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      Phylogenetic analyses of distantly related clades of bent-toed geckos (genus Cyrtodactylus) reveal an unprecedented amount of cryptic diversity in northern and western Thailand

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          Abstract

          Cyrtodactylus species are the most diverse of the geckos and are widely distributed in Southeast Asia, including Thailand. However, their patterns of distribution, especially in northern and western parts of Thailand, remain unknown because few Cyrtodactylus species in these regions have been described. Thus, a data set of mitochondrial NADH dehydrogenase 2 ( ND2) gene and flanking tRNAs from Cyrtodactylus found in northern and western Thailand, including contiguous areas, was assembled to elucidate phylogenetic relationships and identify the distribution patterns of these geckos. The results showed four well-supported clades, a northwestern clade (A), a northern clade (B), a western clade (C), and a special clade characterized by specific morphological features (D). Clades A–C were grouped with strong support by the geography of their localities from northern Thailand (Mae Hong Son and Chiang Mai Provinces) along the Tenasserim mountain ranges to Phang-Nga Province, Thailand. Clade D is a distinct clade of Cyrtodactylus species characterized by a tuberculate and prehensile tail and distributed widely in mainland Southeast Asia. Overall, the results suggest a pattern of geographic separation and distribution of Cyrtodactylus in northern and western Thailand. Additionally, this study provides evidence of a hidden biodiversity of Cyrtodactylus in these regions.

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          Most cited references 55

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          MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

          The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
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            MUSCLE: multiple sequence alignment with high accuracy and high throughput.

             Robert Edgar (2004)
            We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.
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              jModelTest 2: more models, new heuristics and parallel computing.

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                Author and article information

                Contributors
                siriwadee.submission@gmail.com
                gsp621@163.com
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                27 January 2021
                27 January 2021
                2021
                : 11
                Affiliations
                [1 ]GRID grid.7132.7, ISNI 0000 0000 9039 7662, Department of Biology, Faculty of Science, , Chiang Mai University, ; Chiang Mai, 50200 Thailand
                [2 ]GRID grid.7132.7, ISNI 0000 0000 9039 7662, Research Center in Bioresources for Agriculture, Industry and Medicine, , Chiang Mai University, ; Chiang Mai, 50200 Thailand
                [3 ]GRID grid.412996.1, ISNI 0000 0004 0625 2209, School of Agriculture and Natural Resources, , University of Phayao, ; Phayao, 56000 Thailand
                [4 ]GRID grid.7132.7, ISNI 0000 0000 9039 7662, Department of Veterinary Bioscience and Veterinary Public Health, Faculty of Veterinary Medicine, , Chiang Mai University, ; Chiang Mai, 50100 Thailand
                [5 ]GRID grid.7132.7, ISNI 0000 0000 9039 7662, Excellence Center in Veterinary Bioscience, , Chiang Mai University, ; Chiang Mai, 50200 Thailand
                [6 ]GRID grid.14476.30, ISNI 0000 0001 2342 9668, Biological Faculty, Department of Vertebrate Zoology, , Moscow State University, ; Moscow, Russia 119234
                [7 ]Laboratory of Tropical Ecology, Joint Russian-Vietnamese Tropical Research and Technological Center, Hanoi, Vietnam
                [8 ]GRID grid.9227.e, ISNI 0000000119573309, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, , Chinese Academy of Sciences, ; Kunming, 650223 Yunnan China
                [9 ]Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, 05282 Myanmar
                [10 ]GRID grid.464309.c, ISNI 0000 0004 6431 5677, Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, , Guangdong Academy of Science, ; Guangzhou, 510260 Guangdong China
                Article
                70640
                10.1038/s41598-020-70640-8
                7840752
                33504821
                © The Author(s) 2021

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                Funding
                Funded by: Thailand Science Research and Innovation (TSRI)
                Award ID: DBG6180025
                Award Recipient :
                Funded by: Unit of Excellence 2020 on Biodiversity and Natural Resources Management, University of Phayao
                Award ID: UoE63005
                Award Recipient :
                Funded by: Russian Science Foundation
                Award ID: 19-14-00050
                Award Recipient :
                Funded by: Southeast Asia Biodiversity Research Institute, CAS
                Award ID: Y4ZK111B01: 2017CASSEABRIQG002
                Award Recipient :
                Funded by: International Partnership Program of Chinese Academy of Sciences (CAS)
                Award ID: 152453KYSB20170033
                Award Recipient :
                Funded by: GDAS Special Project of Science and Technology Development
                Award ID: No.2018GDASCX-0107
                Award Recipient :
                Funded by: National Natural Science Foundation of China
                Award ID: No. 31471966
                Award Recipient :
                Categories
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                © The Author(s) 2021

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                phylogenetics, biogeography

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