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du Plessis SJ, Blaxter M, Koepfli KP, Chadwick EA, Hailer F. Genomics Reveals Complex Population History and Unexpected Diversity of Eurasian Otters (Lutra lutra) in Britain Relative to Genetic Methods. Mol Biol Evol 2023; 40:msad207. [PMID: 37713621 PMCID: PMC10630326 DOI: 10.1093/molbev/msad207] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/04/2023] [Accepted: 09/06/2023] [Indexed: 09/17/2023] Open
Abstract
Conservation genetic analyses of many endangered species have been based on genotyping of microsatellite loci and sequencing of short fragments of mtDNA. The increase in power and resolution afforded by whole genome approaches may challenge conclusions made on limited numbers of loci and maternally inherited haploid markers. Here, we provide a matched comparison of whole genome sequencing versus microsatellite and control region (CR) genotyping for Eurasian otters (Lutra lutra). Previous work identified four genetically differentiated "stronghold" populations of otter in Britain, derived from regional populations that survived the population crash of the 1950s-1980s. Using whole genome resequencing data from 45 samples from across the British stronghold populations, we confirmed some aspects of population structure derived from previous marker-driven studies. Importantly, we showed that genomic signals of the population crash bottlenecks matched evidence from otter population surveys. Unexpectedly, two strongly divergent mitochondrial lineages were identified that were undetectable using CR fragments, and otters in the east of England were genetically distinct and surprisingly variable. We hypothesize that this previously unsuspected variability may derive from past releases of Eurasian otters from other, non-British source populations in England around the time of the population bottleneck. Our work highlights that even reasonably well-studied species may harbor genetic surprises, if studied using modern high-throughput sequencing methods.
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Affiliation(s)
| | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, USA
- Centre for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, USA
| | | | - Frank Hailer
- School of Biosciences, Cardiff University, Cardiff, UK
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Wei Q, Wang X, Dong Y, Shang Y, Sun G, Wu X, Zhao C, Sha W, Yang G, Zhang H. Analysis of the Complete Mitochondrial Genome of Pteronura brasiliensis and Lontra canadensis. Animals (Basel) 2023; 13:3165. [PMID: 37893890 PMCID: PMC10603698 DOI: 10.3390/ani13203165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/25/2023] [Accepted: 10/08/2023] [Indexed: 10/29/2023] Open
Abstract
P. brasiliensis and L. canadensis are two otter species, which successfully occupied semi-aquatic habitats and diverged from other Mustelidae. Herein, the full-length mitochondrial genome sequences were constructed for these two otter species for the first time. Comparative mitochondrial genome, selection pressure, and phylogenetic independent contrasts (PICs) analyses were conducted to determine the structure and evolutionary characteristics of their mitochondrial genomes. Phylogenetic analyses were also conducted to confirm these two otter species' phylogenetic position. The results demonstrated that the mitochondrial genome structure of P. brasiliensis and L. canadensis were consistent across Mustelidae. However, selection pressure analyses demonstrated that the evolutionary rates of mitochondrial genome protein-coding genes (PCGs) ND1, ND4, and ND4L were higher in otters than in terrestrial Mustelidae, whereas the evolutionary rates of ND2, ND6, and COX1 were lower in otters. Additionally, PIC analysis demonstrated that the evolutionary rates of ND2, ND4, and ND4L markedly correlated with a niche type. Phylogenetic analysis showed that P. brasiliensis is situated at the base of the evolutionary tree of otters, and then L. canadensis diverged from it. This study suggests a divergent evolutionary pattern of Mustelidae mitochondrial genome PCGs, prompting the otters' adaptation to semi-aquatic habitats.
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Affiliation(s)
- Qinguo Wei
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (Q.W.); (G.Y.)
- College of Life Sciences, Qufu Normal University, Qufu 273165, China; (X.W.); (Y.D.); (Y.S.); (G.S.); (X.W.); (C.Z.); (W.S.)
| | - Xibao Wang
- College of Life Sciences, Qufu Normal University, Qufu 273165, China; (X.W.); (Y.D.); (Y.S.); (G.S.); (X.W.); (C.Z.); (W.S.)
| | - Yuehuan Dong
- College of Life Sciences, Qufu Normal University, Qufu 273165, China; (X.W.); (Y.D.); (Y.S.); (G.S.); (X.W.); (C.Z.); (W.S.)
| | - Yongquan Shang
- College of Life Sciences, Qufu Normal University, Qufu 273165, China; (X.W.); (Y.D.); (Y.S.); (G.S.); (X.W.); (C.Z.); (W.S.)
| | - Guolei Sun
- College of Life Sciences, Qufu Normal University, Qufu 273165, China; (X.W.); (Y.D.); (Y.S.); (G.S.); (X.W.); (C.Z.); (W.S.)
| | - Xiaoyang Wu
- College of Life Sciences, Qufu Normal University, Qufu 273165, China; (X.W.); (Y.D.); (Y.S.); (G.S.); (X.W.); (C.Z.); (W.S.)
| | - Chao Zhao
- College of Life Sciences, Qufu Normal University, Qufu 273165, China; (X.W.); (Y.D.); (Y.S.); (G.S.); (X.W.); (C.Z.); (W.S.)
| | - Weilai Sha
- College of Life Sciences, Qufu Normal University, Qufu 273165, China; (X.W.); (Y.D.); (Y.S.); (G.S.); (X.W.); (C.Z.); (W.S.)
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (Q.W.); (G.Y.)
| | - Honghai Zhang
- College of Life Sciences, Qufu Normal University, Qufu 273165, China; (X.W.); (Y.D.); (Y.S.); (G.S.); (X.W.); (C.Z.); (W.S.)
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Baeza JA, Macdonald-Shedd A, Latorre-Cárdenas MC, Griffin E, Gutiérrez-Rodríguez C. The first genomic resource for the ‘near threatened’ Neotropical otter Lontra longicaudis (Carnivora: Mustelidae): mitochondrial genome characterisation and insights into phylomitogenomic relationships in the family Mustelidae. J NAT HIST 2023. [DOI: 10.1080/00222933.2023.2186809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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Shan S, Wang Y. Complete mitochondrial genomes of Boigakraepelini and Hebiuscraspedogaster (Reptilia, Squamata, Colubridae) and their phylogenetic implications. Zookeys 2022; 1124:191-206. [PMID: 36762359 PMCID: PMC9836618 DOI: 10.3897/zookeys.1124.87861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/25/2022] [Indexed: 11/12/2022] Open
Abstract
The complete sequence of the mitochondrial genome is a powerful tool for studying phylogenetic relationships and molecular evolution in various species. In this work, the mitogenomes of Boigakraepelini and Hebiuscraspedogaster were sequenced and characterized for the first time. The lengths of the B.kraepelini and H.craspedogaster mitogenomes were 17,124 bp and 17,120 bp, respectively, and both included 13 protein-coding genes, 22 tRNAs, two rRNAs and two control regions. The arrangements of these mitochondrial genes were the same in B.kraepelini and H.craspedogaster. In addition, both genome compositions showed A+T bias (59.03%, 60.93%) and had positive AT skews (0.179, 0.117) and negative GC skews (-0.397, -0.348). The phylogenetic results illustrated a close relationship between B.kraepelini and the genus Lycodon. Moreover, H.craspedogaster was clustered with other Hebius snakes and closely related to other Natricinae species. These results will provide references for further research on the phylogeny of Colubridae.
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Affiliation(s)
- Shuangshuang Shan
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, ChinaZhejiang Normal UniversityJinhuaChina
| | - Yu Wang
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, ChinaZhejiang Normal UniversityJinhuaChina
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Skorupski J. Characterisation of the Complete Mitochondrial Genome of Critically Endangered Mustela lutreola (Carnivora: Mustelidae) and Its Phylogenetic and Conservation Implications. Genes (Basel) 2022; 13:genes13010125. [PMID: 35052465 PMCID: PMC8774856 DOI: 10.3390/genes13010125] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/28/2021] [Accepted: 01/06/2022] [Indexed: 02/07/2023] Open
Abstract
In this paper, a complete mitochondrial genome of the critically endangered European mink Mustela lutreola L., 1761 is reported. The mitogenome was 16,504 bp in length and encoded the typical 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes, and harboured a putative control region. The A+T content of the entire genome was 60.06% (A > T > C > G), and the AT-skew and GC-skew were 0.093 and −0.308, respectively. The encoding-strand identity of genes and their order were consistent with a collinear gene order characteristic for vertebrate mitogenomes. The start codons of all protein-coding genes were the typical ATN. In eight cases, they were ended by complete stop codons, while five had incomplete termination codons (TA or T). All tRNAs had a typical cloverleaf secondary structure, except tRNASer(AGC) and tRNALys, which lacked the DHU stem and had reduced DHU loop, respectively. Both rRNAs were capable of folding into complex secondary structures, containing unmatched base pairs. Eighty-one single nucleotide variants (substitutions and indels) were identified. Comparative interspecies analyses confirmed the close phylogenetic relationship of the European mink to the so-called ferret group, clustering the European polecat, the steppe polecat and the black-footed ferret. The obtained results are expected to provide useful molecular data, informing and supporting effective conservation measures to save M. lutreola.
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Affiliation(s)
- Jakub Skorupski
- Institute of Marine and Environmental Sciences, University of Szczecin, Adama Mickiewicza 16 St., 70-383 Szczecin, Poland; ; Tel.: +48-91-444-16-85
- Polish Society for Conservation Genetics LUTREOLA, Maciejkowa 21 St., 71-784 Szczecin, Poland
- The European Mink Centre, 71-415 Szczecin, Poland
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Genetic and viability assessment of a reintroduced Eurasian otter Lutra lutra population on the River Ticino, Italy. ORYX 2021. [DOI: 10.1017/s0030605321000107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Abstract
On the River Ticino in northern Italy, a small number of captive Eurasian otters Lutra lutra, belonging to the European breeding programme for self-sustaining captive populations, were reintroduced in 1997, after the species had been declared locally extinct in the 1980s. We surveyed for otter signs in 2008, 2010, 2016–2017 and 2018, confirming the presence of what is probably a small population. To assess the abundance and viability of the population, we genotyped fresh spraints collected during the last two surveys, using 11 microsatellite markers, and modelled the population trend using Vortex. A minimum of six individuals were identified from 25 faecal samples. The analysis of mitochondrial DNA determined that the reintroduced otters share a transversion that is characteristic of the Asiatic subspecies Lutra lutra barang, confirming the contribution of the Asiatic subspecies to the genetic pool of the captive-bred founder population. Population size was consistent with the release of three pairs of otters and all models implied that the number of founders was too small to ensure the long-term survival of the population. Stochastic factors are therefore likely to threaten the success of this reintroduction.
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Vivas-Toro I, Ortega J, Baeza JA. The complete mitochondrial genome of the Honduran white bat Ectophylla alba (Allen 1982) (Chiroptera: Phyllostomidae). Gene 2021; 802:145868. [PMID: 34364911 DOI: 10.1016/j.gene.2021.145868] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/01/2021] [Accepted: 07/30/2021] [Indexed: 11/18/2022]
Abstract
The Honduran white bat, Ectophylla alba (Allen 1982), is one of eight species belonging to the family Phyllostomidae that exclusively roosts in tents. Due to its restricted distribution, habitat specificity, and diet requirements, E. alba has been strongly affected by habitat loss and fragmentation during the last decade. In this study, we developed the first genomic resource for this species; we assembled and analyzed in detail the complete mitochondrial genome of E. alba. The mitogenome of E. alba is 16,664 bp in length and is comprised of 13 protein coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes (tRNAs), and a putative Control Region (CR) 1,232 bp in length. Gene arrangement in the mitochondrial chromosome of E. alba is identical to that reported before in other species of co-familiar bats. All PCGs are under purifying selection, with atp8 experiencing the least selective pressure. In all PCGs, codons ending with adenine are preferred over others ending in thymine and cytosine. Except tRNA-Serine 1, all tRNAs exhibit a cloverleaf secondary structure. The CR of E. alba exhibits three domains commonly described in other mammals, including bats; extended terminal associated sequences (ETAS), central, and conserved sequence block (CSB). A ML phylogenetic reconstruction of the family Phyllostomidae based on all 13 mitochondrial PCGs confirms the monophyletic status of the subfamily Sternodermatinae and indicates the close relationship between E. alba and the genus Artibeus. This is the first genomic resource developed for E. alba and represents the first step to improving our understanding of the genomic underpinnings involved in the evolution of specialization as well as acclimatization and adaptation to local and global change of specialist bats.
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Affiliation(s)
- Isabela Vivas-Toro
- Laboratorio de Bioconservación y Manejo, Posgrado en Ciencias Quimicobiológicas, Departamento de Zoologia, Escuela Nacional de Ciencias Biologicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Sto. Tomas, 11340 CDMX, Mexico
| | - Jorge Ortega
- Laboratorio de Bioconservación y Manejo, Posgrado en Ciencias Quimicobiológicas, Departamento de Zoologia, Escuela Nacional de Ciencias Biologicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Sto. Tomas, 11340 CDMX, Mexico
| | - J Antonio Baeza
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC 29634, USA; Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, FL 34949, USA; Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile.
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8
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Kim HN, Jo YS. Complete mitochondrial genome sequencing of Lutra lutra (Linnaeus, 1758) (Carnivora: Mustelidae) and its phylogenetic status in Mustelidae. Mitochondrial DNA B Resour 2021; 6:2066-2068. [PMID: 34212100 PMCID: PMC8218852 DOI: 10.1080/23802359.2021.1942274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/06/2021] [Indexed: 11/16/2022] Open
Abstract
We report the complete mitochondrial genome sequence of the endangered Eurasian otter, Lutra lutra. The complete mitochondrial genome is 16,537 bp in length and contains 13 protein-coding genes, 22 transfer RNA, two ribosomal RNA, and one control region. The mitogenome is A + T rich, with a composition of 32.2% A, 27.5% C, 14.5% G, and 25.8% T. Phylogenetic analysis based on 13 protein-coding mitochondrial genes of Mustelidae supports the conventional systematic treatment with eight subfamilies. Lutra lutra is closely related to Lutra sumatrana and the subfamily Lutrinae was closely grouped with the Ictonychinae. This study provides genetic and taxonomic information for future studies of Eurasian otters and the Mustelidae.
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Affiliation(s)
- Han-Na Kim
- Biology Education, Daegu University, Gyeongsan, South Korea
| | - Yeong-Seok Jo
- Biology Education, Daegu University, Gyeongsan, South Korea
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Tian J, Du J, Han J, Li D, Song X. Complete Mitochondrial Genome of the South American Fur Seal Arctocephalus australis (Carnivora: Otariidae) and Its Phylogenetic Implications. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421050124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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10
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Park HC, Kurihara N, Kim KS, Min MS, Han S, Lee H, Kimura J. What is the taxonomic status of East Asian otter species based on molecular evidence?: focus on the position of the Japanese otter holotype specimen from museum. Anim Cells Syst (Seoul) 2019; 23:228-234. [PMID: 31231587 PMCID: PMC6567078 DOI: 10.1080/19768354.2019.1601133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 02/17/2019] [Accepted: 03/24/2019] [Indexed: 11/06/2022] Open
Abstract
The Japanese otter (Lutra nippon), once inhabited in most islands of Japan, is now considered as an extinct species. Although the Japanese otter is regarded as a distinct species from the Eurasian otter (L. lutra), its phylogeny and taxonomic status are based on limited information on morphological and genetic data, and thus further clarification is required. Here, we assessed the phylogenetic relationship among the genus Lutra and taxonomic status of L. nippon by using the complete sequences of cytochrome b gene of its holotype. The present phylogenic trees supported that the genus Lutra specimens largely formed monophyletic group, with L. sumatrana as a basal to other Lutra species. Within Lutra species, L. nippon was distantly related with L. lutra. The European otter population of L. l. lutra were clustered together with its subspecies, L. l. chinensis rather than the same subspecies, Korean otter population. The discrepancy between the genetic data and traditional taxonomy justifies the necessity of reexamination of the current subspecific classification system of Eurasian otters. Level of genetic divergence between the holotype of L. nippon and L. lutra was two to three-fold lower than those among the other sister species of the Lutrinae. Based on the level of divergence between the L. nippon and L. lutra, and insufficient evidence of morphological difference between them, it is suggested that designation of Japanese otter as a separate species from L. lutra will be reconsidered.
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Affiliation(s)
- Han-Chan Park
- Conservation Genome Resource Bank for Korean Wildlife, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Nozomi Kurihara
- The United Graduate School of Veterinary Science, Yamaguchi University, Yamaguchi, Japan
| | - Kyung Seok Kim
- Department of Natural Resource Ecology and Management, Iowa State University, Ames, IA, USA
| | - Mi-Sook Min
- Conservation Genome Resource Bank for Korean Wildlife, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Sungyong Han
- Korean Otter Research Center, Hwacheon, Republic of Korea
| | - Hang Lee
- Conservation Genome Resource Bank for Korean Wildlife, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Junpei Kimura
- Department of Anatomy and Cell Biology, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
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Madisha MT, du Plessis M, Kotzé A, Dalton DL. Complete mitochondrial genomes of the African clawless ( Aonyx capensis) and spotted necked ( Hydrictis maculicollis) otter: structure, annotation, and interspecies variation. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1602003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- M. Thabang Madisha
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
- National Zoological Garden, South African National Biodiversity Institute, Pretoria, South Africa
| | - Morné du Plessis
- National Zoological Garden, South African National Biodiversity Institute, Pretoria, South Africa
- Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Antoinette Kotzé
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
- National Zoological Garden, South African National Biodiversity Institute, Pretoria, South Africa
| | - Desiré L. Dalton
- National Zoological Garden, South African National Biodiversity Institute, Pretoria, South Africa
- Department of Zoology, University of Venda, Thohoyandou, South Africa
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12
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Hwang JY, Cho GJ. Identification of novel haplotypes and interpretation of gene flow of mitochondrial DNA control region of Eurasian otter (Lutra lutra) for the effective conservation. J Vet Med Sci 2018; 80:1791-1800. [PMID: 30224573 PMCID: PMC6261830 DOI: 10.1292/jvms.17-0678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The number and distribution of Eurasian otters have declined during twentieth century due to human activity and water pollution. The global conservation status of Eurasian otter is
presently ‘Near Threatened (NT)’ and strictly protected by being listed on the international legislation and conventions. A number of studies using the mitochondrial DNA (mtDNA) control
region (CR) have been conducted in order to effectively apply conservation and reintroduction programs, especially in Europe. However, aside from Europe, there have been few studies
concerning genetic diversity and phylogeny of Eurasian otters. Therefore, in this study, we sequenced partial mtDNA CR sequences (232 bp) from five South Korean Eurasian otters and analyzed
27 otters originating from parts of northeast Asia (South Korea, China, Japan and Russia (Sakhalin)), and Europe. Out of 232 bp partial mtDNA CR sequences, 13 polymorphic sites (5.6%) were
identified and 4 novel mtDNA CR haplotypes (Lut16–19) were discovered from 12 Eurasian otters originating from northeast Asian region. In this study, a comprehensive analysis of genetic
diversity and population structure of Eurasian otter between Europe and northeast Asia continents were conducted. Of these, different past demographic histories in Pleistocene period might
have largely impacted the genetic structure of each population differently. In addition, low degree of gene flow, isolation by distance (IBD) pattern from geographically wide distanced
dataset and analysis of molecular variance (AMOVA) also represented distinct genetic characteristics of Eurasian otter between Europe and northeast Asia.
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Affiliation(s)
- Ji-Yong Hwang
- Institute of Equine Science, College of Veterinary Medicine, Kyungpook National University, 80, Daehak-ro, Buk-gu, Daegu, 41566, Republic of Korea
| | - Gil-Jae Cho
- Institute of Equine Science, College of Veterinary Medicine, Kyungpook National University, 80, Daehak-ro, Buk-gu, Daegu, 41566, Republic of Korea
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13
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Santaquiteria A, Nielsen J, Klemetsen T, Willassen NP, Præbel K. The complete mitochondrial genome of the long-lived Greenland shark (Somniosus microcephalus): characterization and phylogenetic position. CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-016-0676-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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14
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Waku D, Segawa T, Yonezawa T, Akiyoshi A, Ishige T, Ueda M, Ogawa H, Sasaki H, Ando M, Kohno N, Sasaki T. Evaluating the Phylogenetic Status of the Extinct Japanese Otter on the Basis of Mitochondrial Genome Analysis. PLoS One 2016; 11:e0149341. [PMID: 26938434 PMCID: PMC4777564 DOI: 10.1371/journal.pone.0149341] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 01/29/2016] [Indexed: 11/19/2022] Open
Abstract
The Japanese otter lived throughout four main Japanese islands, but it has not been observed in the wild since 1979 and was declared extinct in 2012. Although recent taxonomic and molecular phylogenetic studies suggest that it should be treated as an independent species, International Union for Conservation of Nature Red List considers it as subspecies of Lutra lutra. Therefore, the taxonomic status of this species needs to be resolved. Here we determined the complete mitochondrial genome of two Japanese otters caught in Kanagawa and Kochi prefectures and five Eurasian otters (L. lutra). We reconstructed a molecular phylogenetic tree to estimate the phylogenetic position of the Japanese otter in Lutrinae using the Japanese otters and the other 11 Lutrinae species on the basis of ND5 (692 bp) and cytochrome b (1,140 bp) sequences. We observed that the two Japanese otters had close relationships with Eurasian otters, forming a monophyletic group (100% bootstrap probability). To elucidate detailed phylogenetic relationships among the Japanese and Eurasian otters, we reconstructed a maximum likelihood tree according to mitochondrial genome sequences (14,740 bp). The Japanese otter (JO1) collected in Kanagawa was deeply nested in the Eurasian otter clade, whereas the Japanese otter (JO2) collected in Kochi formed a distinct independent lineage in the Lutra clade. The estimated molecular divergences time for the ancestral lineages of the Japanese otters was 0.10 Ma (95%: 0.06-0.16 Ma) and 1.27 Ma (95%: 0.98-1.59 Ma) for JO1 and JO2 lineages, respectively. Thus, JO1 was identified as a member of L. lutra; JO2 represented the old Japanese otter lineage, which may be a distinct new species or subspecies of Lutra. We suggest that the ancestral population of the JO2 lineage migrated to Japan via the land bridge that existed between western Japanese islands and Asian continent at 1.27 Ma.
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Affiliation(s)
- Daisuke Waku
- Graduate School of Human and Animal-Plant Relationships, Tokyo University of Agriculture, Funako, Atsugi, Kanagawa, Japan
| | - Takahiro Segawa
- National Institute of Polar Research, Midori-cho, Tachikawa-shi, Tokyo, Japan
- Transdisciplinary Research Integration Center, Toranomon, Minato-ku, Tokyo, Japan
| | - Takahiro Yonezawa
- School of Life Sciences, Fudan University, SongHu Rd., Shanghai, China
- School of Advanced Science, The Graduate University for Advanced Studies, Shonan, Hayama-cho, Miura-gun, Kanagawa, Japan
| | - Ayumi Akiyoshi
- National Institute of Polar Research, Midori-cho, Tachikawa-shi, Tokyo, Japan
- Transdisciplinary Research Integration Center, Toranomon, Minato-ku, Tokyo, Japan
| | - Taichiro Ishige
- NODAI Genome Research Center, Nodai Research Institute, Tokyo University of Agriculture, Sakuragaoka, Setagaya-ku, Tokyo, Japan
| | - Miya Ueda
- Yokohama Zoological Gardens, Kamishirane-cho, Asahi-ku, Yokohama-shi, Kanagawa, Japan
| | - Hiroshi Ogawa
- Graduate School of Human and Animal-Plant Relationships, Tokyo University of Agriculture, Funako, Atsugi, Kanagawa, Japan
| | - Hiroshi Sasaki
- Department of Contemporary Social Studies, Chikushi Jogakuen University, Ishizaka, Dazaifu, Fukuoka, Japan
| | - Motokazu Ando
- Graduate School of Human and Animal-Plant Relationships, Tokyo University of Agriculture, Funako, Atsugi, Kanagawa, Japan
| | - Naoki Kohno
- Department of Geology and Paleontology, National Museum of Nature and Science, Tokyo, Amakubo, Tsukuba, Ibaraki, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennoudai, Tsukuba, Ibaraki, Japan
| | - Takeshi Sasaki
- Graduate School of Human and Animal-Plant Relationships, Tokyo University of Agriculture, Funako, Atsugi, Kanagawa, Japan
- * E-mail:
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15
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Shan WJ, Liu YG. The complete mitochondrial DNA sequence of the cape hare Lepus capensis pamirensis. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4572-4573. [PMID: 26642737 DOI: 10.3109/19401736.2015.1101569] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Lepus capensis pamirensis is a specific cape hare species that is only distributed in the Pamirs, with a cruel natural environment. The complete mitochondrial genome of the cape hare L. c. pamirensis was first determined (accession number LC073697), in a total length of 17 597 nucleotides, of which 15 310 nucleotides are coding DNA and 2287 nucleotides are non-coding DNA. It has the common feature with those of other hares with respect to genome structure and gene arrangement. It contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer tRNA genes and 1 control region (D-loop region). The complete mitochondrial genome of the cape hare L. c. pamirensis provides an important data set for further study on its classification.
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Affiliation(s)
- Wen-Juan Shan
- a Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Sciences and Technology, Xinjiang University , Urumqi , China
| | - Yun-Guo Liu
- a Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Sciences and Technology, Xinjiang University , Urumqi , China
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16
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Lehoczky I, Dalton DL, Lanszki J, Sallai Z, Madisha MT, Nupen LJ, Kotzé A. Assessment of population structure in Hungarian otter populations. J Mammal 2015. [DOI: 10.1093/jmammal/gyv136] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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17
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Ma H, Ma C, Li C, Lu J, Zou X, Gong Y, Wang W, Chen W, Ma L, Xia L. First mitochondrial genome for the red crab (Charybdis feriata) with implication of phylogenomics and population genetics. Sci Rep 2015. [PMID: 26225473 PMCID: PMC4520191 DOI: 10.1038/srep11524] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In this study, we first described the complete mitochondrial genome for the red crab (Charybdis feriata), elucidated its phylogenetic relationship among 20 species within Decapoda, and estimated the population genetic diversity. The mitochondrial genome was 15,660 bp in size and encoded 13 protein-coding genes, 22 transfer RNA (tRNA) genes, and two ribosomal RNA genes. The gene arrangement of the mitochondrial genome was the same as that of its sister species, C. japonica. Phylogenomic analysis suggested that genus Charybdis should be classified into subfamily Portuninae but not into subfamily Thalamitinae. Moreover, a total of 33 haplotypes of complete cytochrome c oxidase subunit I gene were defined in 70 individuals of C. feriata derived from three localities. Haplotype diversity and nucleotide diversity values among three localities indicated a high level of genetic diversity in C. feriata. AMOVA analysis suggested a low level of genetic differentiation among the three localities (FST = 0.0023, P > 0.05). Neutrality tests and mismatch analysis revealed that C. feriata might have undergone a population expansion event that possibly occurred in the last 61,498 to 43,814 years. This study should be helpful to better understand the evolutionary status, and population genetic diversity of C. feriata and related species.
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Affiliation(s)
- Hongyu Ma
- 1] East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China [2] Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai 200090, China
| | - Chunyan Ma
- 1] East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China [2] Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai 200090, China
| | - Chenhong Li
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Jianxue Lu
- 1] East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China [2] Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai 200090, China
| | - Xiong Zou
- 1] East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China [2] Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai 200090, China
| | - Yangyang Gong
- 1] East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China [2] Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai 200090, China
| | - Wei Wang
- 1] East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China [2] Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai 200090, China
| | - Wei Chen
- 1] East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China [2] Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai 200090, China
| | - Lingbo Ma
- 1] East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China [2] Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai 200090, China
| | - Lianjun Xia
- 1] East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China [2] Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai 200090, China
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Zhang T, Lu H, Chen C, Jiang H, Wu S. Genetic Diversity of mtDNA D-loop and Maternal Origin of Three Chinese Native Horse Breeds. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 25:921-6. [PMID: 25049645 PMCID: PMC4092969 DOI: 10.5713/ajas.2011.11483] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Revised: 05/04/2012] [Accepted: 02/16/2012] [Indexed: 11/27/2022]
Abstract
In order to protect the genetic resource of native horse breeds, the genetic diversity of mitochondrial DNA (mtDNA) D-loop of three native horse breeds in western China were investigated. Forty-three 600 bp mtDNA D-loop sequences were analyzed by PCR and sequencing techniques, 33 unique haplotypes with 70 polymorphic sites were detected in these horses, which account for 11.67% of 600 bp sequence analyzed, showing the abundant genetic diversity of the three native horse breeds in western China. The Neighbour-Joining (NJ) phylogenetic tree based on 247 bp of 43 D-loop sequences demonstrated the presence of seven major lineages (A to G), indicating that the three native horse breeds in western China originated from multiple maternal origins. Consistent with the front, the NJ phylogenetic tree based on 600 bp of mtDNA D-loop sequences of 43 Chinese western native horses and 81 sequences of six horse breeds from GenBank indicated that the three horse breeds had distributed into the seven major lineages (A to G). The structure of the phylogenic tree is often blurred because the variation in a short segment of the mitochondrial genome is often accompanied by high levels of recurrent mutations. Consequently, longer D-loop sequences are helpful in achieving a higher level of molecular resolution in horses.
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Sun WY, Sun SC. A description of the complete mitochondrial genomes of Amphiporus formidabilis, Prosadenoporus spectaculum and Nipponnemertes punctatula (Nemertea: Hoplonemertea: Monostilifera). Mol Biol Rep 2014; 41:5681-92. [PMID: 24939507 DOI: 10.1007/s11033-014-3438-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 05/27/2014] [Indexed: 11/30/2022]
Abstract
We sequenced the complete mitochondrial genomes (mitogenomes) of three Hoplonemertea species, Amphiporus formidabilis, Prosadenoporus spectaculum and Nipponnemertes punctatula, which are 14,616, 14,655 and 15,354 bp in length, respectively. Each of the three circular mitogenomes consists of 37 typical genes and some non-coding regions. The nucleotide composition of the coding strand is biased toward T, almost a half of total nucleotides in these mitogenomes. There are many poly-T tracts across these mitogenomes, which exhibit T-number variation within different clones of protein-coding genes, mainly resulting from false PCR amplification. The major non-coding regions have tandem repeat motifs and hairpin-like structures that may be associated with the initiation of replication or transcription. Data published to date for nemerteans show that Palaeonemertea species usually bear the largest mitogenomes, while representatives in the more recently derived Distromatonemertea clade bear the smallest ones; and that the gene arrangement of mitogenomes seems to be variable within the phylum Nemertea, but stable within either of Heteronemertea and Hoplonemertea.
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Affiliation(s)
- Wen-Yan Sun
- Institute of Evolution & Marine Biodiversity, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
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Ma H, Ma C, Li X, Xu Z, Feng N, Ma L. The complete mitochondrial genome sequence and gene organization of the mud crab (Scylla paramamosain) with phylogenetic consideration. Gene 2013; 519:120-7. [PMID: 23384716 DOI: 10.1016/j.gene.2013.01.028] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 01/14/2013] [Accepted: 01/17/2013] [Indexed: 11/24/2022]
Abstract
The complete mitochondrial genome is of great importance for better understanding the genome-level characteristics and phylogenetic relationships among related species. In the present study, we determined the complete mitochondrial genome DNA sequence of the mud crab (Scylla paramamosain) by 454 deep sequencing and Sanger sequencing approaches. The complete genome DNA was 15,824 bp in length and contained a typical set of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and a putative control region (CR). Of 37 genes, twenty-three were encoded by the heavy strand (H-strand), while the other ones were encoded by light strand (L-strand). The gene order in the mitochondrial genome was largely identical to those obtained in most arthropods, although the relative position of gene tRNA(His) differed from other arthropods. Among 13 protein-coding genes, three (ATPase subunit 6 (ATP6), NADH dehydrogenase subunits 1 (ND1) and ND3) started with a rare start codon ATT, whereas, one gene cytochrome c oxidase subunit I (COI) ended with the incomplete stop codon TA. All 22 tRNAs could fold into a typical clover-leaf secondary structure, with the gene sizes ranging from 63 to 73 bp. The phylogenetic analysis based on 12 concatenated protein-coding genes showed that the molecular genetic relationship of 19 species of 11 genera was identical to the traditional taxonomy.
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Affiliation(s)
- Hongyu Ma
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200090, China
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21
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Miller AD, Good RT, Coleman RA, Lancaster ML, Weeks AR. Microsatellite loci and the complete mitochondrial DNA sequence characterized through next generation sequencing and de novo genome assembly for the critically endangered orange-bellied parrot, Neophema chrysogaster. Mol Biol Rep 2012; 40:35-42. [DOI: 10.1007/s11033-012-1950-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2012] [Accepted: 10/01/2012] [Indexed: 11/28/2022]
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22
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Groenenberg DSJ, Pirovano W, Gittenberger E, Schilthuizen M. The complete mitogenome of Cylindrus obtusus (Helicidae, Ariantinae) using Illumina next generation sequencing. BMC Genomics 2012; 13:114. [PMID: 22448618 PMCID: PMC3474148 DOI: 10.1186/1471-2164-13-114] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Accepted: 03/26/2012] [Indexed: 12/04/2022] Open
Abstract
Background This study describes how the complete mitogenome of a terrestrial snail, Cylindrus obtusus (Draparnaud, 1805) was sequenced without PCRs from a collection specimen that had been in 70% ethanol for 8 years. The mitogenome was obtained with Illumina GAIIx shot gun sequencing. Although the used specimen was collected relatively recently and kept in a DNA-friendly preservative (not formalin as frequently used with old museum specimens), we believe that the exclusion of PCRs as facilitated by NGS (Next Generation Sequencing) removes a great obstacle in DNA sequencing of collection specimens. A brief comparison is made between our Illumina GAIIx approach and a similar study that made use of the Roche 454-FLX platform. Results The mtDNA sequence of C. obtusus is 14,610 bases in length (about 0.5 kb larger than other stylommatophoran mitogenomes reported hitherto) and contains the 37 genes (13 protein coding genes, two rRNAs and 22 tRNAs) typical for metazoans. Except for a swap between the position of tRNA-Pro and tRNA-Ala, the gene arrangement of C. obtusus is identical to that reported for Cepaea nemoralis. The 'aberrant' rearrangement of tRNA-Thr and COIII compared to that of other Sigmurethra (and the majority of gastropods), is not unique for C. nemoralis (subfamily Helicinae), but is also shown to occur in C. obtusus (subfamily Ariantinae) and might be a synapomorphy for the family Helicidae. Conclusions Natural history collections potentially harbor a wealth of information for the field of evolutionary genetics, but it can be difficult to amplify DNA from such specimens (due to DNA degradation for instance). Because NGS techniques do not rely on primer-directed amplification (PCR) and allow DNA to be fragmented (DNA gets sheared during library preparation), NGS could be a valuable tool for retrieving DNA sequence data from such specimens. A comparison between Illumina GAIIx and the Roche 454 platform suggests that the former might be more suited for de novo sequencing of mitogenomes.
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Affiliation(s)
- Dick S J Groenenberg
- Netherlands Centre for Biodiversity Naturalis, PO Box 9517, Leiden RA 2300, The Netherlands.
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23
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Sato JJ, Wolsan M, Prevosti FJ, D'Elía G, Begg C, Begg K, Hosoda T, Campbell KL, Suzuki H. Evolutionary and biogeographic history of weasel-like carnivorans (Musteloidea). Mol Phylogenet Evol 2012; 63:745-57. [PMID: 22410652 DOI: 10.1016/j.ympev.2012.02.025] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Revised: 01/06/2012] [Accepted: 02/16/2012] [Indexed: 11/28/2022]
Abstract
We analyzed a concatenated (8492 bp) nuclear-mitochondrial DNA data set from 44 musteloids (including the first genetic data for Lyncodon patagonicus) with parsimony, maximum likelihood, and Bayesian methods of phylogenetic and biogeographic inference and two Bayesian methods of chronological inference. Here we show that Musteloidea emerged approximately 32.4-30.9 million years ago (MYA) in Asia, shortly after the greenhouse-icehouse global climate shift at the Eocene-Oligocene transition. During their Oligocene radiation, which proceeded wholly or mostly in Asia, musteloids diversified into four primary divisions: the Mephitidae lineage separated first, succeeded by Ailuridae and the divergence of the Procyonidae and Mustelidae lineages. Mustelidae arose approximately 16.1 MYA within the Mid-Miocene Climatic Optimum, and extensively diversified in the Miocene, mostly in Asia. The early offshoots of this radiation largely evolved into badger and marten ecological niches (Taxidiinae, Melinae, Mellivorinae, Guloninae, and Helictidinae), whereas the later divergences have adapted to other niches including those of weasels, polecats, minks, and otters (Mustelinae, Ictonychinae, and Lutrinae). Notably, and contrary to traditional beliefs, the morphological adaptations of badgers, martens, weasels, polecats, and minks each evolved independently more than once within Mustelidae. Ictonychinae (which is most closely related to Lutrinae) arose approximately 9.5-8.9 MYA, most likely in Asia, where it diverged into the Old World Ictonychini (Vormela, Poecilictis, Ictonyx, and Poecilogale) and New World Lyncodontini (Lyncodon and Galictis) lineages. Ictonychini presumably entered Africa during the Messinian Salinity Crisis (at the Miocene-Pliocene transition), which interposed the origins of this clade (approximately 6.5-6.0 MYA) and its African Poecilictis-Ictonyx-Poecilogale subclade (approximately 4.8-4.5 MYA). Lyncodontini originated approximately 2.9-2.6 MYA at the Pliocene-Pleistocene transition in South America, slightly after the emergence of the Panamanian land bridge that provided for the Great American Biotic Interchange. As the genera Martes and Ictonyx (as currently circumscribed) are paraphyletic with respect to the genera Gulo and Poecilogale, respectively, we propose that Pekaniaand Poecilictis be treated as valid genera and that "Martes"pennanti and "Ictonyx"libyca, respectively, be assigned to these genera.
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Affiliation(s)
- Jun J Sato
- Laboratory of Animal Cell Technology, Faculty of Life Science and Technology, Fukuyama University, Aza, Sanzo, 985, Fukuyama 729-0292, Japan
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Ma H, Ma C, Ma L. Population genetic diversity of mud crab (Scylla paramamosain) in Hainan Island of China based on mitochondrial DNA. BIOCHEM SYST ECOL 2011. [DOI: 10.1016/j.bse.2011.06.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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25
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Yuan Y, Li Q, Kong L, Yu H. The complete mitochondrial genome of the grand jackknife clam, Solen grandis (Bivalvia: Solenidae): a novel gene order and unusual non-coding region. Mol Biol Rep 2011; 39:1287-92. [PMID: 21598108 DOI: 10.1007/s11033-011-0861-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 05/12/2011] [Indexed: 01/22/2023]
Abstract
Molluscs in general, and bivalves in particular, exhibit an extraordinary degree of mitochondrial gene order variation when compared with other metazoans. The complete mitochondrial genome of Solen grandis (Bivalvia: Solenidae) was determined using long-PCR and genome walking techniques. The entire mitochondrial genome sequence of S. grandis is 16,784 bp in length, and contains 36 genes including 12 protein-coding genes (atp8 is absent), 2 ribosomal RNAs, and 22 tRNAs. All genes are encoded on the same strand. Compared with other species, it bears a novel gene order. Besides these, we find a peculiar non-coding region of 435 bp with a microsatellite-like (TA)(12) element, poly-structures and many hairpin structures. In contrast to the available heterodont mitochondrial genomes from GenBank, the complete mtDNA of S. grandis has the shortest cox3 gene, and the longest atp6, nad4, nad5 genes.
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Affiliation(s)
- Yang Yuan
- Fisheries College, Ocean University of China, Qingdao, China
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The complete mitochondrial genome and phylogenetic analysis of the Debao pony (Equus caballus). Mol Biol Rep 2011; 38:593-9. [PMID: 20390359 DOI: 10.1007/s11033-010-0145-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2010] [Accepted: 03/23/2010] [Indexed: 10/19/2022]
Abstract
The Debao pony (Equus caballus) is the most important local variety of domestic horses, and is strictly protected by the Chinese government. Their average adult withers height is 94.42±3.76 cm for males and 98.35±4.55 cm for females, respectively. In the present study, the complete sequence of the Debao pony mitochondrial genome was determined (GenBank Accession No. EU939445), and was found to be similar to other equine mitochondrial genomes. However, there were 85 nucleotide substitutions in the 13 protein-coding genes; the percentage of substitution was 0.8±0.1. Polymorphisms of mtDNA control regions were analyzed with restriction fragment length polymorphism (RFLP), and 19 haplotypes were found, with a genetic diversity of 0.77. Neighbor-Joining (NJ) and Minimum Evolution (ME) trees based on complete control regions of mtDNA were constructed with the Maximum Composite Likelihood (MCL) method. The analysis indicated that the origins of the Debao pony were scattered in the various branches of the phylogenetic tree. The results from the present study suggest that the Debao pony is derived from multi-matrilineal origins of the species.
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The complete mitochondrial genomes of three cestode species of Taenia infecting animals and humans. Mol Biol Rep 2010; 38:2249-56. [PMID: 20922482 DOI: 10.1007/s11033-010-0355-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2010] [Accepted: 09/16/2010] [Indexed: 02/02/2023]
Abstract
Mitochondrial (mt) genome sequences provide useful markers for investigating population genetic structures, systematics and phylogenetics of organisms. Although Taenia multiceps, T. hydatigena, and T. taeniaeformis are common taeniid tapeworms of ruminants, pigs, dogs, or cats, causing significant economic losses, no published study on their mt genomes is available. The complete mt genomes of T. multiceps, T. hydatigena, and T. taeniaeformis were amplified in two overlapping fragments and then sequenced. The sizes of the entire mt genome were 13700 bp for T. multiceps, 13489 bp for T. hydatigena, and 13647 bp for T. taeniaeformis. Each of the three genomes contains 36 genes, consisting of 12 genes for proteins, 2 genes for rRNA, and 22 genes for tRNA, which are the same as the mt genomes of all other cestode species studied to date. All genes are transcribed in the same direction and have a nucleotide composition high in A and T. The contents of A+T of the complete genomes are 71.3% for T. multiceps, 70.8% for T. hydatigena, and 73.0% for T. taeniaeformis. The AT bias had a significant effect on both the codon usage pattern and amino acid composition of proteins. T. multiceps and T. hydatigena had two noncoding regions, but T. taeniaeformis had only one. Phylogenetic analyses based on concatenated amino acid sequences of 12 protein-coding genes revealed that T. multiceps, T. hydatigena, and T. taeniaeformis were more closely related to the other members of the Taenia genus, consistent with results of previous morphological and molecular studies. The present study determined the complete mt genome sequences for three Taenia species of animal and human health significance, providing useful markers for studying the systematics, population genetics, and molecular epidemiology of these cestode parasites of animals and humans.
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Zhang H, Chen L. The complete mitochondrial genome of dhole Cuon alpinus: phylogenetic analysis and dating evolutionary divergence within Canidae. Mol Biol Rep 2010; 38:1651-60. [PMID: 20859694 DOI: 10.1007/s11033-010-0276-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Accepted: 09/02/2010] [Indexed: 01/20/2023]
Abstract
The dhole (Cuon alpinus) is the only existent species in the genus Cuon (Carnivora: Canidae). In the present study, the complete mitochondrial genome of the dhole was sequenced. The total length is 16672 base pairs which is the shortest in Canidae. Sequence analysis revealed that most mitochondrial genomic functional regions were highly consistent among canid animals except the CSB domain of the control region. The difference in length among the Canidae mitochondrial genome sequences is mainly due to the number of short segments of tandem repeated in the CSB domain. Phylogenetic analysis was progressed based on the concatenated data set of 14 mitochondrial genes of 8 canid animals by using maximum parsimony (MP), maximum likelihood (ML) and Bayesian (BI) inference methods. The genera Vulpes and Nyctereutes formed a sister group and split first within Canidae, followed by that in the Cuon. The divergence in the genus Canis was the latest. The divarication of domestic dogs after that of the Canis lupus laniger is completely supported by all the three topologies. Pairwise sequence divergence data of different mitochondrial genes among canid animals were also determined. Except for the synonymous substitutions in protein-coding genes, the control region exhibits the highest sequence divergences. The synonymous rates are approximately two to six times higher than those of the non-synonymous sites except for a slightly higher rate in the non-synonymous substitution between Cuon alpinus and Vulpes vulpes. 16S rRNA genes have a slightly faster sequence divergence than 12S rRNA and tRNA genes. Based on nucleotide substitutions of tRNA genes and rRNA genes, the times since divergence between dhole and other canid animals, and between domestic dogs and three subspecies of wolves were evaluated. The result indicates that Vulpes and Nyctereutes have a close phylogenetic relationship and the divergence of Nyctereutes is a little earlier. The Tibetan wolf may be an archaic pedigree within wolf subspecies. The genetic distance between wolves and domestic dogs is less than that among different subspecies of wolves. The domestication of dogs was about 1.56-1.92 million years ago or even earlier.
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Affiliation(s)
- Honghai Zhang
- College of Life Science, Qufu Normal University, Qufu 273165, China.
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Jayasankar P, Patel A, Khan M, Das P, Panda S. Mitochondrial DNA diversity and PCR-based sex determination of Irrawaddy dolphin (Orcaella brevirostris) from Chilika Lagoon, India. Mol Biol Rep 2010; 38:1661-8. [PMID: 20857220 DOI: 10.1007/s11033-010-0277-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Accepted: 09/02/2010] [Indexed: 11/28/2022]
Abstract
Of the only known two Lagoon populations of Irrawaddy dolphins (Orcaella) in the world, one is residing in the Chilika Lagoon in Orissa state, India. In addition to accidental deaths in gill net fishery and mechanized boat operations, there has been exploitation of the species for their oil. Extreme patchy distribution and vulnerability to becoming entangled in fishing gear has made it a focus of conservation concern. Information on genetic diversity of populations has considerable potential for informing conservation plans. The present paper reports the first genetic study of O. brevirostris from Chilika Lagoon based on mtDNA sequencing and PCR-based sex identification from 11 individuals. Control region sequence comparison showed two haplotypes and cytochrome b a single haplotype in the Chilika population of the species. Phylogenetic analysis indicated distinct clades within the Asian samples, with the Indian population showing closest genetic proximity to the haplotypes from Thailand. Sex of the animal was determined by PCR-based method. It is important to continue to examine the population discreteness and genetic variation of Irrawaddy dolphin in Chilika Lagoon vis-à-vis its global geographic distribution for formulating the conservation plans of the species.
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Affiliation(s)
- P Jayasankar
- Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751 002 Orissa, India.
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Mucci N, Arrendal J, Ansorge H, Bailey M, Bodner M, Delibes M, Ferrando A, Fournier P, Fournier C, Godoy JA, Hajkova P, Hauer S, Heggberget TM, Heidecke D, Kirjavainen H, Krueger HH, Kvaloy K, Lafontaine L, Lanszki J, Lemarchand C, Liukko UM, Loeschcke V, Ludwig G, Madsen AB, Mercier L, Ozolins J, Paunovic M, Pertoldi C, Piriz A, Prigioni C, Santos-Reis M, Luis TS, Stjernberg T, Schmid H, Suchentrunk F, Teubner J, Tornberg R, Zinke O, Randi E. Genetic diversity and landscape genetic structure of otter (Lutra lutra) populations in Europe. CONSERV GENET 2010. [DOI: 10.1007/s10592-010-0054-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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