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Eleftherakos K, Polymeni RM, Mikropoulou EV, Vougogiannopoulou K, Georgiadis C, Petrakis EA, Skaltsounis LA, Halabalaki M. A skin secretion metabolome analysis of the Greek Dodecanese Lycian salamanders: Preliminary evidence of dietary alkaloid sequestration in urodeles. PLoS One 2024; 19:e0300278. [PMID: 39208286 PMCID: PMC11361651 DOI: 10.1371/journal.pone.0300278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 02/25/2024] [Indexed: 09/04/2024] Open
Abstract
Lyciasalamandra species, like most amphibians, secrete a wide array of compounds from their granular and mucous skin glands, including the internally synthesized samandarine alkaloids, making their skin a complex organ performing a variety of functions. Lyciasalamandra helverseni and L. luschani basoglui are insular endemics of the Dodecanese islands of SE Greece, bearing distinct isolated populations, with well-documented phylogenetic profiles. Here, we employ a metabolomics approach, utilizing UPLC-ESI-HRMS/MS data of the skin secretions sampled from a number of specimens found in the islands of Karpathos, Kasos and Kastellorizo, in an effort to reveal aspects of their chemistry and diversity across populations. The results indicated statistically significant variation between all taxa examined, based on various secreted compounds. The underlying factors of variation highlighted by the multivariate analysis were differences in samandarine and other alkaloid content as well as in animal size. Metabolite annotation, based on dereplication tools and most importantly HRMS and HRMS/MS spectra, yielded a number of known samandarine alkaloids, reported for the first time in the currently studied Lyciasalamandra species. We also present documentation for novel members of the samandarine alkaloid family, as well as preliminary evidence for a possible dietary alkaloid sequestration. This work can set the basis for further research of this often-neglected endemic species of the Salamandridae, as well as the structural investigation of the samandarine alkaloid group.
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Affiliation(s)
- Karolos Eleftherakos
- Section of Zoology–Marine Biology, Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Roza Maria Polymeni
- Section of Zoology–Marine Biology, Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Eleni V. Mikropoulou
- Division of Pharmacognosy and Natural Products Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Konstantina Vougogiannopoulou
- Division of Pharmacognosy and Natural Products Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Christos Georgiadis
- Section of Zoology–Marine Biology, Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Eleftherios A. Petrakis
- Division of Pharmacognosy and Natural Products Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Leandros A. Skaltsounis
- Division of Pharmacognosy and Natural Products Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Halabalaki
- Division of Pharmacognosy and Natural Products Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
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Cronemberger ÁA, Werneck FP, Ávila-Pires TCS. Phylogeography of a Typical Forest Heliothermic Lizard Reveals the Combined Influence of Rivers and Climate Dynamics on Diversification in Eastern Amazonia. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.777172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The formation of the Amazon drainage basin has been considered an important driver of speciation of several taxa, promoting vicariant events or reinforcement of barriers that restrict gene flow between opposite river margins. Several recent studies reported a set of miscellaneous events involving climatic fluctuations, geomorphological changes, and dispersal mechanisms as propellers of diversification of Amazonian rainforest taxa. Here, we show the results of dated phylogenetic, biogeographic, and populational analyses to investigate which events could better explain the current distribution of a heliothermic, active foraging lizard in the central and eastern portions of the Amazonian rainforest (besides a disjunct distribution in part of the Atlantic Forest). We sampled Kentropyx calcarata from most of its area of occurrence in Amazonia and used mitochondrial and nuclear markers to evaluate if the genetic structure agrees with evolutionary scenarios previously proposed for Amazonia. We performed phylogenetic and populational analyses to better understand the dynamics of this species in the Amazonia rainforest over time. Phylogenetic inference recovered ten K. calcarata structured lineages in eastern Amazonia, some of them limited by the Amazon River and its southern tributaries (Tapajós, Xingu, and Tocantins), although we detected occasional haplotype sharing across some of the river banks. According to molecular dating, K. calcarata diversified since Miocene–Pliocene, and some of the lineages presented signs of demographic expansion during the Pleistocene, supposedly triggered by climatic dynamics. The putative ancestral lineage of K. calcarata was distributed on the Guiana Shield, later spreading south and southeastward by dispersion. Our results indicate that Amazonian rivers acted as barriers to the dispersal of Kentropyx calcarata, but they were not the sole drivers of diversification.
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Niwa K, Tran DV, Nishikawa K. Differentiated historical demography and ecological niche forming present distribution and genetic structure in coexisting two salamanders (Amphibia, Urodela, Hynobiidae) in a small island, Japan. PeerJ 2022; 10:e13202. [PMID: 35505683 PMCID: PMC9057287 DOI: 10.7717/peerj.13202] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 03/09/2022] [Indexed: 01/12/2023] Open
Abstract
Background The climatic oscillations in the Quaternary period considerably shaped the distribution and population genetic structure of organisms. Studies on the historical dynamics of distribution and demography not only reflect the current geographic distribution but also allow us to understand the adaption and genetic differentiation of species. However, the process and factors affecting the present distribution and genetic structure of many taxa are still poorly understood, especially for endemic organisms to small islands. Methods Here, we integrated population genetic and ecological niche modelling approaches to investigate the historical distribution and demographic dynamics of two co-existing salamanders on Tsushima Island, Japan: the true H. tsuensis (Group A), and Hynobius sp. (Group B). We also examined the hypothesis on the equivalency and similarity of niches of these groups by identity and background tests for ecological niche space. Results Our result showed that Group A is considered to have undergone a recent population expansion after the Last Glacial Maximum while it is unlikely to have occurred in Group B. The highest suitability was predicted for Group A in southern Tsushima Island, whereas the northern part of Tsushima Island was the potential distribution of Group B. The results also suggested a restricted range of both salamanders during the Last Interglacial and Last Glacial Maximum, and recent expansion in Mid-Holocene. The genetic landscape-shape interpolation analysis and historical suitable area of ecological niche modelling were consistent, and suggested refugia used during glacial ages in southern part for Group A, and in northern part of Tsushima Island for Group B. Additionally, we found evidence of nonequivalence for the ecological niche of the two groups of the salamanders, although our test could not show either niche divergence or conservatism based on the background tests. The environmental predictors affecting the potential distribution of each group also showed distinctiveness, leading to differences in selecting suitable areas. Finally, the combination of population genetics and ecological modeling has revealed the differential demographic/historical response between coexisting two salamanders on a small island.
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Affiliation(s)
- Keita Niwa
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan,Akita Prefectural Office, Akita, Japan
| | - Dung Van Tran
- Graduate School of Global Environmental Studies, Kyoto University, Kyoto, Japan,Wildlife Department, Faculty of Forest Resources and Environmental Management, Vietnam National University of Forestry, Hanoi, Vietnam
| | - Kanto Nishikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan,Graduate School of Global Environmental Studies, Kyoto University, Kyoto, Japan
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Karyological Diversification in the Genus Lyciasalamandra (Urodela: Salamandridae). Animals (Basel) 2021; 11:ani11061709. [PMID: 34201034 PMCID: PMC8228943 DOI: 10.3390/ani11061709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary The Lycian salamanders of the genus Lyciasalamandra are characterized by a debated taxonomy and phylogenetic relationships. They have been the subject of various molecular and phylogenetic analyses, but their chromosomal diversity is completely unknown. We here present a comparative cytogenetic analysis on five out of the seven described species and seven subspecies of Lyciasalamandra, providing the first karyological assessment on the genus and comparing them to closely related representatives of the genus Salamandra. We analyzed the occurrence and distribution of different conserved (chromosome number and morphology) and highly variable karyological features. We found an impressive diversity in the configuration of nucleolus organizing regions (NORs), which alternatively occur either as heteromorphic or homomorphic loci on distinct regions of different chromosome pairs. We highlight that the observed peculiar taxon-specific pattern of chromosome markers supports the taxonomic validity of the different studied evolutionary lineages and is consistent with a scenario of synchronous evolution in the Lycian salamanders. Abstract We performed the first cytogenetic analysis on five out of the seven species of the genus Lyciasalamandra, including seven subspecies, and representatives of its sister genus Salamandra. All the studied species have a similar karyotype of 2n = 24, mostly composed of biarmed elements. C-bands were observed on all chromosomes, at centromeric, telomeric and interstitial position. We found a peculiar taxon-specific NOR configuration, including either heteromorphic and homomorphic NORs on distinct regions of different chromosomes. Lyciasalamandra a.antalyana and L. helverseni showed two homomorphic NORs (pairs 8 and 2, respectively), while heteromorphic NORs were found in L. billae (pairs 6, 12), L. flavimembris (pairs 2, 12), L. l. luschani (pairs 2, 12), L. l. basoglui (pairs 6, 12), L. l. finikensis (pairs 2, 6) and S. lanzai (pairs 8, 10). Homomorphic NORs with an additional supernumerary site were shown by S. s. salamandra (pairs 2, 8) and S. s. gigliolii (pairs 2, 10). This unexpected highly variable NOR configuration is probably derived from multiple independent NOR translocations and paracentric inversions and correlated to lineage divergence in Lyciasalamandra. These results support the taxonomic validity of the studied taxa and are consistent with a hypothesized scenario of synchronous evolution in the genus.
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Niwa K, Kuro-O M, Nishikawa K. Discovery of Two Lineages of Hynobius tsuensis (Amphibia, Caudata) Endemic to Tsushima Island, Japan. Zoolog Sci 2021; 38:259-266. [PMID: 34057351 DOI: 10.2108/zs200149] [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: 10/12/2020] [Accepted: 12/03/2020] [Indexed: 11/17/2022]
Abstract
The Tsushima salamander, Hynobius tsuensis, is a lotic-breeding species endemic to Tsushima Island, Japan. We investigated genetic variation in this species using samples covering all known localities on the island. Phylogenetic analyses based on mitochondrial cytochrome b gene sequences divided H. tsuensis populations into two genetic groups: true H. tsuensis and an unknown species (Hynobius sp.) showing a closer relationship to Hynobius nebulosus than to H. tsuensis. The genetic distance between the two groups was greater than the genetic distances between different species of Hynobius. Both groups were found to breed in mountain streams, sometimes in the same streams syntopically. Population structure analysis based on several nuclear microsatellite loci strongly indicated reproductive isolation between the two groups in the syntopic localities. This is the first report confirming the syntopic occurrence of two lotic salamanders of Hynobius on a small island. We propose that the lotic breeding habits of the two salamanders were independently acquired.
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Affiliation(s)
- Keita Niwa
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan.,Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-Nihonmatsu-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masaki Kuro-O
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Kanto Nishikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-Nihonmatsu-cho, Sakyo-ku, Kyoto 606-8501, Japan,
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6
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Vaissi S. Historic range dynamics in Kaiser's mountain newt ( Neurergus kaiseri): Insights from phylogeographic analyses and species distribution modeling. Ecol Evol 2021; 11:7622-7633. [PMID: 34188839 PMCID: PMC8216884 DOI: 10.1002/ece3.7595] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/01/2021] [Accepted: 04/06/2021] [Indexed: 11/20/2022] Open
Abstract
Vulnerable Kaiser's mountain newt, Neurergus kaiseri, is endemic to highland streams, springs, and pools of the southwestern Zagros mountain, Iran. The present study aimed to use an integration of phylogeographical and species distribution modeling (SDM) approaches to provide new insights into the evolutionary history of the species throughout Quaternary climate oscillations. The phylogeographical analysis was followed by analyzing two mitochondrial DNA (mt-DNA) markers including 127 control region (D-loop) and 72 NADH dehydrogenase 2 (ND2) sequences from 15 populations in the entire species range that were obtained from GenBank. Potential recent and past distribution (the Last Glacial Maximum, LGM, 21 Kya and the Mid-Holocene, 6 Kya) reconstructed by ensemble SDM using nine algorithms with CCSM4, MIROC-ESM, and MPI-ESM-P models. N. kaiseri displayed two distinct lineages in the northern and southern regions that diverged in the Early-Pleistocene. The demographics analysis showed signs of a slight increase in effective population size for both northern and southern populations in the Mid-Pleistocene. Biogeography analysis showed that both vicariance and dispersal events played an important role in the formation of recent species distribution of N. kaiseri. Based on SDM projection onto paleoclimatic data, N. kaiseri displayed a scenario of past range expansion that followed by postglacial contraction. The models showed that the distribution range of the species may have shifted to a lower altitude during LGM while with amelioration of climatic during Mid-Holocene to recent conditions caused the species to shift to the higher altitude. The findings of the current study support the hypothesis that the Zagros mountains may be acting as climatic refugia and play an important role in the protection of isolated populations during climate oscillations.
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Affiliation(s)
- Somaye Vaissi
- Department of BiologyFaculty of ScienceRazi UniversityKermanshahIran
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7
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Macey JR, Pabinger S, Barbieri CG, Buring ES, Gonzalez VL, Mulcahy DG, DeMeo DP, Urban L, Hime PM, Prost S, Elliott AN, Gemmell NJ. Evidence of two deeply divergent co-existing mitochondrial genomes in the Tuatara reveals an extremely complex genomic organization. Commun Biol 2021; 4:116. [PMID: 33514857 PMCID: PMC7846811 DOI: 10.1038/s42003-020-01639-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 12/21/2020] [Indexed: 01/30/2023] Open
Abstract
Animal mitochondrial genomic polymorphism occurs as low-level mitochondrial heteroplasmy and deeply divergent co-existing molecules. The latter is rare, known only in bivalvian mollusks. Here we show two deeply divergent co-existing mt-genomes in a vertebrate through genomic sequencing of the Tuatara (Sphenodon punctatus), the sole-representative of an ancient reptilian Order. The two molecules, revealed using a combination of short-read and long-read sequencing technologies, differ by 10.4% nucleotide divergence. A single long-read covers an entire mt-molecule for both strands. Phylogenetic analyses suggest a 7-8 million-year divergence between genomes. Contrary to earlier reports, all 37 genes typical of animal mitochondria, with drastic gene rearrangements, are confirmed for both mt-genomes. Also unique to vertebrates, concerted evolution drives three near-identical putative Control Region non-coding blocks. Evidence of positive selection at sites linked to metabolically important transmembrane regions of encoded proteins suggests these two mt-genomes may confer an adaptive advantage for an unusually cold-tolerant reptile.
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Affiliation(s)
- J Robert Macey
- Peralta Genomics Institute, Chancellor's Office, Peralta Community College District, 333 East 8th Street, Oakland, CA, 94606, USA.
| | - Stephan Pabinger
- AIT Austrian Institute of Technology, Center for Health and Bioresources, Molecular Diagnostics, Giefinggasse 4, 1210, Vienna, Austria
| | - Charles G Barbieri
- Peralta Genomics Institute, Chancellor's Office, Peralta Community College District, 333 East 8th Street, Oakland, CA, 94606, USA
| | - Ella S Buring
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, 1000 Constitution Ave., Washington, DC, 20560, USA
| | - Vanessa L Gonzalez
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, 1000 Constitution Ave., Washington, DC, 20560, USA
| | - Daniel G Mulcahy
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, 1000 Constitution Ave., Washington, DC, 20560, USA
| | - Dustin P DeMeo
- Peralta Genomics Institute, Chancellor's Office, Peralta Community College District, 333 East 8th Street, Oakland, CA, 94606, USA
| | - Lara Urban
- Department of Anatomy, University of Otago, PO Box 913, Dunedin, 9054, New Zealand
| | - Paul M Hime
- Biodiversity Institute and Natural History Museum, University of Kansas, 1345 Jayhawk Blvd., Lawrence, KS, 66045, USA
| | - Stefan Prost
- LOEWE-Center for Translational Biodiversity Genomics, Senckenberg Museum, 60325, Frankfurt, Germany
- South African National Biodiversity Institute, National Zoological Garden, Pretoria, 0184, South Africa
| | - Aaron N Elliott
- Peralta Genomics Institute, Chancellor's Office, Peralta Community College District, 333 East 8th Street, Oakland, CA, 94606, USA
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, PO Box 913, Dunedin, 9054, New Zealand
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Stuart BL, Beamer DA, Farrington HL, Beane JC, Chek DL, Pusser LT, Som HE, Stephan DL, Sever DM, Braswell AL. A New Two-Lined Salamander (Eurycea bislineata Complex) from the Sandhills of North Carolina. HERPETOLOGICA 2020. [DOI: 10.1655/0018-0831-76.4.423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Bryan L. Stuart
- North Carolina Museum of Natural Sciences, Section of Research & Collections, 11 West Jones Street, Raleigh, NC 27601, USA
| | - David A. Beamer
- Nash Community College, Department of Natural Sciences, 522 North Old Carriage Road, Rocky Mount, NC 27804, USA
| | - Heather L. Farrington
- North Carolina Museum of Natural Sciences, Section of Research & Collections, 11 West Jones Street, Raleigh, NC 27601, USA
| | - Jeffrey C. Beane
- North Carolina Museum of Natural Sciences, Section of Research & Collections, 11 West Jones Street, Raleigh, NC 27601, USA
| | - Danielle L. Chek
- North Carolina Museum of Natural Sciences, Section of Research & Collections, 11 West Jones Street, Raleigh, NC 27601, USA
| | | | - Hannah E. Som
- North Carolina Museum of Natural Sciences, Section of Research & Collections, 11 West Jones Street, Raleigh, NC 27601, USA
| | - David L. Stephan
- North Carolina State University, Department of Entomology & Plant Pathology, Campus Box 7613, Raleigh, NC 27695, USA
| | - David M. Sever
- Southeastern Louisiana University, Biology Department, 151 Biology Building, Hammond, LA 70402, USA
| | - Alvin L. Braswell
- North Carolina Museum of Natural Sciences, Section of Research & Collections, 11 West Jones Street, Raleigh, NC 27601, USA
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9
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Matsui M, Yoshikawa N, Aoki G, Sasamori K, Matsui M, Tanabe S, Misawa Y, Nishikawa K. Wide Distribution but Low Differentiation: Phylogenetic Relationships and Phylogeography of Hynobius nigrescens (Amphibia: Caudata). Zoolog Sci 2020; 37:529-537. [PMID: 33269868 DOI: 10.2108/zs200099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/02/2020] [Indexed: 11/17/2022]
Abstract
We surveyed the genetic structure of Hynobius nigrescens Stejneger, 1907, a lentic breeding salamander widespread throughout montane and lowland regions of northeastern Japan. We performed a mitochondrial DNA analysis to explore intraspecific genetic variation and infer the evolutionary population history of H. nigrescens. Complete 1141 bp sequences of the mitochondrial cytochrome b gene were studied for 134 adult and larval individuals collected from 62 localities, encompassing the known range of the species. Hynobius nigrescens proved to be monophyletic, including two major clades (Clade II from southwestern Hokuriku and Clade I from all other localities). The latter clade comprises four well-supported and geographically structured subclades, which show genetic distances smaller than those seen in the widely sympatric species Hynobius lichenatus. Results of population statistical analyses indicated that Clade II of the westernmost range of H. nigrescens seems to have maintained a constant population size, while Clade I from most of the northeastern species range shows a tendency of recent population expansion, which is evident in Subclades I-A from the northernmost range and I-B from southern Tohoku to northern Kanto and eastern Chubu. In contrast, Subclades I-C from northeastern Chubu and Sado Is. and I-D from northwestern Chubu to Hokuriku seem to have been relatively stable in population size. Hynobius nigrescens differs greatly from other salamander species from northeastern Japan in its much more recent periods of genetic differentiation and its pattern thereof, and is suggested to be a young faunal element in this region.
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Affiliation(s)
- Masafumi Matsui
- Graduate School of Human and Environmental Studies, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Natsuhiko Yoshikawa
- Department of Biology, Keio University, 4-1-1 Hiyoshi, Kohoku-Ku, Yokohama, Kanagawa 223-8521, Japan,
| | - Gen Aoki
- Hokuetsu High School, 5-12-1 Yoneyama, Chuo-ku, Niigata 950-0916, Japan
| | | | | | - Shingo Tanabe
- Kamikatsura-Higashi-no-Kuchi-cho 6-10, Nishikyo-ku, Kyoto 615-8221, Japan
| | - Yasuchika Misawa
- Civil Engineering and Eco-Technology Consultants, Osaka Branch, Minami-senba 1-15-14, Chuo-ku, Osaka 542-0081, Japan
| | - Kanto Nishikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.,Graduate School of Global Environmental Studies, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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10
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Ceríaco LMP, Bernstein J, Sousa AC, Marques MP, Bauer AM, Norder SJ. The reptiles of Tinhosa Grande islet (Gulf of Guinea): A taxonomic update and the role of Quaternary sea level fluctuations in their diversification. AFR J HERPETOL 2020. [DOI: 10.1080/21564574.2020.1832151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Luis MP Ceríaco
- Museu de História Natural e da Ciência, Universidade do Porto, Porto, Portugal
- Departamento de Zoologia e Antropologia (Museu Bocage), Museu Nacional de História Natural e da Ciência, Universidade de Lisboa, Lisbon, Portugal
| | - Justin Bernstein
- Department of Biological Sciences, Rutgers University-Newark, Newark, USA
| | - Ana C Sousa
- Departamento de Biologia, Universidade de Évora, Évora, Portuga
| | - Mariana P Marques
- Departamento de Zoologia e Antropologia (Museu Bocage), Museu Nacional de História Natural e da Ciência, Universidade de Lisboa, Lisbon, Portugal
- Research Center in Biodiversity and Genetic Resources (CIBIO), InBIO, University of Porto, Porto, Portugal
| | - Aaron M Bauer
- Department of Biology and Center for Biodiversity and Ecosystem Stewardship, Villanova University, Pennsylvania, USA
| | - Sietze J Norder
- Leiden University Centre for Linguistics, Leiden, The Netherlands
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11
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Bláha M, Patoka J, Japoshvili B, Let M, Buřič M, Kouba A, Mumladze L. Genetic diversity, phylogenetic position and morphometric analysis of Astacus colchicus (Decapoda, Astacidae): a new insight into Eastern European crayfish fauna. Integr Zool 2020; 16:368-378. [PMID: 32978865 DOI: 10.1111/1749-4877.12493] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The phylogeny of European crayfish fauna, especially with respect to Eastern European species, is still far from being completely resolved. To fill this gap, we analyzed most of the European crayfish species focusing on the phylogenetic position of the endemic crayfish Astacus colchicus, inhabiting Georgia. Three mitochondrial and one nuclear marker were used to study evolutionary relationships among European crayfish species, resulting in the unique phylogenetic position of A. colchicus indicating independent species status to A. astacus. Phylogenetic analyses revealed a deep molecular divergence of A. colchicus in comparison to A. astacus (6.5-10.9% in mtDNA and 1.1% in nDNA) as well as to Pontastacus leptodactylus and P. pachypus (5.5-10.0% in mtDNA and 1.4-2.4% in nDNA). Absent ventral process on second male pleopod and abdominal somites II and III with pleura rounded lacking prominent spines clearly indicate taxonomic assignment to the genus Astacus; however, the species is distributed almost in the middle of Ponto-Caspian area typical by occurrence of the genus Pontastacus. Several morphological indices linked to head length, carapace, and total body length and width were found to demonstrate apparent differences between A. colchicus and A. astacus. Although this study provides a novel insight into European crayfish phylogeography, we also point out the gaps in comprehensive study of the P. leptodactylus species complex, which could reveal details about the potential species status of particular species and subspecies within this genus.
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Affiliation(s)
- Martin Bláha
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Vodňany, Czech Republic
| | - Jiří Patoka
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Praha, Czech Republic
| | | | - Marek Let
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Vodňany, Czech Republic
| | - Miloš Buřič
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Vodňany, Czech Republic
| | - Antonín Kouba
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Vodňany, Czech Republic
| | - Levan Mumladze
- Institute of Zoology of Ilia State University, Tbilisi, Georgia
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12
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Trichas A, Smirli M, Papadopoulou A, Anastasiou I, Keskin B, Poulakakis N. Dispersal versus vicariance in the Aegean: combining molecular and morphological phylogenies of eastern Mediterranean Dendarus (Coleoptera: Tenebrionidae) sheds new light on the phylogeography of the Aegean area. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Abstract
The Aegean archipelago, as an ‘evolutionary laboratory of nature’, is an ideal model for research in phylogeography. In this area, the darkling beetles of the genus Dendarus (distributed from Morocco to the Caucasus) exhibit a high level of diversity with 36 species, 27 of which are island endemics. However, their taxonomy is complex and unstable, having undergone continuous revision to address extensive morphological and ecological plasticity. Here, we examine the phylogenetic relationships of 23 species from Greece and Turkey, using mitochondrial and nuclear DNA sequences and 61 morphological characters, to unveil their phylogeny in the Aegean. This helps to clarify phylogeographic scenarios and historical processes that shaped the observed patterns. The analyses reveal 13 distinct lineages with several para- and polyphyletic cases that correspond to three major phylogroups [south/south-east Aegean (D. foraminosus complex, D. rhodius, D. sporadicus, D. wettsteini); central to north Aegean, Turkey and mainland Greece (D. crenulatus, D. moesiacus group, D. sinuatus complex, D. stygius) and mainland Greece (D. messenius, D. paganettii)], indicating the need for further taxonomic re-evaluation. Lineage topology and phylogeography suggest a spatial and temporal sequence of geographic isolation, following either a vicariant or a dispersal model coincident with major palaeogeographic separations in the Aegean.
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Affiliation(s)
- Apostolos Trichas
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, Irakleio, Greece
| | - Maria Smirli
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, Irakleio, Greece
- Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Irakleio, Greece
| | - Anna Papadopoulou
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Ioannis Anastasiou
- Section of Zoology – Marine Biology, Department of Biology, University of Athens, Panepistimioupoli, GR-157 84 Athens, Greece
| | - Bekir Keskin
- Zoology Department, Section of Biology, Faculty of Science, Ege University, Bornova-Izmir, Turkey
| | - Nikos Poulakakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, Irakleio, Greece
- Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Irakleio, Greece
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Chen Z, Li H, Zhai X, Zhu Y, He Y, Wang Q, Li Z, Jiang J, Xiong R, Chen X. Phylogeography, speciation and demographic history: Contrasting evidence from mitochondrial and nuclear markers of the Odorrana graminea sensu lato (Anura, Ranidae) in China. Mol Phylogenet Evol 2020; 144:106701. [DOI: 10.1016/j.ympev.2019.106701] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 11/21/2019] [Accepted: 12/03/2019] [Indexed: 10/25/2022]
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14
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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: 16] [Impact Index Per Article: 4.0] [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.
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Affiliation(s)
| | - Mozafar Sharifi
- Department of Biology Baghabrisham Razi University Kermanshah Iran
| | - Somaye Vaissi
- Department of Biology Baghabrisham Razi University Kermanshah Iran
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15
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Veith M, Göçmen B, Sotiropoulos K, Eleftherakos K, Lötters S, Godmann O, Karış M, Oğuz A, Ehl S. Phylogeographic analyses point to long-term survival on the spot in micro-endemic Lycian salamanders. PLoS One 2020; 15:e0226326. [PMID: 31929551 PMCID: PMC6957296 DOI: 10.1371/journal.pone.0226326] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 11/25/2019] [Indexed: 11/18/2022] Open
Abstract
Lycian salamanders (genus Lyciasalamandra) constitute an exceptional case of micro-endemism of an amphibian species on the Asian Minor mainland. These viviparous salamanders are confined to karstic limestone formations along the southern Anatolian coast and some islands. We here study the genetic differentiation within and among 118 populations of all seven Lyciasalamandra species across the entire genus’ distribution. Based on circa 900 base pairs of fragments of the mitochondrial 16SrDNA and ATPase genes, we analysed the spatial haplotype distribution as well as the genetic structure and demographic history of populations. We used 253 geo-referenced populations and CHELSA climate data to infer species distribution models which we projected on climatic conditions of the Last Glacial Maximum (LGM). Within all but one species, distinct phyloclades were identified, which only in parts matched current taxonomy. Most haplotypes (78%) were private to single populations. Sometimes population genetic parameters showed contradicting results, although in several cases they indicated recent population expansion of phyloclades. Climatic suitability of localities currently inhabited by salamanders was significantly lower during the LGM compared to recent climate. All data indicated a strong degree of isolation among Lyciasalamandra populations, even within phyloclades. Given the sometimes high degree of haplotype differentiation between adjacent populations, they must have survived periods of deteriorated climates during the Quaternary on the spot. However, the alternative explanation of male biased dispersal combined with a pronounced female philopatry can only be excluded if independent nuclear data confirm this result.
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Affiliation(s)
- Michael Veith
- Department of Biogeography, Trier University, Universitätsring, Trier, Germany
- * E-mail:
| | - Bayram Göçmen
- Ege University, Faculty of Science, Department of Biology, Zoology Section, Bornova, İzmir, Turkey
| | | | - Karolos Eleftherakos
- Section of Zoology-Marine Biology, Department of Biology, University of Athens, Athens, Greece
| | - Stefan Lötters
- Department of Biogeography, Trier University, Universitätsring, Trier, Germany
| | | | - Mert Karış
- Ege University, Faculty of Science, Department of Biology, Zoology Section, Bornova, İzmir, Turkey
| | - Anil Oğuz
- Ege University, Faculty of Science, Department of Biology, Zoology Section, Bornova, İzmir, Turkey
| | - Sarah Ehl
- Department of Biogeography, Trier University, Universitätsring, Trier, Germany
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16
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Matsui M, Yoshikawa N, Tanaka-Ueno T, Sato T, Takenaka S, Terui S, Oppata Y, Tominaga A. A Genetic Study of a Newly Found Population of Siberian Salamander, Salamandrella keyserlingii (Amphibia, Caudata). CURRENT HERPETOLOGY 2019. [DOI: 10.5358/hsj.38.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Masafumi Matsui
- 1Graduate School of Human and Environmental Studies, Kyoto University, Sakyo-ku, Kyoto 606-8501, JAP
| | - Natsuhiko Yoshikawa
- 2Department of Biology, Faculty of Law, Keio University, 4-1-1 Hiyoshi, Kohoku-Ku, Yokohama 223-8521
| | - Tomoko Tanaka-Ueno
- 3Laboratory of Biology, Meiji Gakuin University, Kamikurata-cho 1518, Totsuka-ku, Yokohama 244-8539,
| | - Takanori Sato
- 4Oyasato Institute for the Study of Religion, Tenri University, Somanouchi 1050, Tenri, Nara 632-851
| | - Sen Takenaka
- 5Department of Biology, School of Biological Sciences, Tokai University, 1-1-1 Minamisawa 5, Minami-
| | | | - Yasuyuki Oppata
- 7Higashi Taisetsu Museum of Natural History, Kamishihoro-cho, Hokkaido 080-1403, JAPAN
| | - Atsushi Tominaga
- 8Faculty of Education, University of the Ryukyus, Senbaru 1, Nishihara, Okinawa 903-0213, JAPAN
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Reconstructing evolution at the community level: A case study on Mediterranean amphibians. Mol Phylogenet Evol 2019; 134:211-225. [PMID: 30797941 DOI: 10.1016/j.ympev.2019.02.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 02/14/2019] [Accepted: 02/16/2019] [Indexed: 11/22/2022]
Abstract
Reconstructing reliable timescales for species evolution is an important and indispensable goal of modern biogeography. However, many factors influence the estimation of divergence times, and uncertainty in the inferred time trees remains a major issue that is often insufficiently acknowledged. We here focus on a fundamental problem of time tree analysis: the combination of slow-evolving (nuclear DNA) and fast-evolving (mitochondrial DNA) markers in a single time tree. Both markers differ in their suitability to infer divergences at different time scales (the 'genome-timescale-dilemma'). However, strategies to infer shallow and deep divergences in a single time tree have rarely been compared empirically. Using Mediterranean amphibians as model system that is exceptional in its geographic and taxonomic completeness of available genetic information, we analyze 202 lineages of western Palearctic amphibians across the entire Mediterranean region. We compiled data of four nuclear and five mitochondrial genes and used twelve fossil calibration points widely acknowledged for amphibian evolution. We reconstruct time trees for an extensive lineage-level data set and compare the performances of the different trees: the first tree is based on primary fossil calibration and mitochondrial DNA, while the second tree is based on a combination of primary fossil and on secondary calibrations taken from a nuclear tree using mitochondrial DNA (two-step protocol). Focusing on a set of nodes that are most likely explained by vicariance, we statistically compare the reconstructed alternative time trees by applying a biogeographical plausibility test. Our two-step protocol outperformed the alternative approach in terms of spatial and temporal plausibility. It allows us to infer scenarios for Mediterranean amphibian evolution in eight geographic provinces. We identified several tectonic and climatic events explaining the majority of Mediterranean amphibian divergences, with Plio-Pleistocene climatic fluctuations being the dominant driver for intrageneric evolution. However, often more than one event could be invoked for a specific split. We give recommendations for the use of secondary calibrations in future molecular clock analyses at the community level.
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18
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Göçmen B, Ehl S, Karış M, Thiesmeier B, Kordges T. Molecular and morphological evidence for a new subspecies of Fazila’s Lycian Salamander Lyciasalamandra fazilae in South-west Anatolia. ZOOLOGY IN THE MIDDLE EAST 2018. [DOI: 10.1080/09397140.2018.1511291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Bayram Göçmen
- Zoology Section, Department of Biology, Faculty of Science, Ege University, Bornova, Izmir, Turkey
| | - Sarah Ehl
- Department of Biogeography, Trier University, Trier, Germany
| | - Mert Karış
- Zoology Section, Department of Biology, Faculty of Science, Ege University, Bornova, Izmir, Turkey
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Salvi D, Mendes J, Carranza S, Harris DJ. Evolution, biogeography and systematics of the western Palaearctic Zamenis
ratsnakes. ZOOL SCR 2018. [DOI: 10.1111/zsc.12295] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniele Salvi
- Department of Health, Life and Environmental Sciences; University of L'Aquila; L'Aquila Italy
- CIBIO Research Centre in Biodiversity and Genetic Resources; InBIO; Universidade do Porto; Vairão Vila do Conde Portugal
| | - Joana Mendes
- CIBIO Research Centre in Biodiversity and Genetic Resources; InBIO; Universidade do Porto; Vairão Vila do Conde Portugal
- Institute of Evolutionay Biology (CSIC-Universitat Pompeu Fabra); Barcelona Spain
| | - Salvador Carranza
- Institute of Evolutionay Biology (CSIC-Universitat Pompeu Fabra); Barcelona Spain
| | - David James Harris
- CIBIO Research Centre in Biodiversity and Genetic Resources; InBIO; Universidade do Porto; Vairão Vila do Conde Portugal
- Departamento de Biologia; Faculdade de Ciências; Universidade do Porto; Porto Portugal
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20
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Potential distribution under different climatic scenarios of climate change of the vulnerable Caucasian salamander (Mertensiella caucasica): A case study of the Caucasus Hotspot. Biologia (Bratisl) 2018. [DOI: 10.2478/s11756-018-0020-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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21
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Wray KP, Means DB, Steppan SJ. Revision of the Eurycea quadridigitata (Holbrook 1842) Complex of Dwarf Salamanders (Caudata: Plethodontidae: Hemidactyliinae) with a Description of Two New Species. HERPETOLOGICAL MONOGRAPHS 2017. [DOI: 10.1655/herpmonographs-d-16-00011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Kenneth P. Wray
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA
| | - D. Bruce Means
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA
| | - Scott J. Steppan
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA
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Radenković S, Šašić Zorić L, Djan M, Obreht Vidaković D, Ačanski J, Ståhls G, Veličković N, Markov Z, Petanidou T, Kočiš Tubić N, Vujić A. Cryptic speciation in theMerodon luteomaculatuscomplex (Diptera: Syrphidae) from the eastern Mediterranean. J ZOOL SYST EVOL RES 2017. [DOI: 10.1111/jzs.12193] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Snežana Radenković
- Department of Biology and Ecology; Faculty of Sciences; University of Novi Sad; Novi Sad Serbia
| | - Ljiljana Šašić Zorić
- BioSense Institute - Research Institute for Information Technologies in Biosystems; University of Novi Sad; Novi Sad Serbia
| | - Mihajla Djan
- Department of Biology and Ecology; Faculty of Sciences; University of Novi Sad; Novi Sad Serbia
| | - Dragana Obreht Vidaković
- Department of Forest and Conservation Sciences; University of British Columbia; Vancouver BC Canada
| | - Jelena Ačanski
- BioSense Institute - Research Institute for Information Technologies in Biosystems; University of Novi Sad; Novi Sad Serbia
| | - Gunilla Ståhls
- Zoology Unit; Finnish Museum of Natural History; University of Helsinki; Helsinki Finland
| | - Nevena Veličković
- Department of Biology and Ecology; Faculty of Sciences; University of Novi Sad; Novi Sad Serbia
| | - Zlata Markov
- Department of Biology and Ecology; Faculty of Sciences; University of Novi Sad; Novi Sad Serbia
| | - Theodora Petanidou
- Laboratory of Biogeography and Ecology; Department of Geography; University of the Aegean; Mytilene Greece
| | - Nataša Kočiš Tubić
- Department of Biology and Ecology; Faculty of Sciences; University of Novi Sad; Novi Sad Serbia
| | - Ante Vujić
- Department of Biology and Ecology; Faculty of Sciences; University of Novi Sad; Novi Sad Serbia
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23
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Inferring the shallow phylogeny of true salamanders (Salamandra) by multiple phylogenomic approaches. Mol Phylogenet Evol 2017; 115:16-26. [DOI: 10.1016/j.ympev.2017.07.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 05/31/2017] [Accepted: 07/13/2017] [Indexed: 01/31/2023]
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Wang B, Xie F, Li J, Wang G, Li C, Jiang J. Phylogeographic investigation and ecological niche modelling of the endemic frog species Nanorana pleskei revealed multiple refugia in the eastern Tibetan Plateau. PeerJ 2017; 5:e3770. [PMID: 28924497 PMCID: PMC5598431 DOI: 10.7717/peerj.3770] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 08/16/2017] [Indexed: 11/22/2022] Open
Abstract
The largest plateau Tibetan Plateau supplied an excellent opportunity to investigate the influence of the Pleistocene events on the high-elevation species. To test for the alternative hypotheses of Pleistocene glacial refugia, we used partial sequences of two mitochondrial genes and one nuclear gene to examine the phylogeographic patterns of the endemic frog species Nanorana pleskei across its known range in the eastern Tibetan Plateau, and conducted species distribution modelling (SDM) to explore changes of its distribution range through current and paleo periods. In all data sets, the species was divided into lineage north occupying open plateau platform and lineage south colonizing the mountainous plateau. The divergence of two major clades was estimated at the early Pleistocene. In mtDNA, lineage north contained northeastern and northwestern sublineages, and lineage south had two overlapping-distributed sublineages. Different lineages possessed distinct demographic characteristics, i.e., subdivision in the northeastern sublineage, historical bottleneck effects and recent expansions in the northwestern sublineage and the southeastern sublineage. SDMs depicted that stable suitable habitats had existed in the upper-middle streams of the Yellow River, Dadu River, Jinsha River and Yalong River. These regions were also recognized as the ancestral areas of different lineages. In conclusion, Nanorana pleskei lineages have probably experienced long-term separations. Stable suitable habitats existing in upper-middle streams of major rivers on the eastern Tibetan Plateau and distinct demographic dynamics of different lineages indicated that the lineages possessed independent evolutionary processes in multiple glacial refugia. The findings verified the profound effects of Pleistocene climatic fluctuations on the plateau endemic species.
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Affiliation(s)
- Bin Wang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Feng Xie
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Jiannan Li
- Nanjing Institute of Environmental Sciences Under Ministry of Environmental Protection, Nanjing, Jiangsu, China
| | - Gang Wang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Cheng Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Jianping Jiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
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25
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Sinsch U, Böcking H, Leskovar C, Öz M, Veith M. Demography and lifetime growth patterns in viviparous salamanders (genus Lyciasalamandra): Living underground attenuates interspecific variation. ZOOL ANZ 2017. [DOI: 10.1016/j.jcz.2017.07.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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26
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Allegrucci G, Ketmaier V, Di Russo C, Rampini M, Sbordoni V, Cobolli M. Molecular phylogeography ofTroglophiluscave crickets (Orthoptera, Rhaphidophoridae): A combination of vicariance and dispersal drove diversification in the East Mediterranean region. J ZOOL SYST EVOL RES 2017. [DOI: 10.1111/jzs.12172] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
| | - Valerio Ketmaier
- Department of Biology and Biotechnology “Charles Darwin”; University of Rome Sapienza; Roma Italy
| | - Claudio Di Russo
- Department of Biology and Biotechnology “Charles Darwin”; University of Rome Sapienza; Roma Italy
| | - Mauro Rampini
- Department of Biology and Biotechnology “Charles Darwin”; University of Rome Sapienza; Roma Italy
| | - Valerio Sbordoni
- Department of Biology; University of Rome Tor Vergata; Roma Italy
| | - Marina Cobolli
- Department of Biology and Biotechnology “Charles Darwin”; University of Rome Sapienza; Roma Italy
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The geography and timing of genetic divergence in the lizard Phrynocephalus theobaldi on the Qinghai-Tibetan plateau. Sci Rep 2017; 7:2281. [PMID: 28536444 PMCID: PMC5442162 DOI: 10.1038/s41598-017-02674-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 04/18/2017] [Indexed: 11/27/2022] Open
Abstract
The Qinghai-Tibetan Plateau (QTP) represents one of the earth’s most significant physical features and there is increasing interest in the historical generation of biodiversity within this region. We hypothesized that there should be clear geographically coherent genetic structuring within one of the world’s highest altitude lizards, Phrynocephalus theobaldi, due to considerable historical population fragmentation in this environment. This was tested using a major mitochondrial DNA (mtDNA) survey and sequencing of two nuclear markers (AME and RAG-1) from P. theobaldi, from across the southern QTP. A Bayesian method (BPEC) was used to detect four geographically structured mtDNA clusters. A Bayesian phylogenetic tree, together with associated dating analyses, supported four corresponding evolutionary lineages with a timing of 3.74–7.03 Ma for the most basal P. theobaldi split and Pliocene splits of 2.97–5.79 Ma and 2.40–5.39 Ma in the two daughter lineages. Himalayan uplift and changes in the Jilong basin may have contributed to these divergences, but uplift of the Gangdese mountains is rejected due to its timing. The nuclear markers appeared to be sorted between the four mtDNA groups, and species delimitation analyses supported the four phylogeographical groups as candidate species. The study contributes to our understanding of biodiversity on the QTP.
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28
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Nishikawa K, Dujsebayeva T, Matsui M, Yoshikawa N, Tominaga A. Historical Demography of an Endangered Salamander, Ranodon sibiricus (Amphibia, Urodela, Hynobiidae): A Reassessment. Zoolog Sci 2017; 34:18-25. [PMID: 28148215 DOI: 10.2108/zs160099] [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: 11/17/2022]
Abstract
Chinese populations of the endangered Siberian salamander Ranodon sibiricus are reported to have diverged only about 120 years ago, and to have the lowest genetic diversity of any amphibian. However, these conclusions require verification, as the main range of the species is in Kazakhstan. Moreover, the generation time used for estimating divergence time has a weak ground. In order to clarify these problems, we investigated the molecular phylogenetic relationship and historical demography of the species covering its whole distribution range using the mitochondrial DNA region reported for Chinese population (1072 bp sequences of the control region), while conducting skeletochronological analysis to estimate accurate generation time. As a result, the range expansion was estimated at 88,000-50,000 YA, based on the generation time of 6-10 years. Degree of intraspecific genetic differentiation is actually very small, but, as a single species, is not so small as had been reported for Chinese population alone.
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Affiliation(s)
- Kanto Nishikawa
- 1 Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu-cho Sakyo-ku, Kyoto 606-8501, Japan
| | - Tatjana Dujsebayeva
- 2 Institute of Zoology MES RK, Akademgorodok, al-Farabi Av., 93, Almaty 050060, Republic of Kazakhstan.,3 Association for the Conservation of Biodiversity of Kazakhstan, Beibitshilik Street, 18, Office 406, Astana 010000, Republic of Kazakhstan
| | - Masafumi Matsui
- 1 Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu-cho Sakyo-ku, Kyoto 606-8501, Japan
| | - Natsuhiko Yoshikawa
- 4 Center for Molecular Biodiversity Research, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki 305-0005, Japan
| | - Atsushi Tominaga
- 5 Department of Natural Sciences, Faculty of Education, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan
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29
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Zieliński P, Nadachowska-Brzyska K, Dudek K, Babik W. Divergence history of the Carpathian and smooth newts modelled in space and time. Mol Ecol 2016; 25:3912-28. [PMID: 27288862 DOI: 10.1111/mec.13724] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 06/01/2016] [Accepted: 06/01/2016] [Indexed: 12/24/2022]
Abstract
Information about demographic history is essential for the understanding of the processes of divergence and speciation. Patterns of genetic variation within and between closely related species provide insights into the history of their interactions. Here, we investigated historical demography and genetic exchange between the Carpathian (Lissotriton montandoni, Lm) and smooth (L. vulgaris, Lv) newts. We combine an extensive geographical sampling and multilocus nuclear sequence data with the approximate Bayesian computation framework to test alternative scenarios of divergence and reconstruct the temporal and spatial pattern of gene flow between species. A model of recent (last glacial period) interspecific gene flow was favoured over alternative models. Thus, despite the relatively old divergence (4-6 mya) and presumably long periods of isolation, the species have retained the ability to exchange genes. Nevertheless, the low migration rates (ca. 10(-6) per gene copy per generation) are consistent with strong reproductive isolation between the species. Models allowing demographic changes were favoured, suggesting that the effective population sizes of both species at least doubled as divergence reaching the current ca. 0.2 million in Lm and 1 million in Lv. We found asymmetry in rates of interspecific gene flow between Lm and one evolutionary lineage of Lv. We suggest that intraspecific polymorphism for hybrid incompatibilities segregating within Lv could explain this pattern and propose further tests to distinguish between alternative explanations. Our study highlights the importance of incorporating intraspecific genetic structure into the models investigating the history of divergence.
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Affiliation(s)
- P Zieliński
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - K Nadachowska-Brzyska
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - K Dudek
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - W Babik
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
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Identification of a Rare Gecko from North Island New Zealand, and Genetic Assessment of Its Probable Origin: A Novel Mainland Conservation Priority? J HERPETOL 2016. [DOI: 10.1670/13-128] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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31
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Veith M, Göçmen B, Sotiropoulos K, Kieren S, Godmann O, Steinfartz S. Seven at one blow: the origin of major lineages of the viviparous Lycian salamanders (Lyciasalamandra Veith and Steinfartz, 2004) was triggered by a single paleo-historic event. AMPHIBIA-REPTILIA 2016. [DOI: 10.1163/15685381-00003067] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The number of tectonic and climatic events that are used to explain speciation processes in the eastern Mediterranean region is low compared to the western Mediterranean. Among them, the emergence of the mid-Aegean trench and the Messinian Salinity Crisis (MSC) often concurred with speciation time estimates that were inferred from molecular data. We here present a dated molecular phylogeny of Lyciasalamandra from Turkey and Greece based on ca. 4500 bp of the mitochondrial genome (3000 bp of three nuclear genes appeared to be completely inconclusive due to their extremely low degree of variation among taxa). Seven major lineages emerged simultaneously from a basal hard polytomy. A scenario that dates this polytomy to 12.3 and 10.2 million years ago, around the final emergence of the mid-Aegean trench, appears to be most plausible. The MSC can be made responsible for first intraspecific divergence events within L. luschani, L. fazilae and L. flavimembris. Further diversification can be explained by Pliocene and Pleistocene glaciations. Based on levels of molecular differentiation we suggest the recently described species L. arikani, L. irfani and L. yehudahi to be treated as subspecies of L. billae.
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Affiliation(s)
- Michael Veith
- Department of Biogeography, Trier University, Universitätsring 15, 54296 Trier, Germany
| | - Bayram Göçmen
- Zoology Section, Department of Biology, Faculty of Science, Ege University, 35100 Bornova, İzmir, Turkey
| | - Konstantinos Sotiropoulos
- Department of Biological Applications & Technologies, University of Ioannina, 45110 Ioannina, Greece
| | - Sarah Kieren
- Department of Biogeography, Trier University, Universitätsring 15, 54296 Trier, Germany
| | | | - Sebastian Steinfartz
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstraße 4, 38106 Braunschweig, Germany
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Phillips JG, Deitloff J, Guyer C, Huetteman S, Nicholson KE. Biogeography and evolution of a widespread Central American lizard species complex: Norops humilis, (Squamata: Dactyloidae). BMC Evol Biol 2015; 15:143. [PMID: 26187158 PMCID: PMC4506609 DOI: 10.1186/s12862-015-0391-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 05/26/2015] [Indexed: 11/15/2022] Open
Abstract
Background Caribbean anole lizards (Dactyloidae) have frequently been used as models to study questions regarding biogeography and adaptive radiations, but the evolutionary history of Central American anoles (particularly those of the genus Norops) has not been well studied. Previous work has hypothesized a north-to-south dispersal pattern of Central American Norops, but no studies have examined dispersal within any Norops lineages. Here we test two major hypotheses for the dispersal of the N. humilis/quaggulus complex (defined herein, forming a subset within Savage and Guyer’s N. humilis group). Results Specimens of the N. humilis group were collected in Central America, from eastern Mexico to the Canal Zone of Panama. Major nodes were dated for comparison to the geologic history of Central America, and ancestral ranges were estimated for the N. humilis/quaggulus complex to test hypothesized dispersal patterns. These lineages displayed a northward dispersal pattern. We also demonstrate that the N. humilis/quaggulus complex consists of a series of highly differentiated mitochondrial lineages, with more conserved nuclear evolution. The paraphyly of the N. humilis species group is confirmed. A spatial analysis of molecular variance suggests that current populations are genetically distinct from one another, with limited mitochondrial gene flow occurring among sites. Conclusions The observed south-to-north colonization route within the Norops humilis/quaggulus complex represents the first evidence of a Norops lineage colonizing in a south-to-north pattern, (opposite to the previously held hypothesis for mainland Norops). One previously described taxon (N. quaggulus) was nested within N. humilis, demonstrating the paraphyly of this species; while our analyses also reject the monophyly of the Norops humilis species group (sensu Savage and Guyer), with N. tropidonotus, N. uniformis, and N. marsupialis being distantly related to/highly divergent from the N. humilis/quaggulus complex. Our work sheds light on mainland anole biogeography and past dispersal events, providing a pattern to test against other groups of mainland anoles. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0391-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John G Phillips
- Department of Biology, Central Michigan University, Mt. Pleasant, MI, 48859, USA. .,Present address: Department of Biological Sciences, University of Tulsa, Tulsa, OK, 74104, USA.
| | - Jennifer Deitloff
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA.,Present address: Department of Biological Sciences, Lock Haven University, Lock Haven, PA, 17745, USA
| | - Craig Guyer
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Sara Huetteman
- Department of Biology, Central Michigan University, Mt. Pleasant, MI, 48859, USA
| | - Kirsten E Nicholson
- Department of Biology, Central Michigan University, Mt. Pleasant, MI, 48859, USA
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Wang H, Luo X, Meng S, Bei Y, Song T, Meng T, Li G, Zhang B. The Phylogeography and Population Demography of the Yunnan Caecilian (Ichthyophis bannanicus): Massive Rivers as Barriers to Gene Flow. PLoS One 2015; 10:e0125770. [PMID: 25915933 PMCID: PMC4411157 DOI: 10.1371/journal.pone.0125770] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 03/26/2015] [Indexed: 11/23/2022] Open
Abstract
Ichthyophis bannanicus is the only caecilian species in China. In this study, the phylogeography and population demography of I. bannanicus were explored, based on the mitochondrial DNA genes (cyt b and ND2) and 15 polymorphic microsatellite loci. Altogether 158 individuals were collected from five populations in Yunnan province, Guangxi province, Guangdong province, and Northern Vietnam. Phylogeographical and population structure analysis identified either two groups (Xishuangbanna, Northern Vietnam-Yulin-Yangchun-Deqing) or three groups (Xishuangbanna, Northern Vietnam-Yulin-Yangchun, and Deqing), indicating that the Red River and Pearl River systems may have acted as gene-flow barriers for I. bannanicus. Historical population expansion that happened 15–17 Ka ago was detected for mtDNA data and was possibly triggered by warmer weather after the Last Glacial Maximum. However, the Bayesian simulations of population history based on microsatellite data pinpointed population decline in all populations since 19,123 to 1,029 years ago, demonstrating a significant influence of anthropogenic habitat alteration on I. bannanicus.
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Affiliation(s)
- Hui Wang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
| | - Xia Luo
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
| | - Shaoquan Meng
- College of Life Science & Technology, Yulin Normal University, Yulin, 537000, Guangxi, China
| | - Yongjian Bei
- College of Life Science & Technology, Yulin Normal University, Yulin, 537000, Guangxi, China
| | - Tao Song
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
| | - Tao Meng
- Guangxi Forestry Inventory and Planning Institute, Nanning, 530011, Guangxi, China
| | - Guifen Li
- College of Life Science & Technology, Yulin Normal University, Yulin, 537000, Guangxi, China
- * E-mail: (GL); (BZ)
| | - Baowei Zhang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
- * E-mail: (GL); (BZ)
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Phylogenetic Relationships of Apodemus Kaup, 1829 (Rodentia: Muridae) Species in the Eastern Mediterranean Inferred from Mitochondrial DNA, with Emphasis on Iranian Species. J MAMM EVOL 2015. [DOI: 10.1007/s10914-015-9294-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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35
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Cryptic diversity within the Anatololacerta species complex (Squamata: Lacertidae) in the Anatolian Peninsula: evidence from a multi-locus approach. Mol Phylogenet Evol 2014; 82 Pt A:219-33. [PMID: 25315886 DOI: 10.1016/j.ympev.2014.10.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 09/16/2014] [Accepted: 10/02/2014] [Indexed: 11/21/2022]
Abstract
The rapid development of innovative molecular tools for characterizing biodiversity is leading to an extensive and sometimes unexpected renovation of taxonomic classifications. Particularly, for species having allopatric or parapatric distributions or resulting from recent speciation processes, the absence of clear phenotypic differentiation may hinder the recognition of closely related taxa, while intraspecific polymorphism may be confused with the presence of more than one single species. In the present work, we apply different phylogenetic methods in order to infer relationships within the genus Anatololacerta, and to assess the taxonomy of this morphologically diversified group of lizards endemic to western and southern Anatolia and some neighboring Aegean islands. According to morphology, three species have been recognized (Anatololacerta anatolica, A. oertzeni and A. danfordi) as well as several subspecies, but small variation at immunological markers led some authors to join all the populations into one single taxon, A. danfordi. By selecting both mitochondrial and nuclear informative markers, we tested the effectiveness of classical "gene tree" (i.e. Bayesian Inference) vs. innovative (i.e. coalescent-based) "species tree" methods in resolving the Anatololacerta taxonomic enigma, as a case in point for similar studies on species complexes resulting from non-obvious and cryptic diversification patterns. According to our results, the gene tree method failed in resolving phylogenetic relationships among clades, whereas the multi-locus species tree approach, coupled with species delimitation methods, allowed the identification of four well distinct species. These species probably diversified in different allopatric refugia located in southern and western Anatolia, where isolated populations may have persisted during Pleistocene glacial cycles.
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36
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Lawson GR, Kilpatrick ES. Phylogeographic Patterns Among the Subspecies ofNotophthalmus viridescens(Eastern Newt) in South Carolina. SOUTHEAST NAT 2014. [DOI: 10.1656/058.013.0302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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37
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A stable niche assumption-free test of ecological divergence. Mol Phylogenet Evol 2014; 76:211-26. [DOI: 10.1016/j.ympev.2014.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 02/26/2014] [Accepted: 03/04/2014] [Indexed: 11/23/2022]
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Meng H, Li X, Qiao P. Population structure, historical biogeography and demographic history of the alpine toad Scutiger ningshanensis in the Tsinling Mountains of Central China. PLoS One 2014; 9:e100729. [PMID: 24956389 PMCID: PMC4067352 DOI: 10.1371/journal.pone.0100729] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 05/29/2014] [Indexed: 11/18/2022] Open
Abstract
Population genetic structure, historical biogeography and historical demography of the alpine toad Scutiger ningshanensis were studied using the combined data mtDNA cytochrome b (cyt b) and the mtDNA cytochrome c oxidase subunit I (COI) as the molecular markers. This species has high genetic variation. There was a significant genetic differentiation among most populations. Three lineages were detected. The phylogenetic relationship analyses and the SAMOVA (spatial analysis of molecular variance) results showed significant phylogeographic structure. 82.15% genetic variation occurred among populations whereas differentiation within populations only contributed 17.85% to the total. Mantel test results showed a significant correlation between the pairwise calculated genetic distance and pairwise calculated geographical distance of the populations (regression coefficient = 0.001286, correlation coefficient = 0.77051, p (rrand≥robs) = 0.0185<0.05), indicating the existence of isolation-by-distance pattern of genetic divergence for cyt b + COI sequence, which suggests that the distribution of genetic variation is due to geographical separation rather than natural selection. The population expansion or contraction and genetic differentiation between populations or lineages could be explained by topography and the repetitive uplifts of the Tsinling Mountains and the climatic cycles during the late Pliocene and Pleistocene. S. ningshanensis experienced a rapid population expansion about 40,000 years before present. The current decline in population size was probably caused by anthropogenic disturbance. Current populations of S. ningshanensis are from different refugia though the location of these refugia could not be determined in our study. Topography, climatic changes and repetitive population expansion/contraction together led to the high level of genetic variation in S. ningshanensis. A total of three management units (MUs) was determined, which must be considered when conservation policy is made in the future.
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Affiliation(s)
- Hongzhe Meng
- Co-Innovation Center for Qinba Regions' Sustainable Development, College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Xiaochen Li
- Co-Innovation Center for Qinba Regions' Sustainable Development, College of Life Sciences, Shaanxi Normal University, Xi'an, China
- * E-mail:
| | - Penghai Qiao
- Co-Innovation Center for Qinba Regions' Sustainable Development, College of Life Sciences, Shaanxi Normal University, Xi'an, China
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Pyron RA. Biogeographic Analysis Reveals Ancient Continental Vicariance and Recent Oceanic Dispersal in Amphibians. Syst Biol 2014; 63:779-97. [DOI: 10.1093/sysbio/syu042] [Citation(s) in RCA: 227] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- R. Alexander Pyron
- Department of Biological Sciences, The George Washington University, 2023 G Street NW, Washington, DC 20052, USA
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40
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Poulakakis N, Kapli P, Lymberakis P, Trichas A, Vardinoyiannis K, Sfenthourakis S, Mylonas M. A review of phylogeographic analyses of animal taxa from the Aegean and surrounding regions. J ZOOL SYST EVOL RES 2014. [DOI: 10.1111/jzs.12071] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nikos Poulakakis
- Natural History Museum of Crete; University of Crete; Iraklion Greece
- Biology Department; University of Crete; Iraklion Greece
| | - Paschalia Kapli
- Natural History Museum of Crete; University of Crete; Iraklion Greece
- Biology Department; University of Crete; Iraklion Greece
| | - Petros Lymberakis
- Natural History Museum of Crete; University of Crete; Iraklion Greece
| | - Apostolos Trichas
- Natural History Museum of Crete; University of Crete; Iraklion Greece
| | | | | | - Moisis Mylonas
- Natural History Museum of Crete; University of Crete; Iraklion Greece
- Biology Department; University of Crete; Iraklion Greece
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Vences M, Sanchez E, Hauswaldt JS, Eikelmann D, Rodríguez A, Carranza S, Donaire D, Gehara M, Helfer V, Lötters S, Werner P, Schulz S, Steinfartz S. Nuclear and mitochondrial multilocus phylogeny and survey of alkaloid content in true salamanders of the genus Salamandra (Salamandridae). Mol Phylogenet Evol 2014; 73:208-16. [DOI: 10.1016/j.ympev.2013.12.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 12/27/2013] [Accepted: 12/29/2013] [Indexed: 11/28/2022]
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42
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Lu B, Bi K, Fu J. A phylogeographic evaluation of the Amolops mantzorum species group: cryptic species and plateau uplift. Mol Phylogenet Evol 2014; 73:40-52. [PMID: 24462636 DOI: 10.1016/j.ympev.2014.01.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 01/09/2014] [Accepted: 01/13/2014] [Indexed: 11/24/2022]
Abstract
Phylogeographic analysis brings organism phylogeny, regional geological/climatic history, and population demography together, and provides insights into species history and speciation. Using DNA sequence data from a mitochondrial marker (cytochrome b) and a nuclear marker (cmyc intron 2), we examined phylogeography of the Amolops mantzorum species group. We first constructed Bayesian and maximum-likelihood gene trees and medium-joint networks for the recovered haplotypes, and estimated divergence time for each major lineage. Species boundaries were then delineated using the general mixed Yule-coalescent model (GMYC) and a Bayesian species-delimitation method (BP&P). Potential gene flow between putative species was also estimated using the isolation-with-migration model. Furthermore, species-distribution modeling was used to probe linkage between climatic changes and speciation. Lastly, extended Bayesian skyline plotting was employed to reveal historical demography for each putative species. Our analyses clearly delimit nine species in the group, including four well-recognized species and five putative species, of which three are often listed as synonyms of A. mantzorum. The nominal species A. mantzorum may in fact include two cryptic species. Divergence-time estimates align the speciation events with the recent intense uplift of the Tibetan Plateau in the last 3.6 million years. The species-distribution modeling also reveals different habitat preferences among species that are potentially linked to climatic changes associated with the uplift. Furthermore, three species sustained continuous population growth through the last glaciation, while others expanded only after the last glaciation. The eastern escarpment of Tibet is a biodiversity hotspot; its rich species diversity, unique topography, and well-established geological history provide an excellent system for evolutionary studies.
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Affiliation(s)
- Bin Lu
- Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, Sichuan, China
| | - Ke Bi
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Jinzhong Fu
- Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, Sichuan, China; Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada.
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43
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Sağlam İK, Küçükyıldırım S, Çağlar SS. Diversification of montane species via elevation shifts: the case of the Kaçkar cricket Phonochorion
(Orthoptera). J ZOOL SYST EVOL RES 2013. [DOI: 10.1111/jzs.12051] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- İsmail K. Sağlam
- Department of Biology; Faculty of Science; Hacettepe University; Beytepe, Ankara Turkey
| | - Sibel Küçükyıldırım
- Department of Biology; Faculty of Science; Hacettepe University; Beytepe, Ankara Turkey
| | - Selim S. Çağlar
- Department of Biology; Faculty of Science; Hacettepe University; Beytepe, Ankara Turkey
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Molecular phylogeography and population genetic structure of an endangered species Pachyhynobius shangchengensis (hynobiid Salamander) in a fragmented habitat of southeastern China. PLoS One 2013; 8:e78064. [PMID: 24205092 PMCID: PMC3799735 DOI: 10.1371/journal.pone.0078064] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 09/16/2013] [Indexed: 11/26/2022] Open
Abstract
The salamander Pachyhynobius shangchengensis (Hynobiidae) is a vulnerable species restricted to a patchy distribution associated with small mountain streams surrounded by forested slopes in the Mount Dabieshan region in southeastern China. However, molecular phylogeography and population genetic structure of P. shangchengensis remain poorly investigated. In this study, we explored the genetic structure and phylogeography of P. shangchengensis based on partial sequences of the mitochondrial DNA (mtDNA) cytochrome b and cytochrome c oxidase subunit I genes. Fifty-one haplotypes and four clades were found among 93 samples. Phylogenetic analyses revealed four deeply divergent and reciprocally monophyletic mtDNA lineages that approximately correspond to four geographic regions separated by complicated topography and long distances. The distinct geographic distributions of all lineages and the estimated divergence time suggest spatial and temporal separation coinciding with climatic changes during the Pleistocene. Analysis of molecular variance indicated that most of the observed genetic variation occurred among the four groups, implying long-term interruption of gene flow, and the possible separation of P. shangchengensis into four management units for conservation.
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Species tree reconstruction of a poorly resolved clade of salamanders (Ambystomatidae) using multiple nuclear loci. Mol Phylogenet Evol 2013; 68:671-82. [DOI: 10.1016/j.ympev.2013.04.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 04/14/2013] [Accepted: 04/16/2013] [Indexed: 11/23/2022]
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Aoki G, Matsui M, Nishikawa K. Mitochondrial cytochrome B phylogeny and historical biogeography of the Tohoku salamander, Hynobius lichenatus (Amphibia, Caudata). Zoolog Sci 2013; 30:167-73. [PMID: 23480375 DOI: 10.2108/zsj.30.167] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The Tohoku salamander, Hynobius lichenatus Boulenger, 1883, is a lentic breeding species widespread throughout montane regions of northeastern Japan. To explore intraspecific genetic variation and infer evolutionary history of H. lichenatus, we performed mitochondrial DNA analysis (complete 1141 bp sequences of the mitochondrial cytochrome b gene) using 215 adult and larval individuals collected from 75 localities, encompassing known distributional range of the species. Hynobius lichenatus proved to be monophyletic, including three well-supported and geographically structured clades (Clade I from northern Kanto, Clade II from southern Tohoku, and Clade III from northern Tohoku). These clades, respectively, comprise several subclades, and show genetic distances as large as those seen between different species of Hynobius. Results of population statistic analyses indicate that all clades and most subclades have maintained high genetic diversity and demographic stability over long periods. Molecular dating indicates divergence in H. lichenatus concords with topographic evolution of northeastern Japan from late Miocene to early Pleistocene, suggesting that paleogeographic events in this region, such as orogenesis, sea level change, and volcanic activity, have been crucial for shaping genetic patterns and diversity in this species. Hynobius lichenatus greatly differs from many other animal species from northeastern Japan in its much older periods and the pattern of genetic differentiation, and is suggested as an old faunal element in this region.
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Affiliation(s)
- Gen Aoki
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu-cho Sakyo-ku, Kyoto 606-8501, Japan
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Malyarchuk B, Derenko M, Denisova G. Phylogeny and genetic history of the Siberian salamander (Salamandrella keyserlingii, Dybowski, 1870) inferred from complete mitochondrial genomes. Mol Phylogenet Evol 2013; 67:348-57. [PMID: 23415986 DOI: 10.1016/j.ympev.2013.02.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 01/28/2013] [Accepted: 02/03/2013] [Indexed: 11/15/2022]
Abstract
We assessed phylogeny of the Siberian salamander (Salamandrella keyserlingii, Dybowski, 1870), the most northern ectothermic, terrestrial vertebrate in Eurasia, by sequence analysis of complete mitochondrial genomes in 26 specimens from different localities (China, Khabarovsk region, Sakhalin, Yakutia, Magadan region, Chukotka, Kamchatka, Ural, European part of Russia). In addition, a complete mitochondrial genome of the Schrenck salamander, Salamandrella schrenckii, was determined for the first time. Bayesian phylogenetic analysis of the entire mtDNA genomes of S. keyserlingii demonstrates that two haplotype clades, AB and C, radiated about 1.4 million years ago (Mya). Bayesian skyline plots of population size change through time show an expansion around 250 thousand years ago (kya) and then a decline around the Last Glacial Maximum (25 kya) with subsequent restoration of population size. Climatic changes during the Quaternary period have dramatically affected the population genetic structure of the Siberian salamanders. In addition, complete mtDNA sequence analysis allowed us to recognize that the vast area of Northern Eurasia was colonized only by the Siberian salamander clade C1b during the last 150 kya. Meanwhile, we were unable to find evidence of molecular adaptation in this clade by analyzing the whole mitochondrial genomes of the Siberian salamanders.
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Affiliation(s)
- Boris Malyarchuk
- Institute of Biological Problems of the North, Magadan 685000, Russia.
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Wang B, Jiang J, Xie F, Li C. Phylogeographic patterns of mtDNA variation revealed multiple glacial refugia for the frog species Feirana taihangnica endemic to the Qinling Mountains. J Mol Evol 2013; 76:112-28. [PMID: 23381112 DOI: 10.1007/s00239-013-9544-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2011] [Accepted: 01/19/2013] [Indexed: 11/24/2022]
Abstract
Diversification patterns and demography of montane species are affected by Pleistocene climate fluctuations. Empirical cases from the Qinling Mountains (QM) region, which is a major biogeographic divider of East Asia, are few. We used DNA sequence data of the complete mitochondrial ND2 gene to detect effects of the Pleistocene glaciations on phylogeographic profiles of a frog species, Feirana taihangnica, which is endemic to the QM. Four distinct lineages consisting of seven sublineages were revealed. The strongest signal of biogeographical structure (F(ct) = 0.971, P < 0.01) was found when populations were grouped according to these seven sublineages. One narrow secondary contact zone was detected in the middle QM between the lineage from middle QM and the lineage from eastern QM. Coalescent simulations indicated that this species colonized the QM region by a stepping-stone model. Divergences among lineages had likely been influenced by the uplift of the Tibetan Plateau during the late Miocene-to-late Pleistocene, as well as by the Pleistocene climatic cycles. Coalescent simulations also suggested that F. taihangnica populations have persisted through the Pleistocene glacial periods in multiple refugia across the QM region. Demographic analyses indicated that all lineages, except the lineage in the Funiu Mountains, have been experienced postglacial expansion of population size and distribution range. In conclusion, Pleistocene climate fluctuations and tectonic changes during the late Miocene-late Pleistocene have profoundly influenced the phylogeography and historical demography of F. taihangnica.
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Affiliation(s)
- Bin Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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Zieliński P, Nadachowska-Brzyska K, Wielstra B, Szkotak R, Covaciu-Marcov SD, Cogălniceanu D, Babik W. No evidence for nuclear introgression despite complete mtDNA replacement in the Carpathian newt (Lissotriton montandoni). Mol Ecol 2013; 22:1884-903. [DOI: 10.1111/mec.12225] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 12/11/2012] [Accepted: 12/13/2012] [Indexed: 11/26/2022]
Affiliation(s)
- P. Zieliński
- Institute of Environmental Sciences; Jagiellonian University; Gronostajowa 7 30-387 Kraków Poland
| | - K. Nadachowska-Brzyska
- Institute of Environmental Sciences; Jagiellonian University; Gronostajowa 7 30-387 Kraków Poland
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D SE-75236 Uppsala Sweden
| | - B. Wielstra
- Netherlands Biodiversity Center; P. O. Box 9517 2300 RA Leiden The Netherlands
| | - R. Szkotak
- Institute of Environmental Sciences; Jagiellonian University; Gronostajowa 7 30-387 Kraków Poland
| | - S. D. Covaciu-Marcov
- University of Oradea; Faculty of Sciences; Department of Biology; Universităţii str. 1 410087 Oradea Romania
| | - D. Cogălniceanu
- Faculty of Natural Sciences and Agricultural Sciences; University Ovidius Constanţa; Aleea Universităţii nr. 1, corp B 900470 Constanţa Romania
| | - W. Babik
- Institute of Environmental Sciences; Jagiellonian University; Gronostajowa 7 30-387 Kraków Poland
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Azuma N, Hangui JI, Wakahara M, Michimae H. Population structure of the salamander Hynobius retardatus inferred from a partial sequence of the mitochondrial DNA control region. Zoolog Sci 2013; 30:7-14. [PMID: 23317360 DOI: 10.2108/zsj.30.7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We investigated population structure of the salamander Hynobius retardatus in Hokkaido, Japan using partial sequences of the mitochondrial DNA control region (490 bp) from 105 individuals. The salamanders were collected from 28 localities representing the entire regional distribution of this species. Twenty different haplotypes distributed across three haplotype groups were identified. Group 1 was widely distributed in central, northern, and eastern Hokkaido, except Erimo; Groups 2 and 3 appeared exclusively in Erimo and southern Hokkaido, respectively. The genetic distance between the three groups was not very large, but the distributions of the groups never overlapped spatially, indicating a hierarchical population structure comprising three regional groups, which was also supported by analysis of molecular variance. The results suggest that the present population structure is affected by current genetic barriers, as well as by historical transitions of climate and landscape.
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Affiliation(s)
- Noriko Azuma
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studieis, Onogawa 16-2, Tsukuba, Ibaraki 305-8506, Japan.
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