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Tian L, Xu R, Chen D, Ananjeva NB, Brown RM, Min MS, Cai B, Mijidsuren B, Zhang B, Guo X. Range-Wide Phylogeography and Ecological Niche Modeling Provide Insights into the Evolutionary History of the Mongolian Racerunner ( Eremias argus) in Northeast Asia. Animals (Basel) 2024; 14:1124. [PMID: 38612363 PMCID: PMC11011046 DOI: 10.3390/ani14071124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 04/14/2024] Open
Abstract
The Mongolian racerunner, Eremias argus, is a small lizard endemic to Northeast Asia that can serve as an excellent model for investigating how geography and past climate change have jointly influenced the evolution of biodiversity in this region. To elucidate the processes underlying its diversification and demography, we reconstructed the range-wide phylogeographic pattern and evolutionary trajectory, using phylogenetic, population genetic, landscape genetic, Bayesian phylogeographic reconstruction and ecological niche modeling approaches. Phylogenetic analyses of the mtDNA cyt b gene revealed eight lineages that were unbounded by geographic region. The genetic structure of E. argus was mainly determined by geographic distance. Divergence dating indicated that E. argus and E. brenchleyi diverged during the Mid-Pliocene Warm Period. E. argus was estimated to have coalesced at~0.4351 Ma (Marine Isotope Stage 19). Bayesian phylogeographic diffusion analysis revealed out-of-Inner Mongolia and rapid colonization events from the end of the Last Interglacial to the Last Glacial Maximum, which is consistent with the expanded suitable range of the Last Glacial Maximum. Pre-Last Glacial Maximum growth of population is presented for most lineages of E. argus. The Glacial Maximum contraction model and the previous multiple glacial refugia hypotheses are rejected. This may be due to an increase in the amount of climatically favorable habitats in Northeast Asia. Furthermore, E. argus barbouri most likely represents an invalid taxon. The present study is the first to report a range-wide phylogeography of reptiles over such a large region in Northeast Asia. Our results make a significant contribution towards understanding the biogeography of the entire Northeast Asia.
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Affiliation(s)
- Lili Tian
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610223, China; (L.T.); (R.X.); (B.C.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Xu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610223, China; (L.T.); (R.X.); (B.C.)
| | - Dali Chen
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China;
| | - Natalia B. Ananjeva
- Zoological Institute, Russian Academy of Sciences, St. Petersburg 199034, Russia;
| | - Rafe M. Brown
- Biodiversity Institute, Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA;
| | - Mi-Sook Min
- Conservation Genome Resource Bank for Korean Wildlife, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 151-742, Republic of Korea;
| | - Bo Cai
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610223, China; (L.T.); (R.X.); (B.C.)
| | - Byambasuren Mijidsuren
- Plant Protection Research Institute, Mongolian University of Life Sciences, Ulaanbaatar 210153, Mongolia;
| | - Bin Zhang
- College of Life Sciences and Technology, Inner Mongolia Normal University, Hohhot 010022, China;
| | - Xianguang Guo
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610223, China; (L.T.); (R.X.); (B.C.)
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Dufresnes C, Poyarkov N, Jablonski D. Acknowledging more biodiversity without more species. Proc Natl Acad Sci U S A 2023; 120:e2302424120. [PMID: 37748058 PMCID: PMC10556632 DOI: 10.1073/pnas.2302424120] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023] Open
Abstract
Delimiting and naming biodiversity is a vital step toward wildlife conservation and research. However, species delimitation must be consistent across biota so that the limited resources available for nature protection can be spent effectively and objectively. To date, newly discovered lineages typically are either left undescribed and thus remain unprotected or are being erroneously proposed as new species despite mixed evidence for completed speciation, in turn contributing to the emerging problem of taxonomic inflation. Inspired by recent conceptual and methodological progress, we propose a standardized workflow for species delimitation that combines phylogenetic and hybrid zone analyses of genomic datasets ("genomic taxonomy"), in which phylogeographic lineages that do not freely admix are ranked as species, while those that have remained fully genetically compatible are ranked as subspecies. In both cases, we encourage their formal taxonomic naming, diagnosis, and description to promote social awareness toward biodiversity. The use of loci throughout the genome overcomes the unreliability of widely used barcoding genes when phylogeographic patterns are complex, while the evaluation of divergence and reproductive isolation unifies the long-opposed concepts of lineage species and biological species. We suggest that a shift in conservation assessments from a single level (species) toward a two-level hierarchy (species and subspecies) will lead to a more balanced perception of biodiversity in which both intraspecific and interspecific diversity are valued and more adequately protected.
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Affiliation(s)
- Christophe Dufresnes
- Laboratory of Amphibian Systematics and Evolutionary Research, College of Biology and Environment, Nanjing Forestry University, Nanjing210037, People’s Republic of China
| | - Nikolay Poyarkov
- Joint Russian-Vietnamese Tropical Research and Technological Center, Hanoi122000, Vietnam
- Department of Vertebrate Zoology, Lomonosov Moscow State University, Moscow119234, Russia
| | - Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Bratislava84215, Slovakia
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Liang H, Zhang X, Hou Y, Zheng K, Hao H, He B, Li H, Sun C, Yang T, Song H, Cai R, Wang Y, Jiang H, Qi L, Wang Y. Super-high procoagulant activity of gecko thrombin: A gift from sky dragon. CNS Neurosci Ther 2023; 29:3081-3093. [PMID: 37144588 PMCID: PMC10493662 DOI: 10.1111/cns.14250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 04/06/2023] [Accepted: 04/17/2023] [Indexed: 05/06/2023] Open
Abstract
AIMS Gecko, the "sky dragon" named by Traditional Chinese Medicine, undergoes rapid coagulation and scarless regeneration following tail amputation in the natural ecology, providing a perfect opportunity to develop the efficient and safe drug for blood clotting. Here, gecko thrombin (gthrombin) was recombinantly prepared and comparatively studied on its procoagulant activity. METHODS The 3D structure of gthrombin was constructed using the homology modeling method of I-TASSER. The active gthrombin was prepared by the expression of gecko prethrombin-2 in 293 T cells, followed by purification with Ni2+ -chelating column chromatography prior to activation by snake venom-derived Ecarin. The enzymatic activities of gthrombin were assayed by hydrolysis of synthetic substrate S-2238 and the fibrinogen clotting. The vulnerable nerve cells were used to evaluate the toxicity of gthrombin at molecular and cellular levels. RESULTS The active recombinant gthrombin showed super-high catalytic and fibrinogenolytic efficiency than those of human under different temperatures and pH conditions. In addition, gthrombin made nontoxic effects on the central nerve cells including neurons, contrary to those of mammalian counterparts, which contribute to neuronal damage, astrogliosis, and demyelination. CONCLUSIONS A super-high activity but safe procoagulant candidate drug was identified from reptiles, which provided a promising perspective for clinical application in rapid blood clotting.
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Affiliation(s)
- Hao Liang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co‐innovation Center of NeuroregenerationNantong UniversityNantongPR China
| | - Xingyuan Zhang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co‐innovation Center of NeuroregenerationNantong UniversityNantongPR China
| | - Yuxuan Hou
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co‐innovation Center of NeuroregenerationNantong UniversityNantongPR China
| | - Kang Zheng
- Anti‐aging & Regenerative Medicine Research Institution, School of Life Sciences and MedicineShandong University of TechnologyZiboPR China
| | - Huifei Hao
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co‐innovation Center of NeuroregenerationNantong UniversityNantongPR China
| | - Bingqiang He
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co‐innovation Center of NeuroregenerationNantong UniversityNantongPR China
| | - Hui Li
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co‐innovation Center of NeuroregenerationNantong UniversityNantongPR China
| | - Chunshuai Sun
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co‐innovation Center of NeuroregenerationNantong UniversityNantongPR China
| | - Ting Yang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co‐innovation Center of NeuroregenerationNantong UniversityNantongPR China
| | - Honghua Song
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co‐innovation Center of NeuroregenerationNantong UniversityNantongPR China
| | - Rixin Cai
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co‐innovation Center of NeuroregenerationNantong UniversityNantongPR China
| | - Yingjie Wang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co‐innovation Center of NeuroregenerationNantong UniversityNantongPR China
| | - Haiyan Jiang
- Department of Emergency MedicineAffiliated Hospital of Nantong UniversityNantongPR China
| | - Lei Qi
- Department of Emergency MedicineAffiliated Hospital of Nantong UniversityNantongPR China
| | - Yongjun Wang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co‐innovation Center of NeuroregenerationNantong UniversityNantongPR China
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Wu N, Wang S, Dujsebayeva TN, Chen D, Ali A, Guo X. Geography and past climate changes have shaped the evolution of a widespread lizard in arid Central Asia. Mol Phylogenet Evol 2023; 184:107781. [PMID: 37044189 DOI: 10.1016/j.ympev.2023.107781] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 04/06/2023] [Accepted: 04/06/2023] [Indexed: 04/14/2023]
Abstract
The complex orogenic history and structure of Central Asia, coupled with Pleistocene glacial cycles have generated its stepwise aridification. Such events would have significantly influenced the evolution of many mid-latitude species in arid Central Asia (ACA). In this study, we employed two mitochondrial genes (CO1 and ND2) and genome-wide SNPs, coupled with ecological niche modeling, to investigate the lineage diversification and historical demography within a widespread lizard Phrynocepahlus helioscopus, and their associations with geography and past climate change. We obtained themtDNA dataset for 300 individuals from 96 localities within the known range of the lizard, among which 51 individuals from 27 localities were selected for generating the SNP dataset via genotyping-by-sequencing approach. Phylogenetic analyses of the concatenated mtDNA dataset revealed eight geographically correlated lineages that diverged by 4.21-10.41% for the CO1 gene, which were estimated to have coalesced ∼4.47 million years ago. However, we observed mito-nuclear discordance pattern regarding the population of Clade V (P. helioscopus sergeevi) from Tajikistan. Ancestral area estimations suggested that P. helioscopus originated from the Fergana Valley and then dispersed into the adjacent areas in ACA along with a history of multiple allopatric divergence processes, suggesting that Fergana may have been the cradle of diversification of P. helioscopus. The intensification of aridification across Central Asia during the Late Pliocene may have facilitated the rapid radiation of this arid-adapted lizard throughout this vast territory. Subsequently, the geological events (e.g., uplift of the Hissar-Alay, transgressions of the Caspian Sea) and geographic barriers (e.g., Amu Darya River, Zerarshan River) during the Pleistocene triggered the progressive diversification of P. helioscopus. Interestingly, Clade VIII (P. helioscopus varius) experienced rapid population growth coupled with range expansion while Clade IV (P. helioscopus cameranoi) underwent drastic population expansion associated with range contraction during the Last Glacial Maximum. In Clade IV, but not in Clade VIII, environmental turnover contributes more to mitochondrial genetic distinctiveness than geographic distance. Overall, the SNP dataset demonstrates that geographic distance plays a greater role than environmental distance. Both the mtDNA dataset and the SNP dataset suggest local-scale genetic differentiation in Clade IV and Clade VIII, revealing potential geographic barriers in the Ili River Valley and the Junggar Basin, respectively. Twenty-seven outlier SNPs associated with environmental factors (precipitation and temperature) were identified, which supports the signature of local adaptation to the arid desert environment. Finally, our finding suggests taxonomic implications, such as support for full species status for P. saidalievi (Clade II) and P. meridionalis (Clade I). Future analyses based on further evidence and increased taxon and geographic sampling should be carried out to corroborate our findings.
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Affiliation(s)
- Na Wu
- Chengdu Institute of Biology Chinese Academy of Sciences, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Song Wang
- Chengdu Institute of Biology Chinese Academy of Sciences, Chengdu 610041, China
| | - Tatjana N Dujsebayeva
- Laboratory of Ornithology and Herpetology, Institute of Zoology, Ministry of Sciences and High Education of Republic of Kazakhstan, Almaty 050060, Kazakhstan
| | - Dali Chen
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Abid Ali
- Chengdu Institute of Biology Chinese Academy of Sciences, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianguang Guo
- Chengdu Institute of Biology Chinese Academy of Sciences, Chengdu 610041, China.
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Yushchenko PV, Lee JL, Pham HM, Geissler P, Syromyatnikova EV, Poyarkov Jr. NA. The taxonomic status of the kukri snake Oligodon arenarius Vassilieva, 2015 with a redescription of Oligodon macrurus (Angel, 1927) (Squamata, Serpentes, Colubridae). VERTEBRATE ZOOLOGY 2023. [DOI: 10.3897/vz.73.e96958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We investigated the taxonomic status of the recently described kukri snake Oligodon arenarius Vassilieva, 2015 and the morphologically similar Oligodon macrurus (Angel, 1927), two species endemic to the southern coast of Vietnam. Based on phylogenetic analyses using three mitochondrial genes (12S–16S rRNA, cytochrome b), we recovered O. arenarius and O. macrurus in a clade within the O. cyclurus-taeniatus species group, agreeing with previous intrageneric classifications. Genetic distances between O. arenarius and O. macrurus are extremely low (less than 0.5% based on 12S–16S) and render O. arenarius paraphyletic. All preserved specimens of O. arenarius and O. macrurus convey little to no differences in color pattern, hemipenial morphology and osteological features; the latter of which is based on three dimensional micro computer tomography (µCT) scans of one specimen per species. Contrasting these results, univariate and multivariate analyses revealed significant differences in relative tail length, and the number of ventral and subcaudal scales between both species. Although the molecular and morphological datasets present conflicting results, integrating the evidence leads us to synonymize O. arenarius with O. macrurus. We provide a formal redescription of O. macrurus, designate a neotype specimen to avoid future taxonomic confusion, and provide the first detailed osteological description of this species. Oligodon macrurus sensu stricto is endemic to coastal dunefields and adjacent forest habitats in southern Vietnam, where ongoing human development, tourism and road mortality pose significant threats to its conservation. Consequently, we suggest that O. macrurus should be listed as “Vulnerable” based on the assessment criteria of the International Union for Conservation of Nature (IUCN).
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MacGuigan DJ, Mount GG, Watkins-Colwell GJ, Near TJ, Lambert MR. Genomic Data Clarify Aquarana Systematics and Reveal Isolation-by-Distance Dominates Phylogeography of the Wide-Ranging Frog Rana clamitans. ICHTHYOLOGY & HERPETOLOGY 2022. [DOI: 10.1643/h2021129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Daniel J. MacGuigan
- Department of Biological Sciences, University at Buffalo, Buffalo, New York 14260;
| | | | - Gregory J. Watkins-Colwell
- Division of Vertebrate Zoology, Peabody Museum of Natural History, Yale University, New Haven, Connecticut 06511; (GJWC) gregory.
| | - Thomas J. Near
- Division of Vertebrate Zoology, Peabody Museum of Natural History, Yale University, New Haven, Connecticut 06511; (GJWC) gregory.
| | - Max R. Lambert
- Science Division, Habitat Program, Washington Department of Fish & Wildlife, Olympia, Washington 98501;
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Burbrink FT, Crother BI, Murray CM, Smith BT, Ruane S, Myers EA, Pyron RA. Empirical and philosophical problems with the subspecies rank. Ecol Evol 2022; 12:e9069. [PMID: 35845367 PMCID: PMC9271888 DOI: 10.1002/ece3.9069] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/01/2022] [Accepted: 06/10/2022] [Indexed: 11/12/2022] Open
Abstract
Species-level taxonomy derives from empirical sources (data and techniques) that assess the existence of spatiotemporal evolutionary lineages via various species "concepts." These concepts determine if observed lineages are independent given a particular methodology and ontology, which relates the metaphysical species concept to what "kind" of thing a species is in reality. Often, species concepts fail to link epistemology back to ontology. This lack of coherence is in part responsible for the persistence of the subspecies rank, which in modern usage often functions as a placeholder between the evolutionary events of divergence or collapse of incipient species. Thus, prospective events like lineages merging or diverging require information from unknowable future information. This is also conditioned on evidence that the lineage already has a detectably distinct evolutionary history. Ranking these lineages as subspecies can seem attractive given that many lineages do not exhibit intrinsic reproductive isolation. We argue that using subspecies is indefensible on philosophical and empirical grounds. Ontologically, the rank of subspecies is either identical to that of species or undefined in the context of evolutionary lineages representing spatiotemporally defined individuals. Some species concepts more inclined to consider subspecies, like the Biological Species Concept, are disconnected from evolutionary ontology and do not consider genealogy. Even if ontology is ignored, methods addressing reproductive isolation are often indirect and fail to capture the range of scenarios linking gene flow to species identity over space and time. The use of subspecies and reliance on reproductive isolation as a basis for an operational species concept can also conflict with ethical issues governing the protection of species. We provide a way forward for recognizing and naming species that links theoretical and operational species concepts regardless of the magnitude of reproductive isolation.
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Affiliation(s)
- Frank T. Burbrink
- Department of HerpetologyAmerican Museum of Natural HistoryNew YorkNew YorkUSA
| | - Brian I. Crother
- Department of Biological SciencesSoutheastern Louisiana UniversityHammondLouisianaUSA
| | - Christopher M. Murray
- Department of Biological SciencesSoutheastern Louisiana UniversityHammondLouisianaUSA
| | - Brian Tilston Smith
- Department of OrnithologyAmerican Museum of Natural HistoryNew YorkNew YorkUSA
| | - Sara Ruane
- Life Sciences Section, Negaunee Integrative Research CenterField Museum of Natural HistoryChicagoIllinoisUSA
| | - Edward A. Myers
- Department of HerpetologyAmerican Museum of Natural HistoryNew YorkNew YorkUSA
- Department of Biological SciencesClemson UniversityClemsonSouth CarolinaUSA
- Department of Vertebrate ZoologySmithsonian Institution, National Museum of Natural HistoryWashingtonDistrict of ColumbiaUSA
| | - Robert Alexander Pyron
- Department of Vertebrate ZoologySmithsonian Institution, National Museum of Natural HistoryWashingtonDistrict of ColumbiaUSA
- Department of Biological SciencesThe George Washington UniversityWashingtonDistrict of ColumbiaUSA
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Split it up and see: using proxies to highlight divergent inter-populational performances in aquaculture standardised conditions. BMC Ecol Evol 2021; 21:206. [PMID: 34809572 PMCID: PMC8607704 DOI: 10.1186/s12862-021-01937-z] [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: 02/08/2021] [Accepted: 11/10/2021] [Indexed: 12/02/2022] Open
Abstract
Background Considering wild inter-populational phenotypic differentiation can facilitate domestication and subsequent production of new species. However, comparing all populations across a species range to identify those exhibiting suitable key traits for aquaculture (KTA; i.e. important for domestication and subsequent production) expressions is not feasible. Therefore, proxies highlighting inter-populational divergences in KTA are needed. The use of such proxies would allow to identify, prior to bioassays, the wild population pairs which are likely to present differentiations in KTA expressions in aquaculture conditions. Here, we assessed the relevance of three alternative proxies: (i) genetic distance, (ii) habitat divergence, and (iii) geographic/hydrologic distances. We performed this evaluation on seven allopatric populations of Perca fluviatilis for which divergences in KTA had already been shown. Results We showed differences in the correlation degree between the alternative proxy-based and KTA-based distance matrices, with the genetic proxy being correlated to the highest number of KTA. However, no proxy was correlated to all inter-populational divergences in KTA. Conclusion For future domestication trials, we suggest using a multi-proxy assessment along with a prioritisation strategy to identify population pairs which are of interest for further evaluation in bioassays. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01937-z.
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Population genetic and genomic analyses of Western Massasauga (Sistrurus tergeminus ssp.): implications for subspecies delimitation and conservation. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01420-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Zhu G, Yang S, Savitzky AH, Cheng Y, Mori A, Ding L, Rao D, Wang Q. Cryptic diversity and phylogeography of the Rhabdophis nuchalis group (Squamata: Colubridae). Mol Phylogenet Evol 2021; 166:107325. [PMID: 34655748 DOI: 10.1016/j.ympev.2021.107325] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 10/06/2021] [Accepted: 10/08/2021] [Indexed: 11/18/2022]
Abstract
Previous studies, have found that the rapid uplift of the Tibetan plateau accelerated the diversification of species. However, there are few relevant biogeographic data for the Colubridae in this region. We conducted a comprehensive study of the Rhabdophis nuchalis Group, which presently contains four nominal species, R. nuchalis, R. pentasupralabialis, R. leonardi, and R. chiwen. Building upon previous studies with specimens we have recently examined, greater interspecific and intraspecific diversity has been revealed. Here we address three questions: (1) Do the intraspecific differences represent only geographic variation within lineages, or are there cryptic species? (2) What are the interspecific relationships among members of the R. nuchalis Group? (3) What has been the biogeographic history of this species group? To resolve these questions we used four mitochondrial gene sequences and one nuclear sequence to investigate the molecular phylogenetic and geographic relationships among populations. Our molecular analysis reveals cryptic species diversity within the R. nuchalis Group, and seven clades were identified in the analysis. Ancestral area estimation suggests that the R. nuchalis Group originated in the Hengduan Mountains approximately 6.24 Mya and expanded its range northward to the Qinling-Daba Mountains. The Sichuan Basin appears to have been a barrier to migration. Species divergence seems to have been related to the rapid uplift of the Qinghai-Tibet Plateau.
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Affiliation(s)
- Guangxiang Zhu
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| | - Shijun Yang
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Alan H Savitzky
- Department of Biology, Utah State University, Logan, UT 84322-5305, USA
| | - Yuqi Cheng
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Akira Mori
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Li Ding
- Chengdu Institute of Biology, Chinese Academy of Sciences. Chengdu 610041, China
| | - Dingqi Rao
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Qin Wang
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
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11
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Šmíd J, Aghová T, Velenská D, Moravec J, Balej P, Naumov B, Popgeorgiev G, Üzüm N, Avci A, Jablonski D. Quaternary range dynamics and taxonomy of the Mediterranean collared dwarf racer, Platyceps collaris (Squamata: Colubridae). Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The geological and geographical settings of the Eastern Mediterranean have resulted in complex patterns of intraspecific diversifications and phylogeographical histories that can be observed in squamates. In this study, we examined genetic differentiation of the Collared dwarf racer (Platyceps collaris) using a multilocus genetic dataset with a sampling that covered the entire range of the species. We developed distribution models in current and past climatic conditions to assess the dynamics of the species distribution through time. We sequenced a fragment of the cytochrome b mitochondrial gene of the holotype and eight paratypes of Coluber rubriceps thracius, which is considered a synonym of Platyceps collaris. Our results show that there are two distinct clades within P. collaris, one occupying the Balkans and western and southern Anatolia (termed the Balkan–Anatolian clade), the other in the Levant (termed the Levantine clade). All type specimens of C. r. thracius are genetically identical and cluster within the Balkan–Anatolian clade. Distribution models indicate the presence of two refugia during climatically challenging periods. One was in western Anatolia and served as a source for the colonization of the Balkans and southern Anatolia, and the other was in the northern Levant, from where P. collaris dispersed further south. According to our results, we revise the subspecific taxonomy of P. collaris.
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Affiliation(s)
- Jiří Šmíd
- Department of Zoology, National Museum, Cirkusová, Prague, Czech Republic
- Department of Zoology, Faculty of Science, Charles University, Viničná, Prague, Czech Republic
| | - Tatiana Aghová
- Centre of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University, U Nemocnice, Prague, Czech Republic
| | - Doubravka Velenská
- Department of Zoology, Faculty of Science, Charles University, Viničná, Prague, Czech Republic
| | - Jiří Moravec
- Department of Zoology, National Museum, Cirkusová, Prague, Czech Republic
| | - Petr Balej
- Department of Applied Geoinformatics and Spatial Planning, Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká, Praha—Suchdol, Czech Republic
| | - Borislav Naumov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Georgi Popgeorgiev
- National Museum of Natural History, Bulgarian Academy of Sciences, Tzar Osvoboditel Boulevard, Sofia, Bulgaria
| | - Nazan Üzüm
- Department of Biology, Faculty of Science and Arts, Aydın Adnan Menderes University, Aydın, Turkey
| | - Aziz Avci
- Department of Biology, Faculty of Science and Arts, Aydın Adnan Menderes University, Aydın, Turkey
| | - Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Ilkovičova, Mlynská dolina, Bratislava, Slovakia
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Breuil M, Schikorski D, Vuillaume B, Krauss U, Morton MN, Corry E, Bech N, Jelić M, Grandjean F. Painted black: Iguana melanoderma (Reptilia, Squamata, Iguanidae) a new melanistic endemic species from Saba and Montserrat islands (Lesser Antilles). Zookeys 2020; 926:95-131. [PMID: 32336922 PMCID: PMC7170970 DOI: 10.3897/zookeys.926.48679] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/28/2020] [Indexed: 11/12/2022] Open
Abstract
The Lesser Antilles, in the Eastern Caribbean, is inhabited by three Iguana species: the Lesser Antillean iguanaIguana delicatissima, which is endemic to the northernmost islands of the Lesser Antilles, the introduced common iguana from South America, Iguana iguana iguana, represented also by the two newly described endemic subspecies Iguana iguana sanctaluciae from Saint Lucia and Iguana iguana insularis from Saint Vincent and the Grenadines, and Grenada, and the introduced Iguana rhinolopha from Central America. Drawing on both morphological and genetic data, this paper describes the Iguana populations from Saba and Montserrat as a new species, Iguana melanoderma. This species is recognized on the basis of the following combination of characteristics: private microsatellite alleles, unique mitochondrial ND4 haplotypes, a distinctive black spot between the eye and tympanum, a dorsal carpet pattern on juveniles and young adults, a darkening of body coloration with aging (except for the anterior part of the snout), a black dewlap, pink on the jowl, the high number of large tubercular nape scales, fewer than ten medium sized-triangular dewlap spikes, high dorsal spikes, and lack of horns on the snout. This new melanistic taxon is threatened by unsustainable harvesting (including for the pet trade) and both competition and hybridization from escaped or released invasive alien iguanas (I. iguana iguana and I. rhinolopha) from South and Central America, respectively. The authors call for action to conserve Iguana melanoderma in Saba and Montserrat and for further research to investigate its relationship to other melanistic iguanas from the Virgin Islands and coastal islands of Venezuela.
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Affiliation(s)
- Michel Breuil
- Muséum national d'Histoire naturelle, Laboratoire des Reptiles et Amphibiens, Bâtiment 30, 57, rue Cuvier, CP n° 30, 75231 Paris cedex 05, France Muséum national d'Histoire naturelle Paris France
| | - David Schikorski
- Laboratoire Labofarm-Genindexe, 4 rue Théodore Botrel, 22600 Loudéac, France Laboratoire Labofarm-Genindexe Loudéac France
| | - Barbara Vuillaume
- Laboratoire Labofarm-Genindexe, 4 rue Théodore Botrel, 22600 Loudéac, France Laboratoire Labofarm-Genindexe Loudéac France
| | - Ulrike Krauss
- Maison du Soleil, Dauphin Road, La Borne, P O Box GM 1109, Saint Lucia Unaffliated Saint Lucia Saint Lucia
| | - Matthew N Morton
- Durrell Wildlife Conservation Trust, Les Augres Manor, Trinity, Jersey JE3 5BP, UK Durrell Wildlife Conservation Trust Trinity United Kingdom
| | - Elizabeth Corry
- Durrell Wildlife Conservation Trust, Les Augres Manor, Trinity, Jersey JE3 5BP, UK Durrell Wildlife Conservation Trust Trinity United Kingdom
| | - Nicolas Bech
- Laboratoire Écologie et Biologie des Interactions, équipe EES, UMR CNRS 6556, Université de Poitiers, 5 rue Albert Turpin, 86073 Poitiers Cedex 9, France Université de Poitiers Poitiers France
| | - Mišel Jelić
- Entomological Department, Varaždin City Museum, Šetalište Josipa Jurja Strossmayera 3, 42000 Varaždin, Croatia Varaždin City Museum Varaždin Croatia
| | - Frédéric Grandjean
- Laboratoire Écologie et Biologie des Interactions, équipe EES, UMR CNRS 6556, Université de Poitiers, 5 rue Albert Turpin, 86073 Poitiers Cedex 9, France Université de Poitiers Poitiers France
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Vargas-Ramírez M, Caballero S, Morales-Betancourt MA, Lasso CA, Amaya L, Martínez JG, das Neves Silva Viana M, Vogt RC, Farias IP, Hrbek T, Campbell PD, Fritz U. Genomic analyses reveal two species of the matamata (Testudines: Chelidae: Chelus spp.) and clarify their phylogeography. Mol Phylogenet Evol 2020; 148:106823. [PMID: 32278863 DOI: 10.1016/j.ympev.2020.106823] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 03/30/2020] [Accepted: 04/02/2020] [Indexed: 10/24/2022]
Abstract
The matamata is one of the most charismatic turtles on earth, widely distributed in northern South America. Debates have occurred over whether or not there should be two subspecies or species recognized due to its geographic variation in morphology. Even though the matamata is universally known, its natural history, conservation status and biogeography are largely unexplored. In this study we examined the phylogeographic differentiation of the matamata based on three mitochondrial DNA fragments (2168 bp of the control region, cytochrome oxidase subunit I, and the cytochrome b gene), one nuclear genomic DNA fragment (1068 bp of the R35 intron) and 1661 Single Nucleotide Polymorphisms (SNPs). Our molecular and morphological analyses revealed the existence of two distinct, genetically deeply divergent evolutionary lineages of matamatas that separated in the late Miocene (approximately 12.7 million years ago), corresponding well to the time when the Orinoco Basin was established. As a result of our analyses, we describe the genetically and morphologically highly distinct matamata from the Orinoco and Río Negro Basins and the Essequibo drainage as a species new to science (Chelus orinocensis sp. nov.). Chelus fimbriata sensu stricto is distributed in the Amazon Basin and the Mahury drainage. Additionally, the analyses revealed that each species displays phylogeographic differentiation. For C. orinocensis, there is moderate mitochondrial differentiation between the Orinoco and the Río Negro. For C. fimbriata, there is more pronounced differentiation matching different river systems. One mitochondrial clade was identified from the Amazon, Ucayali, and Mahury Rivers, and another one from the Madeira and Jaci Paraná Rivers. The C. orinocensis in the Essequibo and Branco Rivers have haplotypes that constitute a third clade clustering with C. fimbriata. Phylogenetic analyses of the R35 intron and SNP data link the matamatas from the Essequibo and Branco with the new species, suggesting past gene flow and old mitochondrial introgression. Chelus orinocensis is collected for the pet trade in Colombia and Venezuela. However, neither the extent of the harvest nor its impact are known. Hence, it is crucial to gather more information and to assess its exploitation throughout its distribution range to obtain a better understanding of its conservation status and to design appropriate conservation and management procedures. RESUMEN: La matamata es una de las tortugas más carismáticas del mundo, ampliamente distribuida en el norte de Sudamérica. Debido a su variación morfológica geográfica, se debate sobre el reconocimiento de dos subespecies o especies. A pesar de que la matamata es universalmente conocida, su historia natural, estado de conservación y biogeografía han sido muy poco estudiados. En este estudio examinamos la diferenciación filogeográfica de las matamatas en base a tres fragmentos de ADN mitocondrial (2168 pb de la región de control, la subunidad I del citocromo oxidasa y el gen del citocromo b), un fragmento de ADN genómico nuclear (1068 pb del intrón R35) y 1661 polimorfismos de nucleótido único (SNPs). Nuestros análisis moleculares y morfológicos revelaron la existencia de dos linajes evolutivos distintos de matamatas, genéticamente divergentes que se separaron en el Mioceno tardio (hace aproximadamente 12.7 millones de años), correspondiendo al tiempo en que se estableció la cuenca del Orinoco. Como resultado de nuestros análisis, describimos las genéticamente y morfológicamente distintas matamatas de las cuencas del Orinoco, Río Negro y Essequibo como una especie nueva para la ciencia (Chelus orinocensis sp. nov.). Chelus fimbriata sensu stricto se distribuye en la cuenca del Amazonas y en el drenaje del Mahury. Adicionalmente, los análisis revelaron que cada especie muestra diferenciación filogeográfica. Para C. orinocensis, hay una moderada diferenciación mitocondrial entre el Orinoco y el Río Negro. Para C. fimbriata, hay una diferenciación más pronunciada, concordando con los diferentes sistemas fluviales. Se identificó un clado de los ríos Amazonas, Ucayali y Mahury y otro de los ríos Madeira y Jaci Paraná. Las C. orinocensis de los ríos Essequibo y Branco tienen haplotipos que constituyen un tercer clado que se agrupa con C. fimbriata. Los análisis filogenéticos del intrón R35 y los datos de SNP asocian las matamatas de Essequibo y Branco con la nueva especie, sugiriendo flujo de genes pasado e introgresión mitocondrial antigua. Chelus orinocensis se colecta para el comercio de mascotas en Colombia y Venezuela. Sin embargo, ni se conoce el alcance de las colectas ni su impacto. Por lo tanto, es crucial recopilar más información y evaluar su explotación en todo su rango de distribución, comprender mejor su estado de conservación y para diseñar acciones apropiadas de conservación y manejo.
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Affiliation(s)
- Mario Vargas-Ramírez
- Estación de Biología Tropical Roberto Franco (EBTRF), Universidad Nacional de Colombia, Villavicencio, Colombia; Biodiversidad y Conservación Genética, Instituto de Genética, Universidad Nacional de Colombia, Bogotá, Colombia; Museum of Zoology, Senckenberg Dresden, A. B. Meyer Building, Dresden, Germany.
| | - Susana Caballero
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos-LEMVA, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - Mónica A Morales-Betancourt
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Programa Ciencias de la Biodiversidad, Línea de Recursos Hidrobiológicos, Pesqueros Continentales y Fauna Silvestre, Bogotá, Colombia
| | - Carlos A Lasso
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Programa Ciencias de la Biodiversidad, Línea de Recursos Hidrobiológicos, Pesqueros Continentales y Fauna Silvestre, Bogotá, Colombia
| | - Laura Amaya
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos-LEMVA, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - José Gregorio Martínez
- Grupo de Investigación Biociencias, Facultad de Ciencias de la Salud, Institución Universitaria Colegio Mayor de Antioquia, Medellín, Colombia; Laboratório de Evolução e Genética Animal, Departamento de Genetica, Universidade Federal do Amazonas, Manaus, Brazil
| | - Maria das Neves Silva Viana
- Laboratório de Evolução e Genética Animal, Departamento de Genetica, Universidade Federal do Amazonas, Manaus, Brazil
| | - Richard C Vogt
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Izeni Pires Farias
- Laboratório de Evolução e Genética Animal, Departamento de Genetica, Universidade Federal do Amazonas, Manaus, Brazil
| | - Tomas Hrbek
- Laboratório de Evolução e Genética Animal, Departamento de Genetica, Universidade Federal do Amazonas, Manaus, Brazil
| | - Patrick D Campbell
- Department of Life Sciences, Darwin Centre 1, Natural History Museum, London, UK
| | - Uwe Fritz
- Museum of Zoology, Senckenberg Dresden, A. B. Meyer Building, Dresden, Germany
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Montgelard C, Behrooz R, Arnal V, Asadi A, Geniez P, Kaboli M. Diversification and cryptic diversity of
Ophisops elegans
(Sauria, Lacertidae). J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12369] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Claudine Montgelard
- CEFE PSL‐EPHE (Biogéographie et Ecologie des Vertébrés) CNRS Université de Montpellier Univ Paul Valéry Montpellier 3 IRD Montpellier France
- Department of Zoology Centre for Ecological Genomics and Wildlife Conservation University of Johannesburg Johannesburg South Africa
| | - Roozbeh Behrooz
- CEFE PSL‐EPHE (Biogéographie et Ecologie des Vertébrés) CNRS Université de Montpellier Univ Paul Valéry Montpellier 3 IRD Montpellier France
| | - Véronique Arnal
- CEFE PSL‐EPHE (Biogéographie et Ecologie des Vertébrés) CNRS Université de Montpellier Univ Paul Valéry Montpellier 3 IRD Montpellier France
| | - Atefeh Asadi
- CEFE PSL‐EPHE (Biogéographie et Ecologie des Vertébrés) CNRS Université de Montpellier Univ Paul Valéry Montpellier 3 IRD Montpellier France
| | - Philippe Geniez
- CEFE PSL‐EPHE (Biogéographie et Ecologie des Vertébrés) CNRS Université de Montpellier Univ Paul Valéry Montpellier 3 IRD Montpellier France
| | - Mohammad Kaboli
- Department of Environmental Science Faculty of Natural Resources University of Tehran Karaj Iran
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15
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Lecocq T, Biella P, Martinet B, Rasmont P. Too strict or too loose? Integrative taxonomic assessment ofBombus lapidariuscomplex (Hymenoptera: Apidae). ZOOL SCR 2019. [DOI: 10.1111/zsc.12402] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Thomas Lecocq
- Laboratory of Zoology Research Institute of Biosciences University of Mons Mons Belgium
- Inra URAFPA Université de Lorraine Nancy France
| | - Paolo Biella
- Department of Biotechnology and Biosciences University of Milano-Bicocca Milano Italy
| | - Baptiste Martinet
- Laboratory of Zoology Research Institute of Biosciences University of Mons Mons Belgium
| | - Pierre Rasmont
- Laboratory of Zoology Research Institute of Biosciences University of Mons Mons Belgium
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16
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Behrooz R, Kaboli M, Arnal V, Nazarizadeh M, Asadi A, Salmanian A, Ahmadi M, Montgelard C. Conservation Below the Species Level: Suitable Evolutionarily Significant Units among Mountain Vipers (the Montivipera raddei complex) in Iran. J Hered 2019; 109:416-425. [PMID: 29401236 DOI: 10.1093/jhered/esy005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 01/23/2018] [Indexed: 02/05/2023] Open
Abstract
Northern and western mountains of Iran are among the most important biodiversity and endemism hot spots for reptiles in the Middle East. Among herpetofauna, the montivipers represent an emblematic and fragmented endemic group for which estimating their level of genetic differentiation and defining conservation priorities is urgently needed. Here, we present the most comprehensive phylogenetic study on the Montivipera raddei species group comprising all 5 known taxa, among which 3 are endemic to Iran. Based on 2 mitochondrial genes, phylogenetic and phylogeographic analyses revealed 3 major lineages each presenting very contrasting distribution areas. The Iranian montivipers are highly structured in clades showing low genetic diversity and corresponding to high altitude summits. Molecular dating revealed the role of Quaternary paleo-climatic oscillations and altitudinal movements of montivipers in shaping genetic diversity and differentiation of these sky-island taxa. In addition, the best scenario of historical biogeography allowed identifying 3 possible refugial areas in Iran most likely arising by vicariance. Based on our mitochondrial results and pending additional data, we recognize 3 candidate species among the M. raddei complex: M. raddei, Montivipera latifii, and Montivipera kuhrangica that are coherent with their geographical distribution. We propose that the most appropriate evolutionary significant units for conservation of the montivipers are represented by 13 units among which 6 are recognized as high priority. Finally, we suggest some recommendations to the IUCN as well as to the Iranian conservation policies with respect to conservation prioritization.
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Affiliation(s)
- Roozbeh Behrooz
- CEFE, PSL-EPHE (Biogéographie et Ecologie des Vertébrés), CNRS, Univ. Montpellier, Univ Paul Valéry Montpellier, IRD, Montpellier, France
| | - Mohammad Kaboli
- Department of Environmental Science, Faculty of Natural Resources, University of Tehran, Karaj, Iran
| | - Véronique Arnal
- CEFE, PSL-EPHE (Biogéographie et Ecologie des Vertébrés), CNRS, Univ. Montpellier, Univ Paul Valéry Montpellier, IRD, Montpellier, France
| | - Masoud Nazarizadeh
- Department of Environmental Science, Faculty of Natural Resources, University of Tehran, Karaj, Iran
| | - Atefeh Asadi
- CEFE, PSL-EPHE (Biogéographie et Ecologie des Vertébrés), CNRS, Univ. Montpellier, Univ Paul Valéry Montpellier, IRD, Montpellier, France
| | - Amin Salmanian
- Department of Natural Resources Engineering (Habitats and Biodiversity), Faculty of Environment and Energy (FEE), Tehran Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mohsen Ahmadi
- Department of Natural Resources, Isfahan University of Technology, Isfahan, Iran
| | - Claudine Montgelard
- CEFE, PSL-EPHE (Biogéographie et Ecologie des Vertébrés), CNRS, Univ. Montpellier, Univ Paul Valéry Montpellier, IRD, Montpellier, France.,Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Johannesburg, South Africa
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17
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Liu J, Guo X, Chen D, Li J, Yue B, Zeng X. Diversification and historical demography of the rapid racerunner (Eremias velox) in relation to geological history and Pleistocene climatic oscillations in arid Central Asia. Mol Phylogenet Evol 2019; 130:244-258. [DOI: 10.1016/j.ympev.2018.10.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 10/21/2018] [Accepted: 10/22/2018] [Indexed: 10/28/2022]
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18
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Richardson BJ. Subspecies definitions and legislation: from eastern wallaroo (Osphranter robustus robustus) to euro (Osphranter robustus erubescens). AUSTRALIAN MAMMALOGY 2019. [DOI: 10.1071/am17032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
As a consequence of genetic studies of population structuring, the usefulness of subspecies has been questioned, with opinions divided. The situation is further confused by the use of varying species and subspecies concepts. Most alternatives require each taxon to be following an independent evolutionary trajectory. These include traditional approaches and the more recent phylogenetic species concept. The latter has led to large increases in the apparent number of taxa in some groups, though strong objections have been raised to this approach. An alternative, the ecological species concept, has been opposed by phylogeneticists. These two approaches are compared using morphological and genetic data from common wallaroo (Osphranter robustus) populations. The different taxonomies that might result (many species, one species with two subspecies, one species with no subspecies) can have significant consequences for legislative and management decisions. The ecological approach is considered preferable for subspecies and the present taxonomy is maintained. A potential location of the boundary between the wallaroo subspecies is proposed. How the use of the different subspecies definitions would affect legislative decisions is explored.
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19
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Kessler AE, Santos MA, Flatz R, Batbayar N, Natsagdorj T, Batsuuri D, Bidashko FG, Galbadrakh N, Goroshko O, Khrokov VV, Unenbat T, Vagner II, Wang M, Smith CI. Mitochondrial Divergence between Western and Eastern Great Bustards: Implications for Conservation and Species Status. J Hered 2018; 109:641-652. [PMID: 29917081 DOI: 10.1093/jhered/esy025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 06/01/2018] [Indexed: 11/13/2022] Open
Abstract
The great bustard is the heaviest bird capable of flight and an iconic species of the Eurasian steppe. Populations of both currently recognized subspecies are highly fragmented and critically small in Asia. We used DNA sequence data from the mitochondrial cytochrome b gene and the mitochondrial control region to estimate the degree of mitochondrial differentiation and rates of female gene flow between the subspecies. We obtained genetic samples from 51 individuals of Otis tarda dybowskii representing multiple populations, including the first samples from Kazakhstan and Mongolia and samples from near the Altai Mountains, the proposed geographic divide between the subspecies, allowing for better characterization of the boundary between the 2 subspecies. We compared these with existing sequence data (n = 66) from Otis tarda tarda. Our results suggest, though do not conclusively prove, that O. t. dybowskii and O. t. tarda may be distinct species. The geographic distribution of haplotypes, phylogenetic analysis, analyses of molecular variance, and coalescent estimation of divergence time and female migration rates indicate that O. t. tarda and O. t. dybowskii are highly differentiated in the mitochondrial genome, have been isolated for approximately 1.4 million years, and exchange much less than 1 female migrant per generation. Our findings indicate that the 2 forms should at least be recognized and managed as separate evolutionary units. Populations in Xinjiang, China and Khövsgöl and Bulgan, Mongolia exhibited the highest levels of genetic diversity and should be prioritized in conservation planning.
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Affiliation(s)
| | | | - Ramona Flatz
- Department of Biology, Willamette University, Salem, OR
| | - Nyambayar Batbayar
- Wildlife Science and Conservation Center of Mongolia, Ulaanbaatar, Mongolia
| | - Tseveenmyadag Natsagdorj
- Institute of General and Experimental Biology, Mongolian Academy of Sciences, Ulaanbaatar, Mongolia
| | - Dashnyam Batsuuri
- Department of Environment & Biodiversity, HSESC, Oyu Tolgoi LLC, Ulaanbaatar, Mongolia
| | | | | | - Oleg Goroshko
- Daursky State Nature Biosphere Reserve, Chita, Russia.,Institute of Nature Resources, Ecology and Cryology, Russian Academy of Sciences, Chita, Russia
| | - Valery V Khrokov
- Association for the Conservation of Biodiversity in Kazakhstan, Astana, Kazakhstan
| | | | - Ivan I Vagner
- Hunters' and Fishers' Society of Southern Kazakhstan Province, Shymkent, Kazakhstan
| | - Muyang Wang
- Key Laboratory of Biogeography and Bioresources in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
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20
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Vargas-Ramírez M, del Valle C, Ceballos CP, Fritz U. Trachemys medemin. sp. from northwestern Colombia turns the biogeography of South American slider turtles upside down. J ZOOL SYST EVOL RES 2017. [DOI: 10.1111/jzs.12179] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Mario Vargas-Ramírez
- Grupo Biodiversidad y Conservación Genética; Instituto de Genética; Universidad Nacional de Colombia; Bogotá Colombia
- Museum of Zoology; Senckenberg Dresden; Dresden Germany
| | - Carlos del Valle
- Grupo Biodiversidad y Conservación Genética; Instituto de Genética; Universidad Nacional de Colombia; Bogotá Colombia
| | - Claudia P. Ceballos
- Grupo GaMMA; Escuela de Medicina Veterinaria; Facultad de Ciencias Agrarias; Universidad de Antioquia; Medellín Colombia
| | - Uwe Fritz
- Museum of Zoology; Senckenberg Dresden; Dresden Germany
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21
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Patten MA, Remsen JV. Complementary Roles of Phenotype and Genotype in Subspecies Delimitation. J Hered 2017; 108:462-464. [DOI: 10.1093/jhered/esx013] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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22
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Kaito T, Ota H, Toda M. The evolutionary history and taxonomic reevaluation of the Japanese coral snake, Sinomicrurus japonicus(Serpentes, Elapidae), endemic to the Ryukyu Archipelago, Japan, by use of molecular and morphological analyses. J ZOOL SYST EVOL RES 2017. [DOI: 10.1111/jzs.12162] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Takuma Kaito
- Graduate School of Engineering and Science; University of the Ryukyus; Nishihara Okinawa Japan
| | - Hidetoshi Ota
- Institute of Natural and Environmental Science; University of Hyogo, and Museum of Nature and Human Activities; Sanda Hyogo Japan
| | - Mamoru Toda
- Tropical Biosphere Research Center; University of the Ryukyus; Nishihara Okinawa Japan
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23
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JABLONSKI D, SZABOLCS M, SIMOVIĆ A, MIZSEI E. Color and pattern variation of the Balkan whip snake,Hierophis gemonensis (Laurenti, 1768). TURK J ZOOL 2017. [DOI: 10.3906/zoo-1606-15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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24
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Nazarizadeh M, Kaboli M, Rezaie HR, Harisini JI, Pasquet E. Phylogenetic relationships of Eurasian Nuthatches (Sitta europaea Linnaeus, 1758) from the Alborz and Zagros Mountains, Iran. ZOOLOGY IN THE MIDDLE EAST 2016. [DOI: 10.1080/09397140.2016.1226547] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Masoud Nazarizadeh
- Department of Environmental Sciences, Faculty of Natural Resources, University of Tehran, Karaj, Iran
| | - Mohammad Kaboli
- Department of Environmental Sciences, Faculty of Natural Resources, University of Tehran, Karaj, Iran
| | - Hamid Reza Rezaie
- Department of Environmental Sciences, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
| | - Jalil Imani Harisini
- Department of Environmental Sciences, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
| | - Eric Pasquet
- Muséum National d’Histoire Naturelle, Paris, France
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25
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Guo P, Liu Q, Zhu F, Zhong GH, Chen X, Myers EA, Che J, Zhang L, Ziegler T, Nguyen TQ, Burbrink FT. Complex longitudinal diversification across South China and Vietnam in Stejneger's pit viper,Viridovipera stejnegeri(Schmidt, 1925) (Reptilia: Serpentes: Viperidae). Mol Ecol 2016; 25:2920-36. [DOI: 10.1111/mec.13658] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 03/16/2016] [Accepted: 03/29/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Peng Guo
- College of Life Sciences and Food Engineering; Yibin University; Yibin 644007 China
| | - Qin Liu
- College of Life Sciences and Food Engineering; Yibin University; Yibin 644007 China
| | - Fei Zhu
- College of Life Sciences and Food Engineering; Yibin University; Yibin 644007 China
| | - Guang H. Zhong
- College of Life Sciences and Food Engineering; Yibin University; Yibin 644007 China
| | - Xin Chen
- Department of Biological Sciences; Dartmouth College; Hanover NH 03755 USA
| | - Edward A. Myers
- Department of Biology; The Graduate School and University Center; The City University of New York; 365 5th Avenue New York NY 10016 USA
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals; Kunming Institute of Zoology; Chinese Academy of Sciences; Kunming 650223 China
- Southeast Asia Biodiversity Research Institute; Chinese Academy of Sciences; Menglun Mengla Yunnan 666303 China
| | - Liang Zhang
- South China Institute of Endangered Animals; Guangzhou 510260 China
| | - Thomas Ziegler
- AG Zoologischer Garten Köln; Riehler Strasse 173 D-50735 Cologne Germany
| | - Truong Q. Nguyen
- Institute of Ecology and Biological Resources; Vietnam Academy of Science and Technology; 18 Hoang Quoc Viet Street Hanoi Vietnam
| | - Frank T. Burbrink
- Department of Herpetology; American Museum of Natural History; Central Park West at 79th Street New York NY 10024-5192 USA
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Carlson E, MacDonald AJ, Adamack A, McGrath T, Doucette LI, Osborne WS, Gruber B, Sarre SD. How many conservation units are there for the endangered grassland earless dragons? CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0819-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Folt B, Garrison N, Guyer C, Rodriguez J, Bond JE. Phylogeography and evolution of the Red Salamander (Pseudotriton ruber). Mol Phylogenet Evol 2016; 98:97-110. [PMID: 26872531 DOI: 10.1016/j.ympev.2016.01.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 01/04/2016] [Accepted: 01/28/2016] [Indexed: 11/27/2022]
Abstract
Phylogeographic studies frequently result in the elevation of subspecific taxa to species given monophyly, or the synonymy of subspecies that are not monophyletic. However, given limited or incongruent datasets, retention of subspecies can be useful to describe hypothesized incipient species or to illustrate interesting biological phenomena driving morphological diversity. Four subspecific taxa have been used to describe largely allopatric geographic variation within the species Pseudotriton ruber, a plethodontid salamander occupying stream and spring habitats across eastern North America: P. r. vioscai occurs in lowland Coastal Plain habitats, while P. r. ruber, P. r. nitidus, and P. r. schencki occupy upland regions in and around the Appalachian Mountains. Pseudotriton ruber co-occurs through its distribution with the aposematic newt Notophthalmus viridescens, and both species are hypothesized to be part of a Müllerian mimicry complex. In this study, we sequenced regions of two mitochondrial (cytochrome b, NADH dehydrogenase subunit 2) and one single copy nuclear protein-coding gene (pro-opiomelanocortin) from individuals sampled across much of the distribution of P. ruber and then used maximum-likelihood and Bayesian phylogenetic inference to test the monophyly of subspecies, reconstruct biogeographic history, and make inferences about morphological evolution. Phylogeographic hypotheses from mitochondrial and nuclear datasets described structure among populations of P. ruber which separated Coastal Plain and upland Appalachian populations, but subspecies were not monophyletic. Biogeographic reconstruction estimated the ancestor of all populations to have occupied and initially diverged in the Coastal Plain during the Pliocene (∼3.6mya), before one lineage subsequently invaded upland areas of Appalachia. Bold bright coloration of high elevation subspecies P. r. nitidus and P. r. schencki appears to have evolved twice. We hypothesize that the Müllerian mimicry complex with N. viridescens and P. ruber may provide a selective mechanism driving the co-evolution of striking bright and dull morphological variation among populations of both species. While P. ruber subspecies were not consistent with our criteria for diagnosing species (monophyly) and therefore could not be elevated to species, we advocate for the retention of subspecies because they describe hypotheses about an incipient species (P. r. vioscai) and how Müllerian mimicry may shape morphological diversity of species.
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Affiliation(s)
- Brian Folt
- Department of Biological Sciences and Museum of Natural History, 331 Funchess Hall, Auburn University, AL 36849, USA.
| | - Nicole Garrison
- Department of Biological Sciences and Museum of Natural History, 331 Funchess Hall, Auburn University, AL 36849, USA
| | - Craig Guyer
- Department of Biological Sciences and Museum of Natural History, 331 Funchess Hall, Auburn University, AL 36849, USA
| | - Juanita Rodriguez
- Department of Biological Sciences and Museum of Natural History, 331 Funchess Hall, Auburn University, AL 36849, USA
| | - Jason E Bond
- Department of Biological Sciences and Museum of Natural History, 331 Funchess Hall, Auburn University, AL 36849, USA
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Beukema W, Nicieza AG, Lourenço A, Velo-Antón G. Colour polymorphism inSalamandra salamandra(Amphibia: Urodela), revealed by a lack of genetic and environmental differentiation between distinct phenotypes. J ZOOL SYST EVOL RES 2016. [DOI: 10.1111/jzs.12119] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Wouter Beukema
- CIBIO/InBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; Instituto de Ciências Agrárias de Vairão; Universidade do Porto; Vairão Portugal
- Department of Pathology; Bacteriology and Avian Diseases; Faculty of Veterinary Medicine; Ghent University; Merelbeke Belgium
| | - Alfredo G. Nicieza
- Departamento de Biología de Organismos y Sistemas; Universidad de Oviedo; Oviedo Spain
- Unidad Mixta de Investigación en Biodiversidad (UMIB); CSIC-Universidad de Oviedo-Principado de Asturias; Mieres Spain
| | - André Lourenço
- CIBIO/InBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; Instituto de Ciências Agrárias de Vairão; Universidade do Porto; Vairão Portugal
| | - Guillermo Velo-Antón
- CIBIO/InBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; Instituto de Ciências Agrárias de Vairão; Universidade do Porto; Vairão Portugal
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Kanaan NC, Ray J, Stewart M, Russell KW, Fuller M, Bush SP, Caravati EM, Cardwell MD, Norris RL, Weinstein SA. Wilderness Medical Society Practice Guidelines for the Treatment of Pitviper Envenomations in the United States and Canada. Wilderness Environ Med 2015; 26:472-87. [DOI: 10.1016/j.wem.2015.05.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 05/12/2015] [Accepted: 05/27/2015] [Indexed: 10/22/2022]
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Gekko japonicus genome reveals evolution of adhesive toe pads and tail regeneration. Nat Commun 2015; 6:10033. [PMID: 26598231 PMCID: PMC4673495 DOI: 10.1038/ncomms10033] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 10/26/2015] [Indexed: 01/20/2023] Open
Abstract
Reptiles are the most morphologically and physiologically diverse tetrapods, and have undergone 300 million years of adaptive evolution. Within the reptilian tetrapods, geckos possess several interesting features, including the ability to regenerate autotomized tails and to climb on smooth surfaces. Here we sequence the genome of Gekko japonicus (Schlegel's Japanese Gecko) and investigate genetic elements related to its physiology. We obtain a draft G. japonicus genome sequence of 2.55 Gb and annotated 22,487 genes. Comparative genomic analysis reveals specific gene family expansions or reductions that are associated with the formation of adhesive setae, nocturnal vision and tail regeneration, as well as the diversification of olfactory sensation. The obtained genomic data provide robust genetic evidence of adaptive evolution in reptiles. Geckos are small, agile reptiles with nocturnal habits. Here, the authors sequence the genome of the Schlegel's Japanese Gecko and reveal gene family expansions and reductions associated with formation of adhesive setae, nocturnal vision, tail regeneration, and diversification of olfactory sensation.
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Kindler C, Moosig M, Branch WR, Harvey J, Kehlmaier C, Nagy ZT, Prokop H, Široký P, Fritz U. Comparative phylogeographies of six species of hinged terrapins (Pelusiosspp.) reveal discordant patterns and unexpected differentiation in theP. castaneus/P. chapinicomplex andP. rhodesianus. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12647] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Carolin Kindler
- Museum of Zoology; Senckenberg Dresden; A. B. Meyer Building Dresden 01109 Germany
| | - Maggie Moosig
- Museum of Zoology; Senckenberg Dresden; A. B. Meyer Building Dresden 01109 Germany
| | - William R. Branch
- Department of Herpetology; Port Elizabeth Museum; P.O. Box 13147 Humewood 6013 South Africa
- Department of Zoology; Nelson Mandela Metropolitan University; P.O. Box 77000 Port Elizabeth 6031 South Africa
| | - James Harvey
- 35 Carbis Road Pietermaritzburg 3201 South Africa
| | - Christian Kehlmaier
- Museum of Zoology; Senckenberg Dresden; A. B. Meyer Building Dresden 01109 Germany
| | - Zoltán T. Nagy
- Royal Belgian Institute of Natural Sciences; JEMU; Rue Vautier 29 Brussels 1000 Belgium
| | | | - Pavel Široký
- Department of Biology and Wildlife Diseases; Faculty of Veterinary Hygiene and Ecology; University of Veterinary and Pharmaceutical Sciences Brno; Palackého tř. 1/3 Brno 612 42 Czech Republic
| | - Uwe Fritz
- Museum of Zoology; Senckenberg Dresden; A. B. Meyer Building Dresden 01109 Germany
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Puckett EE, Etter PD, Johnson EA, Eggert LS. Phylogeographic Analyses of American Black Bears (Ursus americanus) Suggest Four Glacial Refugia and Complex Patterns of Postglacial Admixture. Mol Biol Evol 2015; 32:2338-50. [DOI: 10.1093/molbev/msv114] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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