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Nishida S, Uchimura A, Tajima Y, Yamada TK. Comparative analysis of the genetic structures of Kogia spp. populations in the western North Pacific. ADVANCES IN MARINE BIOLOGY 2023; 96:25-37. [PMID: 37980127 DOI: 10.1016/bs.amb.2023.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2023]
Abstract
The two Kogia species, the pygmy sperm whale (K. breviceps) and the dwarf sperm whale (K. sima), have similar morphological and biological features as well as diets. Both species are deep divers, and both have wide distributions from tropical to warm-temperate zones. Although K. breviceps is larger than K. sima, there are few reports of habitat differentiation between the two species. The distribution of K. breviceps is concentrated in higher-latitudes, and this species dives deeper than K. sima. We investigated whether these two species differ in their population structures in the western North Pacific. Using stranded specimens from Japan, we compared the population genetic patterns of the two Kogia species using mtDNA control region variation (941 bp). In total, 34 K. breviceps samples and 54 K. sima samples from stranded individuals around Japan were successfully sequenced. Thirty haplotypes were detected in K. breviceps and 34 in K. sima, indicating high genetic diversity for both. Almost all these haplotypes are unique to the western North Pacific, but did not constitute distinct phylogeographic clades within either species. We detected differences between the species in the shape of haplotype networks and in the potential time of population expansion, indicating that the western North Pacific population of the two biologically similar species could have different population demographies. This may reflect differences in evolutionary histories and in the details of their ecological niches.
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Affiliation(s)
- Shin Nishida
- Biology, Science Education, Faculty of Education, University of Miyazaki. Gakuen-Kibanadai-Nishi, Miyazaki, Miyazaki, Japan.
| | - Atsushi Uchimura
- Biology, Science Education, Faculty of Education, University of Miyazaki. Gakuen-Kibanadai-Nishi, Miyazaki, Miyazaki, Japan
| | - Yuko Tajima
- Department of Zoology, National Museum of Nature and Science, Tokyo, Amakubo, Tsukuba, Ibaraki, Japan
| | - Tadasu K Yamada
- Department of Zoology, National Museum of Nature and Science, Tokyo, Amakubo, Tsukuba, Ibaraki, Japan
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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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Yin D, Chen C, Lin D, Zhang J, Ying C, Liu Y, Liu W, Cao Z, Zhao C, Wang C, Liang L, Xu P, Jian J, Liu K. Gapless genome assembly of East Asian finless porpoise. Sci Data 2022; 9:765. [PMID: 36513679 PMCID: PMC9747978 DOI: 10.1038/s41597-022-01868-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/23/2022] [Indexed: 12/14/2022] Open
Abstract
In recent years, conservation efforts have increased for rare and endangered aquatic wildlife, especially cetaceans. However, the East Asian finless porpoise (Neophocaena asiaeorientalis sunameri), which has a wide distribution in China, has received far less attention and protection. As an endangered small cetacean, the lack of a chromosomal-level reference for the East Asian finless porpoise limits our understanding of its population genetics and conservation biology. To address this issue, we combined PacBio HiFi long reads and Hi-C sequencing data to generate a gapless genome of the East Asian finless porpoise that is approximately 2.5 Gb in size over its 21 autosomes and two sex chromosomes (X and Y). A total of 22,814 protein-coding genes were predicted where ~97.31% were functionally annotated. This high-quality genome assembly of East Asian finless porpoise will not only provide new resources for the comparative genomics of cetaceans and conservation biology of threatened species, but also lay a foundation for more speciation, ecology, and evolutionary studies. Measurement(s) Neophocaena asiaeorientalis sunameri • Gapless genome assembly • sequence annotation Technology Type(s) MGISEQ. 2000 • PacBio HiFi Sequencing • Hi-C Sample Characteristic - Organism Neophocaena asiaeorientalis sunameri Sample Characteristic - Environment seawater Sample Characteristic - Location Yellow Sea near Lianyungang City, Jiangsu Province, China.
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Affiliation(s)
- Denghua Yin
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Chunhai Chen
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Danqing Lin
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Jialu Zhang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Congping Ying
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
| | - Yan Liu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Wang Liu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
| | - Zhichen Cao
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Chenxi Zhao
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Chenhe Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Liping Liang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Pao Xu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China.
| | - Jianbo Jian
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Kai Liu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China.
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China.
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Deppisch P, Helfrich-Förster C, Senthilan PR. The Gain and Loss of Cryptochrome/Photolyase Family Members during Evolution. Genes (Basel) 2022; 13:genes13091613. [PMID: 36140781 PMCID: PMC9498864 DOI: 10.3390/genes13091613] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 11/20/2022] Open
Abstract
The cryptochrome/photolyase (CRY/PL) family represents an ancient group of proteins fulfilling two fundamental functions. While photolyases repair UV-induced DNA damages, cryptochromes mainly influence the circadian clock. In this study, we took advantage of the large number of already sequenced and annotated genes available in databases and systematically searched for the protein sequences of CRY/PL family members in all taxonomic groups primarily focusing on metazoans and limiting the number of species per taxonomic order to five. Using BLASTP searches and subsequent phylogenetic tree and motif analyses, we identified five distinct photolyases (CPDI, CPDII, CPDIII, 6-4 photolyase, and the plant photolyase PPL) and six cryptochrome subfamilies (DASH-CRY, mammalian-type MCRY, Drosophila-type DCRY, cnidarian-specific ACRY, plant-specific PCRY, and the putative magnetoreceptor CRY4. Manually assigning the CRY/PL subfamilies to the species studied, we have noted that over evolutionary history, an initial increase of various CRY/PL subfamilies was followed by a decrease and specialization. Thus, in more primitive organisms (e.g., bacteria, archaea, simple eukaryotes, and in basal metazoans), we find relatively few CRY/PL members. As species become more evolved (e.g., cnidarians, mollusks, echinoderms, etc.), the CRY/PL repertoire also increases, whereas it appears to decrease again in more recent organisms (humans, fruit flies, etc.). Moreover, our study indicates that all cryptochromes, although largely active in the circadian clock, arose independently from different photolyases, explaining their different modes of action.
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Suzuki A, Shirakata C, Anzai H, Sumiyama D, Suzuki M. Vitamin B 12 biosynthesis of Cetobacterium ceti isolated from the intestinal content of captive common bottlenose dolphins ( Tursiops truncatus). MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36178719 DOI: 10.1099/mic.0.001244] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In comparison with terrestrial mammals, dolphins require a large amount of haemoglobin in blood and myoglobin in muscle to prolong their diving time underwater and increase the depth they can dive. The genus Cetobacterium is a common gastrointestinal bacterium in dolphins and includes two species: C. somerae and C. ceti. Whilst the former produces vitamin B12, which is essential for the biosynthesis of haem, a component of haemoglobin and myoglobin, but not produced by mammals, the production ability of the latter remains unknown. The present study aimed to isolate C. ceti from dolphins and reveal its ability to biosynthesize vitamin B12. Three strains of C. ceti, identified by phylogenetic analyses with 16S rRNA gene and genome-based taxonomy assignment and biochemical features, were isolated from faecal samples collected from two captive common bottlenose dolphins (Tursiops truncatus). A microbioassay using Lactobacillus leichmannii ATCC 7830 showed that the average concentration of vitamin B12 produced by the three strains was 11 (standard deviation: 2) pg ml-1. The biosynthesis pathway of vitamin B12, in particular, adenosylcobalamin, was detected in the draft genome of the three strains using blastKOALA. This is the first study to isolate C. ceti from common bottlenose dolphins and reveal its ability of vitamin B12 biosynthesis, and our findings emphasize the importance of C. ceti in supplying haemoglobin and myoglobin to dolphins.
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Affiliation(s)
- Akihiko Suzuki
- Laboratory of Aquatic Animal Physiology, Department of Marine Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, 252-0880 Japan
- National Institute for Environmental Studies, Tsukuba, Ibaraki, 305-8506 Japan
| | - Chika Shirakata
- Enoshima Aquarium, Fujisawa, Kanagawa, 251-0035 Japan
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-0054 Japan
| | - Hiroshi Anzai
- Laboratory of Biotechnology in Dairy Life, Department of Bioscience in Dairy Life, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, 252-0880 Japan
| | - Daisuke Sumiyama
- Laboratory of Biotechnology in Dairy Life, Department of Bioscience in Dairy Life, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, 252-0880 Japan
| | - Miwa Suzuki
- Laboratory of Aquatic Animal Physiology, Department of Marine Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, 252-0880 Japan
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6
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Faria DM, Steel D, Baker CS, da Silva JM, de Meirelles ACO, Souto LRA, Siciliano S, Barbosa LA, Secchi E, Di Tullio JC, de Oliveira LR, Ott PH, Farro APC. Mitochondrial diversity and inter-specific phylogeny among dolphins of the genus Stenella in the Southwest Atlantic Ocean. PLoS One 2022; 17:e0270690. [PMID: 35834534 PMCID: PMC9282552 DOI: 10.1371/journal.pone.0270690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 06/15/2022] [Indexed: 11/18/2022] Open
Abstract
The genus Stenella is comprised of five species occurring in all oceans. Despite its wide distribution, genetic diversity information on these species is still scarce especially in the Southwest Atlantic Ocean. Some features of this genus can enhance opportunities for potential introgressive hybridization, e.g. sympatric distibution along the Brazilian coast, mixed known associations among species, karyotype uniformity and genome permeability. In this study we analyzed three genes of the mitochondrial genome to investigate the genetic diversity and occurrence of genetic mixture among eighty specimens of Stenella. All species exhibited moderate to high levels of genetic diversity (h = 0.833 to h = 1.000 and π = 0.006 to π = 0.015). Specimens of S. longirostris, S. attenuata and S. frontalis were clustered into differentiated haplogroups, in contrast, haplotypes of S. coeruleoalba and S. clymene were clustered together. We detected phylogenetic structure of mixed clades for S. clymene and S. coeruleoalba specimens, in the Southwest Atlantic Ocean, and also between S. frontalis and S. attenuata in the Northeast Atlantic Ocean, and between S. frontalis and S. longirostris in the Northwest Atlantic Ocean. These specimes were morphologically identified as one species but exhibited the maternal lineage of another species, by mitochondrial DNA. Our results demonstrate that ongoing gene flow is occurring among species of the genus Stenella reinforcing that this process could be one of the reasons for the confusing taxonomy and difficulties in elucidating phylogenetic relationships within this group.
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Affiliation(s)
- Drienne Messa Faria
- Laboratório de Genética e Conservação Animal, Departamento de Ciências Agrárias e Biológicas, Universidade Federal do Espírito Santo (UFES), São Mateus, ES, Brazil
- * E-mail:
| | - Debbie Steel
- Marine Mammal Institute, Hatfield Marine Science Center, Oregon State University, Newport, OR, United States of America
| | - C. Scott Baker
- Marine Mammal Institute, Hatfield Marine Science Center, Oregon State University, Newport, OR, United States of America
| | - José Martins da Silva
- Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio), Fernando de Noronha, PE, Brazil
| | | | | | - Salvatore Siciliano
- Departamento de Ciências Biológicas, Escola Nacional de Saúde Pública/Fiocruz, Rio de Janeiro, RJ, Brazil
| | | | - Eduardo Secchi
- Laboratório de Ecologia e Conservação da Megafauna Marinha, Universidade Federal do Rio Grande (FURG), Rio Grande, RS, Brazil
| | - Juliana Couto Di Tullio
- Laboratório de Ecologia e Conservação da Megafauna Marinha, Universidade Federal do Rio Grande (FURG), Rio Grande, RS, Brazil
| | | | - Paulo Henrique Ott
- Grupo de Estudos de Mamíferos Aquáticos do Rio Grande do Sul (GEMARS), Torres, RS, Brazil
- Universidade Estadual do Rio Grande do Sul (Uergs), Osório, RS, Brazil
| | - Ana Paula Cazerta Farro
- Laboratório de Genética e Conservação Animal, Departamento de Ciências Agrárias e Biológicas, Universidade Federal do Espírito Santo (UFES), São Mateus, ES, Brazil
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Extensive Interspecific Gene Flow Shaped Complex Evolutionary History and Underestimated Species Diversity in Rapidly Radiated Dolphins. J MAMM EVOL 2021. [DOI: 10.1007/s10914-021-09581-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AbstractRecently diverged taxa are often characterized by high rates of hybridization, which can complicate phylogenetic reconstruction. For this reason, the phylogenetic relationships and evolutionary history of dolphins are still not very well resolved; the question of whether the genera Tursiops and Stenella are monophyletic is especially controversial. Here, we performed re-sequencing of six dolphin genomes and combined them with eight previously published dolphin SRA datasets and six whole-genome datasets to investigate the phylogenetic relationships of dolphins and test the monophyly hypothesis of Tursiops and Stenella. Phylogenetic reconstruction with the maximum likelihood and Bayesian methods of concatenated loci, as well as with coalescence analyses of sliding window trees, produced a concordant and well-supported tree. Our studies support the non-monophyletic status of Tursiops and Stenella because the species referred these genera do not form exclusive monophyletic clades. This suggests that the current taxonomy of both genera might not reflect their evolutionary history and may underestimate their diversity. A four-taxon D-statistic (ABBA-BABA) test, five-taxon DFOIL test, and tree-based PhyloNet analyses all showed extensive gene flow across dolphin species, which could explain the instability in resolving phylogenetic relationship of oceanic dolphins with different and limited markers. This study could be a good case to demonstrate how genomic data can reveal complex speciation and phylogeny in rapidly radiating animal groups.
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Senevirathna JDM, Yonezawa R, Saka T, Igarashi Y, Yoshitake K, Kinoshita S, Funasaka N, Asakawa S. Another polymorphic mitochondrial genome of Grampus griseus and phylogeny of family Delphinidae. Mitochondrial DNA B Resour 2021; 6:2569-2571. [PMID: 34395884 PMCID: PMC8354156 DOI: 10.1080/23802359.2021.1959453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Risso’s dolphin (Grampus griseus Cuvier, 1812) is the only species of genus Grampus and a cosmopolitan marine inhabitant. Here, we report a polymorphic complete mitochondrial genome of G. griseus. The size of the total mitochondrial genome was 16,386 bp in length and contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a control region. 37 single nucleotide polymorphic sites (SNPs) were identified compared to the references. Based on the available total mitochondrial dolphin genomes’ phylogenetics, G. griseus has formed a clade with 0.1415 distance, sister to the following species of the subfamily Globicephalinae and the taxonomy of Orcinus orca still needs further investigations.
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Affiliation(s)
- Jayan Duminda M. Senevirathna
- Laboratory of Aquatic Molecular Biology and Biotechnology, Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Department of Animal Science, Faculty of Animal Science and Export Agriculture, Uva Wellassa University, Badulla, Sri Lanka
| | - Ryo Yonezawa
- Laboratory of Aquatic Molecular Biology and Biotechnology, Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Taiki Saka
- Laboratory of Aquatic Molecular Biology and Biotechnology, Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yoji Igarashi
- Department of Life Sciences and Chemistry, Graduate School of Bioresources, Mie University, Tsu, Japan
| | - Kazutoshi Yoshitake
- Laboratory of Aquatic Molecular Biology and Biotechnology, Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Shigeharu Kinoshita
- Laboratory of Aquatic Molecular Biology and Biotechnology, Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Noriko Funasaka
- Department of Life Sciences, Graduate School of Bioresources, Mie University, Tsu, Japan
| | - Shuichi Asakawa
- Laboratory of Aquatic Molecular Biology and Biotechnology, Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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9
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The T Cell Receptor (TRB) Locus in Tursiops truncatus: From Sequence to Structure of the Alpha/Beta Heterodimer in the Human/Dolphin Comparison. Genes (Basel) 2021; 12:genes12040571. [PMID: 33919966 PMCID: PMC8070946 DOI: 10.3390/genes12040571] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/27/2021] [Accepted: 04/12/2021] [Indexed: 01/25/2023] Open
Abstract
The bottlenose dolphin (Tursiops truncatus) belongs to the Cetartiodactyla and, similarly to other cetaceans, represents the most successful mammalian colonization of the aquatic environment. Here we report a genomic, evolutionary, and expression study of T. truncatus T cell receptor beta (TRB) genes. Although the organization of the dolphin TRB locus is similar to that of the other artiodactyl species, with three in tandem D-J-C clusters located at its 3' end, its uniqueness is given by the reduction of the total length due essentially to the absence of duplications and to the deletions that have drastically reduced the number of the germline TRBV genes. We have analyzed the relevant mature transcripts from two subjects. The simultaneous availability of rearranged T cell receptor α (TRA) and TRB cDNA from the peripheral blood of one of the two specimens, and the human/dolphin amino acids multi-sequence alignments, allowed us to calculate the most likely interactions at the protein interface between the alpha/beta heterodimer in complex with major histocompatibility class I (MH1) protein. Interacting amino acids located in the complementarity-determining region according to IMGT numbering (CDR-IMGT) of the dolphin variable V-alpha and beta domains were identified. According to comparative modelization, the atom pair contact sites analysis between the human MH1 grove (G) domains and the T cell receptor (TR) V domains confirms conservation of the structure of the dolphin TR/pMH.
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Zhao L, Sakornwimon W, Lin W, Zhang P, Chantra R, Dai Y, Aierken R, Wu F, Li S, Kittiwattanawong K, Wang X. Early divergence and differential population histories of the Indo-Pacific humpback dolphin in the Pacific and Indian Oceans. Integr Zool 2021; 16:612-625. [PMID: 33560551 DOI: 10.1111/1749-4877.12527] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The currently recognized Indo-Pacific humpback dolphin occurs in estuaries and surrounding shallow waters from the South China Sea to the Asian coast of the Indian Ocean. However, a recent study suggested that the humpback dolphin from the Bay of Bengal may represent a distinct phylogenetic species. In this study, we sequenced 915-bp mtDNA segments from five geographic populations in both Chinese and Thai waters; together with previously published sequences, these data revealed that the ancestral Indo-Pacific humpback dolphin might have split during the transition from the Oligocene to Miocene (23.45 Mya, 95% HPD: 16.65-26.55 Mya), and then dispersed along the Pacific and Indian Ocean coasts of Asia. Genetic differentiation was detected between most of the examined populations, except for only a few pairwise populations in the northern South China Sea. Genetic differentiation/distance between the humpback dolphins from the northern and southern South China Sea met the sub-species threshold value proposed for marine mammals, whereas that between the humpback dolphins in the Pacific and the Indian Ocean was above the species threshold. Bayesian inference of historic gene flow indicated low but constant northward gene flow along the Indian Ocean coast; however, there was a recent abrupt increase in gene flow in the Pacific region, likely due to the shortening coastline at the low stand of sea level. Our results revealed that the current taxonomic classification of Indo-Pacific humpback dolphins may not reflect their phylogeography.
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Affiliation(s)
- Liyuan Zhao
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration, Xiamen, China
| | - Watchara Sakornwimon
- Marine and Coastal Resources Research Center, The Middle Gulf of Thailand, Chumphon, Thailand
| | - Wenzhi Lin
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Peijun Zhang
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Rachawadee Chantra
- Marine and Coastal Resources Research Center, The Upper Gulf of Thailand, Samut Sakhon, Thailand
| | - Yufei Dai
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration, Xiamen, China
| | - Reyilamu Aierken
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration, Xiamen, China
| | - Fuxing Wu
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration, Xiamen, China
| | - Songhai Li
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | | | - Xianyan Wang
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration, Xiamen, 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: 89] [Impact Index Per Article: 22.3] [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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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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13
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Chen S, Qing J, Liu Z, Liu Y, Tang M, Murphy RW, Pu Y, Wang X, Tang K, Guo K, Jiang X, Liu S. Multilocus phylogeny and cryptic diversity of white-toothed shrews (Mammalia, Eulipotyphla, Crocidura) in China. BMC Evol Biol 2020; 20:29. [PMID: 32059644 PMCID: PMC7023792 DOI: 10.1186/s12862-020-1588-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 01/27/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Crocidura, the most speciose mammalian genus, occurs across much of Asia, Europe and Africa. The taxonomy of Chinese representatives has been studied primarily based on cursory morphological comparisons and their molecular phylogenetic analyses remain unexplored. In order to understand the phylogeny of this group in China, we estimated the first multilocus phylogeny and conducted species delimitation, including taxon sampling throughout their distribution range. RESULTS We obtained one mitochondrial gene (cytb) (~ 1, 134 bp) and three nuclear genes (ApoB, BRCA1, RAG1) (~ 2, 170 bp) for 132 samples from 57 localities. Molecular analyses identified at least 14 putative species that occur within two major well-supported groups in China. Polyphyletic C. wuchihensis appears to be composed of two putative species. Two subspecies, C. rapax rapax and C. rapax kurodai should be elevated to full species status. A phylogenetic tree based on mitochondrial gene from Asian Crocidura species showed that the C. rapax rapax is embedded within C. attenuata, making the latter a paraphyletic group. Three strongly supported undescribed species (C. sp.1, C. sp.2 and C. sp.3) are revealed from Zada County of Tibet (Western China), Hongjiang County of Hunan Province (Central China) and Dongyang County of Zhejiang Province (Eastern China), Motuo County of Tibet, respectively. The divergence time estimation suggested that China's Crocidura species began to diversify during the late Pliocene (3.66 Ma) and the Early Pleistocene (2.29 Ma), followed by a series of diversifications through the Pleistocene. CONCLUSIONS The cryptic diversity found in this study indicated that the number of species is strongly underestimated under the current taxonomy. We propose that the three undescribed species should be evaluated using extensive taxon sampling and comprehensive morphological and morphometric approaches. Climate change since the late Pliocene and the uplift of the Qinghai-Tibet Plateau may result in the diversification and speciation of China's Crocidura species. In short, the underestimated diversity underlines the need for a taxonomic revision of Chinese Crocidura species.
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Affiliation(s)
- Shunde Chen
- College of Life Sciences, Sichuan Normal University, Chengdu, 610066, China.,Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Jiao Qing
- College of Life Sciences, Sichuan Normal University, Chengdu, 610066, China
| | - Zhu Liu
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, 157011, China
| | - Yang Liu
- Sichuan Academy of Forestry, Chengdu, 610081, China
| | - Mingkun Tang
- Sichuan Academy of Forestry, Chengdu, 610081, China
| | - Robert W Murphy
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, 100 Queen's Park, Toronto, M5S 2C6, Canada
| | - Yingting Pu
- College of Life Sciences, Sichuan Normal University, Chengdu, 610066, China
| | - Xuming Wang
- College of Life Sciences, Sichuan Normal University, Chengdu, 610066, China.,Sichuan Academy of Forestry, Chengdu, 610081, China
| | - Keyi Tang
- College of Life Sciences, Sichuan Normal University, Chengdu, 610066, China
| | - Keji Guo
- Central South Forest Inventory and Planning Institute of State Forestry Administration, Changsha, 410014, China
| | - Xuelong Jiang
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Shaoying Liu
- Sichuan Academy of Forestry, Chengdu, 610081, China.
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14
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Yamada TK, Kitamura S, Abe S, Tajima Y, Matsuda A, Mead JG, Matsuishi TF. Description of a new species of beaked whale (Berardius) found in the North Pacific. Sci Rep 2019; 9:12723. [PMID: 31471538 PMCID: PMC6717206 DOI: 10.1038/s41598-019-46703-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 07/04/2019] [Indexed: 11/21/2022] Open
Abstract
Two types of Berardius are recognised by local whalers in Hokkaido, Japan. The first is the ordinary Baird’s beaked whale, B. bairdii, whereas the other is much smaller and entirely black. Previous molecular phylogenetic analyses revealed that the black type is one recognisable taxonomic unit within the Berardius clade but is distinct from the two known Berardius species. To determine the characteristics of the black type, we summarised external morphology and skull osteometric data obtained from four individuals, which included three individuals from Hokkaido and one additional individual from the United States National Museum of Natural History collection. The whales differed from all of their congeners by having the following unique characters: a substantially smaller body size of physically mature individuals, proportionately shorter beak, and darker body colour. Thus, we conclude that the whales are a third Berardius species.
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Affiliation(s)
- Tadasu K Yamada
- Department of Zoology, National Museum of Nature and Science, Tsukuba, Ibaraki, Japan
| | - Shino Kitamura
- Sanriku Fisheries Research Centre, Iwate University, Kamaishi, Iwate, Japan.,Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido, Japan
| | - Syuiti Abe
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido, Japan
| | - Yuko Tajima
- Department of Zoology, National Museum of Nature and Science, Tsukuba, Ibaraki, Japan
| | - Ayaka Matsuda
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido, Japan
| | - James G Mead
- Division of Mammals, Smithsonian Institution, Washington, D.C., USA
| | - Takashi F Matsuishi
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido, Japan. .,Global Institution for Collaborative Research and Education, Hokkaido University, Hakodate, Hokkaido, Japan.
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15
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Whole Genome Sequencing of Chinese White Dolphin ( Sousa chinensis) for High-Throughput Screening of Antihypertensive Peptides. Mar Drugs 2019; 17:md17090504. [PMID: 31466310 PMCID: PMC6780146 DOI: 10.3390/md17090504] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/16/2019] [Accepted: 08/26/2019] [Indexed: 01/17/2023] Open
Abstract
Chinese white dolphin (Sousa chinensis), also known as the Indo-Pacific humpback dolphin, has been classified as “Vulnerable” on the IUCN Red List of Threatened Species. It is a special cetacean species that lives in tropical and subtropical nearshore waters, with significant differences from other cetaceans. Here, we sequenced and assembled a draft genome of the Chinese white dolphin with a total length of 2.3 Gb and annotation of 18,387 protein-coding genes. Genes from certain expanded families are potentially involved in DNA replication and repairing, suggesting that they may be related to adaptation of this marine mammal to nearshore environments. We also discovered that its historical population had undergone a remarkable bottleneck incident before the Mindel glaciation. In addition, a comparative genomic survey on antihypertensive peptides (AHTPs) among five representative mammals with various residential habitats (such as remarkable differences in exogenous ion concentrations and sea depth) revealed that these small bioactive peptides were highly conserved among these examined mammals, and they had the most abundant hits in collagen subunit proteins, especially for two putative AHTP peptides Gly-Leu-Pro (GLP) and Leu-Gly-Pro (LGP). Our genome assembly will be a valuable resource for further genetic researches on adaptive ecology and conservation biology of cetaceans, and for in-depth investigations into bioactive peptides in aquatic and terrestrial mammals for development of peptide-based drugs to treat various human cardiovascular diseases.
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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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Xu S, Tian R, Lin Y, Yu Z, Zhang Z, Niu X, Wang X, Yang G. Widespread positive selection on cetacean TLR extracellular domain. Mol Immunol 2018; 106:135-142. [PMID: 30597475 DOI: 10.1016/j.molimm.2018.12.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 12/04/2018] [Accepted: 12/20/2018] [Indexed: 12/20/2022]
Abstract
Toll like receptors (TLRs), key members of innate immune system, can recognize a wide diversity of pathogens and initiate both innate and adaptive immune responses in vertebrate. Cetaceans must have faced new challenges of pathogens when their terrestrial relatives transitioned from the terrestrial to aquatic environment. Here, we sequenced the extracellular domain (ECD) of 10 TLRs in cetacean lineages because this region involved in the recognition of pathogens. A total of 148 sites ranging between 5-26 codons (0.01%-4.83%) were identified to be robust candidates of positive selection at the ECD of 10 TLRs. In addition, the majority (90.54%) of these positively selected codons were found to have radical amino acid changes, which strengthen the evidence of positive selection. Importantly, more radical amino acid changes in selected sites were enriched in the period of early evolutionary transition from land to semi-aquatic and from semi-aquatic to full-aquatic habitat, which might endow cetaceans with a faster adaptation to new pathogens as they transitioned into novel habitat. Interestingly, similar selective intensity was detected in both viral and non-viral TLRs in cetaceans, which was not in line with previous studies on primates and birds that reported stronger positive selection in non-viral TLRs than in viral TLRs. This result may be explained by the fact that cetaceans might have faced diversity of bacteria and viruses during its transitions from terrestrial to aquatic environment whereas both primates and birds probably being affected by only a restricted number of related viruses due to their homogeneous habitat.
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Affiliation(s)
- Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China.
| | - Ran Tian
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China.
| | - Yurui Lin
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China.
| | - Zhenpeng Yu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China.
| | - Zepeng Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China.
| | - Xu Niu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China.
| | - Xiaohong Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China.
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China.
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18
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Cryptic lineage differentiation among Indo-Pacific bottlenose dolphins (Tursiops aduncus) in the northwest Indian Ocean. Mol Phylogenet Evol 2018; 122:1-14. [DOI: 10.1016/j.ympev.2017.12.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 12/15/2017] [Accepted: 12/26/2017] [Indexed: 11/19/2022]
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19
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Odontoceti phylogeny and divergence data resolved: evidence from nuclear genes and complete mitochondrial genomes of Neophocaena phocaenoides. CONSERV GENET RESOUR 2018. [DOI: 10.1007/s12686-017-0762-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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20
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Chu H, Li C, Guo X, Zhang H, Luo P, Wu Z, Wang G, Zhao T. The phylogenetic relationships of known mosquito (Diptera: Culicidae) mitogenomes. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 29:31-35. [PMID: 27731651 DOI: 10.1080/24701394.2016.1233533] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The known mosquito mitogenomes, containing a total of 34 species, which belong to five genera, were collected from GenBank, and the practicality and effectiveness of the variation in the complete mitochondrial DNA genome and portions of mitochondrial COI gene were assessed to reconstruct the phylogeny of mosquitoes. Phylogenetic trees were reconstructed on the basis of parsimony, maximum likelihood, and Bayesian (BI) methods. It is concluded that: (1) Both mitogenomes and COI gene support the monophly of following taxa: Subgenus Nyssorhynchus, Subgenus Cellia, Anopheles albitarsis complex, Anopheles gambiae complex, and Anopheles punctulatus group; (2) Genus Aedes is not monophyletic relative to Ochlerotatus vigilax; (3) The mitogenome results indicate a close relationship between Anopheles epiroticus and Anopheles gambiae complex, Anopheles dirus complex and Anopheles punctulatus group, respectively; (4) The Bayesian posterior probability (BPP) within phylogenetic tree reconstructed by mitogenomes is higher than COI tree. The results show that phylogenetic relationships reconstructed using the mitogenomes were more similar to those based on morphological data.
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Affiliation(s)
- Hongliang Chu
- a State Key Laboratory of Pathogen and Biosecurity, Department of Vector Biology and Control, Institute of Microbiology and Epidemiology, Beijing, China.,b Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Chunxiao Li
- a State Key Laboratory of Pathogen and Biosecurity, Department of Vector Biology and Control, Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaoxia Guo
- a State Key Laboratory of Pathogen and Biosecurity, Department of Vector Biology and Control, Institute of Microbiology and Epidemiology, Beijing, China
| | - Hengduan Zhang
- a State Key Laboratory of Pathogen and Biosecurity, Department of Vector Biology and Control, Institute of Microbiology and Epidemiology, Beijing, China
| | - Peng Luo
- c Zhejiang Entry-exit Inspection and Quarantine Bureau, Hangzhou, China
| | - Zhonghua Wu
- c Zhejiang Entry-exit Inspection and Quarantine Bureau, Hangzhou, China
| | - Gang Wang
- c Zhejiang Entry-exit Inspection and Quarantine Bureau, Hangzhou, China
| | - Tongyan Zhao
- a State Key Laboratory of Pathogen and Biosecurity, Department of Vector Biology and Control, Institute of Microbiology and Epidemiology, Beijing, 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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Cammen KM, Andrews KR, Carroll EL, Foote AD, Humble E, Khudyakov JI, Louis M, McGowen MR, Olsen MT, Van Cise AM. Genomic Methods Take the Plunge: Recent Advances in High-Throughput Sequencing of Marine Mammals. J Hered 2016; 107:481-95. [PMID: 27511190 DOI: 10.1093/jhered/esw044] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/12/2016] [Indexed: 12/18/2022] Open
Abstract
The dramatic increase in the application of genomic techniques to non-model organisms (NMOs) over the past decade has yielded numerous valuable contributions to evolutionary biology and ecology, many of which would not have been possible with traditional genetic markers. We review this recent progression with a particular focus on genomic studies of marine mammals, a group of taxa that represent key macroevolutionary transitions from terrestrial to marine environments and for which available genomic resources have recently undergone notable rapid growth. Genomic studies of NMOs utilize an expanding range of approaches, including whole genome sequencing, restriction site-associated DNA sequencing, array-based sequencing of single nucleotide polymorphisms and target sequence probes (e.g., exomes), and transcriptome sequencing. These approaches generate different types and quantities of data, and many can be applied with limited or no prior genomic resources, thus overcoming one traditional limitation of research on NMOs. Within marine mammals, such studies have thus far yielded significant contributions to the fields of phylogenomics and comparative genomics, as well as enabled investigations of fitness, demography, and population structure. Here we review the primary options for generating genomic data, introduce several emerging techniques, and discuss the suitability of each approach for different applications in the study of NMOs.
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Affiliation(s)
- Kristina M Cammen
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise).
| | - Kimberly R Andrews
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Emma L Carroll
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Andrew D Foote
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Emily Humble
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Jane I Khudyakov
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Marie Louis
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Michael R McGowen
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Morten Tange Olsen
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Amy M Van Cise
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
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Comparison of whole mitochondrial genome sequences of northern and southern white rhinoceroses (Ceratotherium simum): the conservation consequences of species definitions. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0861-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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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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Leaché AD, Banbury BL, Linkem CW, de Oca ANM. Phylogenomics of a rapid radiation: is chromosomal evolution linked to increased diversification in north american spiny lizards (Genus Sceloporus)? BMC Evol Biol 2016; 16:63. [PMID: 27000803 PMCID: PMC4802581 DOI: 10.1186/s12862-016-0628-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 02/29/2016] [Indexed: 01/25/2023] Open
Abstract
Background Resolving the short phylogenetic branches that result from rapid evolutionary diversification often requires large numbers of loci. We collected targeted sequence capture data from 585 nuclear loci (541 ultraconserved elements and 44 protein-coding genes) to estimate the phylogenetic relationships among iguanian lizards in the North American genus Sceloporus. We tested for diversification rate shifts to determine if rapid radiation in the genus is correlated with chromosomal evolution. Results The phylogenomic trees that we obtained for Sceloporus using concatenation and coalescent-based species tree inference provide strong support for the monophyly and interrelationships among nearly all major groups. The diversification analysis supported one rate shift on the Sceloporus phylogeny approximately 20–25 million years ago that is associated with the doubling of the speciation rate from 0.06 species/million years (Ma) to 0.15 species/Ma. The posterior probability for this rate shift occurring on the branch leading to the Sceloporus species groups exhibiting increased chromosomal diversity is high (posterior probability = 0.997). Conclusions Despite high levels of gene tree discordance, we were able to estimate a phylogenomic tree for Sceloporus that solves some of the taxonomic problems caused by previous analyses of fewer loci. The taxonomic changes that we propose using this new phylogenomic tree help clarify the number and composition of the major species groups in the genus. Our study provides new evidence for a putative link between chromosomal evolution and the rapid divergence and radiation of Sceloporus across North America. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0628-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adam D Leaché
- Department of Biology, University of Washington, Seattle, Washington, 98195, USA. .,Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington, 98195, USA.
| | - Barbara L Banbury
- Department of Biology, University of Washington, Seattle, Washington, 98195, USA.,Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Mail Stop M4-B402, Seattle, 98109, Washington, USA
| | - Charles W Linkem
- Department of Biology, University of Washington, Seattle, Washington, 98195, USA
| | - Adrián Nieto-Montes de Oca
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, México
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Cunha HA, de Castro RL, Secchi ER, Crespo EA, Lailson-Brito J, Azevedo AF, Lazoski C, Solé-Cava AM. Molecular and Morphological Differentiation of Common Dolphins (Delphinus sp.) in the Southwestern Atlantic: Testing the Two Species Hypothesis in Sympatry. PLoS One 2015; 10:e0140251. [PMID: 26559411 PMCID: PMC4641715 DOI: 10.1371/journal.pone.0140251] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 09/23/2015] [Indexed: 11/18/2022] Open
Abstract
The taxonomy of common dolphins (Delphinus sp.) has always been controversial, with over twenty described species since the original description of the type species of the genus (Delphinus delphis Linnaeus, 1758). Two species and four subspecies are currently accepted, but recent molecular data have challenged this view. In this study we investigated the molecular taxonomy of common dolphins through analyses of cytochrome b sequences of 297 individuals from most of their distribution. We included 37 novel sequences from the Southwestern Atlantic Ocean, a region where the short- and long-beaked morphotypes occur in sympatry, but which had not been well sampled before. Skulls of individuals from the Southwestern Atlantic were measured to test the validity of the rostral index as a diagnostic character and confirmed the presence of the two morphotypes in our genetic sample. Our genetic results show that all common dolphins in the Atlantic Ocean belong to a single species, Delphinus delphis. According to genetic data, the species Delphinus capensis is invalid. Long-beaked common dolphins from the Northeastern Pacific Ocean may constitute a different species. Our conclusions prompt the need for revision of currently accepted common dolphin species and subspecies and of Delphinus delphis distribution.
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Affiliation(s)
- Haydée A. Cunha
- Laboratório de Mamíferos Aquáticos e Bioindicadores (MAQUA), Faculdade de Oceanografia, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratório de Biodiversidade Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rocio Loizaga de Castro
- Laboratorio de Mamíferos Marinos, Centro Nacional Patagónico–CONICET, Puerto Madryn, Chubut, Argentina
| | - Eduardo R. Secchi
- Laboratório de Ecologia e Conservação da Megafauna Marinha (EcoMega), Instituto de Oceanografia, Fundação Universitária do Rio Grande, Rio Grande, Rio Grande do Sul, Brazil
| | - Enrique A. Crespo
- Laboratorio de Mamíferos Marinos, Centro Nacional Patagónico–CONICET, Puerto Madryn, Chubut, Argentina
| | - José Lailson-Brito
- Laboratório de Mamíferos Aquáticos e Bioindicadores (MAQUA), Faculdade de Oceanografia, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexandre F. Azevedo
- Laboratório de Mamíferos Aquáticos e Bioindicadores (MAQUA), Faculdade de Oceanografia, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Cristiano Lazoski
- Laboratório de Biodiversidade Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Antonio M. Solé-Cava
- Laboratório de Biodiversidade Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
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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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Zhu K, Zhou X, Xu S, Sun D, Ren W, Zhou K, Yang G. The loss of taste genes in cetaceans. BMC Evol Biol 2014; 14:218. [PMID: 25305673 PMCID: PMC4232718 DOI: 10.1186/s12862-014-0218-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 10/02/2014] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Five basic taste modalities, sour, sweet, bitter, salt and umami, can be distinguished by humans and are fundamental for physical and ecological adaptations in mammals. Molecular genetic studies of the receptor genes for these tastes have been conducted in terrestrial mammals; however, little is known about the evolution and adaptation of these genes in marine mammals. RESULTS Here, all five basic taste modalities, sour, sweet, bitter, salt and umami, were investigated in cetaceans. The sequence characteristics and evolutionary analyses of taste receptor genes suggested that nearly all cetaceans may have lost all taste modalities except for that of salt. CONCLUSIONS This is the first study to comprehensively examine the five basic taste modalities in cetaceans with extensive taxa sampling. Our results suggest that cetaceans have lost four of the basic taste modalities including sour, sweet, umami, and most of the ability to sense bitter tastes. The integrity of the candidate salt taste receptor genes in all the cetaceans examined may be because of their function in Na(+) reabsorption, which is key to osmoregulation and aquatic adaptation.
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Affiliation(s)
- Kangli Zhu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Xuming Zhou
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
| | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Di Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Wenhua Ren
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Kaiya Zhou
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
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Tanaka Y, Fordyce RE. Fossil dolphin Otekaikea marplesi (latest Oligocene, New Zealand) expands the morphological and taxonomic diversity of Oligocene cetaceans. PLoS One 2014; 9:e107972. [PMID: 25250733 PMCID: PMC4176723 DOI: 10.1371/journal.pone.0107972] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 08/08/2014] [Indexed: 11/18/2022] Open
Abstract
The Oligocene Epoch was a time of major radiation of the Odontoceti (echolocating toothed whales, dolphins). Fossils reveal many odontocete lineages and considerable structural diversity, but whether the clades include some crown taxa or only archaic groups is contentious. The New Zealand fossil dolphin "Prosqualodon" marplesi (latest Oligocene, ≥23.9 Ma) is here identified as a crown odontocete that represents a new genus, Otekaikea, and adds to the generic diversity of Oligocene odontocetes. Otekaikea marplesi is known only from the holotype, which comprises a partial skeleton from the marine Otekaike Limestone of the Waitaki Valley. Otekaikea marplesi was about 2.5 m long; it had procumbent anterior teeth, and a broad dished face for the nasofacial muscles implicated in production of echolocation sounds. The prominent condyles and unfused cervical vertebrae suggest a flexible neck. A phylogenetic analysis based on morphological features places Otekaikea marplesi in the extinct group Waipatiidae, within the clade Platanistoidea. The phylogeny implies an Oligocene origin for the lineage now represented by the endangered Ganges River dolphin (Platanista gangetica), supporting an Oligocene history for the crown Odontoceti.
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Affiliation(s)
- Yoshihiro Tanaka
- Department of Geology, University of Otago, Dunedin, New Zealand
- * E-mail:
| | - R. Ewan Fordyce
- Department of Geology, University of Otago, Dunedin, New Zealand
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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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Chen Z, Zhang J, Zhai X, Zhu Y, Chen X. Complete mitochondrial genome of the green odorous frog Odorrana margaretae (Anura: Ranidae). ACTA ACUST UNITED AC 2014; 26:487-8. [PMID: 24938085 DOI: 10.3109/19401736.2014.926533] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome (mitogenome) of the green odorous frog Odorrana margaretae (Anura: Ranidae) has been studied. The 17,903 bp circular genome contains the typical complement of 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a control region. The AT content of the overall base compositon of H-strand is 56% and the length of control region is 2501 bp with 63.8% AT content. The arrangement of the protein-coding and ribosomal RNA genes was the same as that found in other anurans. The cluster of rearranged LTPF tRNA genes and the translocation of tRNA(His) gene into the D-loop region are observed.
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Affiliation(s)
- Zhuo Chen
- College of Life Sciences, Henan Normal University , Xinxiang, Henan Province , China
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Gravena W, Farias IP, da Silva MNF, da Silva VMF, Hrbek T. Looking to the past and the future: were the Madeira River rapids a geographical barrier to the boto (Cetacea: Iniidae)? CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0565-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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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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Gillett RM, Murray BW, White BN. Characterization of class I- and class II-like major histocompatibility complex loci in pedigrees of North Atlantic right whales. J Hered 2013; 105:188-202. [PMID: 24381183 DOI: 10.1093/jhered/est095] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
North Atlantic right whales have one of the lowest levels of genetic variation at minisatellite loci, microsatellite loci, and mitochondrial control region haplotypes among mammals. Here, adaptive variation at the peptide binding region of class I and class II DRB-like genes of the major histocompatibility complex was assessed. Amplification of a duplicated region in 222 individuals revealed at least 11 class II alleles. Six alleles were assigned to the locus Eugl-DRB1 and 5 alleles were assigned to the locus Eugl-DRB2 by assessing segregation patterns of alleles from 81 parent/offspring pedigrees. Pedigree analysis indicated that these alleles segregated into 12 distinct haplotypes. Genotyping a smaller subset of unrelated individuals (n = 5 and 10, respectively) using different primer sets revealed at least 2 class II pseudogenes (with ≥ 4 alleles) and at least 3 class I loci (with ≥ 6 alleles). Class II sequences were significantly different from neutrality at peptide binding sites suggesting loci may be under the influence of balancing selection. Trans-species sharing of alleles was apparent for class I and class II sequences. Characterization of class II loci represents the first step in determining the relationship between major histocompatibility complex variability and factors affecting health and reproduction in this species.
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Affiliation(s)
- Roxanne M Gillett
- the Natural Resources DNA Profiling and Forensic Centre, Department of Biology, Trent University, 2140 East Bank Drive, Peterborough, Ontario K9J 7B8, Canada
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Viricel A, Pante E, Dabin W, Simon-Bouhet B. Applicability of RAD-tag genotyping for interfamilial comparisons: empirical data from two cetaceans. Mol Ecol Resour 2013; 14:597-605. [DOI: 10.1111/1755-0998.12206] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 11/08/2013] [Accepted: 11/13/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Amélia Viricel
- Littoral, Environnement et Sociétés (LIENSs) UMR 7266 CNRS; Université de La Rochelle; 2 rue Olympe de Gouges La Rochelle 17000 France
| | - Eric Pante
- Littoral, Environnement et Sociétés (LIENSs) UMR 7266 CNRS; Université de La Rochelle; 2 rue Olympe de Gouges La Rochelle 17000 France
| | - Willy Dabin
- Observatoire PELAGIS, UMS 3462 CNRS; Université de La Rochelle; Pôle analytique 5 allées de l'océan La Rochelle 17000 France
| | - Benoit Simon-Bouhet
- Littoral, Environnement et Sociétés (LIENSs) UMR 7266 CNRS; Université de La Rochelle; 2 rue Olympe de Gouges La Rochelle 17000 France
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Multilocus phylogeny of talpine moles (Talpini, Talpidae, Eulipotyphla) and its implications for systematics. Mol Phylogenet Evol 2013; 70:513-21. [PMID: 24140029 DOI: 10.1016/j.ympev.2013.10.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 09/13/2013] [Accepted: 10/03/2013] [Indexed: 11/23/2022]
Abstract
The tribe Talpini is a group of strictly subterranean moles distributed across the Eurasian Continent whose phylogenetic relationships and taxonomy remain unresolved. Here we report a multi-locus nuclear-mitochondrial DNA dataset (9468 bp) from 11 talpine species encompassing all five recognized genera, together with analyses of their divergence times and evolutionary affinities inferred from maximum likelihood and Bayesian approaches. Our results finely resolved all relationships except the root of the four recognized Asian genera, which was placed sister to the genus Talpa. With respect to the Asian clade, we moreover provide the first molecular support for a sister-taxon relationship between Parascaptor and Scaptochirus and confirm that the genus Euroscaptor is paraphyletic. Further, and despite a relatively small sample size (22 specimens), our species delimitation analyses support the existence of at least two genetically distinct, and hence potentially cryptic species. Taken together, these findings argue that generic status should be given to E. mizura and illustrate that the taxonomic diversity of the tribe Talpini in mountainous regions of southwestern China and Southeast Asia is underestimated. Finally, results of our divergence time analyses support a rapid radiation of the endemic Asian genera in the late-Miocene, which temporally corresponds with enhanced aridity and cooling arising from a significant uplift of the Himalayan-Tibetan plateau.
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He K, Jiang XL. Mitochondrial phylogeny reveals cryptic genetic diversity in the genus Niviventer (Rodentia, Muroidea). ACTA ACUST UNITED AC 2013; 26:48-55. [PMID: 24021005 DOI: 10.3109/19401736.2013.823167] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Niviventer is a muroid genus with 17 species widely distributed in East and Southeast Asia. These animals are important components of both extant and fossil small mammal communities, and they are among the most common infectious agents in humans. In this study, we employed partitioned Bayesian and relaxed clock divergence dating analyses and included the Niviventer mitochondrial cytochrome b genes of from GenBank (n = 223). Although the intra-generic relationships were not fully resolved, we recognized four major clades/subclades that could support further division of the genus. Paraphyletic and polyphyletic species were discovered, and 21 putative species were recognized through species delimitation analysis, which indicated an imperfect taxonomy and the existent of cryptic species. Molecular dating supported Niviventer origination in the late Miocene, and relatively higher diversification rates were observed in the late Pliocene and the Pleistocene, which might correlate with climate fluctuations.
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Affiliation(s)
- Kai He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming, Yunnan , China and
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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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Chen Z, Wang Z, Xu S, Zhou K, Yang G. Characterization of hairless (Hr) and FGF5 genes provides insights into the molecular basis of hair loss in cetaceans. BMC Evol Biol 2013; 13:34. [PMID: 23394579 PMCID: PMC3608953 DOI: 10.1186/1471-2148-13-34] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Accepted: 01/30/2013] [Indexed: 11/29/2022] Open
Abstract
Background Hair is one of the main distinguishing characteristics of mammals and it has many important biological functions. Cetaceans originated from terrestrial mammals and they have evolved a series of adaptations to aquatic environments, which are of evolutionary significance. However, the molecular mechanisms underlying their aquatic adaptations have not been well explored. This study provided insights into the evolution of hair loss during the transition from land to water by investigating and comparing two essential regulators of hair follicle development and hair follicle cycling, i.e., the Hairless (Hr) and FGF5 genes, in representative cetaceans and their terrestrial relatives. Results The full open reading frame sequences of the Hr and FGF5 genes were characterized in seven cetaceans. The sequence characteristics and evolutionary analyses suggested the functional loss of the Hr gene in cetaceans, which supports the loss of hair during their full adaptation to aquatic habitats. By contrast, positive selection for the FGF5 gene was found in cetaceans where a series of positively selected amino acid residues were identified. Conclusions This is the first study to investigate the molecular basis of the hair loss in cetaceans. Our investigation of Hr and FGF5, two indispensable regulators of the hair cycle, provide some new insights into the molecular basis of hair loss in cetaceans. The results suggest that positive selection for the FGF5 gene might have promoted the termination of hair growth and early entry into the catagen stage of hair follicle cycling. Consequently, the hair follicle cycle was disrupted and the hair was lost completely due to the loss of the Hr gene function in cetaceans. This suggests that cetaceans have evolved an effective and complex mechanism for hair loss.
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Affiliation(s)
- Zhuo Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
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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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Haug C, Sallam WS, Maas A, Waloszek D, Kutschera V, Haug JT. Tagmatization in Stomatopoda - reconsidering functional units of modern-day mantis shrimps (Verunipeltata, Hoplocarida) and implications for the interpretation of fossils. Front Zool 2012; 9:31. [PMID: 23148643 PMCID: PMC3542093 DOI: 10.1186/1742-9994-9-31] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 11/05/2012] [Indexed: 11/10/2022] Open
Abstract
Introduction We describe the tagmatization pattern of the anterior region of the extant stomatopod Erugosquilla massavensis. For documentation we used the autofluorescence capacities of the specimens, resulting in a significant contrast between sclerotized and membranous areas. Results The anterior body region of E. massavensis can be grouped into three tagmata. Tagma I, the sensorial unit, comprises the segments of the eyes, antennules and antennae. This unit is set-off anteriorly from the posterior head region. Ventrally this unit surrounds a large medial sclerite, interpreted as the anterior part of the hypostome. Dorsally the antennular and antennal segments each bear a well-developed tergite. The dorsal shield is part of tagma II, most of the ventral part of which is occupied in the midline by the large, partly sclerotized posterior part of a complex combining hypostome and labrum. Tagma II includes three more segments behind the labrum, the mandibular, maxillulary and maxillary segments. Tagma III includes the maxillipedal segments, bearing five pairs of sub-chelate appendages. The dorsal sclerite of the first of these tagma-III segments, the segment of the first maxillipeds, is not included in the shield, so this segment is not part of tagma II as generally thought. The second and third segments of tagma III form a unit dorsally and ventrally. The tergites of the segments of tagma III become progressively larger from the anterior to the posterior, possibly resulting from a paedomorphic effect during evolution, which caused this reversed enlargement. Conclusions The described pattern of tagmosis differs from current textbook knowledge. Therefore, our re-description of the anterior body area of stomatopods is of considerable impact for understanding the head evolution of Stomatopoda. Likewise, it has a bearing upon any comparisons with fossil stomatopods, as mainly sclerotized areas are fossilized, and, on a wider scale, upon larger-scale comparisons with other malacostracans and eucrustaceans in general.
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Affiliation(s)
- Carolin Haug
- Zoological Institute and Museum, Department of Cytology and Evolutionary Biology, University of Greifswald, Soldmannstr, 23, 17487, Greifswald, Germany.
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Amaral AR, Jackson JA, Möller LM, Beheregaray LB, Manuela Coelho M. Species tree of a recent radiation: the subfamily Delphininae (Cetacea, Mammalia). Mol Phylogenet Evol 2012; 64:243-53. [PMID: 22503758 DOI: 10.1016/j.ympev.2012.04.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 04/04/2012] [Accepted: 04/04/2012] [Indexed: 10/28/2022]
Abstract
Lineages undergoing rapid radiations provide exceptional opportunities for studying speciation and adaptation, but also represent a challenge for molecular systematics because retention of ancestral polymorphisms and the occurrence of hybridization can obscure relationships among lineages. Dolphins in the subfamily Delphininae are one such case. Non-monophyly, rapid speciation events, and discordance between morphological and molecular characters have made the inference of phylogenetic relationships within this subfamily very difficult. Here we approach this problem by applying multiple methods intended to estimate species trees using a multi-gene dataset for the Delphininae (Sousa, Sotalia, Stenella, Tursiops, Delphinus and Lagenodelphis). Incongruent gene trees obtained indicate that incomplete lineage sorting and possibly hybridization are confounding the inference of species history in this group. Nonetheless, using coalescent-based methods, we have been able to extract an underlying species-tree signal from divergent histories of independent genes. This is the first time a molecular study provides support for such relationships. This study further illustrates how methods of species-tree inference can be very sensitive both to the characteristics of the dataset and the evolutionary processes affecting the evolution of the group under study.
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Affiliation(s)
- Ana R Amaral
- Universidade de Lisboa, Faculdade de Ciências, Centro de Biologia Ambiental, Campo Grande, Lisbon, Portugal.
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Shen T, Xu S, Wang X, Yu W, Zhou K, Yang G. Adaptive evolution and functional constraint at TLR4 during the secondary aquatic adaptation and diversification of cetaceans. BMC Evol Biol 2012; 12:39. [PMID: 22443485 PMCID: PMC3384459 DOI: 10.1186/1471-2148-12-39] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 03/24/2012] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Cetaceans (whales, dolphins and porpoises) are a group of adapted marine mammals with an enigmatic history of transition from terrestrial to full aquatic habitat and rapid radiation in waters around the world. Throughout this evolution, the pathogen stress-response proteins must have faced challenges from the dramatic change of environmental pathogens in the completely different ecological niches cetaceans occupied. For this reason, cetaceans could be one of the most ideal candidate taxa for studying evolutionary process and associated driving mechanism of vertebrate innate immune systems such as Toll-like receptors (TLRs), which are located at the direct interface between the host and the microbial environment, act at the first line in recognizing specific conserved components of microorganisms, and translate them rapidly into a defense reaction. RESULTS We used TLR4 as an example to test whether this traditionally regarded pattern recognition receptor molecule was driven by positive selection across cetacean evolutionary history. Overall, the lineage-specific selection test showed that the dN/dS (ω) values along most (30 out of 33) examined cetartiodactylan lineages were less than 1, suggesting a common effect of functional constraint. However, some specific codons made radical changes, fell adjacent to the residues interacting with lipopolysaccharides (LPS), and showed parallel evolution between independent lineages, suggesting that TLR4 was under positive selection. Especially, strong signatures of adaptive evolution on TLR4 were identified in two periods, one corresponding to the early evolutionary transition of the terrestrial ancestors of cetaceans from land to semi-aquatic (represented by the branch leading to whale + hippo) and from semi-aquatic to full aquatic (represented by the ancestral branch leading to cetaceans) habitat, and the other to the rapid diversification and radiation of oceanic dolphins. CONCLUSIONS This is the first study thus far to characterize the TLR gene in cetaceans. Our data present evidences that cetacean TLR4 has undergone adaptive evolution against the background of purifying selection in response to the secondary aquatic adaptation and rapid diversification in the sea. It is suggested that microbial pathogens in different environments are important factors that promote adaptive changes at cetacean TLR4 and new functions of some amino acid sites specialized for recognizing pathogens in dramatically contrasted environments to enhance the fitness for the adaptation and survival of cetaceans.
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Affiliation(s)
- Tong Shen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, China
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The complete mitochondrial genome of the butterfly Apatura metis (Lepidoptera: Nymphalidae). Mol Biol Rep 2012; 39:6529-36. [DOI: 10.1007/s11033-012-1481-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2011] [Accepted: 01/24/2012] [Indexed: 10/14/2022]
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Pattern and timing of diversification of Cetartiodactyla (Mammalia, Laurasiatheria), as revealed by a comprehensive analysis of mitochondrial genomes. C R Biol 2012; 335:32-50. [DOI: 10.1016/j.crvi.2011.11.002] [Citation(s) in RCA: 369] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 11/07/2011] [Accepted: 11/08/2011] [Indexed: 11/22/2022]
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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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Duchêne S, Archer FI, Vilstrup J, Caballero S, Morin PA. Mitogenome phylogenetics: the impact of using single regions and partitioning schemes on topology, substitution rate and divergence time estimation. PLoS One 2011; 6:e27138. [PMID: 22073275 PMCID: PMC3206919 DOI: 10.1371/journal.pone.0027138] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2011] [Accepted: 10/10/2011] [Indexed: 01/10/2023] Open
Abstract
The availability of mitochondrial genome sequences is growing as a result of recent technological advances in molecular biology. In phylogenetic analyses, the complete mitogenome is increasingly becoming the marker of choice, usually providing better phylogenetic resolution and precision relative to traditional markers such as cytochrome b (CYTB) and the control region (CR). In some cases, the differences in phylogenetic estimates between mitogenomic and single-gene markers have yielded incongruent conclusions. By comparing phylogenetic estimates made from different genes, we identified the most informative mitochondrial regions and evaluated the minimum amount of data necessary to reproduce the same results as the mitogenome. We compared results among individual genes and the mitogenome for recently published complete mitogenome datasets of selected delphinids (Delphinidae) and killer whales (genus Orcinus). Using Bayesian phylogenetic methods, we investigated differences in estimation of topologies, divergence dates, and clock-like behavior among genes for both datasets. Although the most informative regions were not the same for each taxonomic group (COX1, CYTB, ND3 and ATP6 for Orcinus, and ND1, COX1 and ND4 for Delphinidae), in both cases they were equivalent to less than a quarter of the complete mitogenome. This suggests that gene information content can vary among groups, but can be adequately represented by a portion of the complete sequence. Although our results indicate that complete mitogenomes provide the highest phylogenetic resolution and most precise date estimates, a minimum amount of data can be selected using our approach when the complete sequence is unavailable. Studies based on single genes can benefit from the addition of a few more mitochondrial markers, producing topologies and date estimates similar to those obtained using the entire mitogenome.
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Affiliation(s)
- Sebastián Duchêne
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos, Universidad de los Andes, Bogotá, Colombia
| | - Frederick I. Archer
- Protected Resources Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, California, United States of America
| | - Julia Vilstrup
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Susana Caballero
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos, Universidad de los Andes, Bogotá, Colombia
| | - Phillip A. Morin
- Protected Resources Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, California, United States of America
- * E-mail:
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Wang J, Yang G. The complete mitogenome of the snakeheadChanna argus(Perciformes: Channoidei): Genome characterization and phylogenetic implications. ACTA ACUST UNITED AC 2011; 22:120-9. [DOI: 10.3109/19401736.2011.624599] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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