1
|
Liu W, Duan Z, Wang D, Zhao W, Liu P. Phylogenetic relationships and genetic differentiation of two Salamandrella species as revealed via COI gene from Northeastern China. PLoS One 2024; 19:e0298221. [PMID: 38354179 PMCID: PMC10866476 DOI: 10.1371/journal.pone.0298221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 01/21/2024] [Indexed: 02/16/2024] Open
Abstract
Due to traditional classification methods' limitations, some cryptic species remain undiscovered. To better explore the existence of the Schrenck salamander (Salamandrella tridactyla, a cryptic species of Siberian salamander S. keyserlingii) in China, we conducted a molecular phylogenetic analysis to confirm the taxonomic relationship among Salamandrella species and investigate genetic variation. We used complete sequences of the mitochondrial COI gene from 65 specimens collected across a wide range in Northeastern China. Thirty-five haplotypes were obtained from six populations. They showed medium-high haplotype diversity (Hd) and low nucleotide polymorphism (π). The phylogenetic tree and haplotype network analysis revealed that populations from Greater Khingan Ridge (Huma: HM) and Lesser Khingan Ridge (Tieli: TL) belong to S. keyserlingii, while populations from Changbai Mountain (Shangzhi-zhuziying: SZ, Shangzhi-cuijia: SC, Hailin: HL, and Baishan: BS) belong to S. tridactyla. This indicates the monophyly of Salamandrella and each of the two species. There was a substantial level of genetic differentiation between different species and within populations of the same species. This differentiation was significantly related to geographical distance. At last, the mismatch distribution and neutrality analyses indicated that the TL populations have undergone expansion of history. The study supplements the distributional range of Schrenck salamander. And it provides a theoretical basis for species conservation of Salamandrella species.
Collapse
Affiliation(s)
- Wanli Liu
- College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang Province, China
| | - Zhuo Duan
- College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang Province, China
| | - Dingcheng Wang
- College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang Province, China
| | - Wenge Zhao
- College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang Province, China
| | - Peng Liu
- College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang Province, China
- Key Laboratory of Biodiversity of Aquatic Organisms, Harbin Normal University, Harbin, Heilongjiang Province, China
| |
Collapse
|
2
|
Talavera A, Palmada-Flores M, Burriel-Carranza B, Valbuena-Ureña E, Mochales-Riaño G, Adams DC, Tejero-Cicuéndez H, Soler-Membrives A, Amat F, Guinart D, Carbonell F, Obon E, Marquès-Bonet T, Carranza S. Genomic insights into the Montseny brook newt ( Calotriton arnoldi), a Critically Endangered glacial relict. iScience 2024; 27:108665. [PMID: 38226169 PMCID: PMC10788218 DOI: 10.1016/j.isci.2023.108665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/09/2023] [Accepted: 12/05/2023] [Indexed: 01/17/2024] Open
Abstract
The Montseny brook newt (Calotriton arnoldi), considered the most endangered amphibian in Europe, is a relict salamandrid species endemic to a small massif located in northeastern Spain. Although conservation efforts should always be guided by genomic studies, those are yet scarce among urodeles, hampered by the extreme sizes of their genomes. Here, we present the third available genome assembly for the order Caudata, and the first genomic study of the species and its sister taxon, the Pyrenean brook newt (Calotriton asper), combining whole-genome and ddRADseq data. Our results reveal significant demographic oscillations which accurately mirrored Europe's climatic history. Although severe bottlenecks have led to depauperate genomic diversity and long runs of homozygosity along a gigantic genome, inbreeding might have been avoided by assortative mating strategies. Other life history traits, however, seem to have been less advantageous, and the lack of land dispersal has driven to exceptional levels of population fragmentation.
Collapse
Affiliation(s)
- Adrián Talavera
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Marc Palmada-Flores
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Bernat Burriel-Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- Museu de Ciències Naturals de Barcelona, Pº Picasso s/n, Parc Ciutadella, 08003 Barcelona, Spain
| | | | | | - Dean C. Adams
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50010, USA
| | - Héctor Tejero-Cicuéndez
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Anna Soler-Membrives
- Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Fèlix Amat
- Àrea d’Herpetologia, BiBIO, Museu de Granollers – Ciències Naturals. Palaudàries 102, Granollers, Barcelona, Spain
| | - Daniel Guinart
- Servei de Gestió de Parcs Naturals, Diputació de Barcelona, Spain
| | - Francesc Carbonell
- Centre de fauna salvatge de Torreferrussa (Forestal Catalana, SA), Santa Perpètua de Mogoda, Spain
| | - Elena Obon
- Centre de fauna salvatge de Torreferrussa (Forestal Catalana, SA), Santa Perpètua de Mogoda, Spain
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| |
Collapse
|
3
|
Fu J, Wen L. Impacts of Quaternary glaciation, geological history and geography on animal species history in continental East Asia: A phylogeographic review. Mol Ecol 2023; 32:4497-4514. [PMID: 37332105 DOI: 10.1111/mec.17053] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/31/2023] [Accepted: 06/07/2023] [Indexed: 06/20/2023]
Abstract
Continental East Asia has a mild Pleistocene climate and a complex recent geological history. Phylogeographic studies of animals over the last 30 years have produced several distinctive patterns. Glaciation refugia are numerous and are not restricted to any particular regions. Most of them are localized and species-specific, although several large refugia, for example the mountains of SW China, are shared by multiple species and have refugia-within-refugia. Furthermore, postglaciation range expansion events vary greatly in time, scale and direction. Large-scale south-to-north post-LGM expansions are few and mostly occurred in the northern regions. Additionally, several unique geographic features, including the three-step terrain of China and the northern arid belt, have significant impacts on many species histories. Overall, the impacts of Pleistocene glaciations, particularly the LGM, on species history vary drastically from nondetectable to significant. The impacts are the least for species from the southwestern region and are most dominant for species from the north. Geological events play a more significant role in shaping species history than Pleistocene climatic changes. Phylogeographic patterns among animals species are highly consistent with those of plants. Future phylogeographic endeavour in East Asia should be hypothesis-driven and seek processes that underlie common patterns. The wide use of genomic data allow accurate estimates of historical population processes and exploration of older history beyond the Pleistocene.
Collapse
Affiliation(s)
- Jinzhong Fu
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Longying Wen
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
- Key Laboratory of Sichuan Institute for Protecting Endangered Birds in the Southwest Mountains, College of Life Sciences, Leshan Normal University, Leshan, China
| |
Collapse
|
4
|
Jeon JY, Jung JH, Suk HY, Lee H, Min MS. The Asian plethodontid salamander preserves historical genetic imprints of recent northern expansion. Sci Rep 2021; 11:9193. [PMID: 33911092 PMCID: PMC8080585 DOI: 10.1038/s41598-021-88238-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 03/30/2021] [Indexed: 02/02/2023] Open
Abstract
The Korean Peninsula, located at the southern tip of Northeast Asia, has never been covered by ice sheets and was a temperate refugium during the Pleistocene. Karsenia koreana, the sole Asian plethodontid salamander species, occurs only on the southern half of the Korean Peninsula and is thought to have found various climatic refugia. Despite its phylogenetic and biogeographic importance, no population-level genetic analysis has been performed on this species. Here we study the population genetic structure of K. koreana using mitochondrial and microsatellite loci to understand the recent historical dispersion process that shaped its current distribution. Overall, the genetic distance between populations correlated well with the spatial distance, and the genetic structure among populations showed signs of a unilateral northward expansion from a southernmost refugium population. Given the distinct genetic structure formed among the populations, the level of historical gene flow among populations appears to have been very low. As the estimated effective population size of K. koreana was also small, these results suggest that the small, restricted populations of K. koreana are extremely vulnerable to environmental changes that may require high levels of genetic diversity to cope with. Thus, special management strategies are needed to preserve these remnant populations.
Collapse
Affiliation(s)
- Jong Yoon Jeon
- grid.31501.360000 0004 0470 5905Research Institute for Veterinary Science and Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine, Seoul National University, Seoul, 08826 South Korea
| | - Ji-hwa Jung
- grid.31501.360000 0004 0470 5905Department of Forest Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826 South Korea
| | - Ho Young Suk
- grid.413028.c0000 0001 0674 4447Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsangbuk-do 38541 South Korea
| | - Hang Lee
- grid.31501.360000 0004 0470 5905Research Institute for Veterinary Science and Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine, Seoul National University, Seoul, 08826 South Korea
| | - Mi-Sook Min
- grid.31501.360000 0004 0470 5905Research Institute for Veterinary Science and Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine, Seoul National University, Seoul, 08826 South Korea
| |
Collapse
|
5
|
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]
|
6
|
Kelava S, Mans BJ, Shao R, Moustafa MAM, Matsuno K, Takano A, Kawabata H, Sato K, Fujita H, Ze C, Plantard O, Hornok S, Gao S, Barker D, Barker SC, Nakao R. Phylogenies from mitochondrial genomes of 120 species of ticks: Insights into the evolution of the families of ticks and of the genus Amblyomma. Ticks Tick Borne Dis 2020; 12:101577. [PMID: 33120251 DOI: 10.1016/j.ttbdis.2020.101577] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 08/19/2020] [Indexed: 11/28/2022]
Abstract
The evolution and phylogenetic relationships of the ticks at both the family and genus levels are contested. The genus Amblyomma and its subgenera are in a state of flux; moreover, the relationships among the three tick families are controversial due to conflicting phylogenetic support for different arrangements of the three families of living ticks. With 18 newly sequenced mitochondrial (mt) genomes of ticks included, we executed the largest mt genome phylogenetic study of ticks so far. Phylogenetic trees were inferred from one sea spider mt genome, one horseshoe crab, five mite mt genomes and 146 tick mt genomes from 120 species: 153 mt genomes in total. Sixteen phylogenetic trees were inferred from 10 datasets using both maximum likelihood and Bayesian inference methods. We describe the first novel mt gene-arrangement for the metastriate Ixodidae in Amblyomma (Africaniella) transversale. Also, three unusual partial 16S rRNA gene inserts were found in the mt genome of Haemaphysalis (Alloceraea) kitaokai: we consider the possible role of past genome translocation events in the formation of these inserts. Our phylogenies revealed evidence that: (i) the genus Amblyomma is polyphyletic with respect to Amblyomma (Africaniella) transversale; (ii) the subgenus Aponomma is apparently embedded in the genus Amblyomma; (iii) Haemaphysalis (Segalia) parva and Haemaphysalis (Alloceraea) kitaokai form a clade to the exclusion of other Haemaphysalis species; and (iv) the phylogenetic position of the family Nuttalliellidae is unstable among phylogenies from different datasets.
Collapse
Affiliation(s)
- Samuel Kelava
- Department of Parasitology, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Ben J Mans
- Epidemiology, Parasites and Vectors, Agricultural Research Council - Onderstepoort Veterinary Research, Onderstepoort, 0110, South Africa; The Department of Veterinary Tropical Diseases, University of Pretoria, Pretoria, 0110, South Africa; The Department of Life and Consumer Sciences, University of South Africa, Florida, 1709, South Africa
| | - Renfu Shao
- School of Science and Engineering, GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, 4558, Australia
| | | | - Keita Matsuno
- Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Hokkaido, 060-0818, Japan
| | - Ai Takano
- Department of Bacteriology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Hiroki Kawabata
- Department of Bacteriology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Kozue Sato
- Department of Bacteriology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Hiromi Fujita
- Mahara Institute of Medical Acarology, 56-3 Aratano, Anan-shi, Tokushima, 779-1510, Japan
| | - Chen Ze
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, China
| | | | - Sandor Hornok
- Department of Parasitology and Zoology, University of Veterinary Medicine, Budapest, 1078, Hungary
| | - Shan Gao
- College of Life Sciences, Nankai University, Tianjin, PR China
| | - Dayana Barker
- School of Veterinary Science, The University of Queensland, Gatton, Queensland 4343, Australia
| | - Stephen C Barker
- Department of Parasitology, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, 4072, Australia.
| | - Ryo Nakao
- Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Hokkaido, 060-0818, Japan
| |
Collapse
|
7
|
Malekoutian M, Sharifi M, Vaissi S. Mitochondrial DNA sequence analysis reveals multiple Pleistocene glacial refugia for the Yellow-spotted mountain newt, Neurergus derjugini (Caudata: Salamandridae) in the mid-Zagros range in Iran and Iraq. Ecol Evol 2020; 10:2661-2676. [PMID: 32537127 PMCID: PMC7285473 DOI: 10.1002/ece3.6098] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 01/20/2020] [Indexed: 01/14/2023] Open
Abstract
Phylogeography is often used to investigate the effects of glacial cycles on current genetic structure of various plant and animal species. This approach can also identify the number and location of glacial refugia as well as the recolonization routes from those refugia to the current locations. To identify the location of glacial refugia of the Yellow‐spotted mountain newt, Neurergus derjugini, we employed phylogeography patterns and genetic variability of this species by analyzing partial ND4 sequences (867 bp) of 67 specimens from 15 sampling localities from the whole species range in Iran and Iraq. Phylogenetic trees concordant with haplotype networks showed a clear genetic structure among populations as three groups corresponding to the populations in the north, center, and south. Evolutionary ages of clades north and south ranging from 0.15 to 0.17 Myr, while the oldest clade is the central clade, corresponding to 0.32 Myr. Bayesian skyline plots of population size change through time show a relatively slight increase until about 25 kyr (around the last glacial maximum) and a decline of population size about 2.5 kyr. The presence of geographically structured clades in north, center, and south sections of the species range signifies the disjunct populations that have emerged in three different refugium. This study illustrates the importance of the effect of previous glacial cycles in shaping the genetic structure of mountain species in the Zagros range. These areas are important in terms of long‐term species persistence and therefore valuable areas for conservation of biodiversity.
Collapse
Affiliation(s)
| | - Mozafar Sharifi
- Department of Biology Baghabrisham Razi University Kermanshah Iran
| | - Somaye Vaissi
- Department of Biology Baghabrisham Razi University Kermanshah Iran
| |
Collapse
|
8
|
Malyarchuk BA, Derenko MV, Litvinov AN. High Level of Interspecific Divergence in the Salamandrella Genus Based on Variability of the RAG2 Gene. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418070098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
9
|
Li HS, Liang XY, Zou SJ, Liu Y, De Clercq P, Ślipiński A, Pang H. Episodic positive selection at mitochondrial genome in an introduced biological control agent. Mitochondrion 2016; 28:67-72. [PMID: 26994640 DOI: 10.1016/j.mito.2016.03.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 03/15/2016] [Accepted: 03/15/2016] [Indexed: 10/22/2022]
Abstract
Artificial introduction in classical biological control provides a unique opportunity to understand mitochondrial evolution driving adaptation to novel environments. We studied mitochondrial genomes of a world-wide introduced agent, Cryptolaemus montrouzieri. We detected positive selection in complex I genes (ND5 and ND4) against a background of widespread negative selection. We further detected significant signals in neutrality tests within 11 populations at ND5 gene, indicating a recent selective sweep/positive selection. Our results imply that these candidate mutations may contribute local adaptation of exotic biological control agents and these provide new insights into the improvement of classical biological control programs.
Collapse
Affiliation(s)
- Hao-Sen Li
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Science, Sun Yat-sen University, Guangzhou 510275, Guangdong, China.
| | - Xin-Yu Liang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Science, Sun Yat-sen University, Guangzhou 510275, Guangdong, China.
| | - Shang-Jun Zou
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Science, Sun Yat-sen University, Guangzhou 510275, Guangdong, China.
| | - Yang Liu
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Science, Sun Yat-sen University, Guangzhou 510275, Guangdong, China.
| | - Patrick De Clercq
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.
| | - Adam Ślipiński
- Australian National Insect Collection, National Research Collections, CSIRO, GPO Box 1700, Canberra ACT 2601, Australia.
| | - Hong Pang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Science, Sun Yat-sen University, Guangzhou 510275, Guangdong, China.
| |
Collapse
|
10
|
Kinoshita G, Sato JJ, Meschersky IG, Pishchulina SL, Simakin LV, Rozhnov VV, Malyarchuk BA, Derenko MV, Denisova GA, Frisman LV, Kryukov AP, Hosoda T, Suzuki H. Colonization history of the sableMartes zibellina(Mammalia, Carnivora) on the marginal peninsula and islands of northeastern Eurasia. J Mammal 2015. [DOI: 10.1093/jmammal/gyu021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
11
|
Guan DL, Xu SQ. The complete mitogenome of the Asiatic Salamander Batrachuperus tibetanus (Amphibia: Caudata: Hynobiidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4052-4053. [DOI: 10.3109/19401736.2014.1003839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- De-Long Guan
- Co-Innovation Center for Qinba Regions’ Sustainable Development, College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, PR China
| | - Sheng-Quan Xu
- Co-Innovation Center for Qinba Regions’ Sustainable Development, College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, PR China
| |
Collapse
|
12
|
Malyarchuk BA, Derenko MV, Denisova GA. Phylogenetic relationships among Asiatic salamanders of the genus Salamandrella based on variability of nuclear genes. RUSS J GENET+ 2015. [DOI: 10.1134/s102279541501007x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
13
|
Dong J, Mao X, Sun H, Irwin DM, Zhang S, Hua P. Introgression of mitochondrial DNA promoted by natural selection in the Japanese pipistrelle bat (Pipistrellus abramus). Genetica 2014; 142:483-94. [DOI: 10.1007/s10709-014-9794-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 09/23/2014] [Indexed: 10/24/2022]
|
14
|
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
|
15
|
Malyarchuk BA, Derenko MV, Denisova GA. Episodes of adaptive evolution of mitochondrial genome in asiatic salamanders (Amphibia, Caudata, Hynobiidae). RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414020070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|