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      Integrative taxonomy of the rock-dwelling gecko Cnemaspis siamensis complex (Squamata, Gekkonidae) reveals a new species from Nakhon Si Thammarat Province, southern Thailand

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          Abstract

          The rock-dwelling gecko genus Cnemaspis is one of the most species-diverse genera of gekkonid in Thailand. Earlier studies relied on morphological data to identify species, but cryptic morphology often obscured species diversity in Cnemaspis . In this study, an integrative taxonomic approach based on morphological characters and sequences of the mitochondrial NADH dehydrogenase subunit 2 (ND2) gene were used to clarify current taxonomy of the Cnemaspis siamensis complex and delimit a new species from Lan Saka District, Nakhon Si Thammarat Province, southern Thailand. Cnemaspis lineatubercularis sp. nov. is distinguished from other congeneric species by the combination of morphological characters: (1) maximum snout-vent length (SVL) of 40.6 mm (mean 38.8 ± SD 1.4, N = 12) in adult males and maximum SVL of 41.8 mm (mean 39.5 ± SD 1.9, N = 7) in adult females; (2) 8–9 supralabial and infralabial scales; (3) gular, pectoral, abdominal, and subcaudal scales keeled; (4) rostral, interorbitals, supercilium, palmar scales, and ventral scales of brachia smooth; (5) 5–6 small, subconical spine-like tubercles present on flanks; (6) 19–21 paravertebral tubercles linearly arranged; (7) 27–29 subdigital lamellae under the fourth toe; (8) 4–7 pore-bearing precloacal scales, pores rounded arranged in chevron shape and separated only in males; (9) one postcloacal tubercles each side in males; (10) ventrolateral caudal tubercles present anteriorly; (11) caudal tubercles restricted to a single paravertebral row on each side; (12) single median row of subcaudal scales keeled and lacking enlarged median row; and (13) gular region, abdomen, limbs and subcaudal region yellowish only in males. Genetically, the uncorrected pairwise divergences between the new species and their congeners in the C. siamensis group were between 15.53–28.09%. The new species is currently known only from granitic rocky streams at Wang Mai Pak Waterfall in the Nakhon Si Thammarat mountain range. Its discovery suggests that additional unrecognized species of Cnemaspis may still occur in unexplored areas of southern Thailand.

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          MRBAYES: Bayesian inference of phylogenetic trees.

          The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo. MRBAYES, including the source code, documentation, sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html.
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            Discriminant analysis of principal components: a new method for the analysis of genetically structured populations

            Background The dramatic progress in sequencing technologies offers unprecedented prospects for deciphering the organization of natural populations in space and time. However, the size of the datasets generated also poses some daunting challenges. In particular, Bayesian clustering algorithms based on pre-defined population genetics models such as the STRUCTURE or BAPS software may not be able to cope with this unprecedented amount of data. Thus, there is a need for less computer-intensive approaches. Multivariate analyses seem particularly appealing as they are specifically devoted to extracting information from large datasets. Unfortunately, currently available multivariate methods still lack some essential features needed to study the genetic structure of natural populations. Results We introduce the Discriminant Analysis of Principal Components (DAPC), a multivariate method designed to identify and describe clusters of genetically related individuals. When group priors are lacking, DAPC uses sequential K-means and model selection to infer genetic clusters. Our approach allows extracting rich information from genetic data, providing assignment of individuals to groups, a visual assessment of between-population differentiation, and contribution of individual alleles to population structuring. We evaluate the performance of our method using simulated data, which were also analyzed using STRUCTURE as a benchmark. Additionally, we illustrate the method by analyzing microsatellite polymorphism in worldwide human populations and hemagglutinin gene sequence variation in seasonal influenza. Conclusions Analysis of simulated data revealed that our approach performs generally better than STRUCTURE at characterizing population subdivision. The tools implemented in DAPC for the identification of clusters and graphical representation of between-group structures allow to unravel complex population structures. Our approach is also faster than Bayesian clustering algorithms by several orders of magnitude, and may be applicable to a wider range of datasets.
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                Author and article information

                Contributors
                Journal
                Zookeys
                Zookeys
                2
                urn:lsid:arphahub.com:pub:45048D35-BB1D-5CE8-9668-537E44BD4C7E
                urn:lsid:zoobank.org:pub:91BD42D4-90F1-4B45-9350-EEF175B1727A
                ZooKeys
                Pensoft Publishers
                1313-2989
                1313-2970
                2020
                12 May 2020
                : 932
                : 129-159
                Affiliations
                [1 ] Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, 10900 Thailand Kasetsart University Bangkok Thailand
                [2 ] Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok, 10110 Thailand Srinakharinwirot University Bangkok Thailand
                [3 ] Department of Biological Sciences and Museum of Natural History, Auburn University, Auburn, AL, USA Auburn University Auburn United States of America
                [4 ] Section of Research and Collections, North Carolina Museum of Natural Sciences, Raleigh, NC, USA North Carolina Museum of Natural Sciences Raleigh United States of America
                Author notes
                Corresponding author: Anchalee Aowphol ( fsciacl@ 123456ku.ac.th )

                Academic editor: A. Bauer

                Author information
                https://orcid.org/0000-0003-3767-5274
                https://orcid.org/0000-0001-9504-4601
                Article
                50602
                10.3897/zookeys.932.50602
                7237529
                ec1b5ff7-892a-43ad-8c5d-6d7c77fade5c
                Natee Ampai, Perry L. Wood Jr, Bryan L. Stuart, Anchalee Aowphol

                This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 29 January 2020
                : 21 March 2020
                Funding
                Funded by: Thailand Research Fund 501100004396 http://doi.org/10.13039/501100004396
                Categories
                Research Article
                Gekkonidae
                Systematics
                Taxonomy
                Cenozoic
                Asia
                Far East
                Thailand

                Animal science & Zoology
                cnemaspis ,morphology,phylogeny,species diversity,taxonomy,thailand,animalia,squamata,gekkonidae

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