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McGowen MR, Tsagkogeorga G, Álvarez-Carretero S, Dos Reis M, Struebig M, Deaville R, Jepson PD, Jarman S, Polanowski A, Morin PA, Rossiter SJ. Phylogenomic Resolution of the Cetacean Tree of Life Using Target Sequence Capture. Syst Biol 2020; 69:479-501. [PMID: 31633766 PMCID: PMC7164366 DOI: 10.1093/sysbio/syz068] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 10/02/2019] [Accepted: 10/06/2019] [Indexed: 12/20/2022] Open
Abstract
The evolution of cetaceans, from their early transition to an aquatic lifestyle to their subsequent diversification, has been the subject of numerous studies. However, although the higher-level relationships among cetacean families have been largely settled, several aspects of the systematics within these groups remain unresolved. Problematic clades include the oceanic dolphins (37 spp.), which have experienced a recent rapid radiation, and the beaked whales (22 spp.), which have not been investigated in detail using nuclear loci. The combined application of high-throughput sequencing with techniques that target specific genomic sequences provide a powerful means of rapidly generating large volumes of orthologous sequence data for use in phylogenomic studies. To elucidate the phylogenetic relationships within the Cetacea, we combined sequence capture with Illumina sequencing to generate data for \documentclass[12pt]{minimal}
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}{}$\sim $\end{document}3200 protein-coding genes for 68 cetacean species and their close relatives including the pygmy hippopotamus. By combining data from \documentclass[12pt]{minimal}
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}{}$>$\end{document}38,000 exons with existing sequences from 11 cetaceans and seven outgroup taxa, we produced the first comprehensive comparative genomic data set for cetaceans, spanning 6,527,596 aligned base pairs (bp) and 89 taxa. Phylogenetic trees reconstructed with maximum likelihood and Bayesian inference of concatenated loci, as well as with coalescence analyses of individual gene trees, produced mostly concordant and well-supported trees. Our results completely resolve the relationships among beaked whales as well as the contentious relationships among oceanic dolphins, especially the problematic subfamily Delphinidae. We carried out Bayesian estimation of species divergence times using MCMCTree and compared our complete data set to a subset of clocklike genes. Analyses using the complete data set consistently showed less variance in divergence times than the reduced data set. In addition, integration of new fossils (e.g., Mystacodon selenensis) indicates that the diversification of Crown Cetacea began before the Late Eocene and the divergence of Crown Delphinidae as early as the Middle Miocene. [Cetaceans; phylogenomics; Delphinidae; Ziphiidae; dolphins; whales.]
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Affiliation(s)
- Michael R McGowen
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK.,Department of Vertebrate Zoology, Smithsonian Museum of Natural History, 10th & Constitution Ave. NW, Washington DC 20560, USA
| | - Georgia Tsagkogeorga
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Sandra Álvarez-Carretero
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Mario Dos Reis
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Monika Struebig
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Robert Deaville
- Institute of Zoology, Zoological Society of London, Outer Circle, London NW1 4RY, UK
| | - Paul D Jepson
- Institute of Zoology, Zoological Society of London, Outer Circle, London NW1 4RY, UK
| | - Simon Jarman
- School of Biological Sciences, University of Western Australia, 35 Stirling Highway, Perth WA 6009, Australia
| | - Andrea Polanowski
- Australian Antarctic Division, 203 Channel Highway, Kingston TAS 7050, Australia
| | - Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla CA 92037 USA
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
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Mishima Y, Morisaka T, Ishikawa M, Karasawa Y, Yoshida Y. Pulsed call sequences as contact calls in Pacific white-sided dolphins (Lagenorhynchus obliquidens). THE JOURNAL OF THE ACOUSTICAL SOCIETY OF AMERICA 2019; 146:409. [PMID: 31370601 DOI: 10.1121/1.5116692] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 06/25/2019] [Indexed: 06/10/2023]
Abstract
Pacific white-sided dolphins are a group-living species and appear to exchange "contact calls" to maintain group cohesion. The aim of this study was to find and characterize their contact calls. Calls were recorded from two females at Osaka Aquarium KAIYUKAN (OAK) and three females at Izu-Mito Sea Paradise (IMSP). Because they often produced pulsed calls consecutively, a "pulsed call sequence" was defined as three or more successive pulsed calls occurring within 325 ms, which was calculated using a bout analysis. The pulsed call sequences increased during separation periods and decreased during reunions and were used for vocal exchange, suggesting that the sequences are contact calls in Pacific white-sided dolphins. Most of the pulsed call sequences were classified into unique types; several stereotyped, repeated patterns were found. One sequence type was found at OAK and the two dolphins shared the type; they exchanged sequences with type matching. On the other hand, three sequence types were found in IMSP and the three dolphins shared all of the types; however, each dolphin preferentially used different types and frequently exchanged with their own favorite types but not with type matching. These results suggest that the sequence type may function as an individual and/or group identity.
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Affiliation(s)
- Yuka Mishima
- Department of Marine Resources and Energy, Tokyo University of Marine Science and Technology, 4-5-7, Konan, Minato-ku, Tokyo, 108-8477, Japan
| | - Tadamichi Morisaka
- Cetacean Research Center, Graduate School of Bioresources, Mie University, 1577, Kurimamachiya-cho, Tsu-shi, Mie, 514-8507, Japan
| | - Megumi Ishikawa
- Osaka Aquarium KAIYUKAN, 1-1-10, Kaigandori, Minato-ku, Osaka-shi, Osaka, 552-0022, Japan
| | - Yuu Karasawa
- Izu-Mito Sea Paradise, 3-1, Nagahama, Uchiura, Numazu-shi, Shizuoka, 410-0295, Japan
| | - Yayoi Yoshida
- Department of Environmental and Societal Affairs, School of Marine Science and Technology, Tokai University, 3-20-1, Orido, Shimizu-ku, Shizuoka-shi, Shizuoka, 424-8610, Japan
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Cryptic lineage differentiation among Indo-Pacific bottlenose dolphins (Tursiops aduncus) in the northwest Indian Ocean. Mol Phylogenet Evol 2018; 122:1-14. [DOI: 10.1016/j.ympev.2017.12.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 12/15/2017] [Accepted: 12/26/2017] [Indexed: 11/19/2022]
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Galatius A, Goodall RNP. Skull shapes of the Lissodelphininae: radiation, adaptation and asymmetry. J Morphol 2016; 277:776-85. [DOI: 10.1002/jmor.20535] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 02/01/2016] [Accepted: 02/27/2016] [Indexed: 11/05/2022]
Affiliation(s)
| | - R. Natalie P. Goodall
- Museo Acatushún de Aves y Mamiferos Marines Australes (AMMA); Tierra del Fuego Argentina
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Vollmer NL, Rosel PE. Developing genomic resources for the common bottlenose dolphin (
Tursiops truncatus
): isolation and characterization of 153 single nucleotide polymorphisms and 53 genotyping assays. Mol Ecol Resour 2012; 12:1124-32. [DOI: 10.1111/1755-0998.12008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 07/24/2012] [Accepted: 07/28/2012] [Indexed: 01/24/2023]
Affiliation(s)
- N. L. Vollmer
- Department of Biology University of Louisiana at Lafayette P.O. Box 42451 Lafayette LA 70504 USA
- NOAA National Marine Fisheries Service Southeast Fisheries Science Center 646 Cajundome Blvd. Suite 234 Lafayette LA 70506 USA
| | - P. E. Rosel
- NOAA National Marine Fisheries Service Southeast Fisheries Science Center 646 Cajundome Blvd. Suite 234 Lafayette LA 70506 USA
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THOMPSON RICHARDS, BÄRMANN EVAV, ASHER ROBERTJ. The interpretation of hidden support in combined data phylogenetics. J ZOOL SYST EVOL RES 2012. [DOI: 10.1111/j.1439-0469.2012.00670.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Cunha HA, Moraes LC, Medeiros BV, Lailson-Brito J, da Silva VMF, Solé-Cava AM, Schrago CG. Phylogenetic status and timescale for the diversification of Steno and Sotalia dolphins. PLoS One 2011; 6:e28297. [PMID: 22163290 PMCID: PMC3233566 DOI: 10.1371/journal.pone.0028297] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Accepted: 11/04/2011] [Indexed: 11/18/2022] Open
Abstract
Molecular data have provided many insights into cetacean evolution but some unsettled issues still remain. We estimated the topology and timing of cetacean evolutionary relationships using bayesian and maximum likelihood analyses of complete mitochondrial genomes. In order to clarify the phylogenetic placement of Sotalia and Steno within the Delphinidae, we sequenced three new delphinid mitogenomes. Our analyses support three delphinid clades: one joining Steno and Sotalia (supporting the revised subfamily Stenoninae); another placing Sousa within the Delphininae; and a third, the Globicephalinae, which includes Globicephala, Feresa, Pseudorca, Peponocephala and Grampus. We also conclude that Orcinus does not belong in the Globicephalinae, but Orcaella may be part of that subfamily. Divergence dates were estimated using the relaxed molecular clock calibrated with fossil data. We hypothesise that the timing of separation of the marine and Amazonian Sotalia species (2.3 Ma) coincided with the establishment of the modern Amazon River basin.
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Affiliation(s)
- Haydée A. Cunha
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratório de Mamíferos Aquáticos e Bioindicadores, Faculdade de Oceanografia, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lucas C. Moraes
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bruna V. Medeiros
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - José Lailson-Brito
- Laboratório de Mamíferos Aquáticos e Bioindicadores, Faculdade de Oceanografia, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Vera M. F. da Silva
- Laboratório de Mamíferos Aquáticos, Instituto Nacional de Pesquisas da Amazônia, Amazonas, Brazil
| | - Antonio M. Solé-Cava
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carlos G. Schrago
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- * E-mail:
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Toward the resolution of an explosive radiation—A multilocus phylogeny of oceanic dolphins (Delphinidae). Mol Phylogenet Evol 2011; 60:345-57. [DOI: 10.1016/j.ympev.2011.05.003] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Revised: 04/15/2011] [Accepted: 05/03/2011] [Indexed: 11/22/2022]
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Vilstrup JT, Ho SYW, Foote AD, Morin PA, Kreb D, Krützen M, Parra GJ, Robertson KM, de Stephanis R, Verborgh P, Willerslev E, Orlando L, Gilbert MTP. Mitogenomic phylogenetic analyses of the Delphinidae with an emphasis on the Globicephalinae. BMC Evol Biol 2011; 11:65. [PMID: 21392378 PMCID: PMC3065423 DOI: 10.1186/1471-2148-11-65] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Accepted: 03/10/2011] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Previous DNA-based phylogenetic studies of the Delphinidae family suggest it has undergone rapid diversification, as characterised by unresolved and poorly supported taxonomic relationships (polytomies) for some of the species within this group. Using an increased amount of sequence data we test between alternative hypotheses of soft polytomies caused by rapid speciation, slow evolutionary rate and/or insufficient sequence data, and hard polytomies caused by simultaneous speciation within this family. Combining the mitogenome sequences of five new and 12 previously published species within the Delphinidae, we used Bayesian and maximum-likelihood methods to estimate the phylogeny from partitioned and unpartitioned mitogenome sequences. Further ad hoc tests were then conducted to estimate the support for alternative topologies. RESULTS We found high support for all the relationships within our reconstructed phylogenies, and topologies were consistent between the Bayesian and maximum-likelihood trees inferred from partitioned and unpartitioned data. Resolved relationships included the placement of the killer whale (Orcinus orca) as sister taxon to the rest of the Globicephalinae subfamily, placement of the Risso's dolphin (Grampus griseus) within the Globicephalinae subfamily, removal of the white-beaked dolphin (Lagenorhynchus albirostris) from the Delphininae subfamily and the placement of the rough-toothed dolphin (Steno bredanensis) as sister taxon to the rest of the Delphininae subfamily rather than within the Globicephalinae subfamily. The additional testing of alternative topologies allowed us to reject all other putative relationships, with the exception that we were unable to reject the hypothesis that the relationship between L. albirostris and the Globicephalinae and Delphininae subfamilies was polytomic. CONCLUSION Despite their rapid diversification, the increased sequence data yielded by mitogenomes enables the resolution of a strongly supported, bifurcating phylogeny, and a chronology of the divergences within the Delphinidae family. This highlights the benefits and potential application of large mitogenome datasets to resolve long-standing phylogenetic uncertainties.
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Affiliation(s)
- Julia T Vilstrup
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Simon YW 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
| | - Phillip A Morin
- Southwest Fisheries Science Center, NOAA Fisheries, 3333 N. Torrey Pines Ct., La Jolla, CA, 92037 USA
| | - Danielle Kreb
- Yayasan Konservasi RASI, Samarinda, Kalimantan Timur, Indonesia
| | - Michael Krützen
- Evolutionary Genetics Group, Anthropological Institute and Museum, University of Zurich, Winterthurerstr. 190, 8057 Zurich, Switzerland
| | - Guido J Parra
- School of Biological Sciences, Flinders University, Lincoln Marine Science Centre, GPO BOX 2100 Adelaide, SA 5001, Australia
- South Australian Research and Development Institute (Aquatic Sciences), PO Box 120, Henley Beach, SA 5022, Australia
| | - Kelly M Robertson
- Southwest Fisheries Science Center, NOAA Fisheries, 3333 N. Torrey Pines Ct., La Jolla, CA, 92037 USA
| | - Renaud de Stephanis
- CIRCE, Conservation Information and Research on Cetaceans, C/Cabeza de Manzaneda 3, Algeciras-Pelayo, 11390 Cadiz, Spain
- Departamento de Biologia de la Conservación, Estación Biologica de Donana, CSIC, C/Americo Vespucio S/N, Isla de la Cartuja, Sevilla, 41092, Spain
| | - Philippe Verborgh
- CIRCE, Conservation Information and Research on Cetaceans, C/Cabeza de Manzaneda 3, Algeciras-Pelayo, 11390 Cadiz, Spain
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
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BUFALINO ANGELOP, MAYDEN RICHARDL. Phylogenetic evaluation of North American Leuciscidae (Actinopterygii: Cypriniformes: Cyprinoidea) as inferred from analyses of mitochondrial and nuclear DNA sequences. SYST BIODIVERS 2010. [DOI: 10.1080/14772000.2010.516029] [Citation(s) in RCA: 6] [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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McGowen MR, Clark C, Gatesy J. The vestigial olfactory receptor subgenome of odontocete whales: phylogenetic congruence between gene-tree reconciliation and supermatrix methods. Syst Biol 2010; 57:574-90. [PMID: 18686195 DOI: 10.1080/10635150802304787] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The macroevolutionary transition of whales (cetaceans) from a terrestrial quadruped to an obligate aquatic form involved major changes in sensory abilities. Compared to terrestrial mammals, the olfactory system of baleen whales is dramatically reduced, and in toothed whales is completely absent. We sampled the olfactory receptor (OR) subgenomes of eight cetacean species from four families. A multigene tree of 115 newly characterized OR sequences from these eight species and published data for Bos taurus revealed a diverse array of class II OR paralogues in Cetacea. Evolution of the OR gene superfamily in toothed whales (Odontoceti) featured a multitude of independent pseudogenization events, supporting anatomical evidence that odontocetes have lost their olfactory sense. We explored the phylogenetic utility of OR pseudogenes in Cetacea, concentrating on delphinids (oceanic dolphins), the product of a rapid evolutionary radiation that has been difficult to resolve in previous studies of mitochondrial DNA sequences. Phylogenetic analyses of OR pseudogenes using both gene-tree reconciliation and supermatrix methods yielded fully resolved, consistently supported relationships among members of four delphinid subfamilies. Alternative minimizations of gene duplications, gene duplications plus gene losses, deep coalescence events, and nucleotide substitutions plus indels returned highly congruent phylogenetic hypotheses. Novel DNA sequence data for six single-copy nuclear loci and three mitochondrial genes (> 5000 aligned nucleotides) provided an independent test of the OR trees. Nucleotide substitutions and indels in OR pseudogenes showed a very low degree of homoplasy in comparison to mitochondrial DNA and, on average, provided more variation than single-copy nuclear DNA. Our results suggest that phylogenetic analysis of the large OR superfamily will be effective for resolving relationships within Cetacea whether supermatrix or gene-tree reconciliation procedures are used.
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Affiliation(s)
- Michael R McGowen
- Department of Biology, University of California, Riverside, California 92521, USA.
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Divergence date estimation and a comprehensive molecular tree of extant cetaceans. Mol Phylogenet Evol 2009; 53:891-906. [DOI: 10.1016/j.ympev.2009.08.018] [Citation(s) in RCA: 296] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Revised: 08/04/2009] [Accepted: 08/14/2009] [Indexed: 11/20/2022]
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Xiong Y, Brandley MC, Xu S, Zhou K, Yang G. Seven new dolphin mitochondrial genomes and a time-calibrated phylogeny of whales. BMC Evol Biol 2009; 9:20. [PMID: 19166626 PMCID: PMC2656474 DOI: 10.1186/1471-2148-9-20] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2008] [Accepted: 01/25/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The phylogeny of Cetacea (whales) is not fully resolved with substantial support. The ambiguous and conflicting results of multiple phylogenetic studies may be the result of the use of too little data, phylogenetic methods that do not adequately capture the complex nature of DNA evolution, or both. In addition, there is also evidence that the generic taxonomy of Delphinidae (dolphins) underestimates its diversity. To remedy these problems, we sequenced the complete mitochondrial genomes of seven dolphins and analyzed these data with partitioned Bayesian analyses. Moreover, we incorporate a newly-developed "relaxed" molecular clock to model heterogenous rates of evolution among cetacean lineages. RESULTS The "deep" phylogenetic relationships are well supported including the monophyly of Cetacea and Odontoceti. However, there is ambiguity in the phylogenetic affinities of two of the river dolphin clades Platanistidae (Indian River dolphins) and Lipotidae (Yangtze River dolphins). The phylogenetic analyses support a sister relationship between Delphinidae and Monodontidae + Phocoenidae. Additionally, there is statistically significant support for the paraphyly of Tursiops (bottlenose dolphins) and Stenella (spotted dolphins). CONCLUSION Our phylogenetic analysis of complete mitochondrial genomes using recently developed models of rate autocorrelation resolved the phylogenetic relationships of the major Cetacean lineages with a high degree of confidence. Our results indicate that a rapid radiation of lineages explains the lack of support the placement of Platanistidae and Lipotidae. Moreover, our estimation of molecular divergence dates indicates that these radiations occurred in the Middle to Late Oligocene and Middle Miocene, respectively. Furthermore, by collecting and analyzing seven new mitochondrial genomes, we provide strong evidence that the delphinid genera Tursiops and Stenella are not monophyletic, and the current taxonomy masks potentially interesting patterns of morphological, physiological, behavioral, and ecological evolution.
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Affiliation(s)
- Ye Xiong
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, PR China
| | - Matthew C Brandley
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
| | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, PR China
| | - Kaiya Zhou
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, PR China
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, PR China
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Horvath JE, Weisrock DW, Embry SL, Fiorentino I, Balhoff JP, Kappeler P, Wray GA, Willard HF, Yoder AD. Development and application of a phylogenomic toolkit: resolving the evolutionary history of Madagascar's lemurs. Genes Dev 2008; 18:489-99. [PMID: 18245770 PMCID: PMC2259113 DOI: 10.1101/gr.7265208] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2007] [Accepted: 12/19/2007] [Indexed: 12/29/2022]
Abstract
Lemurs and the other strepsirrhine primates are of great interest to the primate genomics community due to their phylogenetic placement as the sister lineage to all other primates. Previous attempts to resolve the phylogeny of lemurs employed limited mitochondrial or small nuclear data sets, with many relationships poorly supported or entirely unresolved. We used genomic resources to develop 11 novel markers from nine chromosomes, representing approximately 9 kb of nuclear sequence data. In combination with previously published nuclear and mitochondrial loci, this yields a data set of more than 16 kb and adds approximately 275 kb of DNA sequence to current databases. Our phylogenetic analyses confirm hypotheses of lemuriform monophyly and provide robust resolution of the phylogenetic relationships among the five lemuriform families. We verify that the genus Daubentonia is the sister lineage to all other lemurs. The Cheirogaleidae and Lepilemuridae are sister taxa and together form the sister lineage to the Indriidae; this clade is the sister lineage to the Lemuridae. Divergence time estimates indicate that lemurs are an ancient group, with their initial diversification occurring around the Cretaceous-Tertiary boundary. Given the power of this data set to resolve branches in a notoriously problematic area of primate phylogeny, we anticipate that our phylogenomic toolkit will be of value to other studies of primate phylogeny and diversification. Moreover, the methods applied will be broadly applicable to other taxonomic groups where phylogenetic relationships have been notoriously difficult to resolve.
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Affiliation(s)
- Julie E Horvath
- Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina 27708, USA.
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Harlin-Cognato AD, Markowitz T, Würsig B, Honeycutt RL. Multi-locus phylogeography of the dusky dolphin (Lagenorhynchus obscurus): passive dispersal via the west-wind drift or response to prey species and climate change? BMC Evol Biol 2007; 7:131. [PMID: 17683557 PMCID: PMC1973136 DOI: 10.1186/1471-2148-7-131] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2007] [Accepted: 08/03/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The dusky dolphin (Lagenorhynchus obscurus) is distributed along temperate, coastal regions of New Zealand, South Africa, Argentina, and Peru where it feeds on schooling anchovy, sardines, and other small fishes and squid tightly associated with temperate ocean sea surface temperatures. Previous studies have suggested that the dusky dolphin dispersed in the Southern Hemisphere eastward from Peru via a linear, temperate dispersal corridor provided by the circumpolar west-wind drift. With new mitochondrial and nuclear DNA sequence data, we propose an alternative phylogeographic history for the dusky dolphin that was structured by paleoceanographic conditions that repeatedly altered the distribution of its temperate prey species during the Plio-Pleistocene. RESULTS In contrast to the west-wind drift hypothesis, phylogenetic analyses support a Pacific/Indian Ocean origin, with a relatively early and continued isolation of Peru from other regions. Dispersal of the dusky dolphin into the Atlantic is correlated with the history of anchovy populations, including multiple migrations from New Zealand to South Africa. Additionally, the cooling of the Eastern Equatorial Pacific led to the divergence of anchovy populations, which in turn explains the north-south equatorial transgression of L. obliquidens and the subsequent divergence of L. obscurus in the Southern Hemisphere. CONCLUSION Overall, our study fails to support the west-wind drift hypothesis. Instead, our data indicate that changes in primary productivity and related abundance of prey played a key role in shaping the phylogeography of the dusky dolphin, with periods of ocean change coincident with important events in the history of this temperate dolphin species. Moderate, short-term changes in sea surface temperatures and current systems have a powerful effect on anchovy populations; thus, it is not infeasible that repeated fluctuations in anchovy populations continue to play an important role in the history of coastal dolphin populations.
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Affiliation(s)
- April D Harlin-Cognato
- Department of Zoology, Michigan State University, 203 Natural Sciences Building, East Lansing, MI 48824, USA
| | - Tim Markowitz
- Dusky Dolphin Research Project, Muritai, 13 Maui Street, Kaikoura, New Zealand
| | - Bernd Würsig
- Marine Mammal Research Program, Department of Marine Biology, Texas A&M University, 4700 Ave. U, Galveston, Texas 77551, USA
| | - Rodney L Honeycutt
- Pepperdine University, Natural Science Division, 24255 Pacific Coast Highway, Malibu, California 90263, USA
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Morisaka T, Connor RC. Predation by killer whales (Orcinus orca) and the evolution of whistle loss and narrow-band high frequency clicks in odontocetes. J Evol Biol 2007; 20:1439-58. [PMID: 17584238 DOI: 10.1111/j.1420-9101.2007.01336.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A disparate selection of toothed whales (Odontoceti) share striking features of their acoustic repertoires including the absence of whistles and high frequency but weak (low peak-to-peak source level) clicks that have a relatively long duration and a narrow bandwidth. The non-whistling, high frequency click species include members of the family Phocoenidae, members of one genus of delphinids, Cephalorhynchus, the pygmy sperm whale, Kogia breviceps, and apparently the sole member of the family Pontoporiidae. Our review supports the 'acoustic crypsis' hypothesis that killer whale predation risk was the primary selective factor favouring an echolocation and communication system in cephalorhynchids, phocoenids and possibly Pontoporiidae and Kogiidae restricted to sounds that killer whales hear poorly or not at all (< 2 and > 100 kHz).
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Affiliation(s)
- T Morisaka
- Laboratory of Animal Ecology, Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan.
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