nuclear markers showed evidence of a single panmictic population in the NE Atlantic according STRUCTURE's highest average likelihood found at K = 1. (4) When K = 2 was accepted, based on the Evanno's test, whales were divided into two more or less equally sized groups that showed significant genetic differentiation between them but without any sign of underlying geographic pattern. However, mtDNA for these individuals did not corroborate the differentiation. (5) In order to further evaluate the potential for cryptic structuring, a set of 100 in silico generated panmictic populations was examined using the same procedures as above showing genetic differentiation between two artificially divided groups, similar to the aforementioned observations. This demonstrates that clustering methods may spuriously reveal cryptic genetic structure. Based upon these data, we find no evidence to support the existence of spatial or cryptic population genetic structure of minke whales within the NE Atlantic. However, in order to conclusively evaluate population structure within this highly mobile species, more markers will be required.
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Patterns of genetic diversity in the polymorphic ground snake (Sonora semiannulata). Genetica 2014; 142:361-70. [DOI: 10.1007/s10709-014-9780-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 07/18/2014] [Indexed: 10/25/2022]
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Straley JM, Schorr GS, Thode AM, Calambokidis J, Lunsford CR, Chenoweth EM, O’Connell VM, Andrews RD. Depredating sperm whales in the Gulf of Alaska: local habitat use and long distance movements across putative population boundaries. ENDANGER SPECIES RES 2014. [DOI: 10.3354/esr00595] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Amano M, Kourogi A, Aoki K, Yoshioka M, Mori K. Differences in sperm whale codas between two waters off Japan: possible geographic separation of vocal clans. J Mammal 2014. [DOI: 10.1644/13-mamm-a-172] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Borrell A, Velásquez Vacca A, Pinela AM, Kinze C, Lockyer CH, Vighi M, Aguilar A. Stable isotopes provide insight into population structure and segregation in eastern North Atlantic sperm whales. PLoS One 2013; 8:e82398. [PMID: 24324782 PMCID: PMC3855748 DOI: 10.1371/journal.pone.0082398] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 11/01/2013] [Indexed: 12/02/2022] Open
Abstract
In pelagic species inhabiting large oceans, genetic differentiation tends to be mild and populations devoid of structure. However, large cetaceans have provided many examples of structuring. Here we investigate whether the sperm whale, a pelagic species with large population sizes and reputedly highly mobile, shows indication of structuring in the eastern North Atlantic, an ocean basin in which a single population is believed to occur. To do so, we examined stable isotope values in sequential growth layer groups of teeth from individuals sampled in Denmark and NW Spain. In each layer we measured oxygen- isotope ratios (δ18O) in the inorganic component (hydroxyapatite), and nitrogen and carbon isotope ratios (δ15N: δ13C) in the organic component (primarily collagenous). We found significant differences between Denmark and NW Spain in δ15N and δ18O values in the layer deposited at age 3, considered to be the one best representing the baseline of the breeding ground, in δ15N, δ13C and δ18O values in the period up to age 20, and in the ontogenetic variation of δ15N and δ18O values. These differences evidence that diet composition, use of habitat and/or migratory destinations are dissimilar between whales from the two regions and suggest that the North Atlantic population of sperm whales is more structured than traditionally accepted.
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Affiliation(s)
- Asunción Borrell
- Department of Animal Biology, Faculty of Biology and Biodiversity Research Institute (IRBio), University of Barcelona, Barcelona, Spain
- * E-mail:
| | - Adriana Velásquez Vacca
- Department of Animal Biology, Faculty of Biology and Biodiversity Research Institute (IRBio), University of Barcelona, Barcelona, Spain
| | - Ana M. Pinela
- Department of Animal Biology, Faculty of Biology and Biodiversity Research Institute (IRBio), University of Barcelona, Barcelona, Spain
| | - Carl Kinze
- Zoological Museum, University of Copenhagen, Copenhagen, Denmark
| | | | - Morgana Vighi
- Department of Animal Biology, Faculty of Biology and Biodiversity Research Institute (IRBio), University of Barcelona, Barcelona, Spain
| | - Alex Aguilar
- Department of Animal Biology, Faculty of Biology and Biodiversity Research Institute (IRBio), University of Barcelona, Barcelona, Spain
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Gero S, Gordon J, Whitehead H. Calves as social hubs: dynamics of the social network within sperm whale units. Proc Biol Sci 2013; 280:20131113. [PMID: 23740785 DOI: 10.1098/rspb.2013.1113] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
It is hypothesized that the primary function of permanent social relationships among female sperm whales (Physeter macrocephalus) is to provide allomothers for calves at the surface while mothers make foraging dives. In order to investigate how reciprocity of allocare within units of sperm whales facilitates group living, we constructed weighted social networks based on yearly matrices of associations (2005-2010) and correlated them across years, through changes in age and social role, to study changes in social relationships within seven sperm whale units. Pairs of association matrices from sequential years showed a greater positive correlation than expected by chance, but as the time lag increased, the correlation coefficients decreased. Over all units considered, calves had high values for all measured network statistics, while mothers had intermediate values for most of the measures, but high values for connectedness and affinity. Mothers showed sharp drops in strength and connectedness in the first year of their new calves' lives. These broad patterns appear to be consistent across units. Calves appeared to be significant nodes in the network of the social unit, and thus provide quantitative support for the theory in which communal care acts as the evolutionary force behind group formation in this species.
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Affiliation(s)
- Shane Gero
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada, Sea Mammal Research Unit, University of St Andrew's, Fife, UK.
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Costa-Urrutia P, Sanvito S, Victoria-Cota N, Enríquez-Paredes L, Gendron D. Fine-scale population structure of blue whale wintering aggregations in the Gulf of California. PLoS One 2013; 8:e58315. [PMID: 23505485 PMCID: PMC3591444 DOI: 10.1371/journal.pone.0058315] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 02/01/2013] [Indexed: 12/21/2022] Open
Abstract
Population differentiation in environments without well-defined geographical barriers represents a challenge for wildlife management. Based on a comprehensive database of individual sighting records (1988–2009) of blue whales from the winter/calving Gulf of California, we assessed the fine-scale genetic and spatial structure of the population using individual-based approaches. Skin samples of 187 individuals were analyzed for nine microsatellite loci. A single population with no divergence among years and months and no isolation by distance (Rxy = 0.1–0.001, p>0.05) were found. We ran two Bayesian clustering methods using Structure and Geneland softwares in two different ways: 1) a general analysis including all individuals in which a single cluster was identified with both softwares; 2) a specific analysis of females only in which two main clusters (Loreto Bay and northern areas, and San Jose-La Paz Bay area) were revealed by Geneland program. This study provides information indicating that blue whales wintering in the Gulf of California are part of a single population unit and showed a fine-scale structure among females, possibly associated with their high site fidelity, particularly when attending calves. It is likely that the loss of genetic variation is minimized by male mediated gene flow, which may reduce the genetic drift effect. Opportunities for kin selection may also influence calf survival and, in consequence, have a positive impact on population demography in this small and endangered population.
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Affiliation(s)
- Paula Costa-Urrutia
- Laboratorio de Ecología Molecular, Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Baja California, Mexico
| | - Simona Sanvito
- Laboratorio de Ecología Molecular, Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Baja California, Mexico
- Elephant Seal Research Group, Sea Lion Island, Falkland Islands
| | - Nelva Victoria-Cota
- Laboratorio de Ecología y Epidemiología Molecular, Escuela de Ciencias de la Salud, Universidad Autónoma de Baja California, Baja California, Mexico
| | - Luis Enríquez-Paredes
- Laboratorio de Ecología Molecular, Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Baja California, Mexico
| | - Diane Gendron
- Laboratorio de Ecología de Cetáceos y Quelonios, Centro Interdisciplinario de Ciencias Marinas, Instituto Politécnico Nacional, Mexico City, Mexico
- * E-mail:
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Satizábal P, Mignucci-Giannoni AA, Duchêne S, Caicedo-Herrera D, Perea-Sicchar CM, García-Dávila CR, Trujillo F, Caballero SJ. Phylogeography and sex-biased dispersal across riverine manatee populations (Trichechus inunguis and Trichechus manatus) in South America. PLoS One 2012; 7:e52468. [PMID: 23285054 PMCID: PMC3527500 DOI: 10.1371/journal.pone.0052468] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 11/13/2012] [Indexed: 11/23/2022] Open
Abstract
Phylogeographic patterns and sex-biased dispersal were studied in riverine populations of West Indian (Trichechus manatus) and Amazonian manatees (T. inunguis) in South America, using 410bp D-loop (Control Region, Mitochondrial DNA) sequences and 15 nuclear microsatellite loci. This multi-locus approach was key to disentangle complex patterns of gene flow among populations. D-loop analyses revealed population structuring among all Colombian rivers for T. manatus, while microsatellite data suggested no structure. Two main populations of T. inunguis separating the Colombian and Peruvian Amazon were supported by analysis of the D-loop and microsatellite data. Overall, we provide molecular evidence for differences in dispersal patterns between sexes, demonstrating male-biased gene flow dispersal in riverine manatees. These results are in contrast with previously reported levels of population structure shown by microsatellite data in marine manatee populations, revealing low habitat restrictions to gene flow in riverine habitats, and more significant dispersal limitations for males in marine environments.
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Affiliation(s)
- Paula Satizábal
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos-LEMVA, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia.
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Elizabeth Alter S, Rosenbaum HC, Postma LD, Whitridge P, Gaines C, Weber D, Egan MG, Lindsay M, Amato G, Dueck L, Brownell RL, Heide-Jørgensen MP, Laidre KL, Caccone G, Hancock BL. Gene flow on ice: the role of sea ice and whaling in shaping Holarctic genetic diversity and population differentiation in bowhead whales (Balaena mysticetus). Ecol Evol 2012; 2:2895-911. [PMID: 23170222 PMCID: PMC3501639 DOI: 10.1002/ece3.397] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 08/21/2012] [Accepted: 08/27/2012] [Indexed: 11/10/2022] Open
Abstract
Sea ice is believed to be a major factor shaping gene flow for polar marine organisms, but it remains unclear to what extent it represents a true barrier to dispersal for arctic cetaceans. Bowhead whales are highly adapted to polar sea ice and were targeted by commercial whalers throughout Arctic and subarctic seas for at least four centuries, resulting in severe reductions in most areas. Both changing ice conditions and reductions due to whaling may have affected geographic distribution and genetic diversity throughout their range, but little is known about range-wide genetic structure or whether it differed in the past. This study represents the first examination of genetic diversity and differentiation across all five putative stocks, including Baffin Bay-Davis Strait, Hudson Bay-Foxe Basin, Bering-Beaufort-Chukchi, Okhotsk, and Spitsbergen. We also utilized ancient specimens from Prince Regent Inlet (PRI) in the Canadian Arctic and compared them with modern stocks. Results from analysis of molecular variance and demographic simulations are consistent with recent and high gene flow between Atlantic and Pacific stocks in the recent past. Significant genetic differences between ancient and modern populations suggest PRI harbored unique maternal lineages in the past that have been recently lost, possibly due to loss of habitat during the Little Ice Age and/or whaling. Unexpectedly, samples from this location show a closer genetic relationship with modern Pacific stocks than Atlantic, supporting high gene flow between the central Canadian Arctic and Beaufort Sea over the past millennium despite extremely heavy ice cover over much of this period.
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Affiliation(s)
- S Elizabeth Alter
- Department of Biology, York College, City University of New York 94-20 Guy R. Brewer Blvd, Jamaica, New York, 11415 ; CUNY Graduate Center, 365 Fifth Avenue New York city, New York, 10016 ; American Museum of Natural History, Sackler Institute for Comparative Genomics 79th St and Central Park West, New York city, New York, 10024
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CARROLL EMMAL, CHILDERHOUSE SIMONJ, CHRISTIE MARK, LAVERY SHANE, PATENAUDE NATHALIE, ALEXANDER ALANA, CONSTANTINE ROCHELLE, STEEL DEBBIE, BOREN LAURA, SCOTT BAKER C. Paternity assignment and demographic closure in the New Zealand southern right whale. Mol Ecol 2012; 21:3960-73. [DOI: 10.1111/j.1365-294x.2012.05676.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Mitochondrial DNA paradox: sex-specific genetic structure in a marine mussel--despite maternal inheritance and passive dispersal. BMC Genet 2012; 13:45. [PMID: 22694765 PMCID: PMC3465189 DOI: 10.1186/1471-2156-13-45] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 06/13/2012] [Indexed: 12/29/2022] Open
Abstract
Background When genetic structure is identified using mitochondrial DNA (mtDNA), but no structure is identified using biparentally-inherited nuclear DNA, the discordance is often attributed to differences in dispersal potential between the sexes. Results We sampled the intertidal rocky shore mussel Perna perna in a South African bay and along the nearby open coast, and sequenced maternally-inherited mtDNA (there is no evidence for paternally-inherited mtDNA in this species) and a biparentally-inherited marker. By treating males and females as different populations, we identified significant genetic structure on the basis of mtDNA data in the females only. Conclusions This is the first study to report sex-specific differences in genetic structure based on matrilineally-inherited mtDNA in a passively dispersing species that lacks social structure or sexual dimorphism. The observed pattern most likely stems from females being more vulnerable to selection in habitats from which they did not originate, which also manifests itself in a male-biased sex ratio. Our results have three important implications for the interpretation of population genetic data. First, even when mtDNA is inherited exclusively in the female line, it also contains information about males. For that reason, using it to identify sex-specific differences in genetic structure by contrasting it with biparentally-inherited markers is problematic. Second, the fact that sex-specific differences were found in a passively dispersing species in which sex-biased dispersal is unlikely highlights the fact that significant genetic structure is not necessarily a function of low dispersal potential or physical barriers. Third, even though mtDNA is typically used to study historical demographic processes, it also contains information about contemporary processes. Higher survival rates of males in non-native habitats can erase the genetic structure present in their mothers within a single generation.
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Karl SA, Toonen RJ, Grant WS, Bowen BW. Common misconceptions in molecular ecology: echoes of the modern synthesis. Mol Ecol 2012; 21:4171-89. [PMID: 22574714 DOI: 10.1111/j.1365-294x.2012.05576.x] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The field of molecular ecology has burgeoned into a large discipline spurred on by technical innovations that facilitate the rapid acquisition of large amounts of genotypic data, by the continuing development of theory to interpret results, and by the availability of computer programs to analyse data sets. As the discipline grows, however, misconceptions have become enshrined in the literature and are perpetuated by routine citations to other articles in molecular ecology. These misconceptions hamper a better understanding of the processes that influence genetic variation in natural populations and sometimes lead to erroneous conclusions. Here, we consider eight misconceptions commonly appearing in the literature: (i) some molecular markers are inherently better than other markers; (ii) mtDNA produces higher F(ST) values than nDNA; (iii) estimated population coalescences are real; (iv) more data are always better; (v) one needs to do a Bayesian analysis; (vi) selective sweeps influence mtDNA data; (vii) equilibrium conditions are critical for estimating population parameters; and (viii) having better technology makes us smarter than our predecessors. This is clearly not an exhaustive list and many others can be added. It is, however, sufficient to illustrate why we all need to be more critical of our own understanding of molecular ecology and to be suspicious of self-evident truths.
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Affiliation(s)
- Stephen A Karl
- Hawai'i Institute of Marine Biology, University of Hawai'i, Mānoa, Kāne'ohe, HI 96744, USA.
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Portnoy DS, Heist EJ. Molecular markers: progress and prospects for understanding reproductive ecology in elasmobranchs. JOURNAL OF FISH BIOLOGY 2012; 80:1120-40. [PMID: 22497375 DOI: 10.1111/j.1095-8649.2011.03206.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Application of modern molecular tools is expanding the understanding of elasmobranch reproductive ecology. High-resolution molecular markers provide information at scales ranging from the identification of reproductively isolated populations in sympatry (i.e. cryptic species) to the relationships among parents, offspring and siblings. This avenue of study has not only augmented the current understanding of the reproductive biology of elasmobranchs but has also provided novel insights that could not be obtained through experimental or observational techniques. Sharing of genetic polymorphisms across ocean basins indicates that for some species there may be gene flow on global scales. The presence, however, of morphologically similar but genetically distinct entities in sympatry suggests that reproductive isolation can occur with minimal morphological differentiation. This review discusses the recent findings in elasmobranch reproductive biology like philopatry, hybridization and polyandry while highlighting important molecular and analytical techniques. Furthermore, the review examines gaps in current knowledge and discusses how new technologies may be applied to further the understanding of elasmobranch reproductive ecology.
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Affiliation(s)
- D S Portnoy
- Department of Wildlife and Fisheries Sciences, Center for Biosystematics and Biodiversity, Texas A&M University, College Station, TX 77843-2258, USA.
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Whitehead H, Antunes R, Gero S, Wong SNP, Engelhaupt D, Rendell L. Multilevel Societies of Female Sperm Whales (Physeter macrocephalus) in the Atlantic and Pacific: Why Are They So Different? INT J PRIMATOL 2012. [DOI: 10.1007/s10764-012-9598-z] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Can genetic differences explain vocal dialect variation in sperm whales, Physeter macrocephalus? Behav Genet 2011; 42:332-43. [PMID: 22015469 DOI: 10.1007/s10519-011-9513-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Accepted: 10/13/2011] [Indexed: 10/16/2022]
Abstract
Sperm whale social groups can be assigned to vocal clans based on their production of codas, short stereotyped patterns of clicks. It is currently unclear whether genetic variation could account for these behavioural differences. We studied mitochondrial DNA (mtDNA) variation among sympatric vocal clans in the Pacific Ocean, using sequences extracted from sloughed skin samples. We sampled 194 individuals from 30 social groups belonging to one of three vocal clans. As in previous studies of sperm whales, mtDNA control region diversity was low (π = 0.003), with just 14 haplotypes present in our sample. Both hierarchical AMOVAs and partial Mantel tests showed that vocal clan was a more important factor in matrilineal population genetic structure than geography, even though our sampling spanned thousands of kilometres. The variance component attributed to vocal dialects (7.7%) was an order of magnitude higher than those previously reported in birds, while the variance component attributed to geographic area was negligible. Despite this, the two most common haplotypes were present in significant quantities in each clan, meaning that variation in the control region cannot account for behavioural variation between clans, and instead parallels the situation in humans where parent-offspring transmission of language variation has resulted in correlations with neutral genes. Our results also raise questions for the management of sperm whale populations, which has traditionally been based on dividing populations into geographic 'stocks', suggesting that culturally-defined vocal clans may be more appropriate management units.
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MESNICK SARAHL, TAYLOR BARBARAL, ARCHER FREDERICKI, MARTIEN KARENK, TREVIÑO SERGIOESCORZA, HANCOCK-HANSER BRITTANYL, MORENO MEDINA SANDRACAROLINA, PEASE VICTORIAL, ROBERTSON KELLYM, STRALEY JANICEM, BAIRD ROBINW, CALAMBOKIDIS JOHN, SCHORR GREGORYS, WADE PAUL, BURKANOV VLADIMIR, LUNSFORD CHRISR, RENDELL LUKE, MORIN PHILLIPA. Sperm whale population structure in the eastern and central North Pacific inferred by the use of single-nucleotide polymorphisms, microsatellites and mitochondrial DNA. Mol Ecol Resour 2011; 11 Suppl 1:278-98. [DOI: 10.1111/j.1755-0998.2010.02973.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Machida RJ, Tsuda A. Dissimilarity of species and forms of planktonic Neocalanus copepods using mitochondrial COI, 12S, nuclear ITS, and 28S gene sequences. PLoS One 2010; 5:e10278. [PMID: 20442767 PMCID: PMC2860979 DOI: 10.1371/journal.pone.0010278] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2009] [Accepted: 03/22/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND A total of six Neocalanus species inhabit the oceans of the world. Of these, three species plus form variants (N. cristatus, N. plumchrus, N. flemingeri large form, and N. flemingeri small form), which constitute a monophyletic group among Neocalanus copepods, occur in the Northwestern Pacific off Japan. In the present study, we have tried to discriminate the three species plus form variants of Neocalanus copepods based on sequences of four DNA marker regions. METHODOLOGY/PRINCIPAL FINDINGS Discrimination was performed based on the DNA sequence information from four genetic markers, including the mitochondrial COI, 12S, nuclear ITS, and 28S gene regions. Sequence dissimilarity was compared using both distance- and character-based approaches. As a result, all three species were confirmed to be distinct based on the four genetic marker regions. On the contrary, distinction of the form variants was only confirmed based on DNA sequence of the mitochondrial COI gene region. CONCLUSIONS/SIGNIFICANCE Although discrimination was not successful for the form variants based on the mitochondrial 12S, nuclear ITS, and 28S genes, diagnostic nucleotide sequence characters were observed in their mitochondrial COI gene sequences. Therefore, these form variants are considered to be an important unit of evolution below the species level, and constitute a part of the Neocalanus biodiversity.
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Affiliation(s)
- Ryuji J Machida
- Ocean Research Institute, University of Tokyo, Tokyo, Japan.
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41
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Teterina VI, Sukhanova LV, Kirilchik SV. Molecular divergence and speciation of Baikal oilfish (Comephoridae): facts and hypotheses. Mol Phylogenet Evol 2010; 56:336-42. [PMID: 20382246 DOI: 10.1016/j.ympev.2010.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Revised: 03/25/2010] [Accepted: 04/02/2010] [Indexed: 11/18/2022]
Abstract
Sympatric speciation was studied in two sister species of cottoid fish from Lake Baikal (East Siberia): big golomyanka or Big Baikal oilfish (Comephorus baicalensis Pallas, 1776) and small golomyanka or Little Baikal oilfish (C. dybowski Korotneff, 1905). Analysis of nucleotide sequences of mitochondrial cytochrome b gene showed that the Little Baikal oilfish (LBO) formed a single population in the lake, whereas the Big Baikal oilfish (BBO) was divided into two genetic groups - BBOI and BBOII, which were not separated geographically. Phylogenetic analysis showed that BBO is a more ancient species than LBO and that the paraphyletic origin of LBO is from the BBO genetic lineage within the genus Comephorus. Population-genetic structure and phylogenetic relationships between the two golomyanka species are considered to be a consequence of paleoenvironmental events that took place in the Baikal region during the past hundreds of thousand years.
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Affiliation(s)
- Veronika I Teterina
- Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia.
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42
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Andrews KR, Karczmarski L, Au WWL, Rickards SH, Vanderlip CA, Bowen BW, Gordon Grau E, Toonen RJ. Rolling stones and stable homes: social structure, habitat diversity and population genetics of the Hawaiian spinner dolphin (Stenella longirostris). Mol Ecol 2010; 19:732-48. [PMID: 20089122 DOI: 10.1111/j.1365-294x.2010.04521.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Spinner dolphins (Stenella longirostris) exhibit different social behaviours at two regions in the Hawaiian Archipelago: off the high volcanic islands in the SE archipelago they form dynamic groups with ever-changing membership, but in the low carbonate atolls in the NW archipelago they form long-term stable groups. To determine whether these environmental and social differences influence population genetic structure, we surveyed spinner dolphins throughout the Hawaiian Archipelago with mtDNA control region sequences and 10 microsatellite loci (n = 505). F-statistics, Bayesian cluster analyses, and assignment tests revealed population genetic separations between most islands, with less genetic structuring among the NW atolls than among the SE high islands. The populations with the most stable social structure (Midway and Kure Atolls) have the highest gene flow between populations (mtDNA Phi(ST) < 0.001, P = 0.357; microsatellite F(ST) = -0.001; P = 0.597), and a population with dynamic groups and fluid social structure (the Kona Coast of the island of Hawai'i) has the lowest gene flow (mtDNA 0.042 < Phi(ST) < 0.236, P < 0.05; microsatellite 0.016 < F(ST) < 0.040, P < 0.001). We suggest that gene flow, dispersal, and social structure are influenced by the availability of habitat and resources at each island. Genetic comparisons to a South Pacific location (n = 16) indicate that Hawaiian populations are genetically depauperate and isolated from other Pacific locations (mtDNA 0.216 < F(ST) < 0.643, P < 0.001; microsatellite 0.058 < F(ST) < 0.090, P < 0.001); this isolation may also influence social and genetic structure within Hawai'i. Our results illustrate that genetic and social structure are flexible traits that can vary between even closely-related populations.
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Affiliation(s)
- Kimberly R Andrews
- Hawai'i Institute of Marine Biology, University of Hawai'i, PO Box 1346, Kaneohe, Hawai'i 96744, USA.
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ENGELHAUPT DANIEL, RUS HOELZEL A, NICHOLSON COLIN, FRANTZIS ALEXANDROS, MESNICK SARAH, GERO SHANE, WHITEHEAD HAL, RENDELL LUKE, MILLER PATRICK, DE STEFANIS RENAUD, CAÑADAS ANA, AIROLDI SABINA, MIGNUCCI-GIANNONI ANTONIOA. Female philopatry in coastal basins and male dispersion across the North Atlantic in a highly mobile marine species, the sperm whale (Physeter macrocephalus). Mol Ecol 2009; 18:4193-205. [DOI: 10.1111/j.1365-294x.2009.04355.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Pinela AM, Quérouil S, Magalhães S, Silva MA, Prieto R, Matos JA, Santos RS. Population genetics and social organization of the sperm whale (Physeter macrocephalus) in the Azores inferred by microsatellite analyses. CAN J ZOOL 2009. [DOI: 10.1139/z09-066] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In the northeast Atlantic Ocean, the archipelago of the Azores is frequented by female–offspring groups of sperm whales ( Physeter macrocephalus L., 1758), as well as large males. The Azores apparently constitute both a feeding ground and a reproduction site. Little is known about the population and group structure of sperm whales in the area. We analysed 151 sloughed skin and biopsy samples collected from 2002 to 2004. Molecular analyses involved genetic tagging using 11 microsatellite loci and molecular sexing. Our objectives were to determine the population genetic structure, compare relatedness within and between social groups, infer kinship, and estimate the age of males at dispersal. Results suggest that individuals visiting the archipelago of the Azores belong to a single population. High genetic diversity and absence of inbreeding suggest that the population is recovering from whaling. Individuals sampled in close association are highly related, as well as those observed in the same area on the same day, suggesting that secondary social groups (i.e., the union of primary social units) are largely but not exclusively composed of relatives. Probable mother–offspring and full-sibling pairs were identified. Age of males at dispersal was estimated at 16.6 years, which was well above previous estimates for this species.
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Affiliation(s)
- A. M. Pinela
- Centro do IMAR da Universidade dos Açores, Departamento de Oceanografia e Pescas, Cais Santa Cruz, 9901-862 Horta, Azores, Portugal
- GBM–Molecular Biology Group/Department of Biotechnology, INETI, Estrada do Paço do Lumiar 22, 1649-038 Lisboa, Portugal
| | - S. Quérouil
- Centro do IMAR da Universidade dos Açores, Departamento de Oceanografia e Pescas, Cais Santa Cruz, 9901-862 Horta, Azores, Portugal
- GBM–Molecular Biology Group/Department of Biotechnology, INETI, Estrada do Paço do Lumiar 22, 1649-038 Lisboa, Portugal
| | - S. Magalhães
- Centro do IMAR da Universidade dos Açores, Departamento de Oceanografia e Pescas, Cais Santa Cruz, 9901-862 Horta, Azores, Portugal
- GBM–Molecular Biology Group/Department of Biotechnology, INETI, Estrada do Paço do Lumiar 22, 1649-038 Lisboa, Portugal
| | - M. A. Silva
- Centro do IMAR da Universidade dos Açores, Departamento de Oceanografia e Pescas, Cais Santa Cruz, 9901-862 Horta, Azores, Portugal
- GBM–Molecular Biology Group/Department of Biotechnology, INETI, Estrada do Paço do Lumiar 22, 1649-038 Lisboa, Portugal
| | - R. Prieto
- Centro do IMAR da Universidade dos Açores, Departamento de Oceanografia e Pescas, Cais Santa Cruz, 9901-862 Horta, Azores, Portugal
- GBM–Molecular Biology Group/Department of Biotechnology, INETI, Estrada do Paço do Lumiar 22, 1649-038 Lisboa, Portugal
| | - J. A. Matos
- Centro do IMAR da Universidade dos Açores, Departamento de Oceanografia e Pescas, Cais Santa Cruz, 9901-862 Horta, Azores, Portugal
- GBM–Molecular Biology Group/Department of Biotechnology, INETI, Estrada do Paço do Lumiar 22, 1649-038 Lisboa, Portugal
| | - R. S. Santos
- Centro do IMAR da Universidade dos Açores, Departamento de Oceanografia e Pescas, Cais Santa Cruz, 9901-862 Horta, Azores, Portugal
- GBM–Molecular Biology Group/Department of Biotechnology, INETI, Estrada do Paço do Lumiar 22, 1649-038 Lisboa, Portugal
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Environmental and social influences on the genetic structure of bottlenose dolphins (Tursiops aduncus) in Southeastern Australia. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9968-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Gonzalez EG, Beerli P, Zardoya R. Genetic structuring and migration patterns of Atlantic bigeye tuna, Thunnus obesus (Lowe, 1839). BMC Evol Biol 2008; 8:252. [PMID: 18798987 PMCID: PMC2559848 DOI: 10.1186/1471-2148-8-252] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2008] [Accepted: 09/17/2008] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Large pelagic fishes are generally thought to have little population genetic structuring based on their cosmopolitan distribution, large population sizes and high dispersal capacities. However, gene flow can be influenced by ecological (e.g. homing behaviour) and physical (e.g. present-day ocean currents, past changes in sea temperature and levels) factors. In this regard, Atlantic bigeye tuna shows an interesting genetic structuring pattern with two highly divergent mitochondrial clades (Clades I and II), which are assumed to have been originated during the last Pleistocene glacial maxima. We assess genetic structure patterns of Atlantic bigeye tuna at the nuclear level, and compare them with mitochondrial evidence. RESULTS We examined allele size variation of nine microsatellite loci in 380 individuals from the Gulf of Guinea, Canary, Azores, Canada, Indian Ocean, and Pacific Ocean. To investigate temporal stability of genetic structure, three Atlantic Ocean sites were re-sampled a second year. Hierarchical AMOVA tests, RST pairwise comparisons, isolation by distance (Mantel) tests, Bayesian clustering analyses, and coalescence-based migration rate inferences supported unrestricted gene flow within the Atlantic Ocean at the nuclear level, and therefore interbreeding between individuals belonging to both mitochondrial clades. Moreover, departures from HWE in several loci were inferred for the samples of Guinea, and attributed to a Wahlund effect supporting the role of this region as a spawning and nursery area. Our microsatellite data supported a single worldwide panmictic unit for bigeye tunas. Despite the strong Agulhas Current, immigration rates seem to be higher from the Atlantic Ocean into the Indo-Pacific Ocean, but the actual number of individuals moving per generation is relatively low compared to the large population sizes inhabiting each ocean basin. CONCLUSION Lack of congruence between mt and nuclear evidences, which is also found in other species, most likely reflects past events of isolation and secondary contact. Given the inferred relatively low number of immigrants per generation around the Cape of Good Hope, the proportions of the mitochondrial clades in the different oceans may keep stable, and it seems plausible that the presence of individuals belonging to the mt Clade I in the Atlantic Ocean may be due to extensive migrations that predated the last glaciation.
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Affiliation(s)
- Elena G Gonzalez
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal, 2; 28006 Madrid, Spain
- Department of Biochemistry and Molecular Biology IV, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Peter Beerli
- Department of Scientific Computing, Florida State University, Tallahassee, FL, 32306-4120
| | - Rafael Zardoya
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal, 2; 28006 Madrid, Spain
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Alter SE, Ramirez SF, Nigenda S, Ramirez JU, Bracho LR, Palumbi SR. Mitochondrial and Nuclear Genetic Variation across Calving Lagoons in Eastern North Pacific Gray Whales (Eschrichtius robustus). J Hered 2008; 100:34-46. [DOI: 10.1093/jhered/esn090] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Hartman KL, Visser F, Hendriks AJ. Social structure of Risso’s dolphins (Grampus griseus) at the Azores: a stratified community based on highly associated social units. CAN J ZOOL 2008. [DOI: 10.1139/z07-138] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this study, we present for the first time a model for the social structure of Risso’s dolphins ( Grampus griseus Cuvier, 1812). Over the period 2004–2006, 1028 Risso’s dolphins were identified at Pico island, Azores. Individuals sighted on 10 or more occasions were included in the analysis of social structure (n = 183). High resighting rates indicate strong site fidelity for at least part of the population. We found that individuals form stable, long-term bonds organised in pairs or in clusters of 3–12 individuals. Social structure is stratified based on age and sex classes, with strong associations between adult males and between adult females. We suggest that clusters form the basic units of Risso’s dolphin society. Thirteen pods consisting solely of adults, likely males, and 3 pods consisting of mother–calf pairs were identified. Males are organised in stable, long-term associations of varying size that occur throughout the complete range of behavioural states observed. For females, associations can be of similar strength, but the time scale may vary depending on the presence of nursing calves. As subadults, associations also occur (pair formation), but are less stable than those observed for adults. We propose a new model for Risso’s dolphin societies known as a stratified social organisation, which differs from the fission–fusion and matrilineal society models.
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Affiliation(s)
- K. L. Hartman
- Nova Atlantis Foundation, Rua Dr A.F. Pimentel 11, 9930-309 Santa Cruz das Ribeiras, Lajes do Pico, Pico island, Azores, Portugal
- University of Amsterdam, Institute for Biodiversity and Ecosystem Dymanics, Nieuwe Achtergracht 127, 1018 WS Amsterdam, the Netherlands
- Netherlands Organisation for Applied Scientific Research, Oude Waalsdorperweg 63, 2597 AK Den Haag, the Netherlands
| | - F. Visser
- Nova Atlantis Foundation, Rua Dr A.F. Pimentel 11, 9930-309 Santa Cruz das Ribeiras, Lajes do Pico, Pico island, Azores, Portugal
- University of Amsterdam, Institute for Biodiversity and Ecosystem Dymanics, Nieuwe Achtergracht 127, 1018 WS Amsterdam, the Netherlands
- Netherlands Organisation for Applied Scientific Research, Oude Waalsdorperweg 63, 2597 AK Den Haag, the Netherlands
| | - A. J.E. Hendriks
- Nova Atlantis Foundation, Rua Dr A.F. Pimentel 11, 9930-309 Santa Cruz das Ribeiras, Lajes do Pico, Pico island, Azores, Portugal
- University of Amsterdam, Institute for Biodiversity and Ecosystem Dymanics, Nieuwe Achtergracht 127, 1018 WS Amsterdam, the Netherlands
- Netherlands Organisation for Applied Scientific Research, Oude Waalsdorperweg 63, 2597 AK Den Haag, the Netherlands
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Chen SF, Jones G, Rossiter SJ. Sex-biased gene flow and colonization in the Formosan lesser horseshoe bat: inference from nuclear and mitochondrial markers. J Zool (1987) 2008. [DOI: 10.1111/j.1469-7998.2007.00391.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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50
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Rogers AD. Evolution and biodiversity of Antarctic organisms: a molecular perspective. Philos Trans R Soc Lond B Biol Sci 2008; 362:2191-214. [PMID: 17553774 PMCID: PMC2443175 DOI: 10.1098/rstb.2006.1948] [Citation(s) in RCA: 151] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The Antarctic biota is highly endemic, and the diversity and abundance of taxonomic groups differ from elsewhere in the world. Such characteristics have resulted from evolution in isolation in an increasingly extreme environment over the last 100 Myr. Studies on Antarctic species represent some of the best examples of natural selection at the molecular, structural and physiological levels. Analyses of molecular genetics data are consistent with the diversity and distribution of marine and terrestrial taxa having been strongly influenced by geological and climatic cooling events over the last 70 Myr. Such events have resulted in vicariance driven by continental drift and thermal isolation of the Antarctic, and in pulses of species range contraction into refugia and subsequent expansion and secondary contact of genetically distinct populations or sister species during cycles of glaciation. Limited habitat availability has played a major role in structuring populations of species both in the past and in the present day. For these reasons, despite the apparent simplicity or homogeneity of Antarctic terrestrial and marine environments, populations of species are often geographically structured into genetically distinct lineages. In some cases, genetic studies have revealed that species defined by morphological characters are complexes of cryptic or sibling species. Climate change will cause changes in the distribution of many Antarctic and sub-Antarctic species through affecting population-level processes such as life history and dispersal.
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