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Ruiz-García M, Escobar-Armel P, Martínez-Agüero M, Gaviria M, Álvarez D, Pinedo M, Shostell JM. Are There Barriers Separating the Pink River Dolphin Populations ( Inia boliviensis, Iniidae, Cetacea) within the Mamoré-Iténez River Basins (Bolivia)? An Analysis of Its Genetic Structure by Means of Mitochondrial and Nuclear DNA Markers. Genes (Basel) 2024; 15:1012. [PMID: 39202372 PMCID: PMC11353456 DOI: 10.3390/genes15081012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 07/27/2024] [Accepted: 07/28/2024] [Indexed: 09/03/2024] Open
Abstract
The pink river dolphin, or bufeo, is one of the dolphins which lives in the rivers of the Orinoco and Amazon basins in South America. The Bolivian bufeo population is considered a differentiated species (Inia boliviensis) from the Amazon and Orinoco species (Inia geoffrensis). Until now, no study has completed an extensive population genetics analysis of the bufeo in Bolivian rivers. We analyzed 82 bufeos from different rivers from the Mamoré and Iténez (Guaporé) river basins for the mt control region (CR), nuclear microsatellites, and DQB-1 gene sequences to determine if the inner rapids of these Bolivian river basins have some influence on the genetic structure of this species. The first relevant result was that the genetic diversity for CR, and the microsatellites were substantially lower in the Bolivian bufeos than in the dolphins studied in other areas of the Amazon and Orinoco. However, the DQB-1 gene sequences yielded similar genetic diversity to those found in other areas. The second relevant result is the existence of some significant genetic heterogeneity among the bufeo populations within Bolivia, although in a small degree, but this differentiation is independent of the inner rapids of the Bolivian rivers we sampled. The third relevant result was the existence of significant isolation by distance for the CR, but not for microsatellites and DQB-1 gene sequences. This was related to differential gene flow capacity of females (philopatric) and males (less philopatric and more migrants) and, possibly, to different selective patterns affecting the molecular markers studied. The fourth relevant result was related to diverse demographic changes of these bufeos. At least two or three bottleneck events and one or two population expansions have occurred in the Bolivian bufeo population. The major part of these events occurred during the Pleistocene.
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Affiliation(s)
- Manuel Ruiz-García
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Unidad de Genética, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Carrera 7A No 43-82, Bogotá 110311, DC, Colombia; (P.E.-A.); (M.G.); (D.Á.); (M.P.)
| | - Pablo Escobar-Armel
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Unidad de Genética, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Carrera 7A No 43-82, Bogotá 110311, DC, Colombia; (P.E.-A.); (M.G.); (D.Á.); (M.P.)
| | - María Martínez-Agüero
- Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá 111321, DC, Colombia;
| | - Magda Gaviria
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Unidad de Genética, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Carrera 7A No 43-82, Bogotá 110311, DC, Colombia; (P.E.-A.); (M.G.); (D.Á.); (M.P.)
| | - Diana Álvarez
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Unidad de Genética, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Carrera 7A No 43-82, Bogotá 110311, DC, Colombia; (P.E.-A.); (M.G.); (D.Á.); (M.P.)
| | - Myreya Pinedo
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Unidad de Genética, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Carrera 7A No 43-82, Bogotá 110311, DC, Colombia; (P.E.-A.); (M.G.); (D.Á.); (M.P.)
| | - Joseph Mark Shostell
- Math, Science and Technology Department, University of Minnesota Crookston, Crookston, MN 56716, USA;
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Morin PA, McCarthy ML, Fung CW, Durban JW, Parsons KM, Perrin WF, Taylor BL, Jefferson TA, Archer FI. Revised taxonomy of eastern North Pacific killer whales ( Orcinus orca): Bigg's and resident ecotypes deserve species status. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231368. [PMID: 38545612 PMCID: PMC10966402 DOI: 10.1098/rsos.231368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/29/2024] [Accepted: 02/10/2024] [Indexed: 04/26/2024]
Abstract
Killer whales (Orcinus orca) are currently recognized as a single ecologically and morphologically diverse, globally distributed species. Multiple morphotypes or ecotypes have been described, often associated with feeding specialization, and several studies have suggested taxonomic revision to include multiple subspecies or species in the genus. We review the ecological, morphological and genetic data for the well-studied 'resident' and Bigg's (aka 'transient') ecotypes in the eastern North Pacific and use quantitative taxonomic guidelines and standards to determine whether the taxonomic status of these killer whale ecotypes should be revised. Our review and new analyses indicate that species-level status is justified in both cases, and we conclude that eastern North Pacific Bigg's killer whales should be recognized as Orcinus rectipinnus (Cope in Scammon, 1869) and resident killer whales should be recognized as Orcinus ater (Cope in Scammon, 1869).
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Affiliation(s)
- Phillip A. Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA92037, USA
| | - Morgan L. McCarthy
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA92037, USA
| | - Charissa W. Fung
- University of British Columbia, Vancouver, British ColumbiaV6T 1Z4, Canada
| | - John W. Durban
- Marine Mammal Institute, Oregon State University, Newport, OR97365, USA
| | - Kim M. Parsons
- Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, WA98112, USA
| | - William F. Perrin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA92037, USA
| | - Barbara L. Taylor
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA92037, USA
| | - Thomas A. Jefferson
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA92037, USA
| | - Frederick I. Archer
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA92037, USA
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Shabangu FW, Daniels R, Jordaan RK, de Bruyn PJN, van den Berg MA, Lamont T. Killer whale acoustic patterns respond to prey abundance and environmental variability around the Prince Edward Islands, Southern Ocean. ROYAL SOCIETY OPEN SCIENCE 2024; 11:230903. [PMID: 38179079 PMCID: PMC10762440 DOI: 10.1098/rsos.230903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 12/01/2023] [Indexed: 01/06/2024]
Abstract
Killer whales are apex predators with temporally and spatially varying distributions throughout the world's oceans. Their ecology and behaviour are poorly understood in most regions due to limited research, often because of logistical challenges. Here, we used a passive acoustic monitoring device to investigate the seasonal acoustic occurrence and diel vocalizing behaviour of killer whales around the remote sub-Antarctic Prince Edward Islands (PEIs), Southern Ocean. Killer whales showed diel vocalizing patterns that varied seasonally in relation to their prey abundance and social activities. Killer whale calls were intermittently detected year-round with a high number of hours containing calls in October to December, and a secondary peak in February to May, corresponding to seal prey abundance. Random forest modelling identified wind speed as the primary predictor of the occurrence of killer whale calls (with a negative correlation) while sea surface height, chlorophyll-a and sea surface temperature were moderately important. We provide the first acoustic evidence that killer whale occurrence around the PEIs might coincide with variability in environmental conditions and prey abundance. Our results provide the first indication of diel vocalizing pattern of killer whales in the Southern Ocean. This knowledge is important for understanding killer whale ecology and adaptation to the changing oceans.
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Affiliation(s)
- Fannie W. Shabangu
- Fisheries Management Branch, Department of Forestry, Fisheries and the Environment, Foreshore, Cape Town, South Africa
- Mammal Research Institute, University of Pretoria, Private Bag X20, Hatfield, Pretoria 0028, South Africa
| | - Robyn Daniels
- Department of Oceanography, University of Cape Town, Cape Town, South Africa
| | - Rowan K. Jordaan
- Mammal Research Institute, University of Pretoria, Private Bag X20, Hatfield, Pretoria 0028, South Africa
| | - P. J. Nico de Bruyn
- Mammal Research Institute, University of Pretoria, Private Bag X20, Hatfield, Pretoria 0028, South Africa
| | - Marcel A. van den Berg
- Oceans and Coasts Research Branch, Department of Forestry, Fisheries and the Environment, Foreshore, Cape Town, South Africa
| | - Tarron Lamont
- Department of Oceanography, University of Cape Town, Cape Town, South Africa
- Nansen–Tutu Centre for Marine Environmental Research, University of Cape Town, Cape Town, South Africa
- Oceans and Coasts Research Branch, Department of Forestry, Fisheries and the Environment, Foreshore, Cape Town, South Africa
- Bayworld Centre for Research and Education, Cape Town, South Africa
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Westbury MV, Cabrera AA, Rey-Iglesia A, De Cahsan B, Duchêne DA, Hartmann S, Lorenzen ED. A genomic assessment of the marine-speciation paradox within the toothed whale superfamily Delphinoidea. Mol Ecol 2023; 32:4829-4843. [PMID: 37448145 DOI: 10.1111/mec.17069] [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: 10/27/2022] [Revised: 06/21/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023]
Abstract
The impact of post-divergence gene flow in speciation has been documented across a range of taxa in recent years, and may have been especially widespread in highly mobile, wide-ranging marine species, such as cetaceans. Here, we studied individual genomes from nine species across the three families of the toothed whale superfamily Delphinoidea (Delphinidae, Phocoenidae and Monodontidae). To investigate the role of post-divergence gene flow in the speciation process, we used a multifaceted approach, including (i) phylogenomics, (ii) the distribution of shared derived alleles and (iii) demographic inference. We found the divergence of lineages within Delphinoidea did not follow a process of pure bifurcation, but was much more complex. Sliding-window phylogenomics reveal a high prevalence of discordant topologies within the superfamily, with further analyses indicating these discordances arose due to both incomplete lineage sorting and gene flow. D-statistics and f-branch analyses supported gene flow between members of Delphinoidea, with the vast majority of gene flow occurring as ancient interfamilial events. Demographic analyses provided evidence that introgressive gene flow has likely ceased between all species pairs tested, despite reports of contemporary interspecific hybrids. Our study provides the first steps towards resolving the large complexity of speciation within Delphinoidea; we reveal the prevalence of ancient interfamilial gene flow events prior to the diversification of each family, and suggest that contemporary hybridisation events may be disadvantageous, as hybrid individuals do not appear to contribute to the parental species' gene pools.
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Affiliation(s)
| | | | | | - Binia De Cahsan
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - David A Duchêne
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Stefanie Hartmann
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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Laczkó L, Jordán S, Sramkó G. The
RadOrgMiner
pipeline: Automated genotyping of organellar loci from
RADseq
data. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Levente Laczkó
- MTA‐DE “Lendület” Evolutionary Phylogenomics Research Group, Egyetem tér 1 H‐4032 Debrecen Hungary
- Department of Botany University of Debrecen Egyetem tér 1, Debrecen, H‐4032 Hungary
- ELKH‐ DE Conservation Biology Research Group, Egyetem tér 1, Debrecen, H‐4032 Hungary
- Department of Metagenomics University of Debrecen Nagyerdei körút 98., Debrecen, H‐4032 Hungary
| | - Sándor Jordán
- Department of Botany University of Debrecen Egyetem tér 1, Debrecen, H‐4032 Hungary
- Juhász‐Nagy Pál Doctoral School University of Debrecen Egyetem tér 1, Debrecen, H‐4032 Hungary
| | - Gábor Sramkó
- MTA‐DE “Lendület” Evolutionary Phylogenomics Research Group, Egyetem tér 1 H‐4032 Debrecen Hungary
- Department of Botany University of Debrecen Egyetem tér 1, Debrecen, H‐4032 Hungary
- ELKH‐ DE Conservation Biology Research Group, Egyetem tér 1, Debrecen, H‐4032 Hungary
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Euclide PT, Jasonowicz A, Sitar S, Fischer G, Goetz FW. Further evidence from common garden rearing experiments of heritable traits separating lean and siscowet lake charr (Salvelinus namaycush) ecotypes. Mol Ecol 2022; 31:3432-3450. [PMID: 35510796 PMCID: PMC9323484 DOI: 10.1111/mec.16492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 03/07/2022] [Accepted: 04/12/2022] [Indexed: 11/30/2022]
Abstract
Genetic evidence of selection for complex and polygenically regulated phenotypes can easily become masked by neutral population genetic structure and phenotypic plasticity. Without direct evidence of genotype‐phenotype associations it can be difficult to conclude to what degree a phenotype is heritable or a product of environment. Common garden laboratory studies control for environmental stochasticity and help to determine the mechanism that regulate traits. Here we assess lipid content, growth, weight, and length variation in full and hybrid F1 crosses of deep and shallow water sympatric lake charr ecotypes reared for nine years in a common garden experiment. Redundancy analysis (RDA) and quantitative‐trait‐loci (QTL) genomic scans are used to identify associations between genotypes at 19,714 single nucleotide polymorphisms (SNPs) aligned to the lake charr genome and individual phenotypes to determine the role that genetic inheritance plays in ecotype phenotypic diversity. Lipid content, growth, length, and weight differed significantly among lake charr crosses throughout the experiment suggesting that pedigree plays a large roll in lake charr development. Polygenic scores of 15 SNPs putatively associated with lipid content and/or condition factor indicated that ecotype distinguishing traits are polygenically regulated and additive. A QTL identified on chromosome 38 contained >200 genes, some of which were associated with lipid metabolism and growth, demonstrating the complex nature of ecotype diversity. The results of our common garden study further indicate that lake charr ecotypes observed in nature are predetermined at birth and that ecotypes differ fundamentally in lipid metabolism and growth.
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Affiliation(s)
- P T Euclide
- Purdue University, Department of Forestry and Natural Resources, West Lafayette, IN, 47907, USA
| | - A Jasonowicz
- The International Halibut Commission, 2320 West Commodore Way, Suite 300, Seattle, WA, 98199-1287, USA
| | - S Sitar
- Michigan Department of Natural Resources, Marquette Fisheries Research Station, 484 Cherry Creek Rd., Marquette, MI, 49855, USA
| | - G Fischer
- University of Wisconsin-Stevens Point, Northern Aquaculture Demonstration Facility, 36445 State Hwy 13, Bayfield, WI, 54814, USA
| | - F W Goetz
- University of Wisconsin - Milwaukee, School of Freshwater Sciences, 600 East Greenfield Ave., Milwaukee, WI, 53204, USA
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7
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Stronen AV, Norman AJ, Vander Wal E, Paquet PC. The relevance of genetic structure in ecotype designation and conservation management. Evol Appl 2022; 15:185-202. [PMID: 35233242 PMCID: PMC8867706 DOI: 10.1111/eva.13339] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 12/02/2021] [Accepted: 12/20/2021] [Indexed: 11/28/2022] Open
Abstract
The concept of ecotypes is complex, partly because of its interdisciplinary nature, but the idea is intrinsically valuable for evolutionary biology and applied conservation. The complex nature of ecotypes has spurred some confusion and inconsistencies in the literature, thereby limiting broader theoretical development and practical application. We provide suggestions for how incorporating genetic analyses can ease confusion and help define ecotypes. We approach this by systematically reviewing 112 publications across taxa that simultaneously mention the terms ecotype, conservation and management, to examine the current use of the term in the context of conservation and management. We found that most ecotype studies involve fish, mammals and plants with a focus on habitat use, which at 60% was the most common criterion used for categorization of ecotypes. Only 53% of the studies incorporated genetic analyses, and major discrepancies in available genomic resources among taxa could have contributed to confusion about the role of genetic structure in delineating ecotypes. Our results show that the rapid advances in genetic methods, also for nonmodel organisms, can help clarify the spatiotemporal distribution of adaptive and neutral genetic variation and their relevance to ecotype designations. Genetic analyses can offer empirical support for the ecotype concept and provide a timely measure of evolutionary potential, especially in changing environmental conditions. Genetic variation that is often difficult to detect, including polygenic traits influenced by small contributions from several genes, can be vital for adaptation to rapidly changing environments. Emerging ecotypes may signal speciation in progress, and findings from genome-enabled organisms can help clarify important selective factors driving ecotype development and persistence, and thereby improve preservation of interspecific genetic diversity. Incorporation of genetic analyses in ecotype studies will help connect evolutionary biology and applied conservation, including that of problematic groups such as natural hybrid organisms and urban or anthropogenic ecotypes.
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Affiliation(s)
- Astrid V. Stronen
- Department of BiologyBiotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
- Department of Biotechnology and Life SciencesInsubria UniversityVareseItaly
- Department of Chemistry and BioscienceAalborg UniversityAalborgDenmark
| | - Anita J. Norman
- Department of Fish, Wildlife and Environmental StudiesSwedish University of Agricultural SciencesUmeåSweden
| | - Eric Vander Wal
- Department of BiologyMemorial University of NewfoundlandSt. John’sNLCanada
| | - Paul C. Paquet
- Department of GeographyUniversity of VictoriaVictoriaBCCanada
- Raincoast Conservation FoundationSidneyBCCanada
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Prada C, Hellberg ME. Speciation-by-depth on coral reefs: Sympatric divergence with gene flow or cryptic transient isolation? J Evol Biol 2021; 34:128-137. [PMID: 33140895 PMCID: PMC7894305 DOI: 10.1111/jeb.13731] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 07/21/2020] [Accepted: 09/29/2020] [Indexed: 12/30/2022]
Abstract
The distributions of many sister species in the sea overlap geographically but are partitioned along depth gradients. The genetic changes leading to depth segregation may evolve in geographic isolation as a prerequisite to coexistence or may emerge during primary divergence leading to new species. These alternatives can now be distinguished via the power endowed by the thousands of scorable loci provided by second-generation sequence data. Here, we revisit the case of two depth-segregated, genetically isolated ecotypes of the nominal Caribbean candelabrum coral Eunicea flexuosa. Previous analyses based on a handful of markers could not distinguish between models of genetic exchange after a period of isolation (consistent with secondary contact) and divergence with gene flow (consistent with primary divergence). Analyses of the history of isolation, genetic exchange and population size based on 15,640 new SNP markers derived from RNAseq data best support models where divergence began 800K BP and include epochs of divergence with gene flow, but with an intermediate period of transient isolation. Results also supported the previous conclusion that recent exchange between the ecotypes occurs asymmetrically from the Shallow lineage to the Deep. Parallel analyses of data from two other corals with depth-segregated populations (Agaricia fragilis and Pocillopora damicornis) suggest divergence leading to depth-segregated populations may begin with a period of symmetric exchange, but that an epoch of population isolation precedes more complete isolation marked by asymmetric introgression. Thus, while divergence-with-gene flow may account for much of the differentiation that separates closely related, depth-segregated species, it remains to be seen whether any critical steps in the speciation process only occur when populations are isolated.
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Affiliation(s)
- Carlos Prada
- Department of Biological SciencesUniversity of Rhode IslandKingstonRIUSA
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9
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Jordaan RK, Oosthuizen WC, Reisinger RR, Nico De Bruyn PJ. Abundance, survival and population growth of killer whales Orcinus orca at subantarctic Marion Island. WILDLIFE BIOLOGY 2020. [DOI: 10.2981/wlb.00732] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
| | | | - Ryan R. Reisinger
- R. R. Reisinger (https://orcid.org/0000-0002-8933-6875), Centre d'Etudes Biologiques de Chizé (CEBC), UMR 7372 CNRS-La Rochelle Univ., Villiers-en-Bois, France, and: Inst. of Marine Sciences, Univ. of California Santa Cruz, Santa Cruz, California, US
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10
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Lawson TM, Ylitalo GM, O'Neill SM, Dahlheim ME, Wade PR, Matkin CO, Burkanov V, Boyd DT. Concentrations and profiles of organochlorine contaminants in North Pacific resident and transient killer whale (Orcinus orca) populations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 722:137776. [PMID: 32199362 DOI: 10.1016/j.scitotenv.2020.137776] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/08/2020] [Accepted: 03/05/2020] [Indexed: 06/10/2023]
Abstract
Organochlorine (OC) profiles have been used as chemical "fingerprints" to infer an animal's foraging area. North Pacific killer whale (Orcinus orca) populations are exposed to different levels and patterns of OCs based on their prey, distribution, and amount of time spent in a particular area. To characterize concentrations and profiles of OCs found in various populations of North Pacific killer whales, polychlorinated biphenyls (PCBs), including dioxin-like congeners, DDTs, and hexachlorobenzene (HCB), were measured in biopsy blubber samples of photo-identified resident (fish-eating) and transient (mammal-eating) killer whales collected from 1994 through 2002 from Russian Far East waters to the waters of the west coast of the United States, representing 10 populations. We compared blubber OC concentrations based on ecotype (resident vs. transient), sex and reproductive maturity, and geographic area. We also examined OC mixtures to determine if we could detect segregated geographical areas (foraging areas) among the six populations with sufficient sample sizes. Transients had significantly higher OC concentrations than residents and adult male whales had consistently higher OC levels compared to adult females, regardless of ecotype. Our OC profile findings indicate segregated foraging areas for the North Pacific killer whales, consistent with observations of their geographic distributions. Several potential health risks have also been associated with exposure to high levels of contaminants in top-level predators including reproductive impairment, immune suppression, skeletal deformities, and carcinoma. The results of this baseline study provide information on the geographic distribution of OCs found in North Pacific killer whales, results which are crucial for assessing the potential health risks associated with OC exposure in this species.
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Affiliation(s)
- Teresa M Lawson
- West Coast Region, National Marine Fisheries Services, National Oceanic and Atmospheric Administration, United States Department of Commerce, 7600 Sand Point Way NE, Seattle, WA 98115, United States of America.
| | - Gina M Ylitalo
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Services, National Oceanic and Atmospheric Administration, United States Department of Commerce, 2725 Montlake Blvd. East, Seattle, WA 98112, United States of America
| | - Sandra M O'Neill
- Washington Department of Fish and Wildlife, P.O. Box 43200, Olympia, WA 98504-3200, United States of America
| | - Marilyn E Dahlheim
- Retired employee of the Marine Mammal Laboratory, Alaska Fisheries Science Center, National Marine Fisheries Services, National Oceanic and Atmospheric Administration, United States Department of Commerce, 7600 Sand Point Way NE, Seattle, WA 98115, United States of America
| | - Paul R Wade
- Marine Mammal Laboratory, Alaska Fisheries Science Center, National Marine Fisheries Services, National Oceanic and Atmospheric Administration, United States Department of Commerce, 7600 Sand Point Way NE, Seattle, WA 98115
| | - Craig O Matkin
- North Gulf Oceanic Society, P.O. Box 15244, Homer, AK 99603, United States of America
| | - Vladimir Burkanov
- Marine Mammal Laboratory, Alaska Fisheries Science Center, National Marine Fisheries Services, National Oceanic and Atmospheric Administration, United States Department of Commerce, 7600 Sand Point Way NE, Seattle, WA 98115
| | - Daryle T Boyd
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Services, National Oceanic and Atmospheric Administration, United States Department of Commerce, 2725 Montlake Blvd. East, Seattle, WA 98112, United States of America
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11
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Moura AE, Shreves K, Pilot M, Andrews KR, Moore DM, Kishida T, Möller L, Natoli A, Gaspari S, McGowen M, Chen I, Gray H, Gore M, Culloch RM, Kiani MS, Willson MS, Bulushi A, Collins T, Baldwin R, Willson A, Minton G, Ponnampalam L, Hoelzel AR. Phylogenomics of the genus Tursiops and closely related Delphininae reveals extensive reticulation among lineages and provides inference about eco-evolutionary drivers. Mol Phylogenet Evol 2020; 146:106756. [DOI: 10.1016/j.ympev.2020.106756] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 01/02/2020] [Accepted: 01/28/2020] [Indexed: 12/30/2022]
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12
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Foote AD, Martin MD, Louis M, Pacheco G, Robertson KM, Sinding MHS, Amaral AR, Baird RW, Baker CS, Ballance L, Barlow J, Brownlow A, Collins T, Constantine R, Dabin W, Dalla Rosa L, Davison NJ, Durban JW, Esteban R, Ferguson SH, Gerrodette T, Guinet C, Hanson MB, Hoggard W, Matthews CJD, Samarra FIP, de Stephanis R, Tavares SB, Tixier P, Totterdell JA, Wade P, Excoffier L, Gilbert MTP, Wolf JBW, Morin PA. Killer whale genomes reveal a complex history of recurrent admixture and vicariance. Mol Ecol 2019; 28:3427-3444. [PMID: 31131963 DOI: 10.1111/mec.15099] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 04/06/2019] [Accepted: 04/08/2019] [Indexed: 02/06/2023]
Abstract
Reconstruction of the demographic and evolutionary history of populations assuming a consensus tree-like relationship can mask more complex scenarios, which are prevalent in nature. An emerging genomic toolset, which has been most comprehensively harnessed in the reconstruction of human evolutionary history, enables molecular ecologists to elucidate complex population histories. Killer whales have limited extrinsic barriers to dispersal and have radiated globally, and are therefore a good candidate model for the application of such tools. Here, we analyse a global data set of killer whale genomes in a rare attempt to elucidate global population structure in a nonhuman species. We identify a pattern of genetic homogenisation at lower latitudes and the greatest differentiation at high latitudes, even between currently sympatric lineages. The processes underlying the major axis of structure include high drift at the edge of species' range, likely associated with founder effects and allelic surfing during postglacial range expansion. Divergence between Antarctic and non-Antarctic lineages is further driven by ancestry segments with up to four-fold older coalescence time than the genome-wide average; relicts of a previous vicariance during an earlier glacial cycle. Our study further underpins that episodic gene flow is ubiquitous in natural populations, and can occur across great distances and after substantial periods of isolation between populations. Thus, understanding the evolutionary history of a species requires comprehensive geographic sampling and genome-wide data to sample the variation in ancestry within individuals.
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Affiliation(s)
- Andrew D Foote
- CMPG, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | | | - Marie Louis
- Department of Biology, Section for Evolutionary Genomics, University of Copenhagen, Copenhagen, Denmark.,Scottish Oceans Institute, East Sands, University of St. Andrews, St. Andrews, UK
| | - George Pacheco
- Department of Biology, Section for Evolutionary Genomics, University of Copenhagen, Copenhagen, Denmark
| | - Kelly M Robertson
- Marine Mammal and Turtle Division, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, Southwest Fisheries Science Center, La Jolla, California
| | - Mikkel-Holger S Sinding
- Department of Biology, Section for Evolutionary Genomics, University of Copenhagen, Copenhagen, Denmark.,Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Ana R Amaral
- American Museum of Natural History, New York City, New York.,Faculdade de Ciências Universidade de Lisboa, Centre for Ecology, Evolution and Environmental Changes, Lisboa, Portugal
| | | | - Charles Scott Baker
- Department of Fisheries and Wildlife, Marine Mammal Institute, Oregon State University, Newport, Oregon.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Lisa Ballance
- Marine Mammal and Turtle Division, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, Southwest Fisheries Science Center, La Jolla, California
| | - Jay Barlow
- Marine Mammal and Turtle Division, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, Southwest Fisheries Science Center, La Jolla, California
| | - Andrew Brownlow
- Scottish Marine Animal Stranding Scheme, SRUC Veterinary Services Drummondhill, Inverness, UK
| | - Tim Collins
- Ocean Giants Program, Wildlife Conservation Society, New York City, New York
| | | | - Willy Dabin
- Observatoire Pelagis, Université de La Rochelle-CNRS, La Rochelle, France
| | - Luciano Dalla Rosa
- Laboratório de Ecologia e Conservação da Megafauna Marinha, Instituto de Oceanografia, Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Nicholas J Davison
- Scottish Marine Animal Stranding Scheme, SRUC Veterinary Services Drummondhill, Inverness, UK
| | - John W Durban
- Marine Mammal and Turtle Division, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, Southwest Fisheries Science Center, La Jolla, California
| | - Ruth Esteban
- CIRCE, Conservation, Information and Research on Cetaceans, Algeciras, Spain
| | | | - Tim Gerrodette
- Marine Mammal and Turtle Division, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, Southwest Fisheries Science Center, La Jolla, California
| | - Christophe Guinet
- Centre d'Etudes Biologiques de Chizé (CEBC), CNRS-ULR, UMR, Chizé, France
| | - M Bradley Hanson
- National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Northwest Fisheries Science Center, Seattle, Washington
| | - Wayne Hoggard
- National Marine Fisheries Service, NOAA, Southeast Fisheries Science Center, Pascagoula, Mississippi
| | | | | | - Renaud de Stephanis
- CIRCE, Conservation, Information and Research on Cetaceans, Algeciras, Spain
| | - Sara B Tavares
- Scottish Oceans Institute, East Sands, University of St. Andrews, St. Andrews, UK
| | - Paul Tixier
- Centre d'Etudes Biologiques de Chizé (CEBC), CNRS-ULR, UMR, Chizé, France.,School of Life and Environmental Sciences (Burwood Campus), Deakin University, Geelong, Victoria, Australia
| | - John A Totterdell
- Marine Information and Research Group-Australia (MIRG), Quinns Rocks, Western Australia, Australia
| | - Paul Wade
- National Marine Mammal Laboratory, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Alaska Fisheries Science Center, Seattle, Washington
| | - Laurent Excoffier
- CMPG, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - M Thomas P Gilbert
- NTNU University Museum, Trondheim, Norway.,Department of Biology, Section for Evolutionary Genomics, University of Copenhagen, Copenhagen, Denmark
| | - Jochen B W Wolf
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany.,Department of Evolutionary Biology, Science of Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Phillip A Morin
- Marine Mammal and Turtle Division, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, Southwest Fisheries Science Center, La Jolla, California
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13
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Grady JM, Maitner BS, Winter AS, Kaschner K, Tittensor DP, Record S, Smith FA, Wilson AM, Dell AI, Zarnetske PL, Wearing HJ, Alfaro B, Brown JH. Metabolic asymmetry and the global diversity of marine predators. Science 2019; 363:363/6425/eaat4220. [DOI: 10.1126/science.aat4220] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 12/13/2018] [Indexed: 01/13/2023]
Abstract
Species richness of marine mammals and birds is highest in cold, temperate seas—a conspicuous exception to the general latitudinal gradient of decreasing diversity from the tropics to the poles. We compiled a comprehensive dataset for 998 species of sharks, fish, reptiles, mammals, and birds to identify and quantify inverse latitudinal gradients in diversity, and derived a theory to explain these patterns. We found that richness, phylogenetic diversity, and abundance of marine predators diverge systematically with thermoregulatory strategy and water temperature, reflecting metabolic differences between endotherms and ectotherms that drive trophic and competitive interactions. Spatial patterns of foraging support theoretical predictions, with total prey consumption by mammals increasing by a factor of 80 from the equator to the poles after controlling for productivity.
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14
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Tavares SB, Samarra FIP, Pascoal S, Graves JA, Miller PJO. Killer whales ( Orcinus orca) in Iceland show weak genetic structure among diverse isotopic signatures and observed movement patterns. Ecol Evol 2018; 8:11900-11913. [PMID: 30598785 PMCID: PMC6303705 DOI: 10.1002/ece3.4646] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 09/26/2018] [Accepted: 09/28/2018] [Indexed: 11/07/2022] Open
Abstract
Local adaption through ecological niche specialization can lead to genetic structure between and within populations. In the Northeast Pacific, killer whales (Orcinus orca) of the same population have uniform specialized diets that are non-overlapping with other sympatric, genetically divergent, and socially isolated killer whale ecotypes. However, killer whales in Iceland show intrapopulation variation of isotopic niches and observed movement patterns: some individuals appear to specialize on herring and follow it year-round while others feed upon herring only seasonally or opportunistically. We investigated genetic differentiation among Icelandic killer whales with different isotopic signatures and observed movement patterns. This information is key for management and conservation purposes but also for better understanding how niche specialization drives genetic differentiation. Photo-identified individuals (N = 61) were genotyped for 22 microsatellites and a 611 bp portion of the mitochondrial DNA (mtDNA) control region. Photo-identification of individuals allowed linkage of genetic data to existing data on individual isotopic niche, observed movement patterns, and social associations. Population subdivision into three genetic units was supported by a discriminant analysis of principal components (DAPC). Genetic clustering corresponded to the distribution of isotopic signatures, mtDNA haplotypes, and observed movement patterns, but genetic units were not socially segregated. Genetic differentiation was weak (F ST < 0.1), suggesting ongoing gene flow or recent separation of the genetic units. Our results show that killer whales in Iceland are not as genetically differentiated, ecologically discrete, or socially isolated as the Northeast Pacific prey-specialized killer whales. If any process of ecological divergence and niche specialization is taking place among killer whales in Iceland, it is likely at a very early stage and has not led to the patterns observed in the Northeast Pacific.
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Affiliation(s)
- Sara B. Tavares
- Sea Mammal Research Unit, Scottish Oceans InstituteUniversity of St AndrewsSt Andrews, FifeUK
| | - Filipa I. P. Samarra
- Sea Mammal Research Unit, Scottish Oceans InstituteUniversity of St AndrewsSt Andrews, FifeUK
- Marine and Freshwater Research InstituteReykjavíkIceland
| | - Sonia Pascoal
- Department of ZoologyUniversity of CambridgeCambridgeUK
| | - Jeff A. Graves
- Scottish Oceans InstituteUniversity of St AndrewsSt Andrews, FifeUK
| | - Patrick J. O. Miller
- Sea Mammal Research Unit, Scottish Oceans InstituteUniversity of St AndrewsSt Andrews, FifeUK
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15
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Stobie CS, Cunningham MJ, Oosthuizen CJ, Bloomer P. Finding stories in noise: Mitochondrial portraits from RAD data. Mol Ecol Resour 2018; 19:191-205. [DOI: 10.1111/1755-0998.12953] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Cora Sabriel Stobie
- Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology University of Pretoria Hatfield, Pretoria South Africa
| | - Michael J. Cunningham
- Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology University of Pretoria Hatfield, Pretoria South Africa
| | - Carel J. Oosthuizen
- Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology University of Pretoria Hatfield, Pretoria South Africa
| | - Paulette Bloomer
- Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology University of Pretoria Hatfield, Pretoria South Africa
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16
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Filatova OA, Borisova EA, Meschersky IG, Logacheva MD, Kuzkina NV, Shpak OV, Morin PA, Hoyt E. Colonizing the Wild West: Low Diversity of Complete Mitochondrial Genomes in Western North Pacific Killer Whales Suggests a Founder Effect. J Hered 2018; 109:735-743. [PMID: 30053000 DOI: 10.1093/jhered/esy037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 07/17/2018] [Indexed: 11/13/2022] Open
Abstract
In the North Pacific, fish-eating R-type "resident" and mammal-eating T-type "transient" killer whales do not interbreed and differ in ecology and behavior. Full-length mitochondrial genomes (about 16.4 kbp) were sequenced and assembled for 12 R-type and 14 T-type killer whale samples from different areas of the western North Pacific. All R-type individuals had the same haplotype, previously described for R-type killer whales from both eastern and western North Pacific. However, haplotype diversity of R-type killer whales was much lower in the western North Pacific than in the Aleutian Islands and the eastern North Pacific. T-type whales had 3 different haplotypes, including one previously undescribed. Haplotype diversity of T-type killer whales in the Okhotsk Sea was also much lower than in the Aleutian Islands and the eastern North Pacific. The highest haplotype diversity for both R- and T-type killer whales was observed in the Aleutian Islands. We discuss how the environmental conditions during the last glacial period might have shaped the history of killer whale populations in the North Pacific. Our results suggest the recent colonization or re-colonization of the western North Pacific by small groups of killer whales originating from the central or eastern North Pacific, possibly due to favorable environmental changes after the Last Glacial Maximum.
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Affiliation(s)
- Olga A Filatova
- Department of Vertebrate Zoology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Ekaterina A Borisova
- Department of Vertebrate Zoology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Ilya G Meschersky
- Molecular Diagnostic Center, A.N. Severtsov Institute of Ecology and Evolution RAS, Moscow, Russia
| | - Maria D Logacheva
- Department of Evolutionary Biochemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Nataliia V Kuzkina
- Laboratory of Translational Research and Personalized Medicine, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Olga V Shpak
- Laboratory of Behavior and Behavioral Ecology, A.N. Severtsov Institute of Ecology and Evolution RAS, Moscow, Russia
| | - Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA
| | - Erich Hoyt
- Global Critical Habitat Marine Protected Areas Programme, Whale and Dolphin Conservation, UK
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17
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Pohjoismäki JLO, Lampi S, Donner J, Anderson H. Origins and wanderings of the Finnish hunting spitzes. PLoS One 2018; 13:e0199992. [PMID: 29958296 PMCID: PMC6025854 DOI: 10.1371/journal.pone.0199992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 06/17/2018] [Indexed: 11/18/2022] Open
Abstract
Deducing the evolutionary histories of dog breeds can be challenging due to convergent traits and frequent admixture. In this report, we have explored the relationships of indigenous Finnish hunting spitz breeds among other northern Eurasian hunting breeds using commercially available SNP analysis (the MyDogDNA panel test). We find that Nordic hunting breeds Finnish Spitz, Nordic Spitz and the Karelian Bear Dog, as well as the reindeer herding Lapphund and Lapponian herder are all closely related and have common origins with the northeastern Eurasian Laika breeds, rather than with other Scandinavian Spitz breeds, such as Elkhounds and Swedish Vallhund. By tracing admixture events and direction of gene flow, we also elucidate the complex interactions between the breeds and provide new insight into the history of Swedish Elkhound and Russian-European Laika. The findings, together with an analysis of genetic differentiation between the populations, not only help to understand the origins of the breeds but also provide interesting possibilities to revive genetic diversity, lost during the breeding history, by backcrossing breeds to their hypothetical ancestry.
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Affiliation(s)
- Jaakko L O Pohjoismäki
- University of Eastern Finland, Department of Environmental and Biological Sciences, Joensuu, Finland
| | - Sara Lampi
- University of Eastern Finland, Department of Environmental and Biological Sciences, Joensuu, Finland
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18
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Segura-García I, Rojo-Arreola L, Rocha-Olivares A, Heckel G, Gallo-Reynoso JP, Hoelzel R. Eco-Evolutionary Processes Generating Diversity Among Bottlenose Dolphin, Tursiops truncatus, Populations off Baja California, Mexico. Evol Biol 2018; 45:223-236. [PMID: 29755152 PMCID: PMC5938318 DOI: 10.1007/s11692-018-9445-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 01/09/2018] [Indexed: 11/02/2022]
Abstract
For highly mobile species that nevertheless show fine-scale patterns of population genetic structure, the relevant evolutionary mechanisms determining structure remain poorly understood. The bottlenose dolphin (Tursiops truncatus) is one such species, exhibiting complex patterns of genetic structure associated with local habitat dependence in various geographic regions. Here we studied bottlenose dolphin populations in the Gulf of California and Pacific Ocean off Baja California where habitat is highly structured to test associations between ecology, habitat dependence and genetic differentiation. We investigated population structure at a fine geographic scale using both stable isotope analysis (to assess feeding ecology) and molecular genetic markers (to assess population structure). Our results show that there are at least two factors affecting population structure for both genetics and feeding ecology (as indicated by stable isotope profiles). On the one hand there is a signal for the differentiation of individuals by ecotype, one foraging more offshore than the other. At the same time, there is differentiation between the Gulf of California and the west coast of Baja California, meaning that for example, nearshore ecotypes were both genetically and isotopically differentiated either side of the peninsula. We discuss these data in the context of similar studies showing fine-scale population structure for delphinid species in coastal waters, and consider possible evolutionary mechanisms.
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Affiliation(s)
- Iris Segura-García
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE UK
| | - Liliana Rojo-Arreola
- CONACYT-Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Mar Bermejo 195, Col. Playa Palo de Santa Rita, 23096 La Paz, BCS Mexico
| | - Axayácatl Rocha-Olivares
- Centro de Investigación Científica y Educación Superior de Ensenada (CICESE), 22860 Ensenada, Baja California Mexico
| | - Gisela Heckel
- Centro de Investigación Científica y Educación Superior de Ensenada (CICESE), 22860 Ensenada, Baja California Mexico
| | - Juan Pablo Gallo-Reynoso
- Centro de Investigación en Alimentación y Desarrollo, A.C. Unidad Guaymas, Carretera a Varadero Nacional km 66, Col. Las Playitas, 85480 Guaymas, Sonora Mexico
| | - Rus Hoelzel
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE UK
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19
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Abstract
Whales and dolphins (Cetacea) have excellent social learning skills as well as a long and strong mother-calf bond. These features produce stable cultures, and, in some species, sympatric groups with different cultures. There is evidence and speculation that this cultural transmission of behavior has affected gene distributions. Culture seems to have driven killer whales into distinct ecotypes, which may be incipient species or subspecies. There are ecotype-specific signals of selection in functional genes that correspond to cultural foraging behavior and habitat use by the different ecotypes. The five species of whale with matrilineal social systems have remarkably low diversity of mtDNA. Cultural hitchhiking, the transmission of functionally neutral genes in parallel with selective cultural traits, is a plausible hypothesis for this low diversity, especially in sperm whales. In killer whales the ecotype divisions, together with founding bottlenecks, selection, and cultural hitchhiking, likely explain the low mtDNA diversity. Several cetacean species show habitat-specific distributions of mtDNA haplotypes, probably the result of mother-offspring cultural transmission of migration routes or destinations. In bottlenose dolphins, remarkable small-scale differences in haplotype distribution result from maternal cultural transmission of foraging methods, and large-scale redistributions of sperm whale cultural clans in the Pacific have likely changed mitochondrial genetic geography. With the acceleration of genomics new results should come fast, but understanding gene-culture coevolution will be hampered by the measured pace of research on the socio-cultural side of cetacean biology.
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Affiliation(s)
- Hal Whitehead
- Department of Biology, Dalhousie University, Halifax, NS, Canada B3H 4R2
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20
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Moon KL, Chown SL, Fraser CI. Reconsidering connectivity in the sub-Antarctic. Biol Rev Camb Philos Soc 2017; 92:2164-2181. [DOI: 10.1111/brv.12327] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 02/09/2017] [Accepted: 02/15/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Katherine L. Moon
- School of Biological Sciences; Monash University; Clayton 3800 Australia
- Fenner School of Environment and Society; Australian National University; Acton 2601 Australia
| | - Steven L. Chown
- School of Biological Sciences; Monash University; Clayton 3800 Australia
| | - Ceridwen I. Fraser
- Fenner School of Environment and Society; Australian National University; Acton 2601 Australia
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21
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Reisinger RR, Beukes (née Janse van Rensburg) C, Hoelzel AR, de Bruyn PN. Kinship and association in a highly social apex predator population, killer whales at Marion Island. Behav Ecol 2017. [DOI: 10.1093/beheco/arx034] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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22
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Turner Tomaszewicz CN, Seminoff JA, Peckham SH, Avens L, Kurle CM. Intrapopulation variability in the timing of ontogenetic habitat shifts in sea turtles revealed using δ 15 N values from bone growth rings. J Anim Ecol 2017; 86:694-704. [PMID: 28075017 DOI: 10.1111/1365-2656.12618] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 11/24/2016] [Indexed: 11/29/2022]
Abstract
Determining location and timing of ontogenetic shifts in the habitat use of highly migratory species, along with possible intrapopulation variation in these shifts, is essential for understanding mechanisms driving alternate life histories and assessing overall population trends. Measuring variations in multi-year habitat-use patterns is especially difficult for remote oceanic species. To investigate the potential for differential habitat use among migratory marine vertebrates, we measured the naturally occurring stable nitrogen isotope (δ15 N) patterns that differentiate distinct ocean regions to create a 'regional isotope characterization', analysed the δ15 N values from annual bone growth layer rings from dead-stranded animals, and then combined the bone and regional isotope data to track individual animal movement patterns over multiple years. We used humeri from juvenile North Pacific loggerhead turtles (Caretta caretta), animals that undergo long migrations across the North Pacific Ocean (NPO), using multiple discrete regions as they develop to adulthood. Typical of many migratory marine species, ontogenetic changes in habitat use throughout their decades-long juvenile stage is poorly understood, but each potential habitat has unique foraging opportunities and spatially explicit natural and anthropogenic threats that could affect key life-history parameters. We found a bimodal size/age distribution in the timing that juveniles underwent an ontogenetic habitat shift from the oceanic central North Pacific (CNP) to the neritic east Pacific region near the Baja California Peninsula (BCP) (42·7 ± 7·2 vs. 68·3 ± 3·4 cm carapace length, 7·5 ± 2·7 vs. 15·6 ± 1·7 years). Important to the survival of this population, these disparate habitats differ considerably in their food availability, energy requirements and threats, and these differences can influence life-history parameters such as growth, survival and future fecundity. This is the first evidence of alternative ontogenetic shifts and habitat-use patterns for juveniles foraging in the eastern NPO. We combine two techniques, skeletochronology and stable isotope analysis, to reconstruct multi-year habitat-use patterns of a remote migratory species, linked to estimated ages and body sizes of individuals, to reveal variable ontogeny during the juvenile life stage that could drive alternate life histories and that has the potential to illuminate the migration patterns for other species with accretionary tissues.
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Affiliation(s)
- Calandra N Turner Tomaszewicz
- Division of Biological Sciences, Ecology, Behavior, and Evolution Section, University of California, La Jolla, CA, 92093, USA.,Southwest Fisheries Science Center, NOAA-National Marine Fisheries Service, La Jolla, CA, 92037, USA
| | - Jeffrey A Seminoff
- Southwest Fisheries Science Center, NOAA-National Marine Fisheries Service, La Jolla, CA, 92037, USA
| | - S Hoyt Peckham
- Center for Ocean Solutions, Stanford University, Pacific Grove, CA, 93950, USA
| | - Larisa Avens
- Southeast Fisheries Science Center, NOAA-National Marine Fisheries Service, Beaufort, NC, 28516, USA
| | - Carolyn M Kurle
- Division of Biological Sciences, Ecology, Behavior, and Evolution Section, University of California, La Jolla, CA, 92093, USA
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23
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A response to Hoelzel & Moura. Heredity (Edinb) 2016; 118:511-512. [PMID: 27925616 DOI: 10.1038/hdy.2016.118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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24
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Kierepka EM, Latch EK. High gene flow in the American badger overrides habitat preferences and limits broadscale genetic structure. Mol Ecol 2016; 25:6055-6076. [PMID: 27862522 DOI: 10.1111/mec.13915] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 10/13/2016] [Accepted: 11/01/2016] [Indexed: 01/05/2023]
Abstract
Habitat associations are a function of habitat preferences and dispersal capabilities, both of which can influence how species responded to Quaternary climatic changes and contemporary habitat heterogeneity. Predicting resultant genetic structure is not always straightforward, especially in species where high dispersal potential and habitat preferences yield opposing predictions. The American badger has high dispersal capabilities that predict widespread panmixia, but avoids closed-canopy forests and clay soils, which could restrict gene flow and create ecologically based population genetic structure. We used mitochondrial sequence and microsatellite data sets to characterize how these opposing forces contribute to genetic structure in badgers at a continent-wide scale. Our data revealed an overall lack of ecologically based population genetic structure, suggesting that high dispersal capabilities were sufficiently realized to overcome most habitat-based genetic structure. At a broadscale, badger gene flow is limited only by geographic distance (isolation by distance) and large water barriers (Lake Michigan and the Mississippi River). The absence of genetic structure in a species with strong avoidance of unsuitable habitats advances our understanding of when and how genetic structure emerges in widespread, highly mobile species.
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Affiliation(s)
- E M Kierepka
- Behavioral and Molecular Ecology Research Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, 53211, USA
| | - E K Latch
- Behavioral and Molecular Ecology Research Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, 53211, USA
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25
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Killer whales differentiating in geographic sympatry facilitated by divergent behavioural traditions. Heredity (Edinb) 2016; 117:481-482. [PMID: 27804965 DOI: 10.1038/hdy.2016.112] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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26
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Haarsma A, Siepel H, Gravendeel B. Added value of metabarcoding combined with microscopy for evolutionary studies of mammals. ZOOL SCR 2016. [DOI: 10.1111/zsc.12214] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anne‐Jifke Haarsma
- Radboud University Animal Ecology and Physiology department Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
- Naturalis Biodiversity Center Endless Forms group Darwinweg 2 2333 CR Leiden The Netherlands
| | - Henk Siepel
- Radboud University Animal Ecology and Physiology department Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
- Wageningen University Plant Ecology and Nature Conservation group Droevendaalsesteeg 3 6708 AA Wageningen The Netherlands
| | - Barbara Gravendeel
- Naturalis Biodiversity Center Endless Forms group Darwinweg 2 2333 CR Leiden The Netherlands
- University of Applied Sciences Leiden Life Sciences cluster Zernikedreef 11 2333 CK Leiden The Netherlands
- Leiden University Institute Biology Leiden Sylviusweg 72 2333 BE Leiden The Netherlands
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27
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Genome-wide SNP data suggest complex ancestry of sympatric North Pacific killer whale ecotypes. Heredity (Edinb) 2016; 117:316-325. [PMID: 27485668 DOI: 10.1038/hdy.2016.54] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 06/17/2016] [Accepted: 06/21/2016] [Indexed: 02/07/2023] Open
Abstract
Three ecotypes of killer whale occur in partial sympatry in the North Pacific. Individuals assortatively mate within the same ecotype, resulting in correlated ecological and genetic differentiation. A key question is whether this pattern of evolutionary divergence is an example of incipient sympatric speciation from a single panmictic ancestral population, or whether sympatry could have resulted from multiple colonisations of the North Pacific and secondary contact between ecotypes. Here, we infer multilocus coalescent trees from >1000 nuclear single-nucleotide polymorphisms (SNPs) and find evidence of incomplete lineage sorting so that the genealogies of SNPs do not all conform to a single topology. To disentangle whether uncertainty in the phylogenetic inference of the relationships among ecotypes could also result from ancestral admixture events we reconstructed the relationship among the ecotypes as an admixture graph and estimated f4-statistics using TreeMix. The results were consistent with episodes of admixture between two of the North Pacific ecotypes and the two outgroups (populations from the Southern Ocean and the North Atlantic). Gene flow may have occurred via unsampled 'ghost' populations rather than directly between the populations sampled here. Our results indicate that because of ancestral admixture events and incomplete lineage sorting, a single bifurcating tree does not fully describe the relationship among these populations. The data are therefore most consistent with the genomic variation among North Pacific killer whale ecotypes resulting from multiple colonisation events, and secondary contact may have facilitated evolutionary divergence. Thus, the present-day populations of North Pacific killer whale ecotypes have a complex ancestry, confounding the tree-based inference of ancestral geography.
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Genome-culture coevolution promotes rapid divergence of killer whale ecotypes. Nat Commun 2016; 7:11693. [PMID: 27243207 PMCID: PMC4895049 DOI: 10.1038/ncomms11693] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Accepted: 04/18/2016] [Indexed: 12/22/2022] Open
Abstract
Analysing population genomic data from killer whale ecotypes, which we estimate have globally radiated within less than 250,000 years, we show that genetic structuring including the segregation of potentially functional alleles is associated with socially inherited ecological niche. Reconstruction of ancestral demographic history revealed bottlenecks during founder events, likely promoting ecological divergence and genetic drift resulting in a wide range of genome-wide differentiation between pairs of allopatric and sympatric ecotypes. Functional enrichment analyses provided evidence for regional genomic divergence associated with habitat, dietary preferences and post-zygotic reproductive isolation. Our findings are consistent with expansion of small founder groups into novel niches by an initial plastic behavioural response, perpetuated by social learning imposing an altered natural selection regime. The study constitutes an important step towards an understanding of the complex interaction between demographic history, culture, ecological adaptation and evolution at the genomic level. Killer whales have evolved into specialized ecotypes based on hunting strategies and ecological niches. Here, Andrew Foote and colleagues sequenced the whole genome of individual killer whales representing 5 different ecotypes from North Pacific and Antarctic, and show expansion of small founder groups to adapt to specific ecological niches.
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Morin PA, Parsons KM, Archer FI, Ávila-Arcos MC, Barrett-Lennard LG, Dalla Rosa L, Duchêne S, Durban JW, Ellis GM, Ferguson SH, Ford JK, Ford MJ, Garilao C, Gilbert MTP, Kaschner K, Matkin CO, Petersen SD, Robertson KM, Visser IN, Wade PR, Ho SYW, Foote AD. Geographic and temporal dynamics of a global radiation and diversification in the killer whale. Mol Ecol 2015; 24:3964-79. [PMID: 26087773 DOI: 10.1111/mec.13284] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 06/09/2015] [Accepted: 06/17/2015] [Indexed: 02/05/2023]
Abstract
Global climate change during the Late Pleistocene periodically encroached and then released habitat during the glacial cycles, causing range expansions and contractions in some species. These dynamics have played a major role in geographic radiations, diversification and speciation. We investigate these dynamics in the most widely distributed of marine mammals, the killer whale (Orcinus orca), using a global data set of over 450 samples. This marine top predator inhabits coastal and pelagic ecosystems ranging from the ice edge to the tropics, often exhibiting ecological, behavioural and morphological variation suggestive of local adaptation accompanied by reproductive isolation. Results suggest a rapid global radiation occurred over the last 350 000 years. Based on habitat models, we estimated there was only a 15% global contraction of core suitable habitat during the last glacial maximum, and the resources appeared to sustain a constant global effective female population size throughout the Late Pleistocene. Reconstruction of the ancestral phylogeography highlighted the high mobility of this species, identifying 22 strongly supported long-range dispersal events including interoceanic and interhemispheric movement. Despite this propensity for geographic dispersal, the increased sampling of this study uncovered very few potential examples of ancestral dispersal among ecotypes. Concordance of nuclear and mitochondrial data further confirms genetic cohesiveness, with little or no current gene flow among sympatric ecotypes. Taken as a whole, our data suggest that the glacial cycles influenced local populations in different ways, with no clear global pattern, but with secondary contact among lineages following long-range dispersal as a potential mechanism driving ecological diversification.
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Affiliation(s)
- Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla, CA, 92037, USA
| | - Kim M Parsons
- Alaska Fisheries Science Center, National Marine Fisheries Service, NOAA, 7600 Sand Point Way NE, Seattle, WA, 98115, USA
| | - Frederick I Archer
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla, CA, 92037, USA
| | - María C Ávila-Arcos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Lance G Barrett-Lennard
- Vancouver Aquarium Marine Science Centre, 845 Avison Way, Vancouver, British Columbia, V6G 3E2, Canada
| | - Luciano Dalla Rosa
- Laboratório de Ecologia e Conservação da Megafauna Marinha, Instituto de Oceanografia, Universidade Federal do Rio Grande, Av. Itália km. 8 s/n, Campus Carreiros, Rio Grande, RS, 96201-900, Brazil
| | - Sebastián Duchêne
- School of Biological Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - John W Durban
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla, CA, 92037, USA.,Alaska Fisheries Science Center, National Marine Fisheries Service, NOAA, 7600 Sand Point Way NE, Seattle, WA, 98115, USA
| | - Graeme M Ellis
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Rd, Nanaimo, British Columbia, Canada
| | - Steven H Ferguson
- Fisheries & Oceans Canada, 501 University Crescent, Winnipeg, Manitoba, R3T 2N6, Canada
| | - John K Ford
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Rd, Nanaimo, British Columbia, Canada
| | - Michael J Ford
- Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA 2725 Montlake Blvd E, Seattle, WA, USA
| | - Cristina Garilao
- GEOMAR Helmholtz-Zentrum für Ozeanforschung Kiel Düsternbrooker Weg 2, 24105, Kiel, Germany
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark.,Trace and Environmental DNA laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia, 6845, Australia
| | - Kristin Kaschner
- Department of Biometry and Environmental System Analysis, Albert-Ludwigs-University of Freiburg, Tennenbacher Strasse 4, 79106, Freiburg, Germany
| | - Craig O Matkin
- North Gulf Oceanic Society, 3430 Main St. Ste. B1, Homer, AK, 99603, USA
| | - Stephen D Petersen
- Assiniboine Park Zoo, 2595 Roblin Blvd, Winnipeg, Manitoba, R3P 2N7, Canada
| | - Kelly M Robertson
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla, CA, 92037, USA
| | - Ingrid N Visser
- Orca Research Trust, P.O. Box 402043, Tutukaka, Northland, 0153, New Zealand
| | - Paul R Wade
- Alaska Fisheries Science Center, National Marine Fisheries Service, NOAA, 7600 Sand Point Way NE, Seattle, WA, 98115, USA
| | - Simon Y W Ho
- School of Biological Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Andrew D Foote
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark.,Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
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Filatova OA, Miller PJO, Yurk H, Samarra FIP, Hoyt E, Ford JKB, Matkin CO, Barrett-Lennard LG. Killer whale call frequency is similar across the oceans, but varies across sympatric ecotypes. THE JOURNAL OF THE ACOUSTICAL SOCIETY OF AMERICA 2015; 138:251-7. [PMID: 26233024 DOI: 10.1121/1.4922704] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Killer whale populations may differ in genetics, morphology, ecology, and behavior. In the North Pacific, two sympatric populations ("resident" and "transient") specialize on different prey (fish and marine mammals) and retain reproductive isolation. In the eastern North Atlantic, whales from the same populations have been observed feeding on both fish and marine mammals. Fish-eating North Pacific "residents" are more genetically related to eastern North Atlantic killer whales than to sympatric mammal-eating "transients." In this paper, a comparison of frequency variables in killer whale calls recorded from four North Pacific resident, two North Pacific transient, and two eastern North Atlantic populations is reported to assess which factors drive the large-scale changes in call structure. Both low-frequency and high-frequency components of North Pacific transient killer whale calls have significantly lower frequencies than those of the North Pacific resident and North Atlantic populations. The difference in frequencies could be related to ecological specialization or to the phylogenetic history of these populations. North Pacific transient killer whales may have genetically inherited predisposition toward lower frequencies that may shape their learned repertoires.
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Affiliation(s)
- Olga A Filatova
- Department of Vertebrate Zoology, Faculty of Biology, Moscow State University, Moscow 119991, Russia
| | - Patrick J O Miller
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St. Andrews, St. Andrews, Fife KY16 8LB, Scotland
| | - Harald Yurk
- JASCO Applied Sciences Ltd., 2305-4464 Markham Street, Victoria, British Columbia V8Z 7X8, Canada
| | | | - Erich Hoyt
- Whale and Dolphin Conservation, Park House, Allington Park, Bridport, Dorset DT6 5DD, United Kingdom
| | - John K B Ford
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Road, Nanaimo, British Columbia V9T 1K6, Canada
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Resource specialisation and the divergence of killer whale populations. Heredity (Edinb) 2015; 115:93-5. [PMID: 25990875 DOI: 10.1038/hdy.2015.45] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Drivers of Population Structure of the Bottlenose Dolphin (Tursiops truncatus) in the Eastern Mediterranean Sea. Evol Biol 2015. [DOI: 10.1007/s11692-015-9309-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Moura AE, Kenny JG, Chaudhuri R, Hughes MA, J Welch A, Reisinger RR, de Bruyn PJN, Dahlheim ME, Hall N, Hoelzel AR. Population genomics of the killer whale indicates ecotype evolution in sympatry involving both selection and drift. Mol Ecol 2014; 23:5179-92. [PMID: 25244680 PMCID: PMC4237148 DOI: 10.1111/mec.12929] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 09/09/2014] [Accepted: 09/15/2014] [Indexed: 12/30/2022]
Abstract
The evolution of diversity in the marine ecosystem is poorly understood, given the relatively high potential for connectivity, especially for highly mobile species such as whales and dolphins. The killer whale (Orcinus orca) has a worldwide distribution, and individual social groups travel over a wide geographic range. Even so, regional populations have been shown to be genetically differentiated, including among different foraging specialists (ecotypes) in sympatry. Given the strong matrifocal social structure of this species together with strong resource specializations, understanding the process of differentiation will require an understanding of the relative importance of both genetic drift and local adaptation. Here we provide a high-resolution analysis based on nuclear single-nucleotide polymorphic markers and inference about differentiation at both neutral loci and those potentially under selection. We find that all population comparisons, within or among foraging ecotypes, show significant differentiation, including populations in parapatry and sympatry. Loci putatively under selection show a different pattern of structure compared to neutral loci and are associated with gene ontology terms reflecting physiologically relevant functions (e.g. related to digestion). The pattern of differentiation for one ecotype in the North Pacific suggests local adaptation and shows some fixed differences among sympatric ecotypes. We suggest that differential habitat use and resource specializations have promoted sufficient isolation to allow differential evolution at neutral and functional loci, but that the process is recent and dependent on both selection and drift.
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Affiliation(s)
- Andre E Moura
- School of Biological and Biomedical Sciences, Durham University, South Road, Durham, DH1 3LE, UK
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