1
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Nigenda-Morales SF, Lin M, Nuñez-Valencia PG, Kyriazis CC, Beichman AC, Robinson JA, Ragsdale AP, Urbán R J, Archer FI, Viloria-Gómora L, Pérez-Álvarez MJ, Poulin E, Lohmueller KE, Moreno-Estrada A, Wayne RK. The genomic footprint of whaling and isolation in fin whale populations. Nat Commun 2023; 14:5465. [PMID: 37699896 PMCID: PMC10497599 DOI: 10.1038/s41467-023-40052-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/10/2023] [Indexed: 09/14/2023] Open
Abstract
Twentieth century industrial whaling pushed several species to the brink of extinction, with fin whales being the most impacted. However, a small, resident population in the Gulf of California was not targeted by whaling. Here, we analyzed 50 whole-genomes from the Eastern North Pacific (ENP) and Gulf of California (GOC) fin whale populations to investigate their demographic history and the genomic effects of natural and human-induced bottlenecks. We show that the two populations diverged ~16,000 years ago, after which the ENP population expanded and then suffered a 99% reduction in effective size during the whaling period. In contrast, the GOC population remained small and isolated, receiving less than one migrant per generation. However, this low level of migration has been crucial for maintaining its viability. Our study exposes the severity of whaling, emphasizes the importance of migration, and demonstrates the use of genome-based analyses and simulations to inform conservation strategies.
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Affiliation(s)
- Sergio F Nigenda-Morales
- Advanced Genomics Unit, National Laboratory of Genomics for Biodiversity (Langebio), Center for Research and Advanced Studies (Cinvestav), Irapuato, Guanajuato, 36824, Mexico.
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA, 92096, USA.
| | - Meixi Lin
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA.
| | - Paulina G Nuñez-Valencia
- Advanced Genomics Unit, National Laboratory of Genomics for Biodiversity (Langebio), Center for Research and Advanced Studies (Cinvestav), Irapuato, Guanajuato, 36824, Mexico
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
| | - Christopher C Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Annabel C Beichman
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Jacqueline A Robinson
- Institute for Human Genetics, University of California, San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - Aaron P Ragsdale
- Advanced Genomics Unit, National Laboratory of Genomics for Biodiversity (Langebio), Center for Research and Advanced Studies (Cinvestav), Irapuato, Guanajuato, 36824, Mexico
- Department of Integrative Biology, University of Wisconsin, Madison, WI, 53706, USA
| | - Jorge Urbán R
- Departamento de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur (UABCS), La Paz, Baja California Sur, Mexico
| | - Frederick I Archer
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, La Jolla, CA, 92037, USA
| | - Lorena Viloria-Gómora
- Departamento de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur (UABCS), La Paz, Baja California Sur, Mexico
| | - María José Pérez-Álvarez
- Escuela de Medicina Veterinaria, Facultad de Medicina y Ciencias de la Salud, Universidad Mayor, Santiago, Chile
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Universidad de Chile, Santiago, Chile
| | - Elie Poulin
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Universidad de Chile, Santiago, Chile
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA, 90095, USA.
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
| | - Andrés Moreno-Estrada
- Advanced Genomics Unit, National Laboratory of Genomics for Biodiversity (Langebio), Center for Research and Advanced Studies (Cinvestav), Irapuato, Guanajuato, 36824, Mexico.
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
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2
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Suárez-Menéndez M, Bérubé M, Furni F, Rivera-León VE, Heide-Jørgensen MP, Larsen F, Sears R, Ramp C, Eriksson BK, Etienne RS, Robbins J, Palsbøll PJ. Wild pedigrees inform mutation rates and historic abundance in baleen whales. Science 2023; 381:990-995. [PMID: 37651509 DOI: 10.1126/science.adf2160] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 07/25/2023] [Indexed: 09/02/2023]
Abstract
Phylogeny-based estimates suggesting a low germline mutation rate (μ) in baleen whales have influenced research ranging from assessments of whaling impacts to evolutionary cancer biology. We estimated μ directly from pedigrees in four baleen whale species for both the mitochondrial control region and nuclear genome. The results suggest values higher than those obtained through phylogeny-based estimates and similar to pedigree-based values for primates and toothed whales. Applying our estimate of μ reduces previous genetic-based estimates of preexploitation whale abundance by 86% and suggests that μ cannot explain low cancer rates in gigantic mammals. Our study shows that it is feasible to estimate μ directly from pedigrees in natural populations, with wide-ranging implications for ecological and evolutionary research.
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Affiliation(s)
- Marcos Suárez-Menéndez
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Martine Bérubé
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
- Center for Coastal Studies, Provincetown, MA, USA
| | - Fabrício Furni
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Vania E Rivera-León
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | | | - Finn Larsen
- National Institute of Aquatic Resources, Kongens Lyngby, Denmark
| | - Richard Sears
- Mingan Island Cetacean Study Inc., St. Lambert, Quebec, Canada
| | - Christian Ramp
- Mingan Island Cetacean Study Inc., St. Lambert, Quebec, Canada
- Scottish Oceans Institute, University of St. Andrews, St. Andrews, UK
| | - Britas Klemens Eriksson
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Rampal S Etienne
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | | | - Per J Palsbøll
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
- Center for Coastal Studies, Provincetown, MA, USA
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3
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Post-whaling shift in mating tactics in male humpback whales. Commun Biol 2023; 6:162. [PMID: 36797323 PMCID: PMC9935900 DOI: 10.1038/s42003-023-04509-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 01/20/2023] [Indexed: 02/18/2023] Open
Abstract
Recent studies have shown behavioural plasticity in mating strategies can increase a population's ability to cope with anthropogenic impacts. The eastern Australian humpback whale population was whaled almost to extinction in the 1960s (~200 whales) and has recovered to pre-whaling numbers (>20,000 whales). Using an 18-year dataset, where the population increased from approximately 3,700 to 27,000 whales, we found that as male density increased over time, the use of mating tactics shifted towards more males engaging in non-singing physical competition over singing. Singing was the more successful tactic in earlier post-whaling years whereas non-singing behaviour was the more successful tactic in later years. Together, our study uncovers how changes in both local, and population-level male density resulted in a shift in the frequency, and fitness pay-off, of alternative mating tactics in a wild animal. This individual-level plasticity in male humpback whale mating tactics likely contributed to minimising their risk of extinction following a dramatic change in their social landscape due to whaling.
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4
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Pershing AJ, Stamieszkin K. The North Atlantic Ecosystem, from Plankton to Whales. ANNUAL REVIEW OF MARINE SCIENCE 2020; 12:339-359. [PMID: 31226030 DOI: 10.1146/annurev-marine-010419-010752] [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] [Indexed: 06/09/2023]
Abstract
Compared with terrestrial ecosystems, marine ecosystems have a higher proportion of heterotrophic biomass. Building from this observation, we define the North Atlantic biome as the region where the large, lipid-rich copepod Calanus finmarchicus is the dominant mesozooplankton species. This species is superbly adapted to take advantage of the intense pulse of productivity associated with the North Atlantic spring bloom. Most of the characteristic North Atlantic species, including cod, herring, and right whales, rely on C. finmarchicus either directly or indirectly. The notion of a biome rests inherently on an assumption of stability, yet conditions in the North Atlantic are anything but stable. Humans have reduced the abundance of many fish and whales (though some recovery is underway). Humans are also introducing physical and chemical trends associated with global climate change. Thus, the future of the North Atlantic depends on the biome's newest species, Homo sapiens.
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Affiliation(s)
| | - Karen Stamieszkin
- Virginia Institute for Marine Sciences, Gloucester Point, Virginia 23062, USA;
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5
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Tollis M, Robbins J, Webb AE, Kuderna LFK, Caulin AF, Garcia JD, Bèrubè M, Pourmand N, Marques-Bonet T, O’Connell MJ, Palsbøll PJ, Maley CC. Return to the Sea, Get Huge, Beat Cancer: An Analysis of Cetacean Genomes Including an Assembly for the Humpback Whale (Megaptera novaeangliae). Mol Biol Evol 2019; 36:1746-1763. [PMID: 31070747 PMCID: PMC6657726 DOI: 10.1093/molbev/msz099] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Cetaceans are a clade of highly specialized aquatic mammals that include the largest animals that have ever lived. The largest whales can have ∼1,000× more cells than a human, with long lifespans, leaving them theoretically susceptible to cancer. However, large-bodied and long-lived animals do not suffer higher risks of cancer mortality than humans-an observation known as Peto's Paradox. To investigate the genomic bases of gigantism and other cetacean adaptations, we generated a de novo genome assembly for the humpback whale (Megaptera novaeangliae) and incorporated the genomes of ten cetacean species in a comparative analysis. We found further evidence that rorquals (family Balaenopteridae) radiated during the Miocene or earlier, and inferred that perturbations in abundance and/or the interocean connectivity of North Atlantic humpback whale populations likely occurred throughout the Pleistocene. Our comparative genomic results suggest that the evolution of cetacean gigantism was accompanied by strong selection on pathways that are directly linked to cancer. Large segmental duplications in whale genomes contained genes controlling the apoptotic pathway, and genes inferred to be under accelerated evolution and positive selection in cetaceans were enriched for biological processes such as cell cycle checkpoint, cell signaling, and proliferation. We also inferred positive selection on genes controlling the mammalian appendicular and cranial skeletal elements in the cetacean lineage, which are relevant to extensive anatomical changes during cetacean evolution. Genomic analyses shed light on the molecular mechanisms underlying cetacean traits, including gigantism, and will contribute to the development of future targets for human cancer therapies.
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Affiliation(s)
- Marc Tollis
- Biodesign Institute, Arizona State University, Tempe, AZ
- School of Life Sciences, Arizona State University, Tempe, AZ
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ
| | | | - Andrew E Webb
- Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA
| | | | - Aleah F Caulin
- Genomics and Computational Biology Program, University of Pennsylvania, Philadelphia, PA
| | | | - Martine Bèrubè
- Center for Coastal Studies, Provincetown, MA
- Groningen Institute of Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Nader Pourmand
- Jack Baskin School of Engineering, University of California Santa Cruz, Santa Cruz, CA
| | - Tomas Marques-Bonet
- Instituto de Biologia Evolutiva (UPF-CSIC), PRBB, Barcelona, Spain
- CNAG‐CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, Barcelona, Spain
| | - Mary J O’Connell
- Computational and Molecular Evolutionary Biology Research Group, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Per J Palsbøll
- Center for Coastal Studies, Provincetown, MA
- Groningen Institute of Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Carlo C Maley
- Biodesign Institute, Arizona State University, Tempe, AZ
- School of Life Sciences, Arizona State University, Tempe, AZ
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6
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Incorporating non-equilibrium dynamics into demographic history inferences of a migratory marine species. Heredity (Edinb) 2018; 122:53-68. [PMID: 29720718 DOI: 10.1038/s41437-018-0077-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 03/08/2018] [Accepted: 03/17/2018] [Indexed: 01/26/2023] Open
Abstract
Understanding how dispersal and gene flow link geographically separated the populations over evolutionary history is challenging, particularly in migratory marine species. In southern right whales (SRWs, Eubalaena australis), patterns of genetic diversity are likely influenced by the glacial climate cycle and recent history of whaling. Here we use a dataset of mitochondrial DNA (mtDNA) sequences (n = 1327) and nuclear markers (17 microsatellite loci, n = 222) from major wintering grounds to investigate circumpolar population structure, historical demography and effective population size. Analyses of nuclear genetic variation identify two population clusters that correspond to the South Atlantic and Indo-Pacific ocean basins that have similar effective breeder estimates. In contrast, all wintering grounds show significant differentiation for mtDNA, but no sex-biased dispersal was detected using the microsatellite genotypes. An approximate Bayesian computation (ABC) approach with microsatellite markers compared the scenarios with gene flow through time, or isolation and secondary contact between ocean basins, while modelling declines in abundance linked to whaling. Secondary-contact scenarios yield the highest posterior probabilities, implying that populations in different ocean basins were largely isolated and came into secondary contact within the last 25,000 years, but the role of whaling in changes in genetic diversity and gene flow over recent generations could not be resolved. We hypothesise that these findings are driven by factors that promote isolation, such as female philopatry, and factors that could promote dispersal, such as oceanographic changes. These findings highlight the application of ABC approaches to infer the connectivity in mobile species with complex population histories and, currently, low levels of differentiation.
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7
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Cypriano-Souza AL, da Silva TF, Engel MH, Bonatto SL. Effective population size and the genetic consequences of commercial whaling on the humpback whales (Megaptera novaeangliae) from Southwestern Atlantic Ocean. Genet Mol Biol 2018; 41:253-262. [PMID: 29668011 PMCID: PMC5913722 DOI: 10.1590/1678-4685-gmb-2017-0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 08/01/2017] [Indexed: 11/21/2022] Open
Abstract
Genotypes of 10 microsatellite loci of 420 humpback whales from the Southwestern Atlantic Ocean population were used to estimate for the first time its contemporary effective (Ne) and census (Nc) population sizes and to test the genetic effect of commercial whaling. The results are in agreement with our previous studies that found high genetic diversity for this breeding population. Using an approximate Bayesian computation approach, the scenario of constant Ne was significantly supported over scenarios with moderate to strong size changes during the commercial whaling period. The previous generation Nc (Ne multiplied by 3.6), which should corresponds to the years between around 1980 and 1990, was estimated between ~2,600 and 6,800 whales (point estimate ~4,000), and is broadly compatible with the recent abundance surveys extrapolated to the past using a growth rate of 7.4% per annum. The long-term Nc in the constant scenario (point estimate ~15,000) was broadly compatible (considering the confidence interval) with pre-whaling catch records estimates (point estimate ~25,000). Overall, our results shown that the Southwestern Atlantic Ocean humpback whale population is genetically very diverse and resisted well to the strong population reduction during commercial whaling.
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Affiliation(s)
- Ana Lúcia Cypriano-Souza
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil.,Projeto Baleia Jubarte/Instituto Baleia Jubarte, Caravelas, BA, Brazil
| | - Tiago Ferraz da Silva
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil.,Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo (USP), São Paulo, SP, Brazil
| | - Márcia H Engel
- Projeto Baleia Jubarte/Instituto Baleia Jubarte, Caravelas, BA, Brazil
| | - Sandro L Bonatto
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
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8
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Rosenbaum HC, Kershaw F, Mendez M, Pomilla C, Leslie MS, Findlay KP, Best PB, Collins T, Vely M, Engel MH, Baldwin R, Minton G, Meÿer M, Flórez-González L, Poole MM, Hauser N, Garrigue C, Brasseur M, Bannister J, Anderson M, Olavarría C, Baker CS. First circumglobal assessment of Southern Hemisphere humpback whale mitochondrial genetic variation and implications for management. ENDANGER SPECIES RES 2017. [DOI: 10.3354/esr00822] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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9
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Guevara EE, Frankel DC, Ranaivonasy J, Richard AF, Ratsirarson J, Lawler RR, Bradley BJ. A simple, economical protocol for DNA extraction and amplification where there is no lab. CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0758-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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10
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Resetting predator baselines in coral reef ecosystems. Sci Rep 2017; 7:43131. [PMID: 28220895 PMCID: PMC5318939 DOI: 10.1038/srep43131] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 01/19/2017] [Indexed: 11/18/2022] Open
Abstract
What did coral reef ecosystems look like before human impacts became pervasive? Early efforts to reconstruct baselines resulted in the controversial suggestion that pristine coral reefs have inverted trophic pyramids, with disproportionally large top predator biomass. The validity of the coral reef inverted trophic pyramid has been questioned, but until now, was not resolved empirically. We use data from an eight-year tag-recapture program with spatially explicit, capture-recapture models to re-examine the population size and density of a key top predator at Palmyra atoll, the same location that inspired the idea of inverted trophic biomass pyramids in coral reef ecosystems. Given that animal movement is suspected to have significantly biased early biomass estimates of highly mobile top predators, we focused our reassessment on the most mobile and most abundant predator at Palmyra, the grey reef shark (Carcharhinus amblyrhynchos). We estimated a density of 21.3 (95% CI 17.8, 24.7) grey reef sharks/km2, which is an order of magnitude lower than the estimates that suggested an inverted trophic pyramid. Our results indicate that the trophic structure of an unexploited reef fish community is not inverted, and that even healthy top predator populations may be considerably smaller, and more precarious, than previously thought.
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11
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Kershaw F, Carvalho I, Loo J, Pomilla C, Best PB, Findlay KP, Cerchio S, Collins T, Engel MH, Minton G, Ersts P, Barendse J, Kotze PGH, Razafindrakoto Y, Ngouessono S, Meÿer M, Thornton M, Rosenbaum HC. Multiple processes drive genetic structure of humpback whale (Megaptera novaeangliae) populations across spatial scales. Mol Ecol 2017; 26:977-994. [DOI: 10.1111/mec.13943] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 10/01/2016] [Accepted: 11/16/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Francine Kershaw
- Columbia University; 116th Street and Broadway New York NY 10027 USA
| | - Inês Carvalho
- Population and Conservation Genetics Group; Instituto Gulbenkian de Ciência; Rua da Quinta Grande, 6 2780-156 Oeiras Portugal
- Centre for Environmental and Marine Studies (CESAM); Universidade de Aveiro; Campus Universitário de Santiago 3810-193 Aveiro Portugal
| | - Jacqueline Loo
- Department of Biology; New York University; 100 Washington Square New York NY 10012 USA
| | - Cristina Pomilla
- Wellcome Trust Sanger Institute; Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SA UK
| | - Peter B. Best
- Mammal Research Institute; University of Pretoria; c/o Iziko South African Museum, P.O. Box 61 Cape Town 8000 South Africa
| | - Ken P. Findlay
- Mammal Research Institute; University of Pretoria; c/o Iziko South African Museum, P.O. Box 61 Cape Town 8000 South Africa
| | - Salvatore Cerchio
- Wildlife Conservation Society; Ocean Giants Program; 2300 Southern Blvd. Bronx NY 10460-1099 USA
| | - Tim Collins
- Wildlife Conservation Society; Ocean Giants Program; 2300 Southern Blvd. Bronx NY 10460-1099 USA
- Environment Society of Oman; P.O. Box 3955 PC 112 Ruwi Sultanate of Oman
| | - Marcia H. Engel
- Humpback Whale Project/Humpback Whale Institute; Rua Barão do Rio Branco, 125 Caravelas Bahia Brazil
| | - Gianna Minton
- Environment Society of Oman; P.O. Box 3955 PC 112 Ruwi Sultanate of Oman
| | - Peter Ersts
- Center for Biodiversity and Conservation; American Museum of Natural History; Central Park West at 79th Street New York NY 10024 USA
| | - Jaco Barendse
- Mammal Research Institute; University of Pretoria; c/o Iziko South African Museum, P.O. Box 61 Cape Town 8000 South Africa
| | - P. G. H. Kotze
- Department of Environmental Affairs; Branch Oceans and Coasts; Private Bag x2, Roggebaai 8012 Cape Town South Africa
| | - Yvette Razafindrakoto
- Wildlife Conservation Society-Madagascar Program; 2300 Southern Blvd. Bronx NY 10460-1099 USA
| | - Solange Ngouessono
- Agence Nationale des Parcs Nationaux; Batterie 4 BP 20379 Libreville Gabon
| | - Michael Meÿer
- Department of Environmental Affairs; Branch Oceans and Coasts; Private Bag x2, Roggebaai 8012 Cape Town South Africa
| | - Meredith Thornton
- Mammal Research Institute; University of Pretoria; c/o Iziko South African Museum, P.O. Box 61 Cape Town 8000 South Africa
| | - Howard C. Rosenbaum
- Wildlife Conservation Society; Ocean Giants Program; 2300 Southern Blvd. Bronx NY 10460-1099 USA
- Sackler Institute for Comparative Genomics; American Museum of Natural History; Central Park West at 79th Street New York NY 10024 USA
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12
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Drew J, López EH, Gill L, McKeon M, Miller N, Steinberg M, Shen C, McClenachan L. Collateral damage to marine and terrestrial ecosystems from Yankee whaling in the 19th century. Ecol Evol 2016; 6:8181-8192. [PMID: 27878087 PMCID: PMC5108269 DOI: 10.1002/ece3.2542] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 08/29/2016] [Accepted: 09/04/2016] [Indexed: 11/21/2022] Open
Abstract
Yankee whalers of the 19th century had major impacts on populations of large whales, but these leviathans were not the only taxa targeted. Here, we describe the “collateral damage,” the opportunistic or targeted taking of nongreat whale species by the American whaling industry. Using data from 5,064 records from 79 whaling logs occurring between 1840 and 1901, we show that Yankee whalers captured 5,255 animals across three large ocean basins from 32 different taxonomic categories, including a wide range of marine and terrestrial species. The taxa with the greatest number of individuals captured were walruses (Odobenus rosmarus), ducks (family Anatidae), and cod (Gadus sp.). By biomass, the most captured species were walruses, grampus (a poorly defined group within Odontoceti), and seals (family Otariidae). The whalers captured over 2.4 million kg of nongreat whale meat equaling approximately 34 kg of meat per ship per day at sea. The species and areas targeted shifted over time in response to overexploitation of whale populations, with likely intensive local impacts on terrestrial species associated with multiyear whaling camps. Our results show that the ecosystem impacts of whaling reverberated on both marine and coastal environments.
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Affiliation(s)
- Joshua Drew
- Department of Ecology, Evolution and Environmental Biology Columbia University New York NY USA; Department of Vertebrate Zoology American Museum of Natural History New York NY USA
| | - Elora H López
- Department of Ecology, Evolution and Environmental Biology Columbia University New York NY USA; Present address: Hopkins Marine Station Department of Biology Stanford University Pacific Grove CA USA
| | - Lucy Gill
- Department of Ecology, Evolution and Environmental Biology Columbia University New York NY USA
| | - Mallory McKeon
- Department of Ecology, Evolution and Environmental Biology Columbia University New York NY USA
| | - Nathan Miller
- Department of Ecology, Evolution and Environmental Biology Columbia University New York NY USA; Present address: Nichols School of the Environment Duke University Durham NC USA
| | - Madeline Steinberg
- Department of Environmental Science Barnard College Columbia University New York NY USA
| | - Christa Shen
- Department of Ecology, Evolution and Environmental Biology Columbia University New York NY USA
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13
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Cammen KM, Andrews KR, Carroll EL, Foote AD, Humble E, Khudyakov JI, Louis M, McGowen MR, Olsen MT, Van Cise AM. Genomic Methods Take the Plunge: Recent Advances in High-Throughput Sequencing of Marine Mammals. J Hered 2016; 107:481-95. [PMID: 27511190 DOI: 10.1093/jhered/esw044] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/12/2016] [Indexed: 12/18/2022] Open
Abstract
The dramatic increase in the application of genomic techniques to non-model organisms (NMOs) over the past decade has yielded numerous valuable contributions to evolutionary biology and ecology, many of which would not have been possible with traditional genetic markers. We review this recent progression with a particular focus on genomic studies of marine mammals, a group of taxa that represent key macroevolutionary transitions from terrestrial to marine environments and for which available genomic resources have recently undergone notable rapid growth. Genomic studies of NMOs utilize an expanding range of approaches, including whole genome sequencing, restriction site-associated DNA sequencing, array-based sequencing of single nucleotide polymorphisms and target sequence probes (e.g., exomes), and transcriptome sequencing. These approaches generate different types and quantities of data, and many can be applied with limited or no prior genomic resources, thus overcoming one traditional limitation of research on NMOs. Within marine mammals, such studies have thus far yielded significant contributions to the fields of phylogenomics and comparative genomics, as well as enabled investigations of fitness, demography, and population structure. Here we review the primary options for generating genomic data, introduce several emerging techniques, and discuss the suitability of each approach for different applications in the study of NMOs.
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Affiliation(s)
- Kristina M Cammen
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise).
| | - Kimberly R Andrews
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Emma L Carroll
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Andrew D Foote
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Emily Humble
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Jane I Khudyakov
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Marie Louis
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Michael R McGowen
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Morten Tange Olsen
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Amy M Van Cise
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
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14
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Jackson JA, Carroll EL, Smith TD, Zerbini AN, Patenaude NJ, Baker CS. An integrated approach to historical population assessment of the great whales: case of the New Zealand southern right whale. ROYAL SOCIETY OPEN SCIENCE 2016; 3:150669. [PMID: 27069657 PMCID: PMC4821268 DOI: 10.1098/rsos.150669] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 02/16/2016] [Indexed: 05/06/2023]
Abstract
Accurate estimation of historical abundance provides an essential baseline for judging the recovery of the great whales. This is particularly challenging for whales hunted prior to twentieth century modern whaling, as population-level catch records are often incomplete. Assessments of whale recovery using pre-modern exploitation indices are therefore rare, despite the intensive, global nature of nineteenth century whaling. Right whales (Eubalaena spp.) were particularly exploited: slow swimmers with strong fidelity to sheltered calving bays, the species made predictable and easy targets. Here, we present the first integrated population-level assessment of the whaling impact and pre-exploitation abundance of a right whale, the New Zealand southern right whale (E. australis). In this assessment, we use a Bayesian population dynamics model integrating multiple data sources: nineteenth century catches, genetic constraints on bottleneck size and individual sightings histories informing abundance and trend. Different catch allocation scenarios are explored to account for uncertainty in the population's offshore distribution. From a pre-exploitation abundance of 28 800-47 100 whales, nineteenth century hunting reduced the population to approximately 30-40 mature females between 1914 and 1926. Today, it stands at less than 12% of pre-exploitation abundance. Despite the challenges of reconstructing historical catches and population boundaries, conservation efforts of historically exploited species benefit from targets for ecological restoration.
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Affiliation(s)
- Jennifer A. Jackson
- British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge, UK
- Author for correspondence: Jennifer A. Jackson e-mail:
| | - Emma L. Carroll
- Scottish Oceans Institute, School of Biology, University of St Andrews, Fife, St Andrews KY16 8LB, UK
| | | | - Alexandre N. Zerbini
- National Marine Mammal Laboratory, Alaska Fisheries Science Center, NOAA Fisheries, 7600 Sand Point Way NE, Seattle, WA 98115-6349, USA
- Cascadia Research Collective, 218 1/2 W 4th Ave, Olympia, WA 98501, USA
- Instituto Aqualie, Av. Dr Paulo Japiassu Coelho, 714, Sala 206, Juiz de Fora, Minas Gerais, Brazil
| | | | - C. Scott Baker
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
- Marine Mammal Institute and Department of Fisheries and Wildlife, Hatfield Marine Science Center, Oregon State University, Newport, OR 97365, USA
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15
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Collins CJ, Chilvers BL, Taylor M, Robertson BC. Historical population size of the threatened New Zealand sea lion
Phocarctos hookeri. J Mammal 2015. [DOI: 10.1093/jmammal/gyv187] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Marine mammal species were exploited worldwide during periods of commercial sealing in the 18th and 19th centuries. For many of these species, an estimate of the pre-exploitation abundance of the species is lacking, as historical catch records are generally scarce and inaccurate. Genetic estimates of long-term effective population size provide a means to estimate the pre-exploitation abundance. Here, we apply genetic methods to estimate the long-term effective population size of the subantarctic lineage of the New Zealand sea lion (NZ sea lion), Phocarctos hookeri . This species is predominantly restricted to the subantarctic islands, south of mainland New Zealand, following commercial sealing in the 19th century. Today, the population consists of ~9,880 animals and population growth is slow. Auckland Island breeding colonies of NZ sea lion are currently impacted by commercial trawl fisheries via regular sea lion deaths as bycatch. In order to estimate sustainable levels of bycatch, an estimate of the population’s carrying capacity ( K ) is required. We apply the genetically estimated long-term effective population size of NZ sea lions as a proxy for the estimated historical carrying capacity of the subantarctic population. The historical abundance of subantarctic NZ sea lions was significantly higher than the target values of K employed by the contemporary management. The current management strategy may allow unsustainable bycatch levels, thereby limiting the recovery of the NZ sea lion population toward historical carrying capacity.
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Affiliation(s)
- Catherine J. Collins
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago , P.O. Box 56, Dunedin 9016 , New Zealand (CJC, MT, BCR)
- Department of Conservation, Marine Species and Threats , Wellington 6011 , New Zealand (BLC)
- Wildbase, IVABS, Massey University , Private Bag 11–222, Palmerston North 4442 , New Zealand (BLC)
| | - B. Louise Chilvers
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago , P.O. Box 56, Dunedin 9016 , New Zealand (CJC, MT, BCR)
- Department of Conservation, Marine Species and Threats , Wellington 6011 , New Zealand (BLC)
- Wildbase, IVABS, Massey University , Private Bag 11–222, Palmerston North 4442 , New Zealand (BLC)
| | - Matthew Taylor
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago , P.O. Box 56, Dunedin 9016 , New Zealand (CJC, MT, BCR)
- Department of Conservation, Marine Species and Threats , Wellington 6011 , New Zealand (BLC)
- Wildbase, IVABS, Massey University , Private Bag 11–222, Palmerston North 4442 , New Zealand (BLC)
| | - Bruce C. Robertson
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago , P.O. Box 56, Dunedin 9016 , New Zealand (CJC, MT, BCR)
- Department of Conservation, Marine Species and Threats , Wellington 6011 , New Zealand (BLC)
- Wildbase, IVABS, Massey University , Private Bag 11–222, Palmerston North 4442 , New Zealand (BLC)
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16
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McClenachan L, Cooper AB, McKenzie MG, Drew JA. The Importance of Surprising Results and Best Practices in Historical Ecology. Bioscience 2015. [DOI: 10.1093/biosci/biv100] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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17
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Pomilla C, Amaral AR, Collins T, Minton G, Findlay K, Leslie MS, Ponnampalam L, Baldwin R, Rosenbaum H. The world's most isolated and distinct whale population? Humpback whales of the Arabian Sea. PLoS One 2014; 9:e114162. [PMID: 25470144 PMCID: PMC4254934 DOI: 10.1371/journal.pone.0114162] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 11/04/2014] [Indexed: 11/18/2022] Open
Abstract
A clear understanding of population structure is essential for assessing conservation status and implementing management strategies. A small, non-migratory population of humpback whales in the Arabian Sea is classified as "Endangered" on the IUCN Red List of Threatened Species, an assessment constrained by a lack of data, including limited understanding of its relationship to other populations. We analysed 11 microsatellite markers and mitochondrial DNA sequences extracted from 67 Arabian Sea humpback whale tissue samples and compared them to equivalent datasets from the Southern Hemisphere and North Pacific. Results show that the Arabian Sea population is highly distinct; estimates of gene flow and divergence times suggest a Southern Indian Ocean origin but indicate that it has been isolated for approximately 70,000 years, remarkable for a species that is typically highly migratory. Genetic diversity values are significantly lower than those obtained for Southern Hemisphere populations and signatures of ancient and recent genetic bottlenecks were identified. Our findings suggest this is the world's most isolated humpback whale population, which, when combined with low population abundance estimates and anthropogenic threats, raises concern for its survival. We recommend an amendment of the status of the population to "Critically Endangered" on the IUCN Red List.
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Affiliation(s)
- Cristina Pomilla
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
| | - Ana R. Amaral
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
- Centro de Biologia Ambiental, Faculdade de Ciências Universidade de Lisboa, Lisboa, Portugal
| | - Tim Collins
- Ocean Giants Program, Wildlife Conservation Society, Bronx, New York, United States of America
- Environment Society of Oman, Ruwi, Sultanate of Oman
| | - Gianna Minton
- Environment Society of Oman, Ruwi, Sultanate of Oman
- World Wide Fund for Nature, Gabon, Libreville, Gabon
| | - Ken Findlay
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Matthew S. Leslie
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
- Ocean Giants Program, Wildlife Conservation Society, Bronx, New York, United States of America
| | - Louisa Ponnampalam
- Environment Society of Oman, Ruwi, Sultanate of Oman
- Institute of Ocean and Earth Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | | | - Howard Rosenbaum
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
- Ocean Giants Program, Wildlife Conservation Society, Bronx, New York, United States of America
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18
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Jackson JA, Steel DJ, Beerli P, Congdon BC, Olavarría C, Leslie MS, Pomilla C, Rosenbaum H, Baker CS. Global diversity and oceanic divergence of humpback whales (Megaptera novaeangliae). Proc Biol Sci 2014; 281:20133222. [PMID: 24850919 PMCID: PMC4046397 DOI: 10.1098/rspb.2013.3222] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Accepted: 04/22/2014] [Indexed: 11/12/2022] Open
Abstract
Humpback whales (Megaptera novaeangliae) annually undertake the longest migrations between seasonal feeding and breeding grounds of any mammal. Despite this dispersal potential, discontinuous seasonal distributions and migratory patterns suggest that humpbacks form discrete regional populations within each ocean. To better understand the worldwide population history of humpbacks, and the interplay of this species with the oceanic environment through geological time, we assembled mitochondrial DNA control region sequences representing approximately 2700 individuals (465 bp, 219 haplotypes) and eight nuclear intronic sequences representing approximately 70 individuals (3700 bp, 140 alleles) from the North Pacific, North Atlantic and Southern Hemisphere. Bayesian divergence time reconstructions date the origin of humpback mtDNA lineages to the Pleistocene (880 ka, 95% posterior intervals 550-1320 ka) and estimate radiation of current Northern Hemisphere lineages between 50 and 200 ka, indicating colonization of the northern oceans prior to the Last Glacial Maximum. Coalescent analyses reveal restricted gene flow between ocean basins, with long-term migration rates (individual migrants per generation) of less than 3.3 for mtDNA and less than 2 for nuclear genomic DNA. Genetic evidence suggests that humpbacks in the North Pacific, North Atlantic and Southern Hemisphere are on independent evolutionary trajectories, supporting taxonomic revision of M. novaeangliae to three subspecies.
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Affiliation(s)
- Jennifer A Jackson
- Marine Mammal Institute, Hatfield Marine Science Center, Oregon State University, 2030 SE Marine Science Drive, Newport, OR 97365, USA British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge CB3 0ET, UK
| | - Debbie J Steel
- British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge CB3 0ET, UK
| | - P Beerli
- Department of Scientific Computing, Florida State University, Tallahassee, FL 32306, USA
| | - Bradley C Congdon
- School of Marine and Tropical Biology, James Cook University, Cairns, Queensland 4870, Australia
| | - Carlos Olavarría
- School of Biological Sciences, Auckland University, 3a Symonds Street, Auckland 1010, New Zealand Fundación CEQUA, Punta Arenas, Chile
| | - Matthew S Leslie
- Ocean Giants Program, Global Conservation-Marine, Wildlife Conservation Society, 2300 Southern Boulevard, Bronx, NY 10460, USA Sackler Institute for Comparative Genomics, American Museum of Natural History, 79th Street and Central Park West, New York, NY, USA
| | - Cristina Pomilla
- Ocean Giants Program, Global Conservation-Marine, Wildlife Conservation Society, 2300 Southern Boulevard, Bronx, NY 10460, USA Sackler Institute for Comparative Genomics, American Museum of Natural History, 79th Street and Central Park West, New York, NY, USA
| | - Howard Rosenbaum
- Ocean Giants Program, Global Conservation-Marine, Wildlife Conservation Society, 2300 Southern Boulevard, Bronx, NY 10460, USA Sackler Institute for Comparative Genomics, American Museum of Natural History, 79th Street and Central Park West, New York, NY, USA
| | - C Scott Baker
- Marine Mammal Institute, Hatfield Marine Science Center, Oregon State University, 2030 SE Marine Science Drive, Newport, OR 97365, USA School of Biological Sciences, Auckland University, 3a Symonds Street, Auckland 1010, New Zealand
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