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Morin PA, Martien KK, Lang AR, Hancock-Hanser BL, Pease VL, Robertson KM, Sattler M, Slikas E, Rosel PE, Baker CS, Taylor BL, Archer FI. Guidelines and quantitative standards for improved cetacean taxonomy using full mitochondrial genomes. J Hered 2023; 114:612-624. [PMID: 37647537 DOI: 10.1093/jhered/esad049] [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: 01/31/2023] [Accepted: 08/28/2023] [Indexed: 09/01/2023] Open
Abstract
In many organisms, especially those of conservation concern, traditional lines of evidence for taxonomic delineation, such as morphological data, are often difficult to obtain. In these cases, genetic data are often the only source of information available for taxonomic studies. In particular, population surveys of mitochondrial genomes offer increased resolution and precision in support of taxonomic decisions relative to conventional use of the control region or other gene fragments of the mitochondrial genome. To improve quantitative guidelines for taxonomic decisions in cetaceans, we build on a previous effort targeting the control region and evaluate, for whole mitogenome sequences, a suite of divergence and diagnosability estimates for pairs of recognized cetacean populations, subspecies, and species. From this overview, we recommend new guidelines based on complete mitogenomes, combined with other types of evidence for isolation and divergence, which will improve resolution for taxonomic decisions, especially in the face of small sample sizes or low levels of genetic diversity. We further use simulated data to assist interpretations of divergence in the context of varying forms of historical demography, culture, and ecology.
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Affiliation(s)
- Phillip A Morin
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, United States
| | - Karen K Martien
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, United States
| | - Aimee R Lang
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, United States
| | - Brittany L Hancock-Hanser
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, United States
| | - Victoria L Pease
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, United States
| | - Kelly M Robertson
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, United States
| | - Maya Sattler
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, United States
| | - Elizabeth Slikas
- School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, United States
| | - Patricia E Rosel
- Marine Mammal and Turtle Division, Southeast Fisheries Science Center, National Marine Fisheries Service, NOAA, Lafayette, LA, United States
| | - C Scott Baker
- Marine Mammal Institute, Oregon State University, Newport, OR, United States
| | - Barbara L Taylor
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, United States
| | - Frederick I Archer
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, United States
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2
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Faria DM, Steel D, Baker CS, da Silva JM, de Meirelles ACO, Souto LRA, Siciliano S, Barbosa LA, Secchi E, Di Tullio JC, de Oliveira LR, Ott PH, Farro APC. Mitochondrial diversity and inter-specific phylogeny among dolphins of the genus Stenella in the Southwest Atlantic Ocean. PLoS One 2022; 17:e0270690. [PMID: 35834534 PMCID: PMC9282552 DOI: 10.1371/journal.pone.0270690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 06/15/2022] [Indexed: 11/18/2022] Open
Abstract
The genus Stenella is comprised of five species occurring in all oceans. Despite its wide distribution, genetic diversity information on these species is still scarce especially in the Southwest Atlantic Ocean. Some features of this genus can enhance opportunities for potential introgressive hybridization, e.g. sympatric distibution along the Brazilian coast, mixed known associations among species, karyotype uniformity and genome permeability. In this study we analyzed three genes of the mitochondrial genome to investigate the genetic diversity and occurrence of genetic mixture among eighty specimens of Stenella. All species exhibited moderate to high levels of genetic diversity (h = 0.833 to h = 1.000 and π = 0.006 to π = 0.015). Specimens of S. longirostris, S. attenuata and S. frontalis were clustered into differentiated haplogroups, in contrast, haplotypes of S. coeruleoalba and S. clymene were clustered together. We detected phylogenetic structure of mixed clades for S. clymene and S. coeruleoalba specimens, in the Southwest Atlantic Ocean, and also between S. frontalis and S. attenuata in the Northeast Atlantic Ocean, and between S. frontalis and S. longirostris in the Northwest Atlantic Ocean. These specimes were morphologically identified as one species but exhibited the maternal lineage of another species, by mitochondrial DNA. Our results demonstrate that ongoing gene flow is occurring among species of the genus Stenella reinforcing that this process could be one of the reasons for the confusing taxonomy and difficulties in elucidating phylogenetic relationships within this group.
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Affiliation(s)
- Drienne Messa Faria
- Laboratório de Genética e Conservação Animal, Departamento de Ciências Agrárias e Biológicas, Universidade Federal do Espírito Santo (UFES), São Mateus, ES, Brazil
- * E-mail:
| | - Debbie Steel
- Marine Mammal Institute, Hatfield Marine Science Center, Oregon State University, Newport, OR, United States of America
| | - C. Scott Baker
- Marine Mammal Institute, Hatfield Marine Science Center, Oregon State University, Newport, OR, United States of America
| | - José Martins da Silva
- Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio), Fernando de Noronha, PE, Brazil
| | | | | | - Salvatore Siciliano
- Departamento de Ciências Biológicas, Escola Nacional de Saúde Pública/Fiocruz, Rio de Janeiro, RJ, Brazil
| | | | - Eduardo Secchi
- Laboratório de Ecologia e Conservação da Megafauna Marinha, Universidade Federal do Rio Grande (FURG), Rio Grande, RS, Brazil
| | - Juliana Couto Di Tullio
- Laboratório de Ecologia e Conservação da Megafauna Marinha, Universidade Federal do Rio Grande (FURG), Rio Grande, RS, Brazil
| | | | - Paulo Henrique Ott
- Grupo de Estudos de Mamíferos Aquáticos do Rio Grande do Sul (GEMARS), Torres, RS, Brazil
- Universidade Estadual do Rio Grande do Sul (Uergs), Osório, RS, Brazil
| | - Ana Paula Cazerta Farro
- Laboratório de Genética e Conservação Animal, Departamento de Ciências Agrárias e Biológicas, Universidade Federal do Espírito Santo (UFES), São Mateus, ES, Brazil
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3
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Extensive Interspecific Gene Flow Shaped Complex Evolutionary History and Underestimated Species Diversity in Rapidly Radiated Dolphins. J MAMM EVOL 2021. [DOI: 10.1007/s10914-021-09581-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AbstractRecently diverged taxa are often characterized by high rates of hybridization, which can complicate phylogenetic reconstruction. For this reason, the phylogenetic relationships and evolutionary history of dolphins are still not very well resolved; the question of whether the genera Tursiops and Stenella are monophyletic is especially controversial. Here, we performed re-sequencing of six dolphin genomes and combined them with eight previously published dolphin SRA datasets and six whole-genome datasets to investigate the phylogenetic relationships of dolphins and test the monophyly hypothesis of Tursiops and Stenella. Phylogenetic reconstruction with the maximum likelihood and Bayesian methods of concatenated loci, as well as with coalescence analyses of sliding window trees, produced a concordant and well-supported tree. Our studies support the non-monophyletic status of Tursiops and Stenella because the species referred these genera do not form exclusive monophyletic clades. This suggests that the current taxonomy of both genera might not reflect their evolutionary history and may underestimate their diversity. A four-taxon D-statistic (ABBA-BABA) test, five-taxon DFOIL test, and tree-based PhyloNet analyses all showed extensive gene flow across dolphin species, which could explain the instability in resolving phylogenetic relationship of oceanic dolphins with different and limited markers. This study could be a good case to demonstrate how genomic data can reveal complex speciation and phylogeny in rapidly radiating animal groups.
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4
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Kriangwanich W, Buddhachat K, Poommouang A, Chomdej S, Thitaram C, Kaewmong P, Kittiwattanawong K, Nganvongpanit K. Feasibility of melting fingerprint obtained from ISSR-HRM curves for marine mammal species identification. PeerJ 2021; 9:e11689. [PMID: 34239781 PMCID: PMC8237827 DOI: 10.7717/peerj.11689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/07/2021] [Indexed: 12/19/2022] Open
Abstract
Currently, species identification of stranded marine mammals mostly relies on morphological features, which has inherent challenges. The use of genetic information for marine mammal species identification remains limited, therefore, new approaches that can contribute to a better monitoring of stranded species are needed. In that context, the ISSR-HRM method we have proposed offers a new approach for marine mammal species identification. Consequently, new approaches need to be developed to identify individuals at the species level. Eight primers of the ISSR markers were chosen for HRM analysis resulting in ranges of accuracy of 56.78–75.50% and 52.14–75.93% in terms of precision, while a degree of sensitivity of more than 80% was recorded when each single primer was used. The ISSR-HRM primer combinations revealed a success rate of 100% in terms of discrimination for all marine mammals included in this study. Furthermore, ISSR-HRM analysis was successfully employed in determining marine mammal discrimination among varying marine mammal species. Thus, ISSR-HRM analysis could serve as an effective alternative tool in the species identification process. This option would offer researchers a heightened level of convenience in terms of its performance and success rate. It would also offer field practice to veterinarians, biologists and other field-related people a greater degree of ease with which they could interpret results when effectively classifying stranded marine mammals. However, further studies with more samples and with a broader geographical scope will be required involving distinct populations to account for the high degree of intraspecific variability in cetaceans and to demonstrate the range of applications of this approach.
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Affiliation(s)
- Wannapimol Kriangwanich
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Kittisak Buddhachat
- Excellence Center in Veterinary Bioscience, Chiang Mai University, Chiang Mai, Thailand.,Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, Thailand
| | - Anocha Poommouang
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Siriwadee Chomdej
- Excellence Center in Veterinary Bioscience, Chiang Mai University, Chiang Mai, Thailand.,Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Chatchote Thitaram
- Center of Elephant and Wildlife Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | | | | | - Korakot Nganvongpanit
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
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5
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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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6
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Jedensjö M, Kemper C, Milella M, Willems E, Krützen M. Taxonomy and distribution of bottlenose dolphins (genus Tursiops) in Australian waters: an osteological clarification. CAN J ZOOL 2020. [DOI: 10.1139/cjz-2018-0270] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Species relationships in the bottlenose dolphin (genus Tursiops Gervais, 1855) are controversial. We carried out a comprehensive osteological study of 264 skulls, including type specimens, and 90 postcranial skeletons of Tursiops spp. to address taxonomic uncertainties in Australia using two-dimensional (2D) measurements, and three-dimensional geometric morphometrics (3DGM), tooth and vertebral counts, and categorical data. Analyses provided support for the presence of two forms, aligned to the Indo-Pacific bottlenose dolphin (Tursiops aduncus (Ehrenberg, 1832)) and the common bottlenose dolphin (Tursiops truncatus (Montagu, 1821)), including type specimens. The Burrunan dolphin (Tursiops australis Charlton-Robb, Gershwin, Thompson, Austin, Owen and McKechnie, 2011) fell well within T. truncatus for both 2D and 3DGM methods. Thirteen Tursiops spp. specimens, no T. australis specimens, were of intermediate size (2D) and could not be assigned to either species. For 3DGM data, there was a strong allometric influence and few non-allometric differences between species. Length and width of the cranium and rostrum were important discriminating variables. Tursiops aduncus was smaller, had more teeth, fewer vertebrae, and more erosion on the pterygoids and frontals than T. truncatus. Overall cranium shape was round in T. aduncus and angular in T. truncatus. Skull length of T. aduncus was smaller in low than in high latitudes. This study highlights the importance of large sample size, multiple analytical methods, and extensive geographical coverage when undertaking taxonomic studies.
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Affiliation(s)
- M. Jedensjö
- Department of Anthropology, University of Zurich, Museum of Anthropology, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- South Australian Museum, North Terrace, Adelaide, SA 5000, Australia
| | - C.M. Kemper
- South Australian Museum, North Terrace, Adelaide, SA 5000, Australia
| | - M. Milella
- Department of Anthropology, University of Zurich, Museum of Anthropology, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Department of Anthropology, Institute of Forensic Medicine, University of Bern, Bühlstrasse 20, 3012 Bern, Switzerland
| | - E.P. Willems
- Department of Anthropology, University of Zurich, Museum of Anthropology, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - M. Krützen
- Department of Anthropology, University of Zurich, Museum of Anthropology, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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7
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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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8
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Horreo JL. New insights into the phylogenetic relationships among the oceanic dolphins (Cetacea: Delphinidae). J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12255] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jose L. Horreo
- Department of Biodiversity and Evolutionary BiologyNational Museum of Natural Sciences (MNCN‐CSIC) Madrid Spain
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9
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Gridley T, Elwen SH, Harris G, Moore DM, Hoelzel AR, Lampen F. Hybridization in bottlenose dolphins-A case study of Tursiops aduncus × T. truncatus hybrids and successful backcross hybridization events. PLoS One 2018; 13:e0201722. [PMID: 30208020 PMCID: PMC6135391 DOI: 10.1371/journal.pone.0201722] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 07/20/2018] [Indexed: 11/18/2022] Open
Abstract
The bottlenose dolphin, genus Tursiops is one of the best studied of all the Cetacea with a minimum of two species widely recognised. Common bottlenose dolphins (T. truncatus), are the cetacean species most frequently held in captivity and are known to hybridize with species from at least 6 different genera. In this study, we document several intra-generic hybridization events between T. truncatus and T. aduncus held in captivity. We demonstrate that the F1 hybrids are fertile and can backcross producing apparently healthy offspring, thereby showing introgressive inter-specific hybridization within the genus. We document that female F1 hybrids can reach sexual maturity at 4 yr and 3 mo of age, and can become pregnant and give birth before being fully weaned. The information presented has implications for understanding hybrid reticulation among cetacean species and practical implications for captive facilities housing either Tursiops species or hybrids thereof.
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Affiliation(s)
- T. Gridley
- Centre for Statistics in Ecology, Environment and Conservation, Department of Statistical Sciences, University of Cape Town, C/o Sea Search Research and Conservation NPC, Muizenberg Cape Town, South Africa
- * E-mail:
| | - S. H. Elwen
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, C/o Sea Search Research and Conservation NPC, Muizenberg Cape Town, South Africa
| | - G. Harris
- The South African Association for Marine Biological Research, uShaka Sea World, Point, Durban, South Africa
| | - D. M. Moore
- Department of Biosciences, Durham University, Durham, United Kingdom
| | - A. R. Hoelzel
- Department of Biosciences, Durham University, Durham, United Kingdom
| | - F. Lampen
- The South African Association for Marine Biological Research, uShaka Sea World, Point, Durban, South Africa
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10
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Guidarelli G, Colangelo P, de Francesco MC, Nicolosi P, Meloro C, Loy A. Phenotypic Changes Across a Geographic Gradient: The Case of Three Sympatric Dolphin Species. Evol Biol 2017. [DOI: 10.1007/s11692-017-9435-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Chen I, Nishida S, Yang WC, Isobe T, Tajima Y, Hoelzel AR. Genetic diversity of bottlenose dolphin ( Tursiops sp.) populations in the western North Pacific and the conservation implications. MARINE BIOLOGY 2017; 164:202. [PMID: 28983128 PMCID: PMC5592193 DOI: 10.1007/s00227-017-3232-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 08/29/2017] [Indexed: 06/07/2023]
Abstract
The evolutionary processes that shape patterns of diversity in highly mobile marine species are poorly understood, but important towards transferable inference on their effective conservation. In this study, bottlenose dolphins (Tursiops sp.) are studied to address this broader question. They exhibit remarkable geographical variation for morphology, life history, and genetic diversity, and this high level of variation has made the taxonomy of the genus controversial. A significant population structure has been reported for the most widely distributed species, the common bottlenose dolphin (T. truncatus), in almost all ocean basins, though no data have been available for the western North Pacific Ocean (WNP). The genetic diversity of bottlenose dolphins in the WNP was investigated based on 20 microsatellite and one mitochondrial DNA markers for samples collected from Taiwanese, Japanese, and Philippine waters (9°-39°N, 120°-140°E) during 1986-2012. The results indicated that there are at least four genetically differentiated populations of common bottlenose dolphins in the western and central North Pacific Ocean. The pattern of differentiation appears to correspond to habitat types, resembling results seen in other populations of the same species. Our analyses also showed that there was no evident gene flow between the two "sister species", the common bottlenose dolphins, and the Indo-Pacific bottlenose dolphins (T. aduncus) occurring sympatrically in our study region.
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Affiliation(s)
- Ing Chen
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE UK
- Department of Life Sciences, National Cheng Kung University, 1 Da-Xue Road, East District, Tainan, 70101 Taiwan
| | - Shin Nishida
- Science Education, Faculty of Education and Culture, University of Miyazaki, 1-1 Gakuen-Kibanadai-Nishi, Miyazaki, 889-2192 Japan
| | - Wei-Cheng Yang
- Department of Veterinary Medicine, National Chiayi University, 580 Xinmin Road, Chiayi, 60054 Taiwan
| | - Tomohiko Isobe
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, 305-8506 Japan
| | - Yuko Tajima
- Division of Vertebrates, Department of Zoology, National Museum of Nature and Science, 4–1–1 Amakubo, Tsukuba-shi, Ibaraki, 305-0005 Japan
| | - A. Rus Hoelzel
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE UK
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12
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Farías-Curtidor N, Barragán-Barrera DC, Chávez-Carreño PA, Jiménez-Pinedo C, Palacios DM, Caicedo D, Trujillo F, Caballero S. Range extension for the common dolphin (Delphinus sp.) to the Colombian Caribbean, with taxonomic implications from genetic barcoding and phylogenetic analyses. PLoS One 2017; 12:e0171000. [PMID: 28192446 PMCID: PMC5305112 DOI: 10.1371/journal.pone.0171000] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 01/14/2017] [Indexed: 11/18/2022] Open
Abstract
The nearest known population of common dolphins (Delphinus sp.) to the Colombian Caribbean occurs in a fairly restricted range in eastern Venezuela. These dolphins have not been previously reported in the Colombian Caribbean, likely because of a lack of study of the local cetacean fauna. We collected cetacean observations in waters of the Guajira Department, northern Colombia (~11°N, 73°W) during two separate efforts: (a) a seismic vessel survey (December 2009-March 2010), and (b) three coastal surveys from small boats (May-July 2012, May 2013, and May 2014). Here we document ten sightings of common dolphins collected during these surveys, which extend the known range of the species by ~1000 km into the southwestern Caribbean. We also collected nine skin biopsies in 2013 and 2014. In order to determine the taxonomic identity of the specimens, we conducted genetic barcoding and phylogenetic analyses using two mitochondrial markers, the Control Region (mtDNA) and Cytochrome b (Cytb). Results indicate that these specimens are genetically closer to the short-beaked common dolphin (Delphinus delphis) even though morphologically they resemble a long-beaked form (Delphinus sp.). However, the specific taxonomic status of common dolphins in the Caribbean and in the Western Atlantic remains unresolved. It is also unclear whether the distribution of the species between northern Colombia and eastern Venezuela is continuous or disjoined, or whether they can be considered part of the same stock.
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Affiliation(s)
| | - Dalia C. Barragán-Barrera
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos LEMVA, Departamento de Ciencias Biológicas, Universidad de los Andes, Laboratorio J-202, Bogotá, Colombia
- Fundación Macuáticos Colombia, Medellín, Colombia
| | - Paula Alejandra Chávez-Carreño
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos LEMVA, Departamento de Ciencias Biológicas, Universidad de los Andes, Laboratorio J-202, Bogotá, Colombia
- Nicholas School of the Environment, Duke University, Durham, North Carolina, United States of America
| | | | - Daniel M. Palacios
- Marine Mammal Institute, Oregon State University, Hatfield Marine Science Center, Newport, Oregon, United States of America
| | | | | | - Susana Caballero
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos LEMVA, Departamento de Ciencias Biológicas, Universidad de los Andes, Laboratorio J-202, Bogotá, Colombia
- * E-mail:
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13
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do Amaral KB, Amaral AR, Ewan Fordyce R, Moreno IB. Historical Biogeography of Delphininae Dolphins and Related Taxa (Artiodactyla: Delphinidae). J MAMM EVOL 2016. [DOI: 10.1007/s10914-016-9376-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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14
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Segura-García I, Gallo JP, Chivers S, Díaz-Gamboa R, Hoelzel AR. Post-glacial habitat release and incipient speciation in the genus Delphinus. Heredity (Edinb) 2016; 117:400-407. [PMID: 27599576 DOI: 10.1038/hdy.2016.66] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 06/23/2016] [Accepted: 06/29/2016] [Indexed: 11/09/2022] Open
Abstract
The role of ecological and changing environmental factors in the radiation of species diversity is a fundamental question in evolutionary biology. Of particular interest is the potential for these factors to determine the boundary between what we would consider differentiation among populations and incipient speciation. Dolphins in the genus Delphinus provide a useful test case, exhibiting morphological variation in beak length, coloration and body size across their wide geographic distribution, and in particular among coastal and more pelagic habitats. Two species have been proposed, D. delphis and D. capensis, but morphologically similar allopatric populations are not monophyletic, indicating that the mostly coastal 'long-beaked' D. capensis form is not a single globally distributed species. However, the sympatric populations in the Eastern North Pacific currently designated as these two species are both morphologically and genetically differentiated. Here we use microsatellite DNA and mitochondrial DNA markers to investigate the evolutionary mechanisms that led to this incipient speciation event. We used coalescent and assignment methods to investigate the timing and extent of reproductive isolation. Our data indicate that although there is some level of on-going gene flow, the putative species found in the Eastern North Pacific are reciprocally monophyletic. The timing of isolation appears to be associated with regional changes in paleoceanographic conditions within the Holocene timeframe.
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Affiliation(s)
- I Segura-García
- School of Biological and Biomedical Sciences, Durham University, Durham, UK
| | - J P Gallo
- Centro de Investigación en Alimentación y Desarrollo-Carretera al Varadero Nacional Km 6.6, Guaymas, Mexico
| | - S Chivers
- Southwest Fisheries Science Center, La Jolla, CA, USA
| | - R Díaz-Gamboa
- Departamento de Biología Marina, Universidad Autónoma de Yucatán, Mérida, Mexico
| | - A R Hoelzel
- School of Biological and Biomedical Sciences, Durham University, Durham, UK
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15
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Allen SJ, Bryant KA, Kraus RHS, Loneragan NR, Kopps AM, Brown AM, Gerber L, Krützen M. Genetic isolation between coastal and fishery-impacted, offshore bottlenose dolphin (Tursiopsspp.) populations. Mol Ecol 2016; 25:2735-53. [DOI: 10.1111/mec.13622] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 02/17/2016] [Accepted: 03/11/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Simon J. Allen
- Cetacean Research Unit; School of Veterinary and Life Sciences; Murdoch University; Perth Western Australia 6150 Australia
- Centre for Marine Futures; School of Animal Biology and Oceans Institute; University of Western Australia; Perth Western Australia 6009 Australia
| | - Kate A. Bryant
- School of Veterinary and Life Sciences; Murdoch University; Murdoch Western Australia 6150 Australia
| | - Robert H. S. Kraus
- Department of Biology; University of Konstanz; 78457 Konstanz Germany
- Department of Migration and Immuno-Ecology; Max Planck Institute for Ornithology; Am Obstberg 1 78315 Radolfzell Germany
| | - Neil R. Loneragan
- School of Veterinary and Life Sciences; Murdoch University; Murdoch Western Australia 6150 Australia
| | - Anna M. Kopps
- Evolutionary Genetics Group; Department of Anthropology; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
- Evolution and Ecology Research Centre; School of Biological; Earth and Environmental Sciences; University of New South Wales; Sydney New South Wales 2052 Australia
| | - Alexander M. Brown
- Cetacean Research Unit; School of Veterinary and Life Sciences; Murdoch University; Perth Western Australia 6150 Australia
| | - Livia Gerber
- Evolutionary Genetics Group; Department of Anthropology; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Michael Krützen
- Evolutionary Genetics Group; Department of Anthropology; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
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16
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Yan F, Jiang K, Wang K, Jin JQ, Suwannapoom C, Li C, Vindum JV, Brown RM, Che J. The Australasian frog family Ceratobatrachidae in China, Myanmar and Thailand: discovery of a new Himalayan forest frog clade. DONG WU XUE YAN JIU = ZOOLOGICAL RESEARCH 2016; 37:7-14. [PMID: 26828029 DOI: 10.13918/j.issn.2095-8137.2016.1.7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
In an effort to study the systematic affinities and specieslevel phylogenetic relationships of the enigmatic anurans variably assigned to the genera Ingerana or Limnonectes (family Dicroglossidae), we collected new molecular sequence data for five species including four Himalayan taxa, Limnonectes xizangensis, Lim. medogensis, Lim. alpina, [corrected] Ingerana borealis and one southeast Asian species, I. tasanae, and analyzed these together with data from previous studies involving other ostensibly related taxa. Our surprising results demonstrate unequivocally that Lim. xizangensis, Lim. medogensis and Lim. alpina [corrected] form a strongly supported clade, the sister-group of the family Australasian forest frog family Ceratobatrachidae. This discovery requires an expansion of the definition of Ceratobatrachidae and represents the first record of this family in China. These three species are distinguished from the species of Ingerana and Limnonectes by the: (1) absence of interdigital webbing of the foot, (2) absence of terminal discs on fingers and toes, (3) absence of circumarginal grooves on the fingers and toes, and (4) absence of tarsal folds. Given their phylogenetic and morphological distinctiveness, we assign them to the oldest available generic name for this clade, Liurana Dubois 1987, and transfer Liurana from Dicroglossidae to the family Ceratobatrachidae. In contrast, Ingerana tasanae was found to be clustered with strong support with the recently described genus Alcalus (Ceratobatrachidae), a small clade of otherwise Sundaic species; this constitutes a new record of the family Ceratobatrachidae for Myanmar and Thailand. Finally, Ingerana borealis clustered with the "true" Ingerana (family Dicroglossidae), for which the type species is I. tenasserimensis.
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Affiliation(s)
- Fang Yan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China;Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw 05282, Myanmar
| | - Ke Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China;Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw 05282, Myanmar
| | - Kai Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China; Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman OK 73072-7029, U.S.A
| | - Jie-Qiong Jin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Chatmongkon Suwannapoom
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China; School of Agriculture and Natural Resources, University of Phayao, Phayao 56000, Thailand
| | - Cheng Li
- Imaging Biodiversity Expedition, Beijing 100107, China
| | - Jens V Vindum
- Department of Herpetology, California Academy of Sciences, California 94118, U.S.A
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, 1345 Jayhawk Blvd, University of Kansas, Lawrence KS 66045, U.S.A
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China.
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Mrinalini, Thorpe RS, Creer S, Lallias D, Dawnay L, Stuart BL, Malhotra A. Convergence of multiple markers and analysis methods defines the genetic distinctiveness of cryptic pitvipers. Mol Phylogenet Evol 2015; 92:266-79. [DOI: 10.1016/j.ympev.2015.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 04/24/2015] [Accepted: 06/03/2015] [Indexed: 10/23/2022]
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Qi D, Guo S, Chao Y, Kong Q, Li C, Xia M, Xie B, Zhao K. The biogeography and phylogeny of schizothoracine fishes (Schizopygopsis) in the Qinghai-Tibetan Plateau. ZOOL SCR 2015. [DOI: 10.1111/zsc.12116] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Delin Qi
- Animal Science Department of Agriculture and Animal Husbandry College; Qinghai University; Xining 810016 China
| | - Songchang Guo
- Key laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining 810001 China
| | - Yan Chao
- Animal Science Department of Agriculture and Animal Husbandry College; Qinghai University; Xining 810016 China
| | - Qinghui Kong
- Animal Science Department of Agriculture and Animal Husbandry College; Qinghai University; Xining 810016 China
| | - Changzhong Li
- College of Eco-Environmental Engineering; Qinghai University; Xining 810016 China
| | - Mingzhe Xia
- Animal Science Department of Agriculture and Animal Husbandry College; Qinghai University; Xining 810016 China
| | - Baosheng Xie
- College of Eco-Environmental Engineering; Qinghai University; Xining 810016 China
| | - Kai Zhao
- Key laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining 810001 China
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Hybrid speciation in a marine mammal: the clymene dolphin (Stenella clymene). PLoS One 2014; 9:e83645. [PMID: 24421898 PMCID: PMC3885441 DOI: 10.1371/journal.pone.0083645] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 11/05/2013] [Indexed: 11/19/2022] Open
Abstract
Natural hybridization may result in the exchange of genetic material between divergent lineages and even the formation of new taxa. Many of the Neo-Darwinian architects argued that, particularly for animal clades, natural hybridization was maladaptive. Recent evidence, however, has falsified this hypothesis, instead indicating that this process may lead to increased biodiversity through the formation of new species. Although such cases of hybrid speciation have been described in plants, fish and insects, they are considered exceptionally rare in mammals. Here we present evidence for a marine mammal, Stenella clymene, arising through natural hybridization. We found phylogenetic discordance between mitochondrial and nuclear markers, which, coupled with a pattern of transgressive segregation seen in the morphometric variation of some characters, support a case of hybrid speciation. S. clymene is currently genetically differentiated from its putative parental species, Stenella coerueloalba and Stenella longisrostris, although low levels of introgressive hybridization may be occurring. Although non-reticulate forms of evolution, such as incomplete lineage sorting, could explain our genetic results, we consider that the genetic and morphological evidence taken together argue more convincingly towards a case of hybrid speciation. We anticipate that our study will bring attention to this important aspect of reticulate evolution in non-model mammal species. The study of speciation through hybridization is an excellent opportunity to understand the mechanisms leading to speciation in the context of gene flow.
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Kirchberger PC, Sefc KM, Sturmbauer C, Koblmüller S. Outgroup effects on root position and tree topology in the AFLP phylogeny of a rapidly radiating lineage of cichlid fish. Mol Phylogenet Evol 2014; 70:57-62. [PMID: 24055738 PMCID: PMC3842234 DOI: 10.1016/j.ympev.2013.09.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 09/04/2013] [Accepted: 09/06/2013] [Indexed: 11/26/2022]
Abstract
Phylogenetic analyses of rapid radiations are particularly challenging as short basal branches and incomplete lineage sorting complicate phylogenetic inference. Multilocus data of presence-absence polymorphisms such as obtained by AFLP genotyping overcome some of the difficulties, but also present their own intricacies. Here we analyze >1000 AFLP markers to address the evolutionary history of the Limnochromini, a cichlid fish lineage endemic to Lake Tanganyika, and to test for potential effects of outgroup composition on tree topology. The data support previous mitochondrial evidence on the tribe's taxonomy by confirming the polyphyly of the genus Limnochromis and - in contradiction to a recent taxonomic revision - nesting the genus Greenwoodochromis within the Limnochromini. Species relationships suggest that ecological segregation occurred during the rapid basal radiation of the Limnochromini. The large phylogenetic distance between candidate outgroup taxa and the Limnochromini radiation caused random outgroup effects. Bootstrap support for ingroup nodes was lower in outgroup-rooted than in midpoint-rooted trees, and root positions and ingroup tree topologies varied in response to the composition of the outgroup. These observations suggest that the predisposition for homoplastic evolution makes AFLP-based phylogenetic analyses particularly susceptible to random biases introduced by too-distant outgroup taxa.
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Affiliation(s)
| | | | | | - Stephan Koblmüller
- Department of Zoology, Karl-Franzens-University Graz, Universitätsplatz 2, A-8010 Graz, Austria
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Alfonsi E, Méheust E, Fuchs S, Carpentier FG, Quillivic Y, Viricel A, Hassani S, Jung JL. The use of DNA barcoding to monitor the marine mammal biodiversity along the French Atlantic coast. Zookeys 2013:5-24. [PMID: 24453548 PMCID: PMC3890668 DOI: 10.3897/zookeys.365.5873] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 09/11/2013] [Indexed: 01/09/2023] Open
Abstract
In the last ten years, 14 species of cetaceans and five species of pinnipeds stranded along the Atlantic coast of Brittany in the North West of France. All species included, an average of 150 animals strand each year in this area. Based on reports from the stranding network operating along this coast, the most common stranding events comprise six cetacean species (Delphinus delphis, Tursiops truncatus, Stenella coeruleoalba, Globicephala melas, Grampus griseus, Phocoena phocoena)and one pinniped species (Halichoerus grypus). Rare stranding events include deep-diving or exotic species, such as arctic seals. In this study, our aim was to determine the potential contribution of DNA barcoding to the monitoring of marine mammal biodiversity as performed by the stranding network. We sequenced more than 500 bp of the 5’ end of the mitochondrial COI gene of 89 animals of 15 different species (12 cetaceans, and three pinnipeds). Except for members of the Delphininae, all species were unambiguously discriminated on the basis of their COI sequences. We then applied DNA barcoding to identify some “undetermined” samples. With again the exception of the Delphininae, this was successful using the BOLD identification engine. For samples of the Delphininae, we sequenced a portion of the mitochondrial control region (MCR), and using a non-metric multidimentional scaling plot and posterior probability calculations we were able to determine putatively each species. We then showed, in the case of the harbour porpoise, that COI polymorphisms, although being lower than MCR ones, could also be used to assess intraspecific variability. All these results show that the use of DNA barcoding in conjunction with a stranding network could clearly increase the accuracy of the monitoring of marine mammal biodiversity.
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Affiliation(s)
- Eric Alfonsi
- Laboratoire BioGeMME (Biologie et Génétique des Mammifères Marins dans leur Environnement), Université Européenne de Bretagne & Université de Bretagne Occidentale, UFR Sciences et Techniques, 6 Av. Victor Le Gorgeu - CS93837 - 29238 Brest Cedex 3, France ; Laboratoire d'Etude des Mammifères Marins (LEMM), Océanopolis, port de plaisance, BP 91039, 29210 Brest Cedex 1, France
| | - Eleonore Méheust
- Laboratoire BioGeMME (Biologie et Génétique des Mammifères Marins dans leur Environnement), Université Européenne de Bretagne & Université de Bretagne Occidentale, UFR Sciences et Techniques, 6 Av. Victor Le Gorgeu - CS93837 - 29238 Brest Cedex 3, France ; Laboratoire d'Etude des Mammifères Marins (LEMM), Océanopolis, port de plaisance, BP 91039, 29210 Brest Cedex 1, France
| | - Sandra Fuchs
- Laboratoire d'Etude des Mammifères Marins (LEMM), Océanopolis, port de plaisance, BP 91039, 29210 Brest Cedex 1, France
| | - François-Gilles Carpentier
- Laboratoire BioGeMME (Biologie et Génétique des Mammifères Marins dans leur Environnement), Université Européenne de Bretagne & Université de Bretagne Occidentale, UFR Sciences et Techniques, 6 Av. Victor Le Gorgeu - CS93837 - 29238 Brest Cedex 3, France
| | - Yann Quillivic
- Laboratoire d'Etude des Mammifères Marins (LEMM), Océanopolis, port de plaisance, BP 91039, 29210 Brest Cedex 1, France
| | - Amélia Viricel
- Observatoire PELAGIS, UMS 3462, CNRS-Université de La Rochelle, Pôle analytique, 5 allée de l'océan, 17000 La Rochelle, France ; Littoral, Environnement et Sociétés, UMR 7266, CNRS-Université de La Rochelle, 2 rue Olympe de Gouges, 17000 La Rochelle, France
| | - Sami Hassani
- Laboratoire d'Etude des Mammifères Marins (LEMM), Océanopolis, port de plaisance, BP 91039, 29210 Brest Cedex 1, France
| | - Jean-Luc Jung
- Laboratoire BioGeMME (Biologie et Génétique des Mammifères Marins dans leur Environnement), Université Européenne de Bretagne & Université de Bretagne Occidentale, UFR Sciences et Techniques, 6 Av. Victor Le Gorgeu - CS93837 - 29238 Brest Cedex 3, France
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Viricel A, Pante E, Dabin W, Simon-Bouhet B. Applicability of RAD-tag genotyping for interfamilial comparisons: empirical data from two cetaceans. Mol Ecol Resour 2013; 14:597-605. [DOI: 10.1111/1755-0998.12206] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 11/08/2013] [Accepted: 11/13/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Amélia Viricel
- Littoral, Environnement et Sociétés (LIENSs) UMR 7266 CNRS; Université de La Rochelle; 2 rue Olympe de Gouges La Rochelle 17000 France
| | - Eric Pante
- Littoral, Environnement et Sociétés (LIENSs) UMR 7266 CNRS; Université de La Rochelle; 2 rue Olympe de Gouges La Rochelle 17000 France
| | - Willy Dabin
- Observatoire PELAGIS, UMS 3462 CNRS; Université de La Rochelle; Pôle analytique 5 allées de l'océan La Rochelle 17000 France
| | - Benoit Simon-Bouhet
- Littoral, Environnement et Sociétés (LIENSs) UMR 7266 CNRS; Université de La Rochelle; 2 rue Olympe de Gouges La Rochelle 17000 France
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Moura AE, Nielsen SCA, Vilstrup JT, Moreno-Mayar JV, Gilbert MTP, Gray HWI, Natoli A, Möller L, Hoelzel AR. Recent diversification of a marine genus (Tursiops spp.) tracks habitat preference and environmental change. Syst Biol 2013; 62:865-77. [PMID: 23929779 DOI: 10.1093/sysbio/syt051] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Understanding the evolution of diversity and the resulting systematics in marine systems is confounded by the lack of clear boundaries in oceanic habitats, especially for highly mobile species like marine mammals. Dolphin populations and sibling species often show differentiation between coastal and offshore habitats, similar to the pelagic/littoral or benthic differentiation seen for some species of fish. Here we test the hypothesis that lineages within the polytypic genus Tursiops track past changes in the environment reflecting ecological drivers of evolution facilitated by habitat release. We used a known recent time point for calibration (the opening of the Bosphorus) and whole mitochondrial genome (mitogenome) sequences for high phylogenetic resolution. The pattern of lineage formation suggested an origin in Australasia and several early divisions involving forms currently inhabiting coastal habitats. Radiation in pelagic environments was relatively recent, and was likely followed by a return to coastal habitat in some regions. The timing of some nodes defining different ecotypes within the genus clustered near the two most recent interglacial transitions. A signal for an increase in diversification was also seen for dates after the last glacial maximum. Together these data suggest the tracking of habitat preference during geographic expansions, followed by transition points reflecting habitat shifts, which were likely associated with periods of environmental change.
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Affiliation(s)
- Andre E Moura
- School of Biological and Biomedical Sciences, Durham University, South Road, DH1 3LE, UK; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, Denmark; Biological Department, UAE University, P.O.Box 17551, Al Ain, UAE; and School of Biological Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
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Poczai P, Varga I, Laos M, Cseh A, Bell N, Valkonen JPT, Hyvönen J. Advances in plant gene-targeted and functional markers: a review. PLANT METHODS 2013; 9:6. [PMID: 23406322 PMCID: PMC3583794 DOI: 10.1186/1746-4811-9-6] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 02/05/2013] [Indexed: 05/03/2023]
Abstract
Public genomic databases have provided new directions for molecular marker development and initiated a shift in the types of PCR-based techniques commonly used in plant science. Alongside commonly used arbitrarily amplified DNA markers, other methods have been developed. Targeted fingerprinting marker techniques are based on the well-established practices of arbitrarily amplified DNA methods, but employ novel methodological innovations such as the incorporation of gene or promoter elements in the primers. These markers provide good reproducibility and increased resolution by the concurrent incidence of dominant and co-dominant bands. Despite their promising features, these semi-random markers suffer from possible problems of collision and non-homology analogous to those found with randomly generated fingerprints. Transposable elements, present in abundance in plant genomes, may also be used to generate fingerprints. These markers provide increased genomic coverage by utilizing specific targeted sites and produce bands that mostly seem to be homologous. The biggest drawback with most of these techniques is that prior genomic information about retrotransposons is needed for primer design, prohibiting universal applications. Another class of recently developed methods exploits length polymorphism present in arrays of multi-copy gene families such as cytochrome P450 and β-tubulin genes to provide cross-species amplification and transferability. A specific class of marker makes use of common features of plant resistance genes to generate bands linked to a given phenotype, or to reveal genetic diversity. Conserved DNA-based strategies have limited genome coverage and may fail to reveal genetic diversity, while resistance genes may be under specific evolutionary selection. Markers may also be generated from functional and/or transcribed regions of the genome using different gene-targeting approaches coupled with the use of RNA information. Such techniques have the potential to generate phenotypically linked functional markers, especially when fingerprints are generated from the transcribed or expressed region of the genome. It is to be expected that these recently developed techniques will generate larger datasets, but their shortcomings should also be acknowledged and carefully investigated.
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Affiliation(s)
- Péter Poczai
- Plant Biology, Department of Biosciences, University of Helsinki, PO Box 65, 00014, Helsinki, FIN, Finland
| | - Ildikó Varga
- Plant Biology, Department of Biosciences, University of Helsinki, PO Box 65, 00014, Helsinki, FIN, Finland
| | - Maarja Laos
- Institute of Biotechnology, University of Helsinki, PO Box 65, 00014, Helsinki, FIN, Finland
| | - András Cseh
- Agricultural Institute, Centre of Agricultural Research, Hungarian Academy of Sciences, PO Box 19, H-2462, Martonvásár, Hungary
| | - Neil Bell
- Plant Biology, Department of Biosciences, University of Helsinki, PO Box 65, 00014, Helsinki, FIN, Finland
- Botanical Museum, University of Helsinki, PO Box 7, 00014, Helsinki, FIN, Finland
| | - Jari PT Valkonen
- Department of Agricultural Sciences, University of Helsinki, PO Box 27, 00014, Helsinki, FIN, Finland
| | - Jaakko Hyvönen
- Plant Biology, Department of Biosciences, University of Helsinki, PO Box 65, 00014, Helsinki, FIN, Finland
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Kück P, Greve C, Misof B, Gimnich F. Automated masking of AFLP markers improves reliability of phylogenetic analyses. PLoS One 2012; 7:e49119. [PMID: 23152859 PMCID: PMC3494671 DOI: 10.1371/journal.pone.0049119] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 10/04/2012] [Indexed: 12/24/2022] Open
Abstract
The amplified fragment length polymorphisms (AFLP) method has become an attractive tool in phylogenetics due to the ease with which large numbers of characters can be generated. In contrast to sequence-based phylogenetic approaches, AFLP data consist of anonymous multilocus markers. However, potential artificial amplifications or amplification failures of fragments contained in the AFLP data set will reduce AFLP reliability especially in phylogenetic inferences. In the present study, we introduce a new automated scoring approach, called “AMARE” (AFLP MAtrix REduction). The approach is based on replicates and makes marker selection dependent on marker reproducibility to control for scoring errors. To demonstrate the effectiveness of our approach we record error rate estimations, resolution scores, PCoA and stemminess calculations. As in general the true tree (i.e. the species phylogeny) is not known, we tested AMARE with empirical, already published AFLP data sets, and compared tree topologies of different AMARE generated character matrices to existing phylogenetic trees and/or other independent sources such as morphological and geographical data. It turns out that the selection of masked character matrices with highest resolution scores gave similar or even better phylogenetic results than the original AFLP data sets.
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Affiliation(s)
- Patrick Kück
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Carola Greve
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
- * E-mail:
| | - Bernhard Misof
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - France Gimnich
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
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Amaral AR, Jackson JA, Möller LM, Beheregaray LB, Manuela Coelho M. Species tree of a recent radiation: the subfamily Delphininae (Cetacea, Mammalia). Mol Phylogenet Evol 2012; 64:243-53. [PMID: 22503758 DOI: 10.1016/j.ympev.2012.04.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 04/04/2012] [Accepted: 04/04/2012] [Indexed: 10/28/2022]
Abstract
Lineages undergoing rapid radiations provide exceptional opportunities for studying speciation and adaptation, but also represent a challenge for molecular systematics because retention of ancestral polymorphisms and the occurrence of hybridization can obscure relationships among lineages. Dolphins in the subfamily Delphininae are one such case. Non-monophyly, rapid speciation events, and discordance between morphological and molecular characters have made the inference of phylogenetic relationships within this subfamily very difficult. Here we approach this problem by applying multiple methods intended to estimate species trees using a multi-gene dataset for the Delphininae (Sousa, Sotalia, Stenella, Tursiops, Delphinus and Lagenodelphis). Incongruent gene trees obtained indicate that incomplete lineage sorting and possibly hybridization are confounding the inference of species history in this group. Nonetheless, using coalescent-based methods, we have been able to extract an underlying species-tree signal from divergent histories of independent genes. This is the first time a molecular study provides support for such relationships. This study further illustrates how methods of species-tree inference can be very sensitive both to the characteristics of the dataset and the evolutionary processes affecting the evolution of the group under study.
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Affiliation(s)
- Ana R Amaral
- Universidade de Lisboa, Faculdade de Ciências, Centro de Biologia Ambiental, Campo Grande, Lisbon, Portugal.
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Pattern and timing of diversification of Cetartiodactyla (Mammalia, Laurasiatheria), as revealed by a comprehensive analysis of mitochondrial genomes. C R Biol 2012; 335:32-50. [DOI: 10.1016/j.crvi.2011.11.002] [Citation(s) in RCA: 369] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 11/07/2011] [Accepted: 11/08/2011] [Indexed: 11/22/2022]
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Charlton-Robb K, Gershwin LA, Thompson R, Austin J, Owen K, McKechnie S. A new dolphin species, the Burrunan Dolphin Tursiops australis sp. nov., endemic to southern Australian coastal waters. PLoS One 2011; 6:e24047. [PMID: 21935372 PMCID: PMC3173360 DOI: 10.1371/journal.pone.0024047] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 08/04/2011] [Indexed: 11/23/2022] Open
Abstract
Small coastal dolphins endemic to south-eastern Australia have variously been assigned to described species Tursiops truncatus, T. aduncus or T. maugeanus; however the specific affinities of these animals is controversial and have recently been questioned. Historically 'the southern Australian Tursiops' was identified as unique and was formally named Tursiops maugeanus but was later synonymised with T. truncatus. Morphologically, these coastal dolphins share some characters with both aforementioned recognised Tursiops species, but they also possess unique characters not found in either. Recent mtDNA and microsatellite genetic evidence indicates deep evolutionary divergence between this dolphin and the two currently recognised Tursiops species. However, in accordance with the recommendations of the Workshop on Cetacean Systematics, and the Unified Species Concept the use of molecular evidence alone is inadequate for describing new species. Here we describe the macro-morphological, colouration and cranial characters of these animals, assess the available and new genetic data, and conclude that multiple lines of evidence clearly indicate a new species of dolphin. We demonstrate that the syntype material of T. maugeanus comprises two different species, one of which is the historical 'southern form of Tursiops' most similar to T. truncatus, and the other is representative of the new species and requires formal classification. These dolphins are here described as Tursiops australis sp. nov., with the common name of 'Burrunan Dolphin' following Australian aboriginal narrative. The recognition of T. australis sp. nov. is particularly significant given the endemism of this new species to a small geographic region of southern and south-eastern Australia, where only two small resident populations in close proximity to a major urban and agricultural centre are known, giving them a high conservation value and making them susceptible to numerous anthropogenic threats.
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Affiliation(s)
- Kate Charlton-Robb
- Centre for Environmental Stress and Adaptation Research, School of Biological Sciences, Monash University, Clayton, Victoria, Australia.
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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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Jakovlić I, Gui JF. Recent invasion and low level of divergence between diploid and triploid forms of Carassius auratus complex in Croatia. Genetica 2011; 139:789-804. [PMID: 21644055 DOI: 10.1007/s10709-011-9584-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Accepted: 05/23/2011] [Indexed: 10/18/2022]
Abstract
Carassius auratus is an invasive species in European waters, comprising a complex of diploid and polyploid forms with different modes of reproduction. However, the evolutionary history and relationships between the diploids and polyploids are still unresolved. In this study, 51.5% diploids and 48.5% triploids, including four triploid males, were discovered among the 363 individuals sampled in Croatia. We used eight microsatellite loci and mitochondrial displacement loop sequences to analyze the structure and origin of populations; and to attempt to infer the evolutionary history of the two different forms in Croatia. Microsatellite analyses revealed high allelic and clonal diversity, corroborating that high propagule vectors can compensate for the negative effects of genetic bottlenecks in successful invasive species. The absence of significant population structuring confirmed recent origin and rapid spreading of populations. No evidence was found for the existence of native European populations. Distances between individuals using both nuclear and mtDNA markers revealed the absence of substantial clustering on the ploidy level, while the split between the different ploidies on population level was only partial, suggesting that the reproductive isolation between the two forms is either of a very recent origin, or that there exists uni-, or bidirectional gene flow between the diploid and triploid forms.
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Affiliation(s)
- Ivan Jakovlić
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Graduate School of the Chinese Academy of Sciences, 430072 Wuhan, People's Republic of China
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31
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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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Owen K, Charlton-Robb K, Thompson R. Resolving the trophic relations of cryptic species: an example using stable isotope analysis of dolphin teeth. PLoS One 2011; 6:e16457. [PMID: 21364748 PMCID: PMC3041760 DOI: 10.1371/journal.pone.0016457] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Accepted: 12/17/2010] [Indexed: 11/18/2022] Open
Abstract
Understanding the foraging ecology and diet of animals can play a crucial role in conservation of a species. This is particularly true where species are cryptic and coexist in environments where observing feeding behaviour directly is difficult. Here we present the first information on the foraging ecology of a recently identified species of dolphin (Southern Australian bottlenose dolphin (SABD)) and comparisons to the common bottlenose dolphin (CBD) in Victoria, Australia, using stable isotope analysis of teeth. Stable isotope signatures differed significantly between SABD and CBD for both δ13C (−14.4‰ vs. −15.5‰ respectively) and δ15N (15.9‰ vs. 15.0‰ respectively), suggesting that the two species forage in different areas and consume different prey. This finding supports genetic and morphological data indicating that SABD are distinct from CBD. In Victoria, the SABD is divided into two distinct populations, one in the large drowned river system of Port Phillip Bay and the other in a series of coastal lakes and lagoons called the Gippsland Lakes. Within the SABD species, population differences were apparent. The Port Phillip Bay population displayed a significantly higher δ15N than the Gippsland Lakes population (17.0‰ vs. 15.5‰), suggesting that the Port Phillip Bay population may feed at a higher trophic level - a result which is supported by analysis of local food chains. Important future work is required to further understand the foraging ecology and diet of this newly described, endemic, and potentially endangered species of dolphin.
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Affiliation(s)
- Kylie Owen
- Australian Centre for Biodiversity and School of Biological Sciences, Monash University, Victoria, Australia.
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Zhou X, Xu S, Yang Y, Zhou K, Yang G. Phylogenomic analyses and improved resolution of Cetartiodactyla. Mol Phylogenet Evol 2011; 61:255-64. [PMID: 21315162 DOI: 10.1016/j.ympev.2011.02.009] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Revised: 01/29/2011] [Accepted: 02/03/2011] [Indexed: 11/26/2022]
Abstract
The remarkable antiquity, diversity, and significance in the ecology and evolution of Cetartiodactyla have inspired numerous attempts to resolve their phylogenetic relationships. However, previous analyses based on limited samples of nuclear genes or mitochondrial DNA sequences have generated results that were either inconsistent with one another, weakly supported, or highly sensitive to analytical conditions. Here, we present strongly supported results based upon over 1.4 Mb of an aligned DNA sequence matrix from 110 single-copy nuclear protein-coding genes of 21 Cetartiodactyla species, which represent major Cetartiodactyla lineages, and three species of Perissodactyla and Carnivora as outgroups. Phylogenetic analysis of this newly developed genomic sequence data using a codon-based model and recently developed models of the rate autocorrelation resolved the phylogenetic relationships of the major cetartiodactylan lineages and of those lineages with a high degree of confidence. Cetacea was found to nest within Artiodactyla as the sister group of Hippopotamidae, and Tylopoda was corroborated as the sole base clade of Cetartiodactyla. Within Cetacea, the monophyletic status of Odontoceti relative to Mysticeti, the basal position of Physeteroidea in Odontoceti, the non-monophyly of the river dolphins, and the sister relationship between Delphinidae and Monodontidae+Phocoenidae were strongly supported. In particular, the groups of Tursiops (bottlenose dolphins) and Stenella (spotted dolphins) were validated as unnatural groups. Additionally, a very narrow time frame of ∼3 My (million years) was found for the rapid diversification of delphinids in the late Miocene, which made it difficult to resolve the phylogenetic relationships within the Delphinidae, especially for previous studies with limited data sets. The present study provides a statistically well-supported phylogenetic framework of Cetartiodactyla, which represents an important step toward ending some of the often-heated, century-long debate on their evolution.
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Affiliation(s)
- Xuming Zhou
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
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Poczai P, Hyvönen J. On the origin of Solanum nigrum: can networks help? Mol Biol Rep 2011; 38:1171-85. [PMID: 20574711 DOI: 10.1007/s11033-010-0215-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Accepted: 06/11/2010] [Indexed: 10/25/2022]
Abstract
Black nightshades are a group of species best known for their 'poisonous' or noxious weedy reputation. It is not so well known that species of this group serve as emerging food source in many countries worldwide especially in the African continent. Despite the fact that the section has recently been studied extensively, taxonomy is still unsettled and debated because of inter- and intraspecific hybridization, phenotypic plasticity and polyploidization. In this study we analyze the genetic relationships among diploid, tetraploid and hexaploid species of sect. Solanum, which have possibly taken part in the formation of Solanum nigrum, utilizing multi-locus (SCoT, ISSR) markers combined with chloroplast trnL-F sequence data and morphological characters. We scored 51 morphological characters united with SCoT (171), ISSR (224) and trnL-F (1042), for simultaneous analysis of 49 terminals and 1488 characters. The topology of the tree is concordant with the results of the network analysis. In the phylogenetic networks, all the accessions of the diploid species shared a split with all of the polyploid species. This reflected a high portion of shared ISSR and SCoT bands between diploids and polyploids. In addition, a strong split divided the diploid species. The history of S. nigrum might be reticulate with hybrid speciation playing an important rule. Genetically differentiated diploids in few combinations have created a series of genetically distinct polyploid populations. The insufficient isolation that permitted further recombination between ancient polyploids and diploids have resulted in high level of genotypic and phenotypic polymorphism. This high level of novel genomic variability obviously enabled species to succeed in their new environment.
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Affiliation(s)
- Péter Poczai
- Plant Biology, University of Helsinki, P.O. Box 65, 00014, Helsinki, Finland.
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Vollmer NL, Viricel A, Wilcox L, Katherine Moore M, Rosel PE. The occurrence of mtDNA heteroplasmy in multiple cetacean species. Curr Genet 2011; 57:115-31. [DOI: 10.1007/s00294-010-0331-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Revised: 12/16/2010] [Accepted: 12/20/2010] [Indexed: 11/30/2022]
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Dissecting comimetic radiations in Heliconius reveals divergent histories of convergent butterflies. Proc Natl Acad Sci U S A 2010; 107:7365-70. [PMID: 20368448 DOI: 10.1073/pnas.0911572107] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mimicry among Heliconius butterflies provides a classic example of coevolution but unresolved relationships among mimetic subspecies have prevented examination of codiversification between species. We present amplified fragment length polymorphism and mtDNA datasets for the major comimetic races of Heliconius erato and H. melpomene. The AFLP data reveal unprecedented resolution, clustering samples by geography and race in both species. Our results show that, although H. erato and H. melpomene co-occur, mimic each other, and exhibit parallel shifts in color pattern, they experienced very different modes of diversification and geographic histories. Our results suggest that H. erato originated on the western side of South America whereas H. melpomene originated in the east. H. erato underwent rapid diversification and expansion with continued gene-flow following diversification, resulting in widely dispersed sister taxa. In contrast, H. melpomene underwent a slower pace of diversification with lower levels of gene flow, producing a stepwise directional expansion from west to east. Our results also suggest that each of the three main wing pattern phenotypes originated and/or was lost multiple times in each species. The rayed pattern is likely to be the ancestral phenotype in H. erato whereas postman or red patch is likely to be ancestral in H. melpomene. Finally, H. cydno and H. himera are monophyletic entities clearly nested within H. melpomene and H. erato, rather than being their respective sister species. Estimates of mtDNA divergence suggest a minimum age of 2.8 and 2.1 My for H. erato and H. melpomene, respectively, placing their origins in the late Pliocene.
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