1
|
Tissaoui G, Suchentrunk F, Awadi A, Smith S, Weber A, Ben Slimen H. Evolutionary characteristics of the mitochondrial NADH dehydrogenase subunit 6 gene in some populations of four sympatric Mustela species (Mustelidae, Mammalia) from central Europe. Mol Biol Rep 2024; 51:575. [PMID: 38664260 DOI: 10.1007/s11033-024-09505-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 04/02/2024] [Indexed: 04/30/2024]
Abstract
BACKGROUND Selection on or reticulate evolution of mtDNA is documented in various mammalian taxa and could lead to misleading phylogenetic conclusions if not recognized. We sequenced the MT-ND6 gene of four sympatric Mustelid species of the genus Mustela from some central European populations. We hypothesised positive selection on MT-ND6, given its functional importance and the different body sizes and life histories of the species, even though climatic differences may be unimportant for adaptation in sympatry. METHODS AND RESULTS MT-ND6 genes were sequenced in 187 sympatric specimens of weasels, Mustela nivalis, stoats, M. erminea, polecats, M. putorius, and steppe polecats, M. eversmannii, from eastern Austria and of fourteen allopatric polecats from eastern-central Germany. Median joining networks, neighbour joining and maximum likelihood analyses as well as Bayesian inference grouped all species according to earlier published phylogenetic models. However, polecats and steppe polecats, two very closely related species, shared the same two haplotypes. We found only negative selection within the Mustela sequences, including 131 downloaded ones covering thirteen species. Positive selection was observed on three MT-ND6 codons of other mustelid genera retrieved from GenBank. CONCLUSIONS Negative selection for MT-ND6 within the genus Mustela suggests absence of both environmental and species-specific effects of cellular energy metabolism despite large species-specific differences in body size. The presently found shared polymorphism in European polecats and steppe polecats may result from ancestral polymorphism before speciation and historical or recent introgressive hybridization; it may indicate mtDNA capture of steppe polecats by M. putorius in Europe.
Collapse
Affiliation(s)
- Ghada Tissaoui
- Laboratory of Functional Physiology and Valorization of Bioresources, Higher Institute of Biotechnology of Béja, University of Jendouba, Jendouba, Tunisia
| | - Franz Suchentrunk
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstrasse 1, Vienna, 1160, Austria
| | - Asma Awadi
- Laboratory of Functional Physiology and Valorization of Bioresources, Higher Institute of Biotechnology of Béja, University of Jendouba, Jendouba, Tunisia
| | - Steve Smith
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstrasse 1, Vienna, 1160, Austria
| | - Antje Weber
- Landesamt für Umweltschutz Sachsen-Anhalt, Dez. 44 WZI, Lindenstraße 18, 39606, Iden, Germany
| | - Hichem Ben Slimen
- Laboratory of Functional Physiology and Valorization of Bioresources, Higher Institute of Biotechnology of Béja, University of Jendouba, Jendouba, Tunisia.
| |
Collapse
|
2
|
Mei X, Liu G, Yan J, Zhao C, Wang X, Zhou S, Wei Q, Zhao S, Liu Z, Sha W, Zhang H. A chromosome-level genome assembly of the yellow-throated marten (Martes flavigula). Sci Data 2023; 10:216. [PMID: 37069236 PMCID: PMC10110515 DOI: 10.1038/s41597-023-02120-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 03/29/2023] [Indexed: 04/19/2023] Open
Abstract
The yellow-throated marten (Martes flavigula) is a medium-sized carnivore that is widely distributed across much of Asia and occupies an extensive variety of habitats. We reported a high-quality genome assembly of this organism that was generated using Oxford Nanopore and Hi-C technologies. The final genome sequences contained 215 contigs with a total size of 2,449.15 Mb and a contig N50 length of 68.60 Mb. Using Hi-C analysis, 2,419.20 Mb (98.78%) of the assembled sequences were anchored onto 21 linkage groups. Merqury evaluation suggested that the genome was 94.95% complete with a QV value of 43.75. Additionally, the genome was found to comprise approximately 39.74% repeat sequences, of which long interspersed elements (LINE) that accounted for 26.13% of the entire genome, were the most abundant. Of the 20,464 protein-coding genes, prediction and functional annotation was successfully performed for 20,322 (99.31%) genes. The high-quality, chromosome-level genome of the marten reported in this study will serve as a reference for future studies on genetic diversity, evolution, and conservation biology.
Collapse
Affiliation(s)
- Xuesong Mei
- School of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Guangshuai Liu
- School of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Jiakuo Yan
- School of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Chao Zhao
- School of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Xibao Wang
- School of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Shengyang Zhou
- School of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Qinguo Wei
- School of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Shihu Zhao
- School of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Zhao Liu
- School of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Weilai Sha
- School of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Honghai Zhang
- School of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China.
| |
Collapse
|
3
|
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]
|
4
|
Gray A, Brito JC, Edwards CW, Figueiró HV, Koepfli KP. First complete mitochondrial genome of the Saharan striped polecat ( Ictonyx libycus). MITOCHONDRIAL DNA PART B 2022; 7:1957-1960. [DOI: 10.1080/23802359.2022.2141080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Autumn Gray
- Department of Environmental Science and Policy, George Mason University, Fairfax, VA, USA
- Smithsonian-Mason School of Conservation, George Mason University, Fairfax, VA, USA
| | - José C. Brito
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Cody W. Edwards
- Smithsonian-Mason School of Conservation, George Mason University, Fairfax, VA, USA
- Department of Biology, George Mason University, Fairfax, VA, USA
| | - Henrique V. Figueiró
- Smithsonian-Mason School of Conservation, George Mason University, Fairfax, VA, USA
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Fairfax, VA, USA
- Center for Species Survival, Smithsonian’s National Zoo and Conservation Biology Institute, Virginia, USA
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Schwartz MK, Walters AD, Pilgrim KL, Moriarty KM, Slauson KM, Zielinski WJ, Aubry KB, Sacks BN, Zarn KE, Quinn CB, Young MK. Pliocene-Early Pleistocene Geological Events Structure Pacific Martens (Martes caurina). J Hered 2021; 111:169-181. [PMID: 32161974 DOI: 10.1093/jhered/esaa005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 02/10/2020] [Indexed: 11/15/2022] Open
Abstract
The complex topography, climate, and geological history of Western North America have shaped contemporary patterns of biodiversity and species distributions in the region. Pacific martens (Martes caurina) are distributed along the northern Pacific Coast of North America with disjunct populations found throughout the Northwestern Forested Mountains and Marine West Coast Forest ecoregions of the West Coast. Martes in this region have been classified into subspecies; however, the subspecific designation has been extensively debated. In this study, we use genomic data to delineate conservation units of Pacific marten in the Sierra-Cascade-Coastal montane belt in the western United States. We analyzed the mitochondrial genome for 94 individuals to evaluate the spatial distribution and divergence times of major lineages. We further genotyped 401 individuals at 13 microsatellite loci to investigate major patterns of population structure. Both nuclear and mitochondrial DNA suggest substantial genetic substructure concordant with historical subspecies designations. Our results revealed that the region contains 2 distinct mitochondrial lineages: a Cascades/Sierra lineage that diverged from the Cascades/coastal lineage 2.23 (1.48-3.14 mya), consistent with orogeny of the Cascade Mountain chain. Interestingly, Pacific Martes share phylogeographic patterns similar with other sympatric taxa, suggesting that the complex geological history has shaped the biota of this region. The information is critical for conservation and management efforts, and further investigation of adaptive diversity is warranted following appropriate revision of conservation management designations.
Collapse
Affiliation(s)
- Michael K Schwartz
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Missoula, MT
| | - Ashley D Walters
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Missoula, MT
| | - Kristine L Pilgrim
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Missoula, MT
| | - Katie M Moriarty
- National Council for Air and Stream Improvement, Inc., Corvallis, OR
| | - Keith M Slauson
- USDA Forest Service, Pacific Southwest Research Station, Arcata, CA
| | - William J Zielinski
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Missoula, MT.,USDA Forest Service, Pacific Southwest Research Station, Arcata, CA
| | - Keith B Aubry
- USDA Forest Service, Pacific Northwest Research Station, Olympia, WA
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, Davis, CA
| | - Katherine E Zarn
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Missoula, MT
| | - Cate B Quinn
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, Davis, CA
| | - Michael K Young
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Missoula, MT
| |
Collapse
|
7
|
Li B, Lu J, Monakhov V, Kang H, Xu Y, An B, Ghani MU, Li M, Peng W, Ma X. Phylogeography of subspecies of the sable (Martes zibellina L.) based on mitochondrial genomes: implications for evolutionary history. Mamm Biol 2021. [DOI: 10.1007/s42991-020-00092-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
8
|
Abstract
Abstract
The subspecies concept is one of the most controversial in Linnean taxonomy. In the past, subspecies were described without a clear conceptual framework, triggering confusion and motivating criticism of the very concept of a subspecies. At present, subspecies are conceived as aggregates of populations that are geographically isolated, are composed of interfertile individuals, and are morphologically diagnosable. The tayra, Eira barbara, was described in 1758 and has had a stable taxonomic history at the species level. However, below the species level, 16 subspecies have been named, with from two to seven subspecies recognized as valid by different authors. None of the subspecies were, however, described within a clear conceptual framework. Using the modern concept of a subspecies, I analyzed subspecies of E. barbara recognized by recent authors. I gathered morphometric data from 155 specimens in mammal collections, georeferenced each specimen, and recorded membership to subspecies assigned by different references and by its location. I gathered climate and geographic data for each location. I analyzed data using Principal Components Analysis (PCA) and analysis of variance (ANOVA). Specimens exhibited sexual dimorphism in size but not in skull shape. I used regression analysis to test for associations between skull shape and size and climate data. Geographic analyses documented that subspecies are not allopatric, violating one of the main properties of the subspecies concept. ANOVA showed significant differences in skull morphology between some pairs of recognized subspecies but not others. However, none of the subspecies segregated in the PCA. Thus, the recognized subspecies could not be diagnosed from morphological data, violating another property of the subspecies concept. Size varied greatly between the sexes using different schemes for recognized subspecies. Climate variables explained between 4% and 6% of size variation for males and females. Skull shape proved not to be geographically variable.
Collapse
Affiliation(s)
- Mauro Ignacio Schiaffini
- CIEMEP, Centro de Investigación Esquel de Montaña y Estepa Patagónica (Universidad Nacional de la Patagonia San Juan Bosco- Consejo Nacional de Investigaciones Científicas y Técnicas), LIEB, Laboratorio de Investigaciones en Evolución y Biodiversidad. Facultad de Ciencias Naturales y Ciencias de la Salud, Universidad Nacional de la Patagonia San Juan Bosco, Esquel, Chubut, Argentina
| |
Collapse
|
9
|
Liu G, Zhao C, Xu D, Zhang H, Monakhov V, Shang S, Gao X, Sha W, Ma J, Zhang W, Tang X, Li B, Hua Y, Cao X, Liu Z, Zhang H. First Draft Genome of the Sable, Martes zibellina. Genome Biol Evol 2020; 12:59-65. [PMID: 32058545 PMCID: PMC7144822 DOI: 10.1093/gbe/evaa029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2020] [Indexed: 11/28/2022] Open
Abstract
Members of genus Martes provide early warning signals about forest ecosystem health and are designated as a Management Indicator Species. As one of the most widespread members in Martes, the sable (Martes zibellina) is a circumboreal small predator found throughout all taiga zoogeographical zones of Eurasia and shows distinct population differentiation and morphological variations. To support further studies on striking local adaptation and population evolution, we present the first sable genome, assembled de novo from an individual originating in the Great Khingan Mountains (China). The assembled genome is 2.42 Gb, consisting of 15,814 scaffolds with a scaffold N50 of 5.20 Mb. Searches for complete Mammalia BUSCO (Benchmarking Universal Single-Copy Ortholog) gene groups found that 95.15% of the curated single-copy orthologs were assembled as complete, suggesting a high level of completeness of the genome. We totally predicted 19,413 protein-coding genes, and 0.82 Gb of repeat sequences was annotated. We also detected 1,257 olfactory receptor genes and found more functional olfactory receptor genes in sable than in other Mustelidae species, which provide a possible genetic explanation for the acute sense of smell of the sable for searching the preys under deep snow. Phylogenetic analyses revealed that the ferret (Mustela putorius furo) and sea otter (Enhydra lutris) form a clade that is sister to the sable, which was dated ∼16.4 Ma. Overall, our study provided the first reference genome for research in a broad range of areas including local adaptations, population evolution, conservation, and management for sable.
Collapse
Affiliation(s)
- Guangshuai Liu
- College of Life Science, Qufu Normal University, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Chao Zhao
- College of Life Science, Qufu Normal University, China
| | - Dongming Xu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Huanxin Zhang
- College of Marine Life Science, Ocean University of China, Qingdao, Shandong, China
| | - Vladimir Monakhov
- Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Yekaterinburg, Russia
| | - Shuai Shang
- College of Marine Life Science, Ocean University of China, Qingdao, Shandong, China
- College of Biological and Environmental Engineering, Binzhou University, China
| | - Xiaodong Gao
- College of Life Science, Qufu Normal University, China
| | - Weilai Sha
- College of Life Science, Qufu Normal University, China
| | - Jianzhang Ma
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
| | - Wei Zhang
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
| | - Xuexi Tang
- College of Marine Life Science, Ocean University of China, Qingdao, Shandong, China
| | - Bo Li
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
| | - Yan Hua
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
| | - Xiaofang Cao
- Novogene Bioinformatics Institute, Beijing, China
| | - Zhen Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Honghai Zhang
- College of Life Science, Qufu Normal University, China
| |
Collapse
|
10
|
Gao W, Lu Z, Liang Y, Ren ZM. Complete mitochondrial genome of Mustela sibirica (Carnivora: Mustelidae), a protected and endangered species in China. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:1081-1083. [PMID: 33366884 PMCID: PMC7748545 DOI: 10.1080/23802359.2020.1723447] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
We sequenced the complete mitochondrial genome (mitogenome) of Mustela sibirica in China by the shotgun genome skimming methods. The mitogenome of M. sibirica is 16,558bp in length with the base composition of 32.9% A, 27.3% T, 26.0% C, and 13.9% G, and consists of 13 protein-coding genes (PCGs), 22 tRNAs, two rRNAs, and one non-coding control region. The 13 PCGs use ATG as initiation codons except ND3, ND5 and ND2 which initiate with codons ATA and ATT, respectively. Four (COX3, ND1, ND2 and ND4) of the 13 PCGs terminate with a single T– –, and the remainder with a TAA termination codon except ND3 and CYT B using TA– and AGA as termination codon. The phylogenetic tree based on 13 protein-coding genes indicated that M. sibirica is sister to the clade grouped with three species M. nigripes, M. eversmannii, and M. putorius, and Mustelinae species formed a monophyletic group, which is close to the Lutrinae clade within Mustelidae.
Collapse
Affiliation(s)
- Wei Gao
- School of Life Science, Shanxi University, Taiyuan, China
| | - Zhihao Lu
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Yukang Liang
- School of Life Science, Shanxi University, Taiyuan, China
| | - Zhu-Mei Ren
- School of Life Science, Shanxi University, Taiyuan, China
| |
Collapse
|
11
|
Arslan Y, Demi̇rtaş S, Herman JS, Pustilnik JD, Searle JB, Gündüz İ. The Anatolian glacial refugium and human-mediated colonization: a phylogeographical study of the stone marten (Martes foina) in Turkey. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz180] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractThe Anatolian Peninsula, comprising most of modern Turkey, is situated at the junction of Europe, the Middle East and Asia. Together with its complex geomorphological and climatic history, this has given rise to a rich fauna and flora, which exhibits a wide range of historical biogeographical patterns. The stone marten (Martes foina) is a small carnivore that is found across the temperate Palaearctic region including Anatolia, where it is often associated with habitats modified by humans, but few genetic data exist for this species. We sequenced a 1840-bp region of the mitochondrial genome from 97 martens sampled across the peninsula and intron 7 of the nuclear β-fibrinogen gene from 53 of these. Two mitochondrial lineages were recovered, with overlapping eastern and western distributions, but there was no geographical structure for the autosomal marker. Coalescent analyses indicated that both of the lineages originated during the Last Glacial Maximum, one of them within an eastern Anatolian refugium and the other in a western Anatolian or Balkan refugium. The western lineage colonized most of Europe in the Holocene, while the eastern lineage may be endemic to Anatolia, from where it colonized the Iberian Peninsula via human translocation. The presence of at least one refugial stone marten population highlights the importance of Anatolia to the preservation of genetic variation and biodiversity.
Collapse
Affiliation(s)
- Yağmur Arslan
- Department of Biology, Faculty of Arts and Sciences, Ondokuz Mayis University, Samsun, Turkey
| | - Sadik Demi̇rtaş
- Department of Biology, Faculty of Arts and Sciences, Ondokuz Mayis University, Samsun, Turkey
| | - Jeremy S Herman
- Department of Natural Sciences, National Museums Scotland, Edinburgh, UK
| | - Jeremy D Pustilnik
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - İslam Gündüz
- Department of Biology, Faculty of Arts and Sciences, Ondokuz Mayis University, Samsun, Turkey
| |
Collapse
|
12
|
Beichman AC, Koepfli KP, Li G, Murphy W, Dobrynin P, Kliver S, Tinker MT, Murray MJ, Johnson J, Lindblad-Toh K, Karlsson EK, Lohmueller KE, Wayne RK. Aquatic Adaptation and Depleted Diversity: A Deep Dive into the Genomes of the Sea Otter and Giant Otter. Mol Biol Evol 2019; 36:2631-2655. [PMID: 31212313 PMCID: PMC7967881 DOI: 10.1093/molbev/msz101] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Despite its recent invasion into the marine realm, the sea otter (Enhydra lutris) has evolved a suite of adaptations for life in cold coastal waters, including limb modifications and dense insulating fur. This uniquely dense coat led to the near-extinction of sea otters during the 18th-20th century fur trade and an extreme population bottleneck. We used the de novo genome of the southern sea otter (E. l. nereis) to reconstruct its evolutionary history, identify genes influencing aquatic adaptation, and detect signals of population bottlenecks. We compared the genome of the southern sea otter with the tropical freshwater-living giant otter (Pteronura brasiliensis) to assess common and divergent genomic trends between otter species, and with the closely related northern sea otter (E. l. kenyoni) to uncover population-level trends. We found signals of positive selection in genes related to aquatic adaptations, particularly limb development and polygenic selection on genes related to hair follicle development. We found extensive pseudogenization of olfactory receptor genes in both the sea otter and giant otter lineages, consistent with patterns of sensory gene loss in other aquatic mammals. At the population level, the southern sea otter and the northern sea otter showed extremely low genomic diversity, signals of recent inbreeding, and demographic histories marked by population declines. These declines may predate the fur trade and appear to have resulted in an increase in putatively deleterious variants that could impact the future recovery of the sea otter.
Collapse
Affiliation(s)
- Annabel C Beichman
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA
| | - Klaus-Peter Koepfli
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Gang Li
- College of Life Science, Shaanxi Normal University, Xi’an, Shaanxi, China
| | - William Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX
| | - Pasha Dobrynin
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Sergei Kliver
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Martin T Tinker
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA
| | | | - Jeremy Johnson
- Vertebrate Genome Biology, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Kerstin Lindblad-Toh
- Vertebrate Genome Biology, Broad Institute of MIT and Harvard, Cambridge, MA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Elinor K Karlsson
- Vertebrate Genome Biology, Broad Institute of MIT and Harvard, Cambridge, MA
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA
| |
Collapse
|
13
|
Rozhnov VV, Korablev MP, Abramov AV. Systematics and Distribution of Ferret Badgers Melogale (Mammalia, Mustelidae) in Vietnam: First Genetic Data. DOKLADY BIOLOGICAL SCIENCES : PROCEEDINGS OF THE ACADEMY OF SCIENCES OF THE USSR, BIOLOGICAL SCIENCES SECTIONS 2019; 485:47-51. [PMID: 31197594 DOI: 10.1134/s001249661902008x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 12/04/2018] [Accepted: 12/04/2018] [Indexed: 11/23/2022]
Abstract
Genetic studies of the ferret badgers Melogale conducted in Vietnam have shown that this area is inhabited by three species, M. moschata, M. personata, and M. cucphuongensis, which can be attributed to sibling species (cryptic species). M. personata was found to be widespread not only in southern and central Vietnam, but also in the northern provinces (Lang Son, Ha Giang, Ninh Binh), while M. cucphuongensis was found in the provinces Lang Son, Ha Giang, Cao Bang, and Dak Lak, apart from Ninh Binh, from where it was described. The data obtained suggest a sympatric distribution of all three species over the Vietnam area and confirm sympatry of M. personata and M. moschata in southern Vietnam, which has been earlier established on the basis of morphological data.
Collapse
Affiliation(s)
- V V Rozhnov
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia. .,Vietnamese-Russian Tropical Center, Hanoi, Vietnam.
| | - M P Korablev
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - A V Abramov
- Vietnamese-Russian Tropical Center, Hanoi, Vietnam.,Zoological Institute, Russian Academy of Sciences, St. Petersburg, Russia
| |
Collapse
|
14
|
Wang X, Zhang Y, Zhang H, Qin G, Lin Q. Complete mitochondrial genomes of eight seahorses and pipefishes (Syngnathiformes: Syngnathidae): insight into the adaptive radiation of syngnathid fishes. BMC Evol Biol 2019; 19:119. [PMID: 31185889 PMCID: PMC6560779 DOI: 10.1186/s12862-019-1430-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/30/2019] [Indexed: 11/17/2022] Open
Abstract
Background The evolution of male pregnancy is the most distinctive characteristic of syngnathids, and their specialized life history traits make syngnathid species excellent model species for many issues in biological evolution. However, the origin of syngnathids and the evolutionary divergence time of different syngnathid species remain poorly resolved. Comprehensive phylogenetic studies of the Syngnathidae will provide critical evidence to elucidate their origin, evolution, and dispersal patterns. Results We sequenced the mitochondrial genomes of eight syngnathid species in this study, and the estimated divergence times suggested that syngnathids diverged from other teleosts approximately 48.8 Mya during the Eocene period. Selection analysis showed that many mitochondrial genes of syngnathids exhibited significantly lower Ka/Ks values than those of other teleosts. The two most frequently used codons in syngnathid fishes were different from those in other teleosts, and a greater proportion of the mitochondrial simple sequence repeats (SSRs) were distributed in non-coding sequences in syngnathids compared with other teleosts. Conclusions Our study indicated that syngnathid fishes experienced an adaptive radiation process during the early explosion of species. Syngnathid mitochondrial OXPHOS genes appear to exhibit depressed Ka/Ks ratios compared with those of other teleosts, and this may suggest that their mitogenomes have experienced strong selective constraints to eliminate deleterious mutations. Electronic supplementary material The online version of this article (10.1186/s12862-019-1430-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Xin Wang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, People's Republic of China.,University of the Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yanhong Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
| | - Huixian Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
| | - Geng Qin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China. .,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, People's Republic of China. .,University of the Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
| |
Collapse
|
15
|
Tsoupas A, Andreadou M, Papakosta MA, Karaiskou N, Bakaloudis DE, Chatzinikos E, Sakoulis A, Triantafyllidis A, Vlachos CG. Phylogeography of Martes foina in Greece. Mamm Biol 2019. [DOI: 10.1016/j.mambio.2019.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
16
|
Li B, Wu D, Cai Y, Vladimir G M, Zhang W, Xu Y. Genetic individualization of sable ( Martes zibellina L. 1758) using microsatellites. Anim Cells Syst (Seoul) 2018; 22:253-258. [PMID: 30460105 PMCID: PMC6138352 DOI: 10.1080/19768354.2018.1494039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 05/22/2018] [Accepted: 06/21/2018] [Indexed: 10/28/2022] Open
Abstract
Genetic individualization based on non-invasive sampling is crucial for estimating the numbers of individuals in endangered mammalian populations. In sable (Martes zibellina)-poaching cases, identifying the number of animals involved is critical for determining the penalty. In addition, investigating animal numbers for wild sable populations requires genetic individualization when collecting several samples in neighboring regions. Microsatellites have been demonstrated to be reliable markers for individual identification. Thirty-three microsatellite loci derived from Mustelidae were selected to develop a genetic individualization method for sable. Three reference populations containing 54 unrelated sables were used to calculate allele number, allelic frequencies, and the polymorphic information content of each locus. The data were subsequently used to assess the validity of a combination of twelve loci for sable individualization. We defined twelve polymorphic loci that were easy to be amplified and genotyped. Four significant deviations from Hardy-Weinberg equilibrium were observed among the 12 loci in the three populations. The match probability of an individual from the reference populations with a random individual based on the 12 loci was 1.37 × 10-13. Using the combination of the twelve loci provides sufficient power to individualize sables considering the levels of microsatellite polymorphism observed. These loci were successfully applied to a case of sable poaching and provided valid evidence to determine the penalty. The genetic individualization of sable based on these loci might also be useful to investigate the numbers of animals in wild populations.
Collapse
Affiliation(s)
- Bo Li
- College of Wildlife Resources, Northeast Forestry University, Harbin, People's Republic of China.,State Forestry Administration Detecting Center of Wildlife Resources, Harbin, People's Republic of China
| | - Dan Wu
- College of Wildlife Resources, Northeast Forestry University, Harbin, People's Republic of China.,College of Biotechnology and Engineering, West Yunnan University, Lincang, People's Republic of China
| | - Yingying Cai
- College of Wildlife Resources, Northeast Forestry University, Harbin, People's Republic of China
| | - Monakhov Vladimir G
- Institute of Plant and Animal Ecology, Ural Division of RAS, Yekaterinburg, Russia
| | - Wei Zhang
- College of Wildlife Resources, Northeast Forestry University, Harbin, People's Republic of China.,State Forestry Administration Detecting Center of Wildlife Resources, Harbin, People's Republic of China
| | - Yanchun Xu
- College of Wildlife Resources, Northeast Forestry University, Harbin, People's Republic of China.,State Forestry Administration Detecting Center of Wildlife Resources, Harbin, People's Republic of China
| |
Collapse
|
17
|
İbiş O, Koepfli KP, Özcan S, Tez C. Genetic analysis of Turkish martens: Do two species of the genusMartesoccur in Anatolia? ZOOL SCR 2018. [DOI: 10.1111/zsc.12289] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Osman İbiş
- Department of Agricultural Biotechnology; Faculty of Agriculture; Erciyes University; Kayseri Turkey
- Genome and Stem Cell Center (GENKOK); Erciyes University; Kayseri Turkey
| | - Klaus-Peter Koepfli
- National Zoological Park; Smithsonian Conservation Biology Institute; Washington District of Columbia
- Theodosius Dobzhansky Center for Genome Bioinformatics; Saint Petersburg State University; Saint Petersburg Russia
| | - Servet Özcan
- Genome and Stem Cell Center (GENKOK); Erciyes University; Kayseri Turkey
- Department of Biology; Faculty of Sciences; Erciyes University; Kayseri Turkey
| | - Coşkun Tez
- Department of Biology; Faculty of Sciences; Erciyes University; Kayseri Turkey
| |
Collapse
|
18
|
Law CJ, Slater GJ, Mehta RS. Lineage Diversity and Size Disparity in Musteloidea: Testing Patterns of Adaptive Radiation Using Molecular and Fossil-Based Methods. Syst Biol 2018; 67:127-144. [PMID: 28472434 DOI: 10.1093/sysbio/syx047] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 04/28/2017] [Indexed: 11/12/2022] Open
Abstract
Adaptive radiation is hypothesized to be a primary mechanism that drives the remarkable species diversity and morphological disparity across the Tree of Life. Tests for adaptive radiation in extant taxa are traditionally estimated from calibrated molecular phylogenies with little input from extinct taxa. With 85 putative species in 33 genera and over 400 described extinct species, the carnivoran superfamily Musteloidea is a prime candidate to investigate patterns of adaptive radiation using both extant- and fossil-based macroevolutionary methods. The species diversity and equally impressive ecological and phenotypic diversity found across Musteloidea is often attributed to two adaptive radiations coinciding with two major climate events, the Eocene-Oligocene transition and the Mid-Miocene Climate Transition. Here, we compiled a novel time-scaled phylogeny for 88% of extant musteloids and used it as a framework for testing the predictions of adaptive radiation hypotheses with respect to rates of lineage diversification and phenotypic evolution. Contrary to expectations, we found no evidence for rapid bursts of lineage diversification at the origin of Musteloidea, and further analyses of lineage diversification rates using molecular and fossil-based methods did not find associations between rates of lineage diversification and the Eocene-Oligocene transition or Mid-Miocene Climate Transition as previously hypothesized. Rather, we found support for decoupled diversification dynamics driven by increased clade carrying capacity in the branches leading to a subclade of elongate mustelids. Supporting decoupled diversification dynamics between the subclade of elongate mustelids and the ancestral musteloid regime is our finding of increased rates of body length evolution, but not body mass evolution, within the decoupled mustelid subclade. The lack of correspondence in rates of body mass and length evolution suggest that phenotypic evolutionary rates under a single morphological metric, even one as influential as mass, may not capture the evolution of diversity in clades that exhibit elongate body shapes. The discordance in evolutionary rates between body length and body mass along with evidence of decoupled diversification dynamics suggests that body elongation might be an innovation for the exploitation of novel Mid-Miocene resources, resulting in the radiation of some musteloids.
Collapse
Affiliation(s)
- Chris J Law
- Department of Ecology and Evolutionary Biology, Long Marine Lab, University of California, Santa Cruz, 115 McAllister Way, Santa Cruz, CA 95060, USA
| | - Graham J Slater
- Department of the Geophysical Sciences, University of Chicago, 5734 S. Ellis Avenue, Chicago, IL 60637 USA
| | - Rita S Mehta
- Department of Ecology and Evolutionary Biology, Long Marine Lab, University of California, Santa Cruz, 115 McAllister Way, Santa Cruz, CA 95060, USA
| |
Collapse
|
19
|
Emami-Khoyi A, Hartley DA, Ross JG, Murphy EC, Paterson AM, Cruickshank RH, Else TA. Complete mitochondrial genome of the stoat (Mustela erminea) and New Zealand fur seal (Arctocephalus forsteri) and their significance for mammalian phylogeny. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 27:4597-4599. [PMID: 27246241 DOI: 10.3109/19401736.2015.1101542] [Citation(s) in RCA: 4] [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 of three mustelid species, stoats (Mustela erminea), weasels (Mustela nivalis) and ferrets (Mustela furo), and the New Zealand fur seal (Arctocephalus forsteri) were sequenced using direct mitochondrial DNA extraction and overlapping long PCRs. The usual 37 mammalian mitochondrial genes (13 protein coding genes, 22 t-RNA and 2 r-RNA) were identified in all four mitogenomes. The divergence of stoats from other members of the sub-family Mustelinae was dated 4.5 million years ago. The mitogenomic data were consistent with a bear-like origin of seals.
Collapse
Affiliation(s)
| | | | - James G Ross
- a Department of Ecology , Lincoln University , Lincoln , New Zealand.,c Centre for Wildlife Management and Conservation, Lincoln University , Lincoln , New Zealand
| | - Elaine C Murphy
- a Department of Ecology , Lincoln University , Lincoln , New Zealand.,c Centre for Wildlife Management and Conservation, Lincoln University , Lincoln , New Zealand
| | - Adrian M Paterson
- a Department of Ecology , Lincoln University , Lincoln , New Zealand
| | | | - Terry-Ann Else
- d Touro University - Nevada - College of Osteopathic Medicine, Medical Microbiology/Immunology , Henderson , NV , USA
| |
Collapse
|
20
|
Hua Y, Xu Y. Evolutionary status of the invasive American mink Neovison vison revealed by complete mitochondrial genome. MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:6-7. [PMID: 33473387 PMCID: PMC7799575 DOI: 10.1080/23802359.2015.1137794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The American mink, Neovison vison, is native to North America and listed as one of the most widely distributed invasive species into the Eurasian mainland. Even though facing serious over-hunting and habitat degradation problems, this species has successfully dispersed into most areas of northeast China in the past decades, which may have a huge impact on local species composition and structure. We determined and annotated the whole mitochondrial DNA genome of the American mink N. vison to better understand the evolutionary relationship of this invasive species with other Mustelidae distributing in China. The complete mitogenome is 16 627 bp in length, includes 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and one control region. We built the phylogenetic tree of American mink and other 10 most closely Mustelidae species.
Collapse
Affiliation(s)
- Yan Hua
- College of Wildlife Resources, Northeast Forestry University, Harbin, P.R. China
| | - Yanchun Xu
- College of Wildlife Resources, Northeast Forestry University, Harbin, P.R. China
| |
Collapse
|
21
|
Wang J, Lu B, Zan R, Chai J, Ma W, Jin W, Duan R, Luo J, Murphy RW, Xiao H, Chen Z. Phylogenetic Relationships of Five Asian Schilbid Genera Including Clupisoma (Siluriformes: Schilbeidae). PLoS One 2016; 11:e0145675. [PMID: 26751688 PMCID: PMC4713424 DOI: 10.1371/journal.pone.0145675] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 12/06/2015] [Indexed: 11/19/2022] Open
Abstract
The phylogenetic relationships of Asian schilbid catfishes of the genera Clupisoma, Ailia, Horabagrus, Laides and Pseudeutropius are poorly understood, especially those of Clupisoma. Herein, we reconstruct the phylogeny of 38 species of catfishes belonging to 28 genera and 14 families using the concatenated mitochondrial genes COI, cytb, and 16S rRNA, as well as the nuclear genes RAG1 and RAG2. The resulting phylogenetic trees consistently place Clupisoma as the sister taxon of Laides, and the five representative Asian schilbid genera form two monophyletic groups with the relationships (Ailia (Laides, Clupisoma)) and (Horabagrus, Pseudeutropius). The so-called "Big Asia" lineage relates distantly to African schilbids. Independent analyses of the mitochondrial and nuclear DNA data yield differing trees for the two Asian schilbid groups. Analyses of the mitochondrial gene data support a sister-group relationship for (Ailia (Laides, Clupisoma)) and the Sisoroidea and a sister-taxon association of (Horabagrus, Pseudeutropius) and the Bagridae. In contrast, analyses of the combined nuclear data indicate (Ailia (Laides, Clupisoma)) to be the sister group to (Horabagrus, Pseudeutropius). Our results indicate that the Horabagridae, recognized by some authors as consisting of Horabagrus, Pseudeutropius and Clupisoma does not include the latter genus. We formally erect a new family, Ailiidae fam. nov. for a monophyletic Asian group comprised of the genera Ailia, Laides and Clupisoma.
Collapse
Affiliation(s)
- Jing Wang
- Yunnan University / State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Kunming 650091, China
| | - Bin Lu
- Yunnan University / State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Kunming 650091, China
| | - Ruiguang Zan
- School of Life Science, Yunnan University, Kunming 650091, China
| | - Jing Chai
- Yunnan University / State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Kunming 650091, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Wei Ma
- Yunnan University / State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Kunming 650091, China
| | - Wei Jin
- Yunnan University / State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Kunming 650091, China
| | - Rongyao Duan
- School of Life Science, Yunnan University, Kunming 650091, China
| | - Jing Luo
- Yunnan University / State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Kunming 650091, China
- School of Life Science, Yunnan University, Kunming 650091, China
| | - Robert W. Murphy
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, 100 Queen’s park, Toronto, M5S 2C6, Canada
| | - Heng Xiao
- School of Life Science, Yunnan University, Kunming 650091, China
- * E-mail: (HX); (ZMC)
| | - Ziming Chen
- School of Life Science, Yunnan University, Kunming 650091, China
- * E-mail: (HX); (ZMC)
| |
Collapse
|
22
|
Zhou W, Yu L, Tan B, Liu Y, Zhang L, Hua Y. Phylogenetic relationship of Asian badger Meles leucurus amurensis revealed by complete mitochondrial genome. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 28:403-404. [PMID: 26714063 DOI: 10.3109/19401736.2015.1127365] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Asian badger (Meles leucurus amurensis) is widely distributed throughout the northeast of China, and plays an important role in regulating the prey population stability of forest eco-system as mesopredators. We first determined and annotated the whole mtDNA genome of the Asian badger Meles leucurus amurensis to better understand the evolutionary relationship of this subspecies. The complete mitogenome is 16 497 bp in length, includes 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 control region. We built the phylogenetic tree of Asian badger and other 10 most closely Mustelidae species.
Collapse
Affiliation(s)
- Weiwei Zhou
- a College of Wildlife Resources, Northeast Forestry University , Harbin , P. R. China
| | - Lan Yu
- a College of Wildlife Resources, Northeast Forestry University , Harbin , P. R. China
| | - Buyuan Tan
- a College of Wildlife Resources, Northeast Forestry University , Harbin , P. R. China
| | - Yutang Liu
- a College of Wildlife Resources, Northeast Forestry University , Harbin , P. R. China
| | - Lina Zhang
- a College of Wildlife Resources, Northeast Forestry University , Harbin , P. R. China
| | - Yan Hua
- a College of Wildlife Resources, Northeast Forestry University , Harbin , P. R. China
| |
Collapse
|
23
|
Malyarchuk BA, Derenko MV, Denisova GA. Mitochondrial genome variability in the wolverine (Gulo gulo). RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415090069] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
24
|
Liu G, Yang X, Zhang H, Sun G, Zhao C, Dou H. The complete mitochondrial genome sequence of Mustela eversmannii (Carnivora: Mustelidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3657-8. [PMID: 26367202 DOI: 10.3109/19401736.2015.1079842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, the complete mitochondrial genome of Steppe polecat, Mustela eversmannii, was sequenced for the first time using muscle tissue. The mitochondrial genome is a circular molecule of 16 463 bp in length and overall base composition is A (32.7%), T (27.3%), C (26.1%), and G (13.9%), which indicates a strong A-T bias. A phylogenetic analysis on the basis of 13 protein-coding genes and two rRNA genes of 10 Mustela species' mitochondrial genomes using maximum likelihood (ML) and Bayesian inference (BI) demonstrated that these Mustela species were clustered into two clades and M. eversmannii was close to M. putorius.
Collapse
Affiliation(s)
- Guangshuai Liu
- a College of Wildlife Resources, Northeast Forestry University , Harbin , PR China .,b College of Life Science, Qufu Normal University , Qufu , PR China , and
| | - Xiufeng Yang
- b College of Life Science, Qufu Normal University , Qufu , PR China , and
| | - Honghai Zhang
- b College of Life Science, Qufu Normal University , Qufu , PR China , and
| | - Guolei Sun
- b College of Life Science, Qufu Normal University , Qufu , PR China , and
| | - Chao Zhao
- b College of Life Science, Qufu Normal University , Qufu , PR China , and
| | - Huashan Dou
- c Dailake National Nature Reserve , Hulunbuir , PR China
| |
Collapse
|
25
|
Botero-Castro F, Delsuc F, Douzery EJP. Thrice better than once: quality control guidelines to validate new mitogenomes. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:449-54. [PMID: 24708133 DOI: 10.3109/19401736.2014.900666] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Mitogenomic data are increasingly used in evolutionary biology and ecology, stressing the importance for double checking the authenticity of DNA sequences. For example, Szcześniak et al. (2013) recently published the mitochondrial genome of a bat, the Leschenault's rousette (Rousettus leschenaultii). Here we show using straightforward phylogenetic analyses of available chiropteran sequence data that the taxonomic attribution of the reported mitogenome is erroneous. The purportedly-new complete mitochondrial genome likely belongs to the Egyptian fruit bat (R. aegyptiacus) for which a reference sequence already exists. We propose that future articles reporting complete mitochondrial genome sequences should mandatorily include maximum likelihood trees inferred from (i) the standard barcoding marker for the taxon under focus, which would benefit from the massive data available in public databases, and (ii) the available mitogenomes of closely related species. We also strongly advise these trees be presented as phylograms so that all pertinent phylogenetic information is displayed in the form of a topology and its associated branch lengths. Along with compulsory information on the geographical location and origin of the specimen, these new standards should help avoiding the publication of taxonomically misidentified mitogenomes that might end up as reference sequences in public databases and re-used in subsequent meta-analyses.
Collapse
Affiliation(s)
- Fidel Botero-Castro
- a Université Montpellier 2, CNRS & IRD, Institut des Sciences de l'Evolution (UMR 5554) , Montpellier , France
| | - Frédéric Delsuc
- a Université Montpellier 2, CNRS & IRD, Institut des Sciences de l'Evolution (UMR 5554) , Montpellier , France
| | - Emmanuel J P Douzery
- a Université Montpellier 2, CNRS & IRD, Institut des Sciences de l'Evolution (UMR 5554) , Montpellier , France
| |
Collapse
|
26
|
Malyarchuk BA, Derenko MV, Denisova GA, Litvinov AN. Topological conflicts in phylogenetic analysis of different regions of the sable (Martes zibellina L.) mitochondrial genome. RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415060095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
27
|
High-resolution melting of 12S rRNA and cytochrome b DNA sequences for discrimination of species within distinct European animal families. PLoS One 2014; 9:e115575. [PMID: 25531439 PMCID: PMC4274031 DOI: 10.1371/journal.pone.0115575] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 11/29/2014] [Indexed: 11/19/2022] Open
Abstract
The cheap and easy identification of species is necessary within multiple fields of molecular biology. The use of high-resolution melting (HRM) of DNA provides a fast closed-tube method for analysis of the sequence composition of the mitochondrial genes 12S rRNA and cytochrome b. We investigated the potential use of HRM for species identification within eleven different animal groups commonly found in Europe by animal-group-specific DNA amplification followed by DNA melting. Influence factors as DNA amount, additional single base alterations, and the existence of mixed samples were taken into consideration. Visual inspection combined with mathematical evaluation of the curve shapes did resolve nearly all species within an animal group. The assay can therefore not only be used for identification of animal groups and mixture analysis but also for species identification within the respective groups. The use of a universal 12S rRNA system additionally revealed a possible approach for species discrimination, mostly by exclusion. The use of the HRM assay showed to be a reliable, fast, and cheap method for species discrimination within a broad range of different animal species and can be used in a flexible "modular" manner depending on the question to be solved.
Collapse
|
28
|
Mitochondrial genomes reveal the pattern and timing of marten (Martes), wolverine (Gulo), and fisher (Pekania) diversification. Mol Phylogenet Evol 2014; 80:156-64. [DOI: 10.1016/j.ympev.2014.08.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 07/30/2014] [Accepted: 08/03/2014] [Indexed: 11/18/2022]
|
29
|
Zhao RB, Zhou CY, Lu ZX, Hu P, Liu JQ, Tan WW, Yang TH. The complete mitochondrial genome of black-footed ferret, Mustela nigripes (Mustela, Mustelinae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1595-6. [PMID: 25208186 DOI: 10.3109/19401736.2014.958685] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, the complete mitochondrial genome sequence of black-footed ferret, Mustela nigripes, is determined for the first time. This mitogenome is 16,556 bp in length and contains 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region (D-loop). The overall base composition is A (32.9%), C (26.1%), G (13.8%), and T (27.2%), so the percentage of A and T (60.1%) is higher than that of G and C. Most of the genes are encoded on H-strand, except for the ND6 subunit gene and six tRNA genes. The complete mitochondrial genome sequence reported here would be useful for further phylogenetic analysis and conservation genetic studies in M. nigripes.
Collapse
Affiliation(s)
- Ren-Bin Zhao
- a Department of Hematology , The First People's Hospital of Yunnan Province , Kunming , P.R. China and
| | - Chao-Yang Zhou
- b Department of Hematology , The People's Hospital of Chuxiong Yi Autonomous Prefecture , Chuxiong , P.R. China
| | - Zhi-Xiang Lu
- a Department of Hematology , The First People's Hospital of Yunnan Province , Kunming , P.R. China and
| | - Peng Hu
- a Department of Hematology , The First People's Hospital of Yunnan Province , Kunming , P.R. China and
| | - Jian-Qiong Liu
- a Department of Hematology , The First People's Hospital of Yunnan Province , Kunming , P.R. China and
| | - Wei-Wei Tan
- b Department of Hematology , The People's Hospital of Chuxiong Yi Autonomous Prefecture , Chuxiong , P.R. China
| | - Tong-Hua Yang
- a Department of Hematology , The First People's Hospital of Yunnan Province , Kunming , P.R. China and
| |
Collapse
|
30
|
Malyarchuk B, Derenko M, Denisova G. A mitogenomic phylogeny and genetic history of sable (Martes zibellina). Gene 2014; 550:56-67. [PMID: 25110108 DOI: 10.1016/j.gene.2014.08.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Revised: 07/29/2014] [Accepted: 08/06/2014] [Indexed: 12/21/2022]
Abstract
We assessed phylogeny of sable (Martes zibellina, Linnaeus, 1758) by sequence analysis of nearly complete, new mitochondrial genomes in 36 specimens from different localities in northern Eurasia (Primorye, Khabarovsk and Krasnoyarsk regions, the Kamchatka Peninsula, the Kuril Islands and the Urals). Phylogenetic analysis of mtDNA sequences demonstrates that two clades, A and BC, radiated about 200-300 thousandyears ago (kya) according to results of Bayesian molecular clock and RelTime analyses of different mitogenome alignments (nearly complete mtDNA sequences, protein-coding region, and synonymous sites), while the age estimates of clades A, B and C fall within the Late Pleistocene (~50-140 kya). Bayesian skyline plots (BSPs) of sable population size change based on analysis of nearly complete mtDNAs show an expansion around 40 kya in the warm Karganian time, without a decline of population size around the Last Glacial Maximum (21 kya). The BSPs based on synonymous clock rate indicate that M. zibellina experienced demographic expansions later, approximately 22 kya. The A2a clade that colonized Kamchatka ~23-50 kya (depending on the mutation rate used) survived the last glaciation there as demonstrated by the BSP analysis. In addition, we have found evidence of positive selection acting at ND4 and cytochrome b genes, thereby suggesting adaptive evolution of the A2a clade in Kamchatka.
Collapse
Affiliation(s)
- Boris Malyarchuk
- Institute of Biological Problems of the North, Magadan, 685000 Russia.
| | - Miroslava Derenko
- Institute of Biological Problems of the North, Magadan, 685000 Russia
| | - Galina Denisova
- Institute of Biological Problems of the North, Magadan, 685000 Russia
| |
Collapse
|
31
|
Houssaye A, Tafforeau P, Herrel A. Amniote vertebral microanatomy - what are the major trends? Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12311] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexandra Houssaye
- Steinmann Institut für Geologie; Paläontologie und Mineralogie; Universität Bonn; Nussallee 8 53115 Bonn Germany
- UMR 7179 du CNRS; Département Ecologie et Gestion de la Biodiversité; Muséum National d'Histoire Naturelle; 57 rue Cuvier CP-55 75000 Paris France
| | - Paul Tafforeau
- European Synchrotron Radiation Facility; BP220, 6 rue Jules Horowitz 38043 Grenoble Cedex France
| | - Anthony Herrel
- UMR 7179 du CNRS; Département Ecologie et Gestion de la Biodiversité; Muséum National d'Histoire Naturelle; 57 rue Cuvier CP-55 75000 Paris France
- Evolutionary Morphology of Vertebrates; Ghent University; K.L. Ledeganckstraat 35 B-9000 Ghent Belgium
| |
Collapse
|
32
|
Rose J, Moore A, Russell A, Butcher M. Functional osteology of the forelimb digging apparatus of badgers. J Mammal 2014. [DOI: 10.1644/13-mamm-a-174] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
|
33
|
Scheel DM, Slater GJ, Kolokotronis SO, Potter CW, Rotstein DS, Tsangaras K, Greenwood AD, Helgen KM. Biogeography and taxonomy of extinct and endangered monk seals illuminated by ancient DNA and skull morphology. Zookeys 2014:1-33. [PMID: 24899841 PMCID: PMC4042687 DOI: 10.3897/zookeys.409.6244] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 04/19/2014] [Indexed: 11/12/2022] Open
Abstract
Extinctions and declines of large marine vertebrates have major ecological impacts and are of critical concern in marine environments. The Caribbean monk seal, Monachus tropicalis, last definitively reported in 1952, was one of the few marine mammal species to become extinct in historical times. Despite its importance for understanding the evolutionary biogeography of southern phocids, the relationships of M. tropicalis to the two living species of critically endangered monk seals have not been resolved. In this study we present the first molecular data for M. tropicalis, derived from museum skins. Phylogenetic analysis of cytochrome b sequences indicates that M. tropicalis was more closely related to the Hawaiian rather than the Mediterranean monk seal. Divergence time estimation implicates the formation of the Panamanian Isthmus in the speciation of Caribbean and Hawaiian monk seals. Molecular, morphological and temporal divergence between the Mediterranean and “New World monk seals” (Hawaiian and Caribbean) is profound, equivalent to or greater than between sister genera of phocids. As a result, we classify the Caribbean and Hawaiian monk seals together in a newly erected genus, Neomonachus. The two genera of extant monk seals (Monachus and Neomonachus) represent old evolutionary lineages each represented by a single critically endangered species, both warranting continuing and concerted conservation attention and investment if they are to avoid the fate of their Caribbean relative.
Collapse
Affiliation(s)
- Dirk-Martin Scheel
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Graham J Slater
- Division of Mammals, Smithsonian Institution, National Museum of Natural History, 10th Street and Constitution Ave, NW, Washington, DC 20560-0108, USA ; Department of Paleobiology, Smithsonian Institution, National Museum of Natural History, 10th Street and Constitution Ave, NW, Washington, DC 20560-0108, USA
| | | | - Charles W Potter
- Division of Mammals, Smithsonian Institution, National Museum of Natural History, 10th Street and Constitution Ave, NW, Washington, DC 20560-0108, USA
| | - David S Rotstein
- Marine Mammal Pathology Services, 19117 Bloomfield Road, Olney, MD 20832, USA
| | - Kyriakos Tsangaras
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Alex D Greenwood
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Kristofer M Helgen
- Division of Mammals, Smithsonian Institution, National Museum of Natural History, 10th Street and Constitution Ave, NW, Washington, DC 20560-0108, USA
| |
Collapse
|
34
|
Reproduction and Advances in Reproductive Studies in Carnivores. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 753:205-39. [DOI: 10.1007/978-1-4939-0820-2_10] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
35
|
Ruane S, Bryson RW, Pyron RA, Burbrink FT. Coalescent Species Delimitation in Milksnakes (Genus Lampropeltis) and Impacts on Phylogenetic Comparative Analyses. Syst Biol 2013; 63:231-50. [DOI: 10.1093/sysbio/syt099] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
36
|
Helgen KM, Pinto CM, Kays R, Helgen LE, Tsuchiya MTN, Quinn A, Wilson DE, Maldonado JE. Taxonomic revision of the olingos (Bassaricyon), with description of a new species, the Olinguito. Zookeys 2013; 324:1-83. [PMID: 24003317 PMCID: PMC3760134 DOI: 10.3897/zookeys.324.5827] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Accepted: 08/12/2013] [Indexed: 11/22/2022] Open
Abstract
We present the first comprehensive taxonomic revision and review the biology of the olingos, the endemic Neotropical procyonid genus Bassaricyon, based on most specimens available in museums, and with data derived from anatomy, morphometrics, mitochondrial and nuclear DNA, field observations, and geographic range modeling. Species of Bassaricyon are primarily forest-living, arboreal, nocturnal, frugivorous, and solitary, and have one young at a time. We demonstrate that four olingo species can be recognized, including a Central American species (Bassaricyon gabbii), lowland species with eastern, cis-Andean (Bassaricyon alleni) and western, trans-Andean (Bassaricyon medius) distributions, and a species endemic to cloud forests in the Andes. The oldest evolutionary divergence in the genus is between this last species, endemic to the Andes of Colombia and Ecuador, and all other species, which occur in lower elevation habitats. Surprisingly, this Andean endemic species, which we call the Olinguito, has never been previously described; it represents a new species in the order Carnivora and is the smallest living member of the family Procyonidae. We report on the biology of this new species based on information from museum specimens, niche modeling, and fieldwork in western Ecuador, and describe four Olinguito subspecies based on morphological distinctions across different regions of the Northern Andes.
Collapse
Affiliation(s)
- Kristofer M. Helgen
- Division of Mammals, National Museum of Natural History, NHB 390, MRC 108, Smithsonian Institution, P.O. Box 37012, Washington, DC 20013-7012, USA
| | - C. Miguel Pinto
- Centro de Investigación en Enfermedades Infecciosas, Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Av. 12 de Octubre y Roca, Quito, Ecuador
- Department of Mammalogy, and Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
- The Graduate Center, City University of New York, 365 Fifth Ave., New York, NY, 10016 USA
- Department of Biological Sciences and the Museum, Texas Tech University, Lubbock, Texas 79409-3131, USA
| | - Roland Kays
- North Carolina Museum of Natural Sciences, 11 West Jones Street, Raleigh, NC, 27601, USA
- Fisheries, Wildlife & Conservation Program, North Carolina State University, Raleigh, NC, 27695, USA
- Smithsonian Tropical Research Institute, Balboa Ancón, Republic of Panamá
| | - Lauren E. Helgen
- Division of Mammals, National Museum of Natural History, NHB 390, MRC 108, Smithsonian Institution, P.O. Box 37012, Washington, DC 20013-7012, USA
| | - Mirian T. N. Tsuchiya
- Division of Mammals, National Museum of Natural History, NHB 390, MRC 108, Smithsonian Institution, P.O. Box 37012, Washington, DC 20013-7012, USA
- Department of Environmental Science & Policy, George Mason University, Fairfax, VA, 22030 USA
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC 20008, USA
| | - Aleta Quinn
- Division of Mammals, National Museum of Natural History, NHB 390, MRC 108, Smithsonian Institution, P.O. Box 37012, Washington, DC 20013-7012, USA
- Department of History and Philosophy of Science, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Don E. Wilson
- Division of Mammals, National Museum of Natural History, NHB 390, MRC 108, Smithsonian Institution, P.O. Box 37012, Washington, DC 20013-7012, USA
| | - Jesús E. Maldonado
- Division of Mammals, National Museum of Natural History, NHB 390, MRC 108, Smithsonian Institution, P.O. Box 37012, Washington, DC 20013-7012, USA
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC 20008, USA
| |
Collapse
|
37
|
Next-generation sequencing and phylogenetic signal of complete mitochondrial genomes for resolving the evolutionary history of leaf-nosed bats (Phyllostomidae). Mol Phylogenet Evol 2013; 69:728-39. [PMID: 23850499 DOI: 10.1016/j.ympev.2013.07.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 06/19/2013] [Accepted: 07/03/2013] [Indexed: 12/11/2022]
Abstract
Leaf-nosed bats (Phyllostomidae) are one of the most studied groups within the order Chiroptera mainly because of their outstanding species richness and diversity in morphological and ecological traits. Rapid diversification and multiple homoplasies have made the phylogeny of the family difficult to solve using morphological characters. Molecular data have contributed to shed light on the evolutionary history of phyllostomid bats, yet several relationships remain unresolved at the intra-familial level. Complete mitochondrial genomes have proven useful to deal with this kind of situation in other groups of mammals by providing access to a large number of molecular characters. At present, there are only two mitogenomes available for phyllostomid bats hinting at the need for further exploration of the mitogenomic approach in this group. We used both standard Sanger sequencing of PCR products and next-generation sequencing (NGS) of shotgun genomic DNA to obtain new complete mitochondrial genomes from 10 species of phyllostomid bats, including representatives of major subfamilies, plus one outgroup belonging to the closely-related mormoopids. We then evaluated the contribution of mitogenomics to the resolution of the phylogeny of leaf-nosed bats and compared the results to those based on mitochondrial genes and the RAG2 and VWF nuclear makers. Our results demonstrate the advantages of the Illumina NGS approach to efficiently obtain mitogenomes of phyllostomid bats. The phylogenetic signal provided by entire mitogenomes is highly comparable to the one of a concatenation of individual mitochondrial and nuclear markers, and allows increasing both resolution and statistical support for several clades. This enhanced phylogenetic signal is the result of combining markers with heterogeneous evolutionary rates representing a large number of nucleotide sites. Our results illustrate the potential of the NGS mitogenomic approach for resolving the evolutionary history of phyllostomid bats based on a denser species sampling.
Collapse
|
38
|
Li B, Wu D, Malyarchuk B. Complete mitochondrial genome of European pine marten, Martes martes. ACTA ACUST UNITED AC 2013; 25:372-3. [DOI: 10.3109/19401736.2013.803541] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Bo Li
- Northeast Forestry University, College of Wildlife Resources
No. 26, Hexing Road, Xiangfang District, HarbinChina
- State Forestry Administration Detecting Center of Wildlife
No. 26, Hexing Road, Xiangfang District, HarbinChina
| | - Dan Wu
- Northeast Forestry University, College of Wildlife Resources
No. 26, Hexing Road, Xiangfang District, HarbinChina
| | - Boris Malyarchuk
- Institute of Biological Problems of the North
MagadanRussian Federation
| |
Collapse
|
39
|
Huang J, Yang B, Yan C, Yang C, Tu F, Zhang X, Yue B. Phylogenetic analysis of the Mustela altaica (Carnivora: Mustelidae) based on complete mitochondrial genome. MITOCHONDRIAL DNA 2013; 25:255-6. [PMID: 23795845 DOI: 10.3109/19401736.2013.800491] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The mountain weasel (Mustela altaica) belongs to family Mustelidae, which is the near threatened species in the IUCN Red List. In this study, the complete mitochondrial genome of M. altaica was sequenced and characterized. The genome is 16,521 bases in length (GenBank accession no. KC815122). The nucleotide sequence data of 12 heavy-strand protein-coding genes of M. altaica and other 20 Mustelidae species were used for phylogenetic analyses. Trees constructed by using Bayesian inference, maximum parsimony and maximum likelihood demonstrated that M. altaica was close to Mustela nivalis and they were sister to Mustela putorius and Mustela sibirica.
Collapse
Affiliation(s)
- Jie Huang
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University , Chengdu , P.R. China and
| | | | | | | | | | | | | |
Collapse
|
40
|
Modular real-time PCR screening assay for common European animal families. Int J Legal Med 2013; 128:11-8. [PMID: 23613031 DOI: 10.1007/s00414-013-0857-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 03/27/2013] [Indexed: 10/26/2022]
Abstract
A screening assay based on real-time PCR and melt curve analysis was developed to detect DNA from nine common European animal families/species and human. The assay consists of a 10-cycle universal pre-amplification followed by specific nested PCR and was designed to exploit the different melting temperatures (T m) of family/species-specific 12S ribosomal ribonucleic acid and cytochrome b fragments, which are amplified in duplex reactions. Case-related modular application is possible. Beyond determination of the animal family and discrimination from human DNA, evaluation of the melt curve in some cases additionally allows for species determination (e.g. cat vs. lynx). The method presents a quick, flexible and sample-saving approach to assess non-human DNA at low expenses, and it is especially useful in resolution of DNA mixtures.
Collapse
|
41
|
Quemeneur S, de Buffrénil V, Laurin M. Microanatomy of the amniote femur and inference of lifestyle in limbed vertebrates. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12066] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sonia Quemeneur
- UMR 7207, CNRS/MNHN/UPMC; Département Histoire de la Terre; Muséum National d'Histoire Naturelle; 43 rue Buffon; 75005; Paris; France
| | - Vivian de Buffrénil
- UMR 7207, CNRS/MNHN/UPMC; Département Histoire de la Terre; Muséum National d'Histoire Naturelle; 43 rue Buffon; 75005; Paris; France
| | - Michel Laurin
- UMR 7207, CNRS/MNHN/UPMC; Département Histoire de la Terre; Muséum National d'Histoire Naturelle; 43 rue Buffon; 75005; Paris; France
| |
Collapse
|
42
|
Nagai T, Raichev EG, Tsunoda H, Kaneko Y, Masuda R. Preliminary Study on Microsatellite and Mitochondrial DNA Variation of the Stone MartenMartes foinain Bulgaria. MAMMAL STUDY 2012. [DOI: 10.3106/041.037.0410] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
43
|
Molecular phylogeny of extant equids and effects of ancestral polymorphism in resolving species-level phylogenies. Mol Phylogenet Evol 2012; 65:573-81. [DOI: 10.1016/j.ympev.2012.07.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 05/18/2012] [Accepted: 07/14/2012] [Indexed: 11/19/2022]
|
44
|
Wang XP, Yu L, Roos C, Ting N, Chen CP, Wang J, Zhang YP. Phylogenetic relationships among the colobine monkeys revisited: new insights from analyses of complete mt genomes and 44 nuclear non-coding markers. PLoS One 2012; 7:e36274. [PMID: 22558416 PMCID: PMC3338693 DOI: 10.1371/journal.pone.0036274] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 04/03/2012] [Indexed: 01/05/2023] Open
Abstract
Background Phylogenetic relationships among Asian and African colobine genera have been disputed and are not yet well established. In the present study, we revisit the contentious relationships within the Asian and African Colobinae by analyzing 44 nuclear non-coding genes (>23 kb) and mitochondrial (mt) genome sequences from 14 colobine and 4 non-colobine primates. Principal Findings The combined nuclear gene and the mt genome as well as the combined nuclear and mt gene analyses yielded different phylogenetic relationships among colobine genera with the exception of a monophyletic ‘odd-nosed’ group consisting of Rhinopithecus, Pygathrix and Nasalis, and a monophyletic African group consisting of Colobus and Piliocolobus. The combined nuclear data analyses supported a sister-grouping between Semnopithecus and Trachypithecus, and between Presbytis and the odd-nosed monkey group, as well as a sister-taxon association of Pygathrix and Rhinopithecus within the odd-nosed monkey group. In contrast, mt genome data analyses revealed that Semnopithecus diverged earliest among the Asian colobines and that the odd-nosed monkey group is sister to a Presbytis and Trachypithecus clade, as well as a close association of Pygathrix with Nasalis. The relationships among these genera inferred from the analyses of combined nuclear and mt genes, however, varied with the tree-building methods used. Another remarkable finding of the present study is that all of our analyses rejected the recently proposed African colobine paraphyly and hybridization hypothesis and supported reciprocal monophyly of the African and Asian groups. Significance The phylogenetic utility of large-scale new non-coding genes was assessed using the Colobinae as a model, We found that these markers were useful for distinguishing nodes resulting from rapid radiation episodes such as the Asian colobine radiation. None of these markers here have previously been used for colobine phylogenetic reconstruction, increasing the spectrum of molecular markers available to mammalian systematics.
Collapse
Affiliation(s)
- Xiao Ping Wang
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, Yunnan, China
| | - Li Yu
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, Yunnan, China
- * E-mail: (LY); (YPZ)
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Göttingen, Germany
| | - Nelson Ting
- Department of Anthropology, University of Oregon, Eugene, Oregon, United States of America
| | - Cui Ping Chen
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, Yunnan, China
| | - Jing Wang
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, Yunnan, China
| | - Ya Ping Zhang
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, Yunnan, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- * E-mail: (LY); (YPZ)
| |
Collapse
|
45
|
Han GZ, Worobey M. Endogenous lentiviral elements in the weasel family (Mustelidae). Mol Biol Evol 2012; 29:2905-8. [PMID: 22522310 DOI: 10.1093/molbev/mss126] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Endogenous retroviruses provide molecular fossils for studying the ancient evolutionary history of retroviruses. Here, we report our independent discovery and analysis of endogenous lentiviral insertions (Mustelidae endogenous lentivirus [MELV]) within the genomes of weasel family (Mustelidae). Genome-scale screening identified MELV elements in the domestic ferret (Mustela putorius furo) genome (MELVmpf). MELVmpf exhibits a typical lentiviral genomic organization. Phylogenetic analyses position MELVmpf basal to either primate lentiviruses or feline immunodeficiency virus. Moreover, we verified the presence of MELV insertions in the genomes of several species of the Lutrinae and Mustelinae subfamilies but not the Martinae subfamily, suggesting that the invasion of MELV into the Mustelidae genomes likely took place between 8.8 and 11.8 Ma. The discovery of MELV in weasel genomes extends the host range of lentiviruses to the Caniformia (order Carnivora) and provides important insights into the prehistoric diversity of lentiviruses.
Collapse
Affiliation(s)
- Guan-Zhu Han
- Department of Ecology and Evolutionary Biology, University of Arizona.
| | | |
Collapse
|