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      Hiding on jagged karst pinnacles: A new microendemic genus and species of a limestone-dwelling agamid lizard (Squamata: Agamidae: Draconinae) from Khammouan Province, Laos

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          Abstract

          We describe a unique new species and genus of agamid lizard from the karstic massifs of Khammouan Province, central Laos. Laodracon carsticola Gen. et sp. nov. is an elusive medium-sized lizard (maximum snout-vent length 101 mm) specifically adapted to life on limestone rocks and pinnacles. To assess the phylogenetic position of the new genus amongst other agamids, we generated DNA sequences from two mitochondrial gene fragments (16S rRNA and ND2) and three nuclear loci ( BDNF, RAG1 and c-mos), with a final alignment comprising 7 418 base pairs for 64 agamid species. Phylogenetic analyses unambiguously place the new genus in the mainland Asia subfamily Draconinae, where it forms a clade sister to the genus Diploderma from East Asia and the northern part of Southeast Asia. Morphologically, the new genus is distinguished from all other genera in Draconinae by possessing a notably swollen tail base with enlarged scales on its dorsal and ventral surfaces. Our work provides further evidence that limestone regions of Indochina represent unique “arks of biodiversity” and harbor numerous relict lineages. To date, Laodracon carsticola Gen. et sp. nov. is known from only two adult male specimens and its distribution seems to be restricted to a narrow limestone massif on the border of Khammouan and Bolikhamxai provinces of Laos. Additional studies are required to understand its life history, distribution, and conservation status.

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          MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

          We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge.
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            IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

            Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%.
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              MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.

              K Katoh (2002)
              A multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing methods. MAFFT includes two novel techniques. (i) Homo logous regions are rapidly identified by the fast Fourier transform (FFT), in which an amino acid sequence is converted to a sequence composed of volume and polarity values of each amino acid residue. (ii) We propose a simplified scoring system that performs well for reducing CPU time and increasing the accuracy of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length. Two different heuristics, the progressive method (FFT-NS-2) and the iterative refinement method (FFT-NS-i), are implemented in MAFFT. The performances of FFT-NS-2 and FFT-NS-i were compared with other methods by computer simulations and benchmark tests; the CPU time of FFT-NS-2 is drastically reduced as compared with CLUSTALW with comparable accuracy. FFT-NS-i is over 100 times faster than T-COFFEE, when the number of input sequences exceeds 60, without sacrificing the accuracy.
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                Author and article information

                Contributors
                Journal
                Zool Res
                Zool Res
                ZR
                Zoological Research
                Science Press (16 Donghuangchenggen Beijie, Beijing 100717, China )
                2095-8137
                18 November 2023
                : 44
                : 6
                : 1039-1051
                Affiliations
                [1 ] Faculty of Forestry, National University of Laos, Vientiane 01170, Lao PDR
                [2 ] IUCN Laos PDR, Vientiane 01160, Lao PDR
                [3 ] Faculty of Environmental Sciences, National University of Laos, Vientiane 01170, Lao PDR
                [4 ] Chelonian Conservation Center Laos, World Encyclopedia of Herpetofauna, Vientiane 01000, Lao PDR
                [5 ] Department of Vertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Moscow 119234, Russia
                [6 ] Rabbit in the Moon Foundation (RIM), Suanphueng, Ratchaburi 70180, Thailand
                [7 ] State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
                [8 ] Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin , Nay Pyi Taw 05282, Myanmar
                [9 ] Institute for Research and Training in Medicine, Biology and Pharmacy, Duy Tan University, Da Nang 550000, Vietnam
                [10 ] College of Medicine & Pharmacy, Duy Tan University, Da Nang 550000, Vietnam
                [11 ] Joint Russian-Vietnamese Tropical Research and Technological Center, Nghia Do, Cau Giay, Hanoi 122000, Vietnam
                Author notes
                Article
                zr-44-6-1039
                10.24272/j.issn.2095-8137.2023.062
                10802101
                37872005
                d7c8e29c-def8-49f5-8625-0e6bf02856da
                Copyright © 2023 Editorial Office of Zoological Research, Kunming Institute of Zoology, Chinese Academy of Sciences.

                This is an open-access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/4.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 28 July 2023
                : 9 October 2023
                Funding
                This work was supported by the Russian Science Foundation (22-14-00037) to N.A.P. (phylogenetic analyses), National Natural Science Foundation of China (32130015) to K.W. (data collection), and partially by Rufford Foundation (39897-1) to N.T.V. (data collection)
                Categories
                Article

                biodiversity,endemism,indochina,karstic landscape,laodracon carsticola,phylogeny,southeast asia,taxonomy

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