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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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Louis M, Korlević P, Nykänen M, Archer F, Berrow S, Brownlow A, Lorenzen ED, O'Brien J, Post K, Racimo F, Rogan E, Rosel PE, Sinding MHS, van der Es H, Wales N, Fontaine MC, Gaggiotti OE, Foote AD. Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters. Nat Commun 2023; 14:4020. [PMID: 37463880 DOI: 10.1038/s41467-023-39532-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 06/16/2023] [Indexed: 07/20/2023] Open
Abstract
Parallel evolution provides strong evidence of adaptation by natural selection due to local environmental variation. Yet, the chronology, and mode of the process of parallel evolution remains debated. Here, we harness the temporal resolution of paleogenomics to address these long-standing questions, by comparing genomes originating from the mid-Holocene (8610-5626 years before present, BP) to contemporary pairs of coastal-pelagic ecotypes of bottlenose dolphin. We find that the affinity of ancient samples to coastal populations increases as the age of the samples decreases. We assess the youngest genome (5626 years BP) at sites previously inferred to be under parallel selection to coastal habitats and find it contained coastal-associated genotypes. Thus, coastal-associated variants rose to detectable frequencies close to the emergence of coastal habitat. Admixture graph analyses reveal a reticulate evolutionary history between pelagic and coastal populations, sharing standing genetic variation that facilitated rapid adaptation to newly emerged coastal habitats.
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Affiliation(s)
- Marie Louis
- Centre for Biological Diversity, Sir Harold Mitchell Building and Dyers Brae, University of St Andrews, St Andrews, KY16 9TH, Scotland, UK.
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark.
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands.
- Greenland Institute of Natural Resources, Kivioq 2, Nuuk, 3900, Greenland.
| | - Petra Korlević
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Milaja Nykänen
- Department of Environmental and Biological Sciences, PO Box 111, FI-80101, Joensuu, Finland
- School of Biological, Earth and Environmental Sciences, University College Cork, North Mall, Cork, Ireland
| | - Frederick Archer
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, NOAA, 8901 La Jolla Shores Drive, La Jolla, CA, 92037, USA
| | - Simon Berrow
- Irish Whale and Dolphin Group, Kilrush, Co Clare, Ireland
- Marine and Freshwater Research Centre, Department of Natural Sciences, School of Science and Computing, Atlantic Technological University, Dublin Road, H91 T8NW, Galway, Ireland
| | - Andrew Brownlow
- Scottish Marine Animal Stranding Scheme, Institute of Biodiversity, Animal Health & Comparative Medicine College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Eline D Lorenzen
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark
| | - Joanne O'Brien
- Irish Whale and Dolphin Group, Kilrush, Co Clare, Ireland
- Marine and Freshwater Research Centre, Department of Natural Sciences, School of Science and Computing, Atlantic Technological University, Dublin Road, H91 T8NW, Galway, Ireland
| | - Klaas Post
- Natural History Museum Rotterdam, Westzeedijk 345, 3015 AA, Rotterdam, Netherlands
| | - Fernando Racimo
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark
| | - Emer Rogan
- School of Biological, Earth and Environmental Sciences, University College Cork, North Mall, Cork, Ireland
| | - Patricia E Rosel
- Marine Mammal and Turtle Division, Southeast Fisheries Science Center, NOAA, 646 Cajundome Boulevard, Lafayette, LA, 70506, USA
| | - Mikkel-Holger S Sinding
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Henry van der Es
- Natural History Museum Rotterdam, Westzeedijk 345, 3015 AA, Rotterdam, Netherlands
| | - Nathan Wales
- University of York, BioArCh, Environment Building, Wentworth Way, Heslington, York, YO10 5DD, UK
| | - Michael C Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands
- MIVEGEC (Université de Montpellier, CNRS 5290, IRD 229) Institut de Recherche pour le Développement (IRD), F-34394, Montpellier, France
| | - Oscar E Gaggiotti
- Centre for Biological Diversity, Sir Harold Mitchell Building and Dyers Brae, University of St Andrews, St Andrews, KY16 9TH, Scotland, UK
| | - Andrew D Foote
- Department of Natural History, Norwegian University of Science and Technology (NTNU), NO-7491, Trondheim, Norway.
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0316, Oslo, Norway.
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3
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Abstract
AbstractRensch’s rule entails that male-biased sexual size dimorphism scales allometrically with body size and is assumed to generally apply to polygynous taxa. However, so far only few mammalian groups have been shown to conform to it. Toothed whales (Odontoceti) not only span a substantial range of body sizes, but are commonly presumed to be predominantly polygynous, thus representing a promising candidate group to test for Rensch’s rule. Here we compiled a dataset of sex-specific body lengths in 57 species of toothed whales and demonstrate that sexual size dimorphism in this group does indeed follow Rensch’s rule. When focusing on selected subgroups of toothed whales, conformity to the rule was prominent among lineages of the speciose superfamily Delphinoidea, while it was not found in the beaked whales of the family Ziphiidae. These results support the assumption that polygynous and polygynandrous mating systems and marked precopulatory intrasexual competition between males are common among toothed whales. However, female-biased sexual size dimorphism as well as monomorphism occur at notable frequencies as well, suggesting that reproductive strategies are nevertheless variable among these marine mammals.
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Gut Microbial Characterization of Melon-Headed Whales (Peponocephala electra) Stranded in China. Microorganisms 2022; 10:microorganisms10030572. [PMID: 35336147 PMCID: PMC8950688 DOI: 10.3390/microorganisms10030572] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/27/2022] [Accepted: 03/05/2022] [Indexed: 12/04/2022] Open
Abstract
Although gut microbes are regarded as a significant component of many mammals and play a very important role, there is a paucity of knowledge around marine mammal gut microbes, which may be due to sampling difficulties. Moreover, to date, there are very few, if any, reports on the gut microbes of melon-headed whales. In this study, we opportunistically collected fecal samples from eight stranded melon-headed whales (Peponocephala electra) in China. Using high-throughput sequencing technology of partial 16S rRNA gene sequences, we demonstrate that the main taxa of melon-headed whale gut microbes are Firmicutes, Fusobacteriota, Bacteroidota, and Proteobacteria (Gamma) at the phylum taxonomic level, and Cetobacterium, Bacteroides, Clostridium sensu stricto, and Enterococcus at the genus taxonomic level. Meanwhile, molecular ecological network analysis (MENA) shows that two modules (a set of nodes that have strong interactions) constitute the gut microbial community network of melon-headed whales. Module 1 is mainly composed of Bacteroides, while Module 2 comprises Cetobacterium and Enterococcus, and the network keystone genera are Corynebacterium, Alcaligenes, Acinetobacter, and Flavobacterium. Furthermore, by predicting the functions of the gut microbial community through PICRUSt2, we found that although there are differences in the composition of the gut microbial community in different individuals, the predicted functional profiles are similar. Our study gives a preliminary inside look into the composition of the gut microbiota of stranded melon-headed whales.
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5
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OUP accepted manuscript. J Mammal 2022. [DOI: 10.1093/jmammal/gyac040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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6
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Wang ZT, Supin AY, Akamatsu T, Duan PX, Yang YN, Wang KX, Wang D. Auditory evoked potential in stranded melon-headed whales (Peponocephala electra): With severe hearing loss and possibly caused by anthropogenic noise pollution. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 228:113047. [PMID: 34861441 DOI: 10.1016/j.ecoenv.2021.113047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/27/2021] [Accepted: 11/29/2021] [Indexed: 06/13/2023]
Abstract
Highly concentrated live mass stranding events of dolphins and whales happened in the eastern coast of China between June and October 2021. The current study adopted the non-invasive auditory evoked-potential technique to investigate the hearing threshold of a stranded melon headed whale (Peponocephala electra) at a frequency range of between 9.5 and 181 kHz. It was found that, at the frequency range of from 10 to 100 kHz, hearing thresholds for the animal were between 20 and 65 dB higher than those of its phylogenetically closest species (Pygmy killer whale). The severe hearing loss in the melon headed whale was probably caused by transient intense anthropogenic sonar or chronic shipping noise exposures. The hearing loss could have been the cause for the observed temporal and spatial clustered stranding events. Therefore, there is need for noise mitigation strategies to reduce noise exposure levels for marine mammals in the coastal areas of China.
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Affiliation(s)
- Zhi-Tao Wang
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, 7 South Donghu Road, Wuhan 430072, China
| | - Alexander Ya Supin
- Institute of Ecology and Evolution of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Tomonari Akamatsu
- Ocean Policy Research Institute, the Sasakawa Peace Foundation, Tokyo, Japan
| | - Peng-Xiang Duan
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, 7 South Donghu Road, Wuhan 430072, China
| | - Yi-Ning Yang
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, 7 South Donghu Road, Wuhan 430072, China
| | - Ke-Xiong Wang
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, 7 South Donghu Road, Wuhan 430072, China.
| | - Ding Wang
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, 7 South Donghu Road, Wuhan 430072, China.
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7
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Abramson NI, Bodrov SY, Bondareva OV, Genelt-Yanovskiy EA, Petrova TV. A mitochondrial genome phylogeny of voles and lemmings (Rodentia: Arvicolinae): Evolutionary and taxonomic implications. PLoS One 2021; 16:e0248198. [PMID: 34797834 PMCID: PMC8604340 DOI: 10.1371/journal.pone.0248198] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 11/03/2021] [Indexed: 01/04/2023] Open
Abstract
Arvicolinae is one of the most impressive placental radiations with over 150 extant and numerous extinct species that emerged since the Miocene in the Northern Hemisphere. The phylogeny of Arvicolinae has been studied intensively for several decades using morphological and genetic methods. Here, we sequenced 30 new mitochondrial genomes to better understand the evolutionary relationships among the major tribes and genera within the subfamily. The phylogenetic and molecular dating analyses based on 11,391 bp concatenated alignment of protein-coding mitochondrial genes confirmed the monophyly of the subfamily. While Bayesian analysis provided a high resolution across the entire tree, Maximum Likelihood tree reconstruction showed weak support for the ordering of divergence and interrelationships of tribal level taxa within the most ancient radiation. Both the interrelationships among tribes Lagurini, Ellobiusini and Arvicolini, comprising the largest radiation and the position of the genus Dinaromys within it also remained unresolved. For the first time complex relationships between genus level taxa within the species-rich tribe Arvicolini received full resolution. Particularly Lemmiscus was robustly placed as sister to the snow voles Chionomys in the tribe Arvicolini in contrast with a long-held belief of its affinity with Lagurini. Molecular dating of the origin of Arvicolinae and early divergences obtained from the mitogenome data were consistent with fossil records. The mtDNA estimates for putative ancestors of the most genera within Arvicolini appeared to be much older than it was previously proposed in paleontological studies.
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Affiliation(s)
- Natalia I. Abramson
- Department of Molecular Systematics, Laboratory of Theriology, Zoological Institute RAS, Saint Petersburg, Russia
| | - Semyon Yu. Bodrov
- Department of Molecular Systematics, Laboratory of Theriology, Zoological Institute RAS, Saint Petersburg, Russia
| | - Olga V. Bondareva
- Department of Molecular Systematics, Laboratory of Theriology, Zoological Institute RAS, Saint Petersburg, Russia
| | - Evgeny A. Genelt-Yanovskiy
- Department of Molecular Systematics, Laboratory of Theriology, Zoological Institute RAS, Saint Petersburg, Russia
| | - Tatyana V. Petrova
- Department of Molecular Systematics, Laboratory of Theriology, Zoological Institute RAS, Saint Petersburg, Russia
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8
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Mello CADA, Amorim IC, Silva AFD, Medeiros GRD, Wallau GL, Moura RDCD. Mitogenome of Coprophanaeus ensifer and phylogenetic analysis of the Scarabaeidae family (Coleoptera). Genet Mol Biol 2021; 44:e20200417. [PMID: 34387299 PMCID: PMC8361247 DOI: 10.1590/1678-4685-gmb-2020-0417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 05/02/2021] [Indexed: 12/02/2022] Open
Abstract
Several studies about the phylogenetic relationships of the Scarabaeinae subfamily (Coleoptera: Scarabaeidae) have been performed, but some phylogenetic uncertainties persist including the relationship and monophyly of different tribes and some genera. The aim of this study was to characterize the mitogenome of Coprophanaeus ensifer in order to establish its position within the Scarabaeidae family and to contribute to the resolution of some phylogenetic uncertainties. The mitogenome was sequenced on the Illumina HiSeq 4000, assembled using the Mitobim software and annotated in MITOS WebServer. The phylogenetic trees were reconstructed by Bayesian inference. The C. ensifer mitogenome is a molecule of 14,964 bp that contains the number and organization of the genes similar to those of most Coleoptera species. Phylogenetic reconstruction suggests monophyly of the tribe Phanaeini and supports the hypothesis that Coprini is a sister group of Phanaeini. The results also revealed the position of the tribe Oniticellini which is grouped with Onthophagini and Onitini. The geographic distribution of these species that form the most ancestral clade suggests with Scarabaeinae originated in Africa.
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Affiliation(s)
| | - Igor Costa Amorim
- Universidade de Pernambuco, Instituto de Ciências Biológicas, Laboratório de Biodiversidade e Genética de Insetos, Recife, PE, Brazil
| | | | - Giuliene Rocha de Medeiros
- Universidade de Pernambuco, Instituto de Ciências Biológicas, Laboratório de Biodiversidade e Genética de Insetos, Recife, PE, Brazil
| | - Gabriel Luz Wallau
- Departamento de Entomologia, Instituto Aggeu Magalhães - FIOCRUZ, Recife, Pernambuco, Brazil
| | - Rita de Cássia de Moura
- Universidade de Pernambuco, Instituto de Ciências Biológicas, Laboratório de Biodiversidade e Genética de Insetos, Recife, PE, Brazil
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9
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Lloyd GT, Slater GJ. A Total-Group Phylogenetic Metatree for Cetacea and the Importance of Fossil Data in Diversification Analyses. Syst Biol 2021; 70:922-939. [PMID: 33507304 DOI: 10.1093/sysbio/syab002] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 12/20/2020] [Accepted: 01/10/2021] [Indexed: 01/09/2023] Open
Abstract
Phylogenetic trees provide a powerful framework for testing macroevolutionary hypotheses, but it is becoming increasingly apparent that inferences derived from extant species alone can be highly misleading. Trees incorporating living and extinct taxa are are needed to address fundamental questions about the origins of diversity and disparity but it has proved challenging to generate robust, species-rich phylogenies that include large numbers of fossil taxa. As a result, most studies of diversification dynamics continue to rely on molecular phylogenies. Here, we extend and apply a recently developed meta-analytic approach for synthesizing previously published phylogenetic studies to infer a well-resolved set of species level, time-scaled phylogenetic hypotheses for extinct and extant cetaceans (whales, dolphins and allies). Our trees extend sampling from the ∼ 90 extant species to over 500 living and extinct species, and therefore allow for more robust inference of macroevolutionary dynamics. While the diversification scenarios we recover are broadly concordant with those inferred from molecular phylogenies they differ in critical ways, notably in the relative contributions of extinction and speciation rate shifts in driving rapid radiations. The metatree approach provides the most immediate route for generating higher level phylogenies of extinct taxa, and opens the door to re-evaluation of macroevolutionary hypotheses derived only from extant taxa.
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Affiliation(s)
- Graeme T Lloyd
- School of Earth and Environment, University of Leeds, Leeds, U.K
| | - Graham J Slater
- Department of the Geophysical Sciences, University of Chicago, Chicago, USA
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10
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Chen YX, Sun CH, Li YK, Fei YL, Xue XM, Hou SL, Zhou YW, Jiang J, Guo HT. Complete mitogenome of Treron sphenurus (Aves, Columbiformes): the first representative from the genus Treron, genomic comparisons and phylogenetic analysis of Columbidae. Anim Biotechnol 2021; 33:1003-1013. [PMID: 33439093 DOI: 10.1080/10495398.2020.1862135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The wedge-tailed green pigeon (Treron sphenurus) has a protective value in the evolution of the family Columbidae. In this study, the complete mitogenome of T. sphenurus from Baise City, China, which represents the first sequenced species of the genus Treron in Tribe Treronini, is reported. This was accomplished using PCR-based methods and a primer-walking sequencing strategy with genus-specific primers. The mitogenome was found to be 18,919 bp in length comprising 37 genes, including 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one control region. In terms of structure and composition, many similarities were found between the T. sphenurus and Hemiphaga novaeseelandiae (New Zealand pigeon) mitogenomes. This was further supported by phylogenetic analysis showing that T. sphenurus has a close evolutionary relationship with H. novaeseelandiae. The complete mitogenome of T. sphenurus reported here is expected to provide valuable molecular information for further studies on the phylogeny of the genus Treron and for analyses of the taxonomic status of the family Columbidae.
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Affiliation(s)
- Yun-Xia Chen
- Nanjing Forest Police College, Nanjing, China.,Key Laboratory of Wildlife Evidence Technology State Forest and Grassland Administration, Nanjing, China
| | - Cheng-He Sun
- Department of Ecology, Jinan University, Guangzhou, China
| | - Yao-Kai Li
- Department of Ecology, Jinan University, Guangzhou, China
| | - Yi-Ling Fei
- Nanjing Forest Police College, Nanjing, China.,Key Laboratory of Wildlife Evidence Technology State Forest and Grassland Administration, Nanjing, China
| | - Xiao-Ming Xue
- Nanjing Forest Police College, Nanjing, China.,Key Laboratory of Wildlife Evidence Technology State Forest and Grassland Administration, Nanjing, China
| | - Sen-Lin Hou
- Nanjing Forest Police College, Nanjing, China.,Key Laboratory of Wildlife Evidence Technology State Forest and Grassland Administration, Nanjing, China
| | - Yong-Wu Zhou
- Nanjing Forest Police College, Nanjing, China.,Key Laboratory of Wildlife Evidence Technology State Forest and Grassland Administration, Nanjing, China
| | - Jing Jiang
- Nanjing Forest Police College, Nanjing, China.,Key Laboratory of Wildlife Evidence Technology State Forest and Grassland Administration, Nanjing, China
| | - Hai-Tao Guo
- Nanjing Forest Police College, Nanjing, China.,Key Laboratory of Wildlife Evidence Technology State Forest and Grassland Administration, Nanjing, China
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11
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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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12
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Nykänen M, Kaschner K, Dabin W, Brownlow A, Davison NJ, Deaville R, Garilao C, Kesner-Reyes K, Gilbert MTP, Penrose R, Islas-Villanueva V, Wales N, Ingram SN, Rogan E, Louis M, Foote AD. Postglacial Colonization of Northern Coastal Habitat by Bottlenose Dolphins: A Marine Leading-Edge Expansion? J Hered 2020; 110:662-674. [PMID: 31211393 DOI: 10.1093/jhered/esz039] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 06/14/2019] [Indexed: 11/15/2022] Open
Abstract
Oscillations in the Earth's temperature and the subsequent retreating and advancing of ice-sheets around the polar regions are thought to have played an important role in shaping the distribution and genetic structuring of contemporary high-latitude populations. After the Last Glacial Maximum (LGM), retreating of the ice-sheets would have enabled early colonizers to rapidly occupy suitable niches to the exclusion of other conspecifics, thereby reducing genetic diversity at the leading-edge. Bottlenose dolphins (genus Tursiops) form distinct coastal and pelagic ecotypes, with finer-scale genetic structuring observed within each ecotype. We reconstruct the postglacial colonization of the Northeast Atlantic (NEA) by bottlenose dolphins using habitat modeling and phylogenetics. The AquaMaps model hindcasted suitable habitat for the LGM in the Atlantic lower latitude waters and parts of the Mediterranean Sea. The time-calibrated phylogeny, constructed with 86 complete mitochondrial genomes including 30 generated for this study and created using a multispecies coalescent model, suggests that the expansion to the available coastal habitat in the NEA happened via founder events starting ~15 000 years ago (95% highest posterior density interval: 4 900-26 400). The founders of the 2 distinct coastal NEA populations comprised as few as 2 maternal lineages that originated from the pelagic population. The low effective population size and genetic diversity estimated for the shared ancestral coastal population subsequent to divergence from the pelagic source population are consistent with leading-edge expansion. These findings highlight the legacy of the Late Pleistocene glacial cycles on the genetic structuring and diversity of contemporary populations.
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Affiliation(s)
- Milaja Nykänen
- School of Biological, Earth and Environmental Sciences, University College Cork, Distillery Fields, Cork, Ireland
| | - Kristin Kaschner
- Department of Biometry and Environmental System Analysis, Faculty of Environment and Natural Resources, University of Freiburg, Tennenbacher Straße, Freiburg, Germany
| | - Willy Dabin
- Centre d'Etudes Biologiques de Chizé. UMR 7372 CNRS-Université de La Rochelle, Villiers-en-Bois, France.,Observatoire PELAGIS, UMS 3462 CNRS-Université de La Rochelle, 5 allées de l'Océan, La Rochelle, France
| | - Andrew Brownlow
- Scottish Marine Animal Stranding Scheme, SRUC Veterinary Services, Drummondhill, Inverness, UK
| | - Nicholas J Davison
- Scottish Marine Animal Stranding Scheme, SRUC Veterinary Services, Drummondhill, Inverness, UK
| | - Rob Deaville
- UK Cetacean Strandings Investigation Programme, The Wellcome Building, Institute of Zoology, Zoological Society of London, Regent's Park, London, UK
| | | | | | - M Thomas P Gilbert
- Section for Evolutionary Genomics, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rod Penrose
- Marine Environmental Monitoring, Penwalk, Llechryd, Cardigan, Ceredigion, Wales, UK
| | | | - Nathan Wales
- Section for Evolutionary Genomics, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Simon N Ingram
- Marine Vertebrate Research Group, School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth, UK
| | - Emer Rogan
- School of Biological, Earth and Environmental Sciences, University College Cork, Distillery Fields, Cork, Ireland
| | - Marie Louis
- Centre d'Etudes Biologiques de Chizé. UMR 7372 CNRS-Université de La Rochelle, Villiers-en-Bois, France.,Scottish Oceans Institute, East Sands, St Andrews, UK
| | - Andrew D Foote
- School of Biological, Earth and Environmental Sciences, University College Cork, Distillery Fields, Cork, Ireland.,Section for Evolutionary Genomics, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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13
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Coombs EJ, Clavel J, Park T, Churchill M, Goswami A. Wonky whales: the evolution of cranial asymmetry in cetaceans. BMC Biol 2020; 18:86. [PMID: 32646447 PMCID: PMC7350770 DOI: 10.1186/s12915-020-00805-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 06/01/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Unlike most mammals, toothed whale (Odontoceti) skulls lack symmetry in the nasal and facial (nasofacial) region. This asymmetry is hypothesised to relate to echolocation, which may have evolved in the earliest diverging odontocetes. Early cetaceans (whales, dolphins, and porpoises) such as archaeocetes, namely the protocetids and basilosaurids, have asymmetric rostra, but it is unclear when nasofacial asymmetry evolved during the transition from archaeocetes to modern whales. We used three-dimensional geometric morphometrics and phylogenetic comparative methods to reconstruct the evolution of asymmetry in the skulls of 162 living and extinct cetaceans over 50 million years. RESULTS In archaeocetes, we found asymmetry is prevalent in the rostrum and also in the squamosal, jugal, and orbit, possibly reflecting preservational deformation. Asymmetry in odontocetes is predominant in the nasofacial region. Mysticetes (baleen whales) show symmetry similar to terrestrial artiodactyls such as bovines. The first significant shift in asymmetry occurred in the stem odontocete family Xenorophidae during the Early Oligocene. Further increases in asymmetry occur in the physeteroids in the Late Oligocene, Squalodelphinidae and Platanistidae in the Late Oligocene/Early Miocene, and in the Monodontidae in the Late Miocene/Early Pliocene. Additional episodes of rapid change in odontocete skull asymmetry were found in the Mid-Late Oligocene, a period of rapid evolution and diversification. No high-probability increases or jumps in asymmetry were found in mysticetes or archaeocetes. Unexpectedly, no increases in asymmetry were recovered within the highly asymmetric ziphiids, which may result from the extreme, asymmetric shape of premaxillary crests in these taxa not being captured by landmarks alone. CONCLUSIONS Early ancestors of living whales had little cranial asymmetry and likely were not able to echolocate. Archaeocetes display high levels of asymmetry in the rostrum, potentially related to directional hearing, which is lost in early neocetes-the taxon including the most recent common ancestor of living cetaceans. Nasofacial asymmetry becomes a significant feature of Odontoceti skulls in the Early Oligocene, reaching its highest levels in extant taxa. Separate evolutionary regimes are reconstructed for odontocetes living in acoustically complex environments, suggesting that these niches impose strong selective pressure on echolocation ability and thus increased cranial asymmetry.
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Affiliation(s)
- Ellen J Coombs
- Genetics, Evolution, and Environment Department, University College London, Gower Street, London, WC1E 6BT, UK.
- Department of Life Sciences, Natural History Museum, London, Cromwell Road, London, SW7 5BD, UK.
| | - Julien Clavel
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622, Villeurbanne, France
| | - Travis Park
- Department of Life Sciences, Natural History Museum, London, Cromwell Road, London, SW7 5BD, UK
- Department of Earth Sciences, University of Oxford, Oxford, OX1 3AN, UK
| | - Morgan Churchill
- Department of Biology, University of Wisconsin-Oshkosh, Oshkosh, WI, 54901, USA
| | - Anjali Goswami
- Genetics, Evolution, and Environment Department, University College London, Gower Street, London, WC1E 6BT, UK
- Department of Life Sciences, Natural History Museum, London, Cromwell Road, London, SW7 5BD, UK
- Department of Earth Sciences, University College London, Gower Street, London, WC1E 6BT, UK
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14
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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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15
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Vijay N, Park C, Oh J, Jin S, Kern E, Kim HW, Zhang J, Park JK. Population Genomic Analysis Reveals Contrasting Demographic Changes of Two Closely Related Dolphin Species in the Last Glacial. Mol Biol Evol 2019; 35:2026-2033. [PMID: 29846663 PMCID: PMC6063294 DOI: 10.1093/molbev/msy108] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Population genomic data can be used to infer historical effective population sizes (Ne), which help study the impact of past climate changes on biodiversity. Previous genome sequencing of one individual of the common bottlenose dolphin Tursiops truncatus revealed an unusual, sharp rise in Ne during the last glacial, raising questions about the reliability, generality, underlying cause, and biological implication of this finding. Here we first verify this result by additional sampling of T. truncatus. We then sequence and analyze the genomes of its close relative, the Indo-Pacific bottlenose dolphin T. aduncus. The two species exhibit contrasting demographic changes in the last glacial, likely through actual changes in population size and/or alterations in the level of gene flow among populations. Our findings suggest that even closely related species can have drastically different responses to climatic changes, making predicting the fate of individual species in the ongoing global warming a serious challenge.
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Affiliation(s)
- Nagarjun Vijay
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
| | - Chungoo Park
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, Republic of Korea
| | - Jooseong Oh
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, Republic of Korea
| | - Soyeong Jin
- Division of EcoScience, Ewha Womans University, Seoul, Republic of Korea
| | - Elizabeth Kern
- Division of EcoScience, Ewha Womans University, Seoul, Republic of Korea
| | - Hyun Woo Kim
- Cetacean Research Institute, National Institute of Fisheries Science, Ulsan, Republic of Korea
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
| | - Joong-Ki Park
- Division of EcoScience, Ewha Womans University, Seoul, Republic of Korea
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16
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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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17
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Cortés-Hinojosa G, Subramaniam K, Wellehan JFX, Ng TFF, Delwart E, McCulloch SD, Goldstein JD, Schaefer AM, Fair PA, Reif JS, Bossart GD, Waltzek TB. Genomic sequencing of a virus representing a novel type within the species Dyopipapillomavirus 1 in an Indian River Lagoon bottlenose dolphin. Arch Virol 2019; 164:767-774. [PMID: 30663022 DOI: 10.1007/s00705-018-04117-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 11/14/2018] [Indexed: 10/27/2022]
Abstract
Fecal samples collected from free-ranging Atlantic bottlenose dolphins (BDs) in the Indian River Lagoon of Florida were processed for viral discovery using a next-generation sequencing (NGS) approach. A 693-bp contig identified in the NGS data was nearly identical to the partial L1 gene sequence of a papillomavirus (PV) previously found in a penile papilloma in a killer whale (Orcinus orca). Based on this partial bottlenose dolphin papillomavirus (BDPV) sequence, a nested inverse PCR and primer-walking strategy was employed to generate the complete genome sequence. The full BDPV genome consisted of 7299 bp and displayed a typical PV genome organization. The BDPV E6 protein contained a PDZ-binding motif, which has been shown to be involved in carcinogenic transformation involving high-risk genital human PVs. Screening of 12 individual fecal samples using a specific endpoint PCR assay revealed that the feces from a single female BD displaying a genital papilloma was positive for the BDPV. Genetic analysis indicated that this BDPV (Tursiops truncatus papillomavirus 8; TtPV8) is a new type of Dyopipapillomavirus 1, previously sequenced from an isolate obtained from a penile papilloma in a harbor porpoise (Phocoena phocoena). Although only a partial L1 sequence has been determined for a PV detected in a killer whale genital papilloma, our finding of a nearly identical sequence in an Atlantic BD may indicate that members of this viral species are capable of host jumping. Future work is needed to determine if this virus is a high-risk PV that is capable of inducing carcinogenic transformation and whether it poses a significant health risk to wild delphinid populations.
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Affiliation(s)
- Galaxia Cortés-Hinojosa
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Kuttichantran Subramaniam
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Bldg 1379, Mowry Road, Gainesville, FL, 32611, USA
| | - James F X Wellehan
- Department of Comparative, Diagnostic and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Terry Fei Fan Ng
- College of Veterinary Medicine, University of Georgia, Athens, GA, USA.,Blood Systems Research Institute, San Francisco, USA.,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, USA.,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Stephen D McCulloch
- Division of Marine Mammal Research and Conservation, Center of Marine Ecosystems Health, Harbor Branch Oceanographic Institution, Florida Atlantic University, Fort Pierce, FL, USA.,Protect Wild Dolphins Alliance, 2046 Treasure Coast Plaza, Vero Beach, FL, 32960, USA
| | - Juli D Goldstein
- Division of Marine Mammal Research and Conservation, Center of Marine Ecosystems Health, Harbor Branch Oceanographic Institution, Florida Atlantic University, Fort Pierce, FL, USA.,Protect Wild Dolphins Alliance, 2046 Treasure Coast Plaza, Vero Beach, FL, 32960, USA
| | - Adam M Schaefer
- Division of Marine Mammal Research and Conservation, Center of Marine Ecosystems Health, Harbor Branch Oceanographic Institution, Florida Atlantic University, Fort Pierce, FL, USA
| | - Patricia A Fair
- National Oceanic and Atmospheric Administration, National Ocean Service, Center for Coastal Environmental Health and Biomolecular Research, Charleston, SC, USA
| | - John S Reif
- Department of Environmental and Radiological Health Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Gregory D Bossart
- Georgia Aquarium, 225 Baker Street, NW, Atlanta, GA, 30313, USA.,Division of Comparative Pathology, Miller School of Medicine, University of Miami, PO Box 016960, (R-46), Miami, FL, 33101, USA
| | - Thomas B Waltzek
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Bldg 1379, Mowry Road, Gainesville, FL, 32611, USA.
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18
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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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19
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Eimanifar A, Kimball RT, Braun EL, Ellis JD. Mitochondrial genome diversity and population structure of two western honey bee subspecies in the Republic of South Africa. Sci Rep 2018; 8:1333. [PMID: 29358597 PMCID: PMC5778041 DOI: 10.1038/s41598-018-19759-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 01/08/2018] [Indexed: 11/09/2022] Open
Abstract
Apis mellifera capensis Eschscholtz and A.m. scutellata Lepeletier are subspecies of western honey bees that are indigenous to the Republic of South Africa (RSA). Both subspecies have invasive potential and are organisms of concern for areas outside their native range, though they are important bees to beekeepers, agriculture, and the environment where they are native. The aim of the present study was to examine genetic differentiation among these subspecies and estimate their phylogenetic relationships using complete mitochondrial genomes sequences. We used 25 individuals that were either assigned to one of the subspecies or designated hybrids using morphometric analyses. Phylogenetic analyses of mitogenome sequences by maximum likelihood (ML) and Bayesian inference identified a monophyletic RSA clade, subdivided into two clades. A haplotype network was consistent with the phylogenetic trees. However, members of both subspecies occurred in both clades, indicating that A.m. capensis and A.m. scutellata are neither reciprocally monophyletic nor do they exhibit paraphyly with one subspecies nested within the other subspecies. Furthermore, no mitogenomic features were diagnostic to either subspecies. All bees analyzed from the RSA expressed a substantial level of haplotype diversity (most samples had unique haplotypes) but limited nucleotide diversity. The number of variable codons across protein-coding genes (PCGs) differed among loci, with CO3 exhibiting the most variation and ATP6 the least.
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Affiliation(s)
- Amin Eimanifar
- Honey Bee Research and Extension Laboratory, Entomology and Nematology Department, University of Florida, Gainesville, Florida, 32611-0620, USA.
| | - Rebecca T Kimball
- Department of Biology, University of Florida, Gainesville, Florida, 32611, USA
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, Florida, 32611, USA
| | - James D Ellis
- Honey Bee Research and Extension Laboratory, Entomology and Nematology Department, University of Florida, Gainesville, Florida, 32611-0620, USA
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20
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Gaubert P, Antunes A, Meng H, Miao L, Peigné S, Justy F, Njiokou F, Dufour S, Danquah E, Alahakoon J, Verheyen E, Stanley WT, O’Brien SJ, Johnson WE, Luo SJ. The Complete Phylogeny of Pangolins: Scaling Up Resources for the Molecular Tracing of the Most Trafficked Mammals on Earth. J Hered 2017; 109:347-359. [DOI: 10.1093/jhered/esx097] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/02/2017] [Indexed: 01/08/2023] Open
Affiliation(s)
- Philippe Gaubert
- Institut des Sciences de l’Evolution de Montpellier (ISEM)—UM-CNRS-IRD-EPHE, Université, France
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Portugal
| | - Agostinho Antunes
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Portugal
| | - Hao Meng
- School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, China
| | - Lin Miao
- School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, China
| | - Stéphane Peigné
- Centre de recherche sur la paléobiodiversité et les paléoenvironnements (CR2P)—UMR 7207 MNHN/CNRS/UPMC, Muséum national d’Histoire naturelle—CP38, France
| | - Fabienne Justy
- Institut des Sciences de l’Evolution de Montpellier (ISEM)—UM-CNRS-IRD-EPHE, Université, France
| | - Flobert Njiokou
- Laboratoire de Parasitologie et Ecologie, Université de Yaoundé I, Faculté des Sciences, Cameroon
| | | | - Emmanuel Danquah
- Department of Wildlife and Range Management, Faculty of Renewable Natural Resources, Kwame Nkrumah University of Science and Technology, Ghana
| | | | - Erik Verheyen
- OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Belgium
- Evolutionary Ecology Group, University of Antwerp, Belgium
| | | | - Stephen J O’Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Russia
- Oceanographic Center, Dania Beach, FL
- Nova Southeastern University, Ft Lauderdale, FL
| | - Warren E Johnson
- Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA
| | - Shu-Jin Luo
- School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, China
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21
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Speller C, van den Hurk Y, Charpentier A, Rodrigues A, Gardeisen A, Wilkens B, McGrath K, Rowsell K, Spindler L, Collins M, Hofreiter M. Barcoding the largest animals on Earth: ongoing challenges and molecular solutions in the taxonomic identification of ancient cetaceans. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150332. [PMID: 27481784 PMCID: PMC4971184 DOI: 10.1098/rstb.2015.0332] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2016] [Indexed: 11/30/2022] Open
Abstract
Over the last few centuries, many cetacean species have witnessed dramatic global declines due to industrial overharvesting and other anthropogenic influences, and thus are key targets for conservation. Whale bones recovered from archaeological and palaeontological contexts can provide essential baseline information on the past geographical distribution and abundance of species required for developing informed conservation policies. Here we review the challenges with identifying whale bones through traditional anatomical methods, as well as the opportunities provided by new molecular analyses. Through a case study focused on the North Sea, we demonstrate how the utility of this (pre)historic data is currently limited by a lack of accurate taxonomic information for the majority of ancient cetacean remains. We then discuss current opportunities presented by molecular identification methods such as DNA barcoding and collagen peptide mass fingerprinting (zooarchaeology by mass spectrometry), and highlight the importance of molecular identifications in assessing ancient species' distributions through a case study focused on the Mediterranean. We conclude by considering high-throughput molecular approaches such as hybridization capture followed by next-generation sequencing as cost-effective approaches for enhancing the ecological informativeness of these ancient sample sets.This article is part of the themed issue 'From DNA barcodes to biomes'.
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Affiliation(s)
- Camilla Speller
- BioArCh, Department of Archaeology, University of York, Environment Building, York, North Yorkshire YO10 5DD, UK
| | - Youri van den Hurk
- Institute of Archaeology, University College London, 31-34 Gordon Square, London WC1H 0PY, UK
| | - Anne Charpentier
- CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE - CNRS, Montpellier Cedex 5, France
| | - Ana Rodrigues
- CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE - CNRS, Montpellier Cedex 5, France
| | - Armelle Gardeisen
- Archéologie des Sociétés Méditerranéennes, UMR 5140, CNRS, Labex Archimede IA-ANR-11-LABX-0032-01, Université Paul-Valéry Montpellier, 34970 Lattes, France
| | - Barbara Wilkens
- Dipartimento di Scienze della Natura e del Territorio, Università degli Studi, Sassari, Italy
| | - Krista McGrath
- BioArCh, Department of Archaeology, University of York, Environment Building, York, North Yorkshire YO10 5DD, UK
| | - Keri Rowsell
- BioArCh, Department of Archaeology, University of York, Environment Building, York, North Yorkshire YO10 5DD, UK
| | - Luke Spindler
- BioArCh, Department of Archaeology, University of York, Environment Building, York, North Yorkshire YO10 5DD, UK
| | - Matthew Collins
- BioArCh, Department of Archaeology, University of York, Environment Building, York, North Yorkshire YO10 5DD, UK
| | - Michael Hofreiter
- Institute of Biochemistry and Biology, Faculty of Mathematics and Natural Sciences, University of Potsdam, 14476 Potsdam, Germany
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22
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23
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Montelli S, Peruffo A, Patarnello T, Cozzi B, Negrisolo E. Back to Water: Signature of Adaptive Evolution in Cetacean Mitochondrial tRNAs. PLoS One 2016; 11:e0158129. [PMID: 27336480 PMCID: PMC4919058 DOI: 10.1371/journal.pone.0158129] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 06/11/2016] [Indexed: 11/29/2022] Open
Abstract
The mitochondrion is the power plant of the eukaryotic cell, and tRNAs are the fundamental components of its translational machinery. In the present paper, the evolution of mitochondrial tRNAs was investigated in the Cetacea, a clade of Cetartiodactyla that retuned to water and thus had to adapt its metabolism to a different medium than that of its mainland ancestors. Our analysis focussed on identifying the factors that influenced the evolution of Cetacea tRNA double-helix elements, which play a pivotal role in the formation of the secondary and tertiary structures of each tRNA and consequently manipulate the whole translation machinery of the mitochondrion. Our analyses showed that the substitution pathways in the stems of different tRNAs were influenced by various factors, determining a molecular evolution that was unique to each of the 22 tRNAs. Our data suggested that the composition, AT-skew, and GC-skew of the tRNA stems were the main factors influencing the substitution process. In particular, the range of variation and the fluctuation of these parameters affected the fate of single tRNAs. Strong heterogeneity was observed among the different species of Cetacea. Finally, it appears that the evolution of mitochondrial tRNAs was also shaped by the environments in which the Cetacean taxa differentiated. This latter effect was particularly evident in toothed whales that either live in freshwater or are deep divers.
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Affiliation(s)
- Stefano Montelli
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro (PD), Italy
| | - Antonella Peruffo
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro (PD), Italy
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro (PD), Italy
| | - Bruno Cozzi
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro (PD), Italy
| | - Enrico Negrisolo
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro (PD), Italy
- * E-mail:
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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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Addamo AM, Vertino A, Stolarski J, García-Jiménez R, Taviani M, Machordom A. Merging scleractinian genera: the overwhelming genetic similarity between solitary Desmophyllum and colonial Lophelia. BMC Evol Biol 2016; 16:108. [PMID: 27193263 PMCID: PMC4870751 DOI: 10.1186/s12862-016-0654-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 04/12/2016] [Indexed: 12/16/2022] Open
Abstract
Background In recent years, several types of molecular markers and new microscale skeletal characters have shown potential as powerful tools for phylogenetic reconstructions and higher-level taxonomy of scleractinian corals. Nonetheless, discrimination of closely related taxa is still highly controversial in scleractinian coral research. Here we used newly sequenced complete mitochondrial genomes and 30 microsatellites to define the genetic divergence between two closely related azooxanthellate taxa of the family Caryophylliidae: solitary Desmophyllum dianthus and colonial Lophelia pertusa. Results In the mitochondrial control region, an astonishing 99.8 % of nucleotides between L. pertusa and D. dianthus were identical. Variability of the mitochondrial genomes of the two species is represented by only 12 non-synonymous out of 19 total nucleotide substitutions. Microsatellite sequence (37 loci) analysis of L. pertusa and D. dianthus showed genetic similarity is about 97 %. Our results also indicated that L. pertusa and D. dianthus show high skeletal plasticity in corallum shape and similarity in skeletal ontogeny, micromorphological (septal and wall granulations) and microstructural characters (arrangement of rapid accretion deposits, thickening deposits). Conclusions Molecularly and morphologically, the solitary Desmophyllum and the dendroid Lophelia appear to be significantly more similar to each other than other unambiguous coral genera analysed to date. This consequently leads to ascribe both taxa under the generic name Desmophyllum (priority by date of publication). Findings of this study demonstrate that coloniality may not be a robust taxonomic character in scleractinian corals. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0654-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anna Maria Addamo
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Agostina Vertino
- Dipartimento di Scienze dell'Ambiente e del Territorio e di Scienze della Terra, Università di Milano Bicocca (UNIMIB), Piazza della Scienza 4, 20126, Milan, Italy.,Department of Geology Renard Centre of Marine Geology, Universiteit Ghent, Krijgslaan 281, B-9000, Ghent, Belgium
| | - Jaroslaw Stolarski
- Polskiej Akademii Nauk, Instytut Paleobiologii, Twarda 51/55, PL-00-818, Warsaw, Poland
| | - Ricardo García-Jiménez
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Marco Taviani
- Consiglio Nazionale delle Ricerche, Istituto di Scienze Marine (ISMAR), Via Gobetti 101, 40129, Bologna, Italy.,Biology Department, Woods Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, 02543, MA, USA.,Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Annie Machordom
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006, Madrid, Spain.
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Ritchie AM, Lo N, Ho SYW. Examining the sensitivity of molecular species delimitations to the choice of mitochondrial marker. ORG DIVERS EVOL 2016. [DOI: 10.1007/s13127-016-0275-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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27
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Botero-Castro F, Delsuc F, Douzery EJP. Thrice better than once: quality control guidelines to validate new mitogenomes. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:449-54. [PMID: 24708133 DOI: 10.3109/19401736.2014.900666] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Mitogenomic data are increasingly used in evolutionary biology and ecology, stressing the importance for double checking the authenticity of DNA sequences. For example, Szcześniak et al. (2013) recently published the mitochondrial genome of a bat, the Leschenault's rousette (Rousettus leschenaultii). Here we show using straightforward phylogenetic analyses of available chiropteran sequence data that the taxonomic attribution of the reported mitogenome is erroneous. The purportedly-new complete mitochondrial genome likely belongs to the Egyptian fruit bat (R. aegyptiacus) for which a reference sequence already exists. We propose that future articles reporting complete mitochondrial genome sequences should mandatorily include maximum likelihood trees inferred from (i) the standard barcoding marker for the taxon under focus, which would benefit from the massive data available in public databases, and (ii) the available mitogenomes of closely related species. We also strongly advise these trees be presented as phylograms so that all pertinent phylogenetic information is displayed in the form of a topology and its associated branch lengths. Along with compulsory information on the geographical location and origin of the specimen, these new standards should help avoiding the publication of taxonomically misidentified mitogenomes that might end up as reference sequences in public databases and re-used in subsequent meta-analyses.
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Affiliation(s)
- Fidel Botero-Castro
- a Université Montpellier 2, CNRS & IRD, Institut des Sciences de l'Evolution (UMR 5554) , Montpellier , France
| | - Frédéric Delsuc
- a Université Montpellier 2, CNRS & IRD, Institut des Sciences de l'Evolution (UMR 5554) , Montpellier , France
| | - Emmanuel J P Douzery
- a Université Montpellier 2, CNRS & IRD, Institut des Sciences de l'Evolution (UMR 5554) , Montpellier , France
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Fernández R, Schubert M, Vargas-Velázquez AM, Brownlow A, Víkingsson GA, Siebert U, Jensen LF, Øien N, Wall D, Rogan E, Mikkelsen B, Dabin W, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Guillot G, Orlando L. A genomewide catalogue of single nucleotide polymorphisms in white-beaked and Atlantic white-sided dolphins. Mol Ecol Resour 2015; 16:266-76. [DOI: 10.1111/1755-0998.12427] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Revised: 05/01/2015] [Accepted: 05/05/2015] [Indexed: 11/30/2022]
Affiliation(s)
- R. Fernández
- Centre for GeoGenetics; University of Copenhagen; Øster Volgade 5-7 1350K Copenhagen Denmark
| | - M. Schubert
- Centre for GeoGenetics; University of Copenhagen; Øster Volgade 5-7 1350K Copenhagen Denmark
| | - A. M. Vargas-Velázquez
- Centre for GeoGenetics; University of Copenhagen; Øster Volgade 5-7 1350K Copenhagen Denmark
| | - A. Brownlow
- Wildlife Unit; SAC Veterinary Services; Drummondhill, Stratherrick Road Inverness UK
| | | | - U. Siebert
- Institute for Terrestrial and Aquatic Wildlife Research; University of Veterinary Medicine Hannover, Foundation; Werftstraße 6 Büsum Germany
| | - L. F. Jensen
- Fisheries and Maritime Museum; Tarphagevej 2 Esbjerg Denmark
| | - N. Øien
- Institute for Marine Research; 5817 Bergen Norway
| | - D. Wall
- Irish Whale and Dolphin Group; Merchants Quay, Kilrush, Co.; Clare Ireland
| | - E. Rogan
- School of Biological, Earth and Environmental Sciences; University College Cork; Distillery Fields, North Mall Cork Ireland
| | - B. Mikkelsen
- Natural History Museum; V. U. Hammersheimsgøta 13 100 Tórshavn Faroe Islands
| | - W. Dabin
- Centre de Recherche sur les mammiféres marins; Université La Rochelle; 5 allée de l'Océan La Rochelle France
| | - A. H. Alfarhan
- Zoology Department; College of Science; King Saud University; Riyadh 11451 Saudi Arabia
| | - S. A. Alquraishi
- Zoology Department; College of Science; King Saud University; Riyadh 11451 Saudi Arabia
| | - K. A. S. Al-Rasheid
- Zoology Department; College of Science; King Saud University; Riyadh 11451 Saudi Arabia
| | - G. Guillot
- Department of Applied Mathematics and Computer Science; Technical University of Denmark; Richard Petersens Plads Lyngvy Denmark
| | - L. Orlando
- Centre for GeoGenetics; University of Copenhagen; Øster Volgade 5-7 1350K Copenhagen Denmark
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Caballero S, Duchêne S, Garavito MF, Slikas B, Baker CS. Initial Evidence for Adaptive Selection on the NADH Subunit Two of Freshwater Dolphins by Analyses of Mitochondrial Genomes. PLoS One 2015; 10:e0123543. [PMID: 25946045 PMCID: PMC4422622 DOI: 10.1371/journal.pone.0123543] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Accepted: 03/04/2015] [Indexed: 01/31/2023] Open
Abstract
A small number of cetaceans have adapted to an entirely freshwater environment, having colonized rivers in Asia and South America from an ancestral origin in the marine environment. This includes the ‘river dolphins’, early divergence from the odontocete lineage, and two species of true dolphins (Family Delphinidae). Successful adaptation to the freshwater environment may have required increased demands in energy involved in processes such as the mitochondrial osmotic balance. For this reason, riverine odontocetes provide a compelling natural experiment in adaptation of mammals from marine to freshwater habitats. Here we present initial evidence of positive selection in the NADH dehydrogenase subunit 2 of riverine odontocetes by analyses of full mitochondrial genomes, using tests of selection and protein structure modeling. The codon model with highest statistical support corresponds to three discrete categories for amino acid sites, those under positive, neutral, and purifying selection. With this model we found positive selection at site 297 of the NADH dehydrogenase subunit 2 (dN/dS>1.0,) leading to a substitution of an Ala or Val from the ancestral state of Thr. A phylogenetic reconstruction of 27 cetacean mitogenomes showed that an Ala substitution has evolved at least four times in cetaceans, once or more in the three ‘river dolphins’ (Families Pontoporidae, Lipotidae and Inidae), once in the riverine Sotalia fluviatilis (but not in its marine sister taxa), once in the riverine Orcaella brevirostris from the Mekong River (but not in its marine sister taxa) and once in two other related marine dolphins. We located the position of this amino acid substitution in an alpha-helix channel in the trans-membrane domain in both the E. coli structure and Sotalia fluviatilis model. In E. coli this position is located in a helix implicated in a proton translocation channel of respiratory complex 1 and may have a similar role in the NADH dehydrogenases of cetaceans.
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Affiliation(s)
- Susana Caballero
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos, Biological Sciences Department, Universidad de los Andes, Bogota, Colombia
- * E-mail:
| | - Sebastian Duchêne
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos, Biological Sciences Department, Universidad de los Andes, Bogota, Colombia
- School of Biological Sciences, The University of Sydney, NSW, Australia
| | - Manuel F. Garavito
- Grupo de Investigaciones en Bioquímica y Biología Molecular de Parásitos, Biological Sciences Department, Universidad de los Andes, Bogota, Colombia
| | - Beth Slikas
- Marine Mammal Institute and Department of Fisheries and Wildlife, Hatfield Marine Science Center, Oregon State University, Newport, Oregon, United States of America
| | - C. Scott Baker
- Marine Mammal Institute and Department of Fisheries and Wildlife, Hatfield Marine Science Center, Oregon State University, Newport, Oregon, United States of America
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Poortvliet M, Olsen JL, Croll DA, Bernardi G, Newton K, Kollias S, O'Sullivan J, Fernando D, Stevens G, Galván Magaña F, Seret B, Wintner S, Hoarau G. A dated molecular phylogeny of manta and devil rays (Mobulidae) based on mitogenome and nuclear sequences. Mol Phylogenet Evol 2014; 83:72-85. [PMID: 25462995 DOI: 10.1016/j.ympev.2014.10.012] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Revised: 09/07/2014] [Accepted: 10/08/2014] [Indexed: 12/24/2022]
Abstract
Manta and devil rays are an iconic group of globally distributed pelagic filter feeders, yet their evolutionary history remains enigmatic. We employed next generation sequencing of mitogenomes for nine of the 11 recognized species and two outgroups; as well as additional Sanger sequencing of two mitochondrial and two nuclear genes in an extended taxon sampling set. Analysis of the mitogenome coding regions in a Maximum Likelihood and Bayesian framework provided a well-resolved phylogeny. The deepest divergences distinguished three clades with high support, one containing Manta birostris, Manta alfredi, Mobula tarapacana, Mobula japanica and Mobula mobular; one containing Mobula kuhlii, Mobula eregoodootenkee and Mobula thurstoni; and one containing Mobula munkiana, Mobula hypostoma and Mobula rochebrunei. Mobula remains paraphyletic with the inclusion of Manta, a result that is in agreement with previous studies based on molecular and morphological data. A fossil-calibrated Bayesian random local clock analysis suggests that mobulids diverged from Rhinoptera around 30 Mya. Subsequent divergences are characterized by long internodes followed by short bursts of speciation extending from an initial episode of divergence in the Early and Middle Miocene (19-17 Mya) to a second episode during the Pliocene and Pleistocene (3.6 Mya - recent). Estimates of divergence dates overlap significantly with periods of global warming, during which upwelling intensity - and related high primary productivity in upwelling regions - decreased markedly. These periods are hypothesized to have led to fragmentation and isolation of feeding regions leading to possible regional extinctions, as well as the promotion of allopatric speciation. The closely shared evolutionary history of mobulids in combination with ongoing threats from fisheries and climate change effects on upwelling and food supply, reinforces the case for greater protection of this charismatic family of pelagic filter feeders.
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Affiliation(s)
- Marloes Poortvliet
- Department of Marine Benthic Ecology and Evolution, Centre for Ecological and Evolutionary Studies, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands; Department of Ecology & Evolutionary Biology, University of California Santa Cruz, 100 Shaffer Road, Santa Cruz, CA 95060, USA; Faculty of Biosciences and Aquaculture, Universitetet i Nordland, Universitetsalleen 11, 8049 Bodø, Norway.
| | - Jeanine L Olsen
- Department of Marine Benthic Ecology and Evolution, Centre for Ecological and Evolutionary Studies, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.
| | - Donald A Croll
- Department of Ecology & Evolutionary Biology, University of California Santa Cruz, 100 Shaffer Road, Santa Cruz, CA 95060, USA.
| | - Giacomo Bernardi
- Department of Ecology & Evolutionary Biology, University of California Santa Cruz, 100 Shaffer Road, Santa Cruz, CA 95060, USA.
| | - Kelly Newton
- Department of Ecology & Evolutionary Biology, University of California Santa Cruz, 100 Shaffer Road, Santa Cruz, CA 95060, USA.
| | - Spyros Kollias
- Faculty of Biosciences and Aquaculture, Universitetet i Nordland, Universitetsalleen 11, 8049 Bodø, Norway.
| | - John O'Sullivan
- Monterey Bay Aquarium, 886 Cannery Row, Monterey, CA 93940, USA.
| | - Daniel Fernando
- Department of Biology and Environmental Science, Linnaeus University, SE 39182 Kalmar, Sweden; The Manta Trust, Catemwood House, Corscombe, Dorchester, Dorset DT2 0NT, United Kingdom.
| | - Guy Stevens
- The Manta Trust, Catemwood House, Corscombe, Dorchester, Dorset DT2 0NT, United Kingdom.
| | - Felipe Galván Magaña
- Centro Interdisciplinario de Ciencias Marinas, Instituto Politécnico Nacional, Av. IPN s/n, La Paz, Baja California Sur 23096, Mexico.
| | - Bernard Seret
- Muséum national d'Histoire naturelle, Département Systématique et Evolution, CP 51, rue Buffon, 75231 Paris cedex 05, France.
| | - Sabine Wintner
- KwaZulu-Natal Sharks Board, 1A Herrwood Drive, Umhlanga Rocks 4320, South Africa; Biomedical Resource Unit, University of KwaZulu-Natal, Westville Campus, University Road, Westville 3600, South Africa.
| | - Galice Hoarau
- Faculty of Biosciences and Aquaculture, Universitetet i Nordland, Universitetsalleen 11, 8049 Bodø, Norway.
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Banguera-Hinestroza E, Hayano A, Crespo E, Hoelzel AR. Delphinid systematics and biogeography with a focus on the current genus Lagenorhynchus: multiple pathways for antitropical and trans-oceanic radiation. Mol Phylogenet Evol 2014; 80:217-30. [PMID: 25130419 DOI: 10.1016/j.ympev.2014.08.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 07/20/2014] [Accepted: 08/03/2014] [Indexed: 10/24/2022]
Abstract
The six species currently classified within the genus Lagenorhynchus exhibit a pattern of antitropical distribution common among marine taxa. In spite of their morphological similarities they are now considered an artificial grouping, and include both recent and the oldest representatives of the Delphinidae radiation. They are, therefore, a good model for studying questions about the evolutionary processes that have driven dolphin speciation, dispersion and distribution. Here we used two different approaches. First we constructed a multigenic phylogeny with a minimum amount of missing data (based on 9 genes, 11,030bp, using the 6 species of the genus and their closest relatives) to infer their relationships. Second, we built a supermatrix phylogeny (based on 33 species and 27 genes) to test the effect of taxon sampling on the phylogeny of the genus, to provide inference on biogeographic history, and provide inference on the main events shaping the dispersion and radiation of delphinids. Our analyses suggested an early evolutionary history of marine dolphins in the North Atlantic Ocean and revealed multiple pathways of migration and radiation, probably guided by paleoceanographic changes during the Miocene and Pliocene. L. acutus and L. albirostris likely shared a common ancestor that arose in the North Atlantic around the Middle Miocene, predating the radiation of subfamilies Delphininae, Globicephalinae and Lissodelphininae.
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Affiliation(s)
| | - Azusa Hayano
- Wildlife Research Center, Kyoto University, Sakyo, Kyoto 606-8203, Japan
| | - Enrique Crespo
- Centro Nacional Patagonico (CONICET), Blvd. Brown 3600 (9120), Puerto Madryn, Chubut, Argentina
| | - A Rus Hoelzel
- Department of Biological and Biomedical Sciences, University of Durham, South Road DH1 3LE, UK.
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32
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Wu LW, Lin LH, Lees DC, Hsu YF. Mitogenomic sequences effectively recover relationships within brush-footed butterflies (Lepidoptera: Nymphalidae). BMC Genomics 2014; 15:468. [PMID: 24923777 PMCID: PMC4070565 DOI: 10.1186/1471-2164-15-468] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 06/04/2014] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Mitogenomic phylogenies have revealed well-supported relationships for many eukaryote groups. In the order Lepidoptera, 113 species mitogenomes had been sequenced (May 14, 2014). However, these data are restricted to ten of the forty-three recognised superfamilies, while it has been challenging to recover large numbers of mitogenomes due to the time and cost required for primer design and sequencing. Nuclear rather than mitochondrial genes have been preferred to reconstruct deep-level lepidopteran phylogenies, without seriously evaluating the potential of entire mitogenomes. Next-generation sequencing methods remove these limitations by providing efficiently massive amounts of sequence data. In the present study, we simultaneously obtained a large number of nymphalid butterfly mitogenomes to evaluate the utility of mitogenomic phylogenies by comparing reconstructions to the now quite well established phylogeny of Nymphalidae. RESULTS We newly obtained 30 nymphalid mitogenomes via pyrosequencing on the Roche 454 GS Junior system, and combined these sequences with publicly accessible data to provide a 70-taxa dataset covering 37 genes for a 15,495 bp alignment. Polymorphic sites were not homogeneously distributed across the gene. Two gene regions, nad6 and 3' end of nad5, were most variable, whereas the cox1 and 5' ends of rrnL were most conserved. Phylogenetic relationships inferred by two likelihood methods were congruent and strongly supported (>0.95 posterior probability; ML bootstrap >85%), across the majority of nodes for multiple partitioning strategies and substitution models. Bayes factor results showed that the most highly partitioned dataset is the preferred strategy among different partitioning schemes. The most striking phylogenetic findings were that the subfamily Danainae not Libytheinae was sister of the remaining brush-footed butterflies and that, within Limenitidini, the genus Athyma was clearly polyphyletic. None of the single-gene phylogenies recovered the highly supported topologies generated on the basis of the whole mitogenomic data. CONCLUSIONS Thirty mitogenomes were assembled with 89% completeness from the contigs of pyrosequencing-derived reads. Entire mitogenomes or higher-quality sequences could be obtained by increasing pyrosequencing read coverage or by additional Sanger sequencing. Our mitogenomic phylogenies provide robust nodal support at a range of levels, demonstrating that mitogenomes are both accurate and efficient molecular markers for inferring butterfly phylogeny.
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Affiliation(s)
- Li-Wei Wu
- />Department of Geosciences, National Taiwan University, Taipei, Taiwan
| | - Li-Hung Lin
- />Department of Geosciences, National Taiwan University, Taipei, Taiwan
| | - David C Lees
- />Department of Zoology, University of Cambridge, Cambridge, UK
| | - Yu-Feng Hsu
- />Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
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Hrbek T, da Silva VMF, Dutra N, Gravena W, Martin AR, Farias IP. A new species of river dolphin from Brazil or: how little do we know our biodiversity. PLoS One 2014; 9:e83623. [PMID: 24465386 PMCID: PMC3898917 DOI: 10.1371/journal.pone.0083623] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 10/28/2013] [Indexed: 11/24/2022] Open
Abstract
True river dolphins are some of the rarest and most endangered of all vertebrates. They comprise relict evolutionary lineages of high taxonomic distinctness and conservation value, but are afforded little protection. We report the discovery of a new species of a river dolphin from the Araguaia River basin of Brazil, the first such discovery in nearly 100 years. The species is diagnosable by a series of molecular and morphological characters and diverged from its Amazonian sister taxon 2.08 million years ago. The estimated time of divergence corresponds to the separation of the Araguaia-Tocantins basin from the Amazon basin. This discovery highlights the immensity of the deficit in our knowledge of Neotropical biodiversity, as well as vulnerability of biodiversity to anthropogenic actions in an increasingly threatened landscape. We anticipate that this study will provide an impetus for the taxonomic and conservation reanalysis of other taxa shared between the Araguaia and Amazon aquatic ecosystems, as well as stimulate historical biogeographical analyses of the two basins.
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Affiliation(s)
- Tomas Hrbek
- Laboratory of Evolution and Animal Genetics (LEGAL), Department of Biology, Institute of Biological Sciences, Federal University of Amazonas (UFAM), Manaus, AM, Brazil
| | | | - Nicole Dutra
- Laboratory of Evolution and Animal Genetics (LEGAL), Department of Biology, Institute of Biological Sciences, Federal University of Amazonas (UFAM), Manaus, AM, Brazil
| | - Waleska Gravena
- Laboratory of Evolution and Animal Genetics (LEGAL), Department of Biology, Institute of Biological Sciences, Federal University of Amazonas (UFAM), Manaus, AM, Brazil
| | - Anthony R. Martin
- Centre for Remote Environments, University of Dundee, Dundee, United Kingdom
| | - Izeni Pires Farias
- Laboratory of Evolution and Animal Genetics (LEGAL), Department of Biology, Institute of Biological Sciences, Federal University of Amazonas (UFAM), Manaus, AM, Brazil
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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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35
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Finstermeier K, Zinner D, Brameier M, Meyer M, Kreuz E, Hofreiter M, Roos C. A mitogenomic phylogeny of living primates. PLoS One 2013; 8:e69504. [PMID: 23874967 PMCID: PMC3713065 DOI: 10.1371/journal.pone.0069504] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 06/11/2013] [Indexed: 12/28/2022] Open
Abstract
Primates, the mammalian order including our own species, comprise 480 species in 78 genera. Thus, they represent the third largest of the 18 orders of eutherian mammals. Although recent phylogenetic studies on primates are increasingly built on molecular datasets, most of these studies have focused on taxonomic subgroups within the order. Complete mitochondrial (mt) genomes have proven to be extremely useful in deciphering within-order relationships even up to deep nodes. Using 454 sequencing, we sequenced 32 new complete mt genomes adding 20 previously not represented genera to the phylogenetic reconstruction of the primate tree. With 13 new sequences, the number of complete mt genomes within the parvorder Platyrrhini was widely extended, resulting in a largely resolved branching pattern among New World monkey families. We added 10 new Strepsirrhini mt genomes to the 15 previously available ones, thus almost doubling the number of mt genomes within this clade. Our data allow precise date estimates of all nodes and offer new insights into primate evolution. One major result is a relatively young date for the most recent common ancestor of all living primates which was estimated to 66-69 million years ago, suggesting that the divergence of extant primates started close to the K/T-boundary. Although some relationships remain unclear, the large number of mt genomes used allowed us to reconstruct a robust primate phylogeny which is largely in agreement with previous publications. Finally, we show that mt genomes are a useful tool for resolving primate phylogenetic relationships on various taxonomic levels.
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Affiliation(s)
- Knut Finstermeier
- Research Group Molecular Ecology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Markus Brameier
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Matthias Meyer
- Research Group Molecular Ecology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Eva Kreuz
- Research Group Molecular Ecology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Michael Hofreiter
- Research Group Molecular Ecology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
- Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
- * E-mail:
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36
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Next-generation sequencing and phylogenetic signal of complete mitochondrial genomes for resolving the evolutionary history of leaf-nosed bats (Phyllostomidae). Mol Phylogenet Evol 2013; 69:728-39. [PMID: 23850499 DOI: 10.1016/j.ympev.2013.07.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 06/19/2013] [Accepted: 07/03/2013] [Indexed: 12/11/2022]
Abstract
Leaf-nosed bats (Phyllostomidae) are one of the most studied groups within the order Chiroptera mainly because of their outstanding species richness and diversity in morphological and ecological traits. Rapid diversification and multiple homoplasies have made the phylogeny of the family difficult to solve using morphological characters. Molecular data have contributed to shed light on the evolutionary history of phyllostomid bats, yet several relationships remain unresolved at the intra-familial level. Complete mitochondrial genomes have proven useful to deal with this kind of situation in other groups of mammals by providing access to a large number of molecular characters. At present, there are only two mitogenomes available for phyllostomid bats hinting at the need for further exploration of the mitogenomic approach in this group. We used both standard Sanger sequencing of PCR products and next-generation sequencing (NGS) of shotgun genomic DNA to obtain new complete mitochondrial genomes from 10 species of phyllostomid bats, including representatives of major subfamilies, plus one outgroup belonging to the closely-related mormoopids. We then evaluated the contribution of mitogenomics to the resolution of the phylogeny of leaf-nosed bats and compared the results to those based on mitochondrial genes and the RAG2 and VWF nuclear makers. Our results demonstrate the advantages of the Illumina NGS approach to efficiently obtain mitogenomes of phyllostomid bats. The phylogenetic signal provided by entire mitogenomes is highly comparable to the one of a concatenation of individual mitochondrial and nuclear markers, and allows increasing both resolution and statistical support for several clades. This enhanced phylogenetic signal is the result of combining markers with heterogeneous evolutionary rates representing a large number of nucleotide sites. Our results illustrate the potential of the NGS mitogenomic approach for resolving the evolutionary history of phyllostomid bats based on a denser species sampling.
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Alexander A, Steel D, Slikas B, Hoekzema K, Carraher C, Parks M, Cronn R, Baker CS. Low diversity in the mitogenome of sperm whales revealed by next-generation sequencing. Genome Biol Evol 2013; 5:113-29. [PMID: 23254394 PMCID: PMC3595033 DOI: 10.1093/gbe/evs126] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Large population sizes and global distributions generally associate with high mitochondrial DNA control region (CR) diversity. The sperm whale (Physeter macrocephalus) is an exception, showing low CR diversity relative to other cetaceans; however, diversity levels throughout the remainder of the sperm whale mitogenome are unknown. We sequenced 20 mitogenomes from 17 sperm whales representative of worldwide diversity using Next Generation Sequencing (NGS) technologies (Illumina GAIIx, Roche 454 GS Junior). Resequencing of three individuals with both NGS platforms and partial Sanger sequencing showed low discrepancy rates (454-Illumina: 0.0071%; Sanger-Illumina: 0.0034%; and Sanger-454: 0.0023%) confirming suitability of both NGS platforms for investigating low mitogenomic diversity. Using the 17 sperm whale mitogenomes in a phylogenetic reconstruction with 41 other species, including 11 new dolphin mitogenomes, we tested two hypotheses for the low CR diversity. First, the hypothesis that CR-specific constraints have reduced diversity solely in the CR was rejected as diversity was low throughout the mitogenome, not just in the CR (overall diversity π = 0.096%; protein-coding 3rd codon = 0.22%; CR = 0.35%), and CR phylogenetic signal was congruent with protein-coding regions. Second, the hypothesis that slow substitution rates reduced diversity throughout the sperm whale mitogenome was rejected as sperm whales had significantly higher rates of CR evolution and no evidence of slow coding region evolution relative to other cetaceans. The estimated time to most recent common ancestor for sperm whale mitogenomes was 72,800 to 137,400 years ago (95% highest probability density interval), consistent with previous hypotheses of a bottleneck or selective sweep as likely causes of low mitogenome diversity.
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Affiliation(s)
- Alana Alexander
- Marine Mammal Institute, Hatfield Marine Science Center, Oregon State University, OR, USA.
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38
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Winkelmann I, Campos PF, Strugnell J, Cherel Y, Smith PJ, Kubodera T, Allcock L, Kampmann ML, Schroeder H, Guerra A, Norman M, Finn J, Ingrao D, Clarke M, Gilbert MTP. Mitochondrial genome diversity and population structure of the giant squid Architeuthis: genetics sheds new light on one of the most enigmatic marine species. Proc Biol Sci 2013; 280:20130273. [PMID: 23516246 PMCID: PMC3619516 DOI: 10.1098/rspb.2013.0273] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 02/25/2013] [Indexed: 11/12/2022] Open
Abstract
Despite its charismatic appeal to both scientists and the general public, remarkably little is known about the giant squid Architeuthis, one of the largest of the invertebrates. Although specimens of Architeuthis are becoming more readily available owing to the advancement of deep-sea fishing techniques, considerable controversy exists with regard to topics as varied as their taxonomy, biology and even behaviour. In this study, we have characterized the mitochondrial genome (mitogenome) diversity of 43 Architeuthis samples collected from across the range of the species, in order to use genetic information to provide new and otherwise difficult to obtain insights into the life of this animal. The results show no detectable phylogenetic structure at the mitochondrial level and, furthermore, that the level of nucleotide diversity is exceptionally low. These observations are consistent with the hypotheses that there is only one global species of giant squid, Architeuthis dux (Steenstrup, 1857), and that it is highly vagile, possibly dispersing through both a drifting paralarval stage and migration of larger individuals. Demographic history analyses of the genetic data suggest that there has been a recent population expansion or selective sweep, which may explain the low level of genetic diversity.
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Affiliation(s)
- Inger Winkelmann
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Paula F. Campos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- Museu da Ciência da Universidade de Coimbra, Largo Marquês de Pombal, 3000-272 Coimbra, Portugal
| | - Jan Strugnell
- Department of Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, 3086 Victoria, Australia
| | - Yves Cherel
- Centre d'Etudes Biologiques de Chizé, UPR1934 du CNRS, BP 14, 79360 Villiers-en-Bois, France
| | - Peter J. Smith
- National Museum Victoria, GPO Box 666, Melbourne, Victoria 3001, Australia
| | - Tsunemi Kubodera
- National Museum of Nature and Science, Collection Center, 4-1-1 Amakubo, Tsukuba-shi, Ibaragi-Pref 305-0005, Japan
| | - Louise Allcock
- Department of Zoology, Martin Ryan Marine Science Institute, National University of Ireland, University Road, Galway, Ireland
| | - Marie-Louise Kampmann
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Hannes Schroeder
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Angel Guerra
- Instituto de Investigaciones Marinas (CSIC), Eduardo Cabello 6, 36208 Vigo, Spain
| | - Mark Norman
- Melbourne Museum, Museum Victoria, 11 Nicholson Street, Carlton, Victoria 3053, Australia
| | - Julian Finn
- Melbourne Museum, Museum Victoria, 11 Nicholson Street, Carlton, Victoria 3053, Australia
| | | | - Malcolm Clarke
- Rua do Porto18, 9939 430 Sao Joao, Lajes do Pico, Açores, Portugal
| | - 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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Mitogenomic phylogenetics of fin whales (Balaenoptera physalus spp.): genetic evidence for revision of subspecies. PLoS One 2013; 8:e63396. [PMID: 23691042 PMCID: PMC3656932 DOI: 10.1371/journal.pone.0063396] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 04/02/2013] [Indexed: 11/19/2022] Open
Abstract
There are three described subspecies of fin whales (Balaenoptera physalus): B. p. physalus Linnaeus, 1758 in the Northern Hemisphere, B. p. quoyi Fischer, 1829 in the Southern Hemisphere, and a recently described pygmy form, B. p. patachonica Burmeister, 1865. The discrete distribution in the North Pacific and North Atlantic raises the question of whether a single Northern Hemisphere subspecies is valid. We assess phylogenetic patterns using ~16 K base pairs of the complete mitogenome for 154 fin whales from the North Pacific, North Atlantic--including the Mediterranean Sea--and Southern Hemisphere. A Bayesian tree of the resulting 136 haplotypes revealed several well-supported clades representing each ocean basin, with no haplotypes shared among ocean basins. The North Atlantic haplotypes (n = 12) form a sister clade to those from the Southern Hemisphere (n = 42). The estimated time to most recent common ancestor (TMRCA) for this Atlantic/Southern Hemisphere clade and 81 of the 97 samples from the North Pacific was approximately 2 Ma. 14 of the remaining North Pacific samples formed a well-supported clade within the Southern Hemisphere. The TMRCA for this node suggests that at least one female from the Southern Hemisphere immigrated to the North Pacific approximately 0.37 Ma. These results provide strong evidence that North Pacific and North Atlantic fin whales should not be considered the same subspecies, and suggest the need for revision of the global taxonomy of the species.
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Wang L, Yin Q, He G, Rossiter SJ, Holmes EC, Cui J. Ancient invasion of an extinct gammaretrovirus in cetaceans. Virology 2013; 441:66-9. [PMID: 23545142 DOI: 10.1016/j.virol.2013.03.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 02/08/2013] [Accepted: 03/09/2013] [Indexed: 11/30/2022]
Abstract
Endogenous gammaretroviruses (EGVs) have been widely studied in terrestrial mammals but seldom so in marine species. A genomic mining of the bottlenose dolphin (Tursiops truncatus) genome revealed a new EGV, termed Tursiops truncatus endogenous retrovirus (TTEV), which is divergent from extant mammalian EGVs. Molecular clock dating estimated the invasion time of TTEV into the host genome to be approximately 10-19 million years ago (MYA), while a previously identified killer whale endogenous gammaretrovirus (KWERV) was estimated to have invaded the host genome approximately 3-5 MYA. Using a PCR-based technique, we then verified that similar endogenous viruses exist in nine cetacean genomes. Phylogenetic analysis revealed that these cetacean EGVs are highly divergent from their counterparts in other mammals, including KWERV from the killer whale. In sum, we conclude that there have been at least two invasion episodes of EGVs into cetaceans during their evolutionary history.
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Affiliation(s)
- Lina Wang
- Institute of Molecular Ecology and Evolution, Institutes for Advanced Interdisciplinary Research, East China Normal University, Shanghai 200062, China
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41
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Vilstrup JT, Seguin-Orlando A, Stiller M, Ginolhac A, Raghavan M, Nielsen SCA, Weinstock J, Froese D, Vasiliev SK, Ovodov ND, Clary J, Helgen KM, Fleischer RC, Cooper A, Shapiro B, Orlando L. Mitochondrial phylogenomics of modern and ancient equids. PLoS One 2013; 8:e55950. [PMID: 23437078 PMCID: PMC3577844 DOI: 10.1371/journal.pone.0055950] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 01/07/2013] [Indexed: 11/19/2022] Open
Abstract
The genus Equus is richly represented in the fossil record, yet our understanding of taxonomic relationships within this genus remains limited. To estimate the phylogenetic relationships among modern horses, zebras, asses and donkeys, we generated the first data set including complete mitochondrial sequences from all seven extant lineages within the genus Equus. Bayesian and Maximum Likelihood phylogenetic inference confirms that zebras are monophyletic within the genus, and the Plains and Grevy’s zebras form a well-supported monophyletic group. Using ancient DNA techniques, we further characterize the complete mitochondrial genomes of three extinct equid lineages (the New World stilt-legged horses, NWSLH; the subgenus Sussemionus; and the Quagga, Equus quagga quagga). Comparisons with extant taxa confirm the NWSLH as being part of the caballines, and the Quagga and Plains zebras as being conspecific. However, the evolutionary relationships among the non-caballine lineages, including the now-extinct subgenus Sussemionus, remain unresolved, most likely due to extremely rapid radiation within this group. The closest living outgroups (rhinos and tapirs) were found to be too phylogenetically distant to calibrate reliable molecular clocks. Additional mitochondrial genome sequence data, including radiocarbon dated ancient equids, will be required before revisiting the exact timing of the lineage radiation leading up to modern equids, which for now were found to have possibly shared a common ancestor as far as up to 4 Million years ago (Mya).
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Affiliation(s)
- Julia T. Vilstrup
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Mathias Stiller
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Aurelien Ginolhac
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Maanasa Raghavan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Sandra C. A. Nielsen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Jacobo Weinstock
- Faculty of Humanities, University of Southampton, Southampton, United Kingdom
| | - Duane Froese
- Department of Earth and Atmospheric Sciences, University of Alberta, Alberta, Canada
| | - Sergei K. Vasiliev
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia
| | - Nikolai D. Ovodov
- Laboratory of Archaeology and Paleogeography of Central Siberia, Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia
| | - Joel Clary
- Centre de Conservation et d’Étude des Collections, Musée des Confluences, Lyon, France
| | - Kristofer M. Helgen
- Division of Mammals, National Museum of Natural History, Smithsonian Institution, Washington D.C., United States of America
| | - Robert C. Fleischer
- Center for Conservation and Evolutionary Genetics, Smithsonian National Zoological Park, Smithsonian Institution, Washington D.C., United States of America
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, The University of Adelaide, South Australia, Australia
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
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Dunn KA, Jiang W, Field C, Bielawski JP. Improving evolutionary models for mitochondrial protein data with site-class specific amino acid exchangeability matrices. PLoS One 2013; 8:e55816. [PMID: 23383286 PMCID: PMC3561347 DOI: 10.1371/journal.pone.0055816] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 01/02/2013] [Indexed: 11/24/2022] Open
Abstract
Adequate modeling of mitochondrial sequence evolution is an essential component of mitochondrial phylogenomics (comparative mitogenomics). There is wide recognition within the field that lineage-specific aspects of mitochondrial evolution should be accommodated through lineage-specific amino-acid exchangeability matrices (e.g., mtMam for mammalian data). However, such a matrix must be applied to all sites and this implies that all sites are subject to the same, or largely similar, evolutionary constraints. This assumption is unjustified. Indeed, substantial differences are expected to arise from three-dimensional structures that impose different physiochemical environments on individual amino acid residues. The objectives of this paper are (1) to investigate the extent to which amino acid evolution varies among sites of mitochondrial proteins, and (2) to assess the potential benefits of explicitly modeling such variability. To achieve this, we developed a novel method for partitioning sites based on amino acid physiochemical properties. We apply this method to two datasets derived from complete mitochondrial genomes of mammals and fish, and use maximum likelihood to estimate amino acid exchangeabilities for the different groups of sites. Using this approach we identified large groups of sites evolving under unique physiochemical constraints. Estimates of amino acid exchangeabilities differed significantly among such groups. Moreover, we found that joint estimates of amino acid exchangeabilities do not adequately represent the natural variability in evolutionary processes among sites of mitochondrial proteins. Significant improvements in likelihood are obtained when the new matrices are employed. We also find that maximum likelihood estimates of branch lengths can be strongly impacted. We provide sets of matrices suitable for groups of sites subject to similar physiochemical constraints, and discuss how they might be used to analyze real data. We also discuss how the general approach might be employed to improve a variety of mitogenomic-based research activities.
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Affiliation(s)
- Katherine A Dunn
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada.
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Hancock‐Hanser BL, Frey A, Leslie MS, Dutton PH, Archer FI, Morin PA. Targeted multiplex next‐generation sequencing: advances in techniques of mitochondrial and nuclear
DNA
sequencing for population genomics. Mol Ecol Resour 2013; 13:254-68. [DOI: 10.1111/1755-0998.12059] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 11/30/2012] [Accepted: 12/06/2012] [Indexed: 11/27/2022]
Affiliation(s)
- Brittany L. Hancock‐Hanser
- Protected Resources Division Southwest Fisheries Science Center National Marine Fisheries Service, NOAA 8901 La Jolla Shores Drive La Jolla CA 92037 USA
| | - Amy Frey
- Protected Resources Division Southwest Fisheries Science Center National Marine Fisheries Service, NOAA 8901 La Jolla Shores Drive La Jolla CA 92037 USA
| | - Matthew S. Leslie
- Scripps Institution of Oceanography University of California San Diego 9500 Gilman Drive, MC 0202 La Jolla CA 92093 USA
| | - Peter H. Dutton
- Protected Resources Division Southwest Fisheries Science Center National Marine Fisheries Service, NOAA 8901 La Jolla Shores Drive La Jolla CA 92037 USA
| | - Frederick I. Archer
- Protected Resources Division Southwest Fisheries Science Center National Marine Fisheries Service, NOAA 8901 La Jolla Shores Drive La Jolla CA 92037 USA
| | - Phillip A. Morin
- Protected Resources Division Southwest Fisheries Science Center National Marine Fisheries Service, NOAA 8901 La Jolla Shores Drive La Jolla CA 92037 USA
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Zinner D, Wertheimer J, Liedigk R, Groeneveld LF, Roos C. Baboon phylogeny as inferred from complete mitochondrial genomes. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2012. [PMID: 23180628 PMCID: PMC3572579 DOI: 10.1002/ajpa.22185] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Baboons (genus Papio) are an interesting phylogeographical primate model for the evolution of savanna species during the Pleistocene. Earlier studies, based on partial mitochondrial sequence information, revealed seven major haplogroups indicating multiple para- and polyphylies among the six baboon species. The most basal splits among baboon lineages remained unresolved and the credibility intervals for divergence time estimates were rather large. Assuming that genetic variation within the two studied mitochondrial loci so far was insufficient to infer the apparently rapid early radiation of baboons we used complete mitochondrial sequence information of ten specimens, representing all major baboon lineages, to reconstruct a baboon phylogeny and to re-estimate divergence times. Our data confirmed the earlier tree topology including the para- and polyphyletic relationships of most baboon species; divergence time estimates are slightly younger and credibility intervals narrowed substantially, thus making the estimates more precise. However, the most basal relationships could not be resolved and it remains open whether (1) the most southern population of baboons diverged first or (2) a major split occurred between southern and northern clades. Our study shows that complete mitochondrial genome sequences are more effective to reconstruct robust phylogenies and to narrow down estimated divergence time intervals than only short portions of the mitochondrial genome, although there are also limitations in resolving phylogenetic relationships. Am J Phys Anthropol, 2013. © 2012 Wiley Periodicals, Inc.
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Affiliation(s)
- Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Göttingen, Germany.
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Amaral AR, Beheregaray LB, Bilgmann K, Freitas L, Robertson KM, Sequeira M, Stockin KA, Coelho MM, Möller LM. Influences of past climatic changes on historical population structure and demography of a cosmopolitan marine predator, the common dolphin (genus Delphinus). Mol Ecol 2012; 21:4854-71. [PMID: 22891814 DOI: 10.1111/j.1365-294x.2012.05728.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2011] [Revised: 06/05/2012] [Accepted: 06/16/2012] [Indexed: 11/29/2022]
Abstract
Climatic oscillations during the Pleistocene have greatly influenced the distribution and connectivity of many organisms, leading to extinctions but also generating biodiversity. While the effects of such changes have been extensively studied in the terrestrial environment, studies focusing on the marine realm are still scarce. Here we used sequence data from one mitochondrial and five nuclear loci to assess the potential influence of Pleistocene climatic changes on the phylogeography and demographic history of a cosmopolitan marine predator, the common dolphin (genus Delphinus). Population samples representing the three major morphotypes of Delphinus were obtained from 10 oceanic regions. Our results suggest that short-beaked common dolphins are likely to have originated in the eastern Indo-Pacific Ocean during the Pleistocene and expanded into the Atlantic Ocean through the Indian Ocean. On the other hand, long-beaked common dolphins appear to have evolved more recently and independently in several oceans. Our results also suggest that short-beaked common dolphins had recurrent demographic expansions concomitant with changes in sea surface temperature during the Pleistocene and its associated increases in resource availability, which differed between the North Atlantic and Pacific Ocean basins. By proposing how past environmental changes had an effect on the demography and speciation of a widely distributed marine mammal, we highlight the impacts that climate change may have on the distribution and abundance of marine predators and its ecological consequences for marine ecosystems.
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Affiliation(s)
- Ana R Amaral
- Centro de Biologia Ambiental, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal.
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Soares AE, Schrago CG. The influence of taxon sampling and tree shape on molecular dating: an empirical example from Mammalian mitochondrial genomes. Bioinform Biol Insights 2012; 6:129-43. [PMID: 22693422 PMCID: PMC3370833 DOI: 10.4137/bbi.s9677] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Over the last decade, molecular dating methods have been among the most studied subjects in statistical phylogenetics. Although the evolutionary modelling of substitution rates and the handling of calibration information are the primary focus of species divergence time research, parameters that influence topological estimation, such as taxon sampling and tree shape, also have the potential to influence evolutionary age estimates. However, the impact of topological parameters on chronological estimates is rarely considered. In this study, we use mitochondrial genomes to evaluate the influence of tree shape and taxon sampling on the divergence times of selected nodes of the mammalian tree. Our results show that taxon sampling affects divergence time estimates; the credibility intervals for age estimates decrease as taxonomic sampling increases (i.e., estimates become more precise). The influence of taxonomic sampling was not observed on nodes that lay deep in the mammalian phylogeny, although the means of the posterior distributions tend to converge with increased taxon sampling, an effect that is independent of the location of the node. In the majority of cases, the effect of tree shape was negligible.
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Affiliation(s)
- André E.R. Soares
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carlos G. Schrago
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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JACOBSEN MAGNUSW, HANSEN MICHAELM, ORLANDO LUDOVIC, BEKKEVOLD DORTE, BERNATCHEZ LOUIS, WILLERSLEV ESKE, GILBERT MTHOMASP. Mitogenome sequencing reveals shallow evolutionary histories and recent divergence time between morphologically and ecologically distinct European whitefish (Coregonusspp.). Mol Ecol 2012; 21:2727-42. [DOI: 10.1111/j.1365-294x.2012.05561.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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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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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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Parra GJ, Corkeron PJ, Arnold P. Grouping and fission–fusion dynamics in Australian snubfin and Indo-Pacific humpback dolphins. Anim Behav 2011. [DOI: 10.1016/j.anbehav.2011.09.027] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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