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      A new species of Leptobrachella Smith 1925 (Anura, Megophryidae) from Lai Chau Province, Vietnam

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          Abstract

          Background

          The genus Leptobrachella ( Anura , Megophryidae ) was originally described, based on the type species from Sarawak (Malaysia), Leptobrachella mjöbergi Smith. The taxa in the group were previously classified into different genera, i.e, Paramegophrys Liu; Leptolalax Dubois; Lalax Delorme, Dubois, Grosjean & Ohler; and Lalos Dubois, Grosjean, Ohler, Adler & Zhao. However, Yuan et al. synonymised Leptolalax with Leptobrachella in 2017. Members of Leptobrachella inhabit the forest floor and rocky streams in hilly evergreen forests. They are widely distributed from southern China and Myanmar through mainland Indochina to Peninsular Malaysia and the island of Borneo. However, the species diversity of the genus was indicated to be underestimated by phylogenetic analyses and a series of new species have been discovered recently. In Vietnam, 34 species of Leptobrachella are currently known and 75% (or 24 species) have been described or newly recorded from the country since 2010.

          New information

          We describe a new species, Leptobrachella huynhi sp. nov., from Sin Ho District, Lai Chau Province. The new species is distinguished from its congeners by genetic divergences ranging from 3.62 to 18.51% (16S rRNA gene) and morphological differences: size medium (SVL 37.8–40.2 mm in adult females); head longer than wide; tympanum distinct; skin on entire dorsum shagreened; toes without webbing and with narrow lateral fringes; supratympanic ridge slightly rough with few nodules; dorsum grey-brown with indistinct dark brown markings; an interorbital region with a stacking double Y-shaped marking; centre of belly creamy-white, outer edges of belly brown with small whitish spots; iris copper. The new species is the 35 th species of the genus Leptobrachella known from Vietnam.

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          Most cited references35

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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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            MEGA11: Molecular Evolutionary Genetics Analysis Version 11

            The Molecular Evolutionary Genetics Analysis (MEGA) software has matured to contain a large collection of methods and tools of computational molecular evolution. Here, we describe new additions that make MEGA a more comprehensive tool for building timetrees of species, pathogens, and gene families using rapid relaxed-clock methods. Methods for estimating divergence times and confidence intervals are implemented to use probability densities for calibration constraints for node-dating and sequence sampling dates for tip-dating analyses. They are supported by new options for tagging sequences with spatiotemporal sampling information, an expanded interactive Node Calibrations Editor , and an extended Tree Explorer to display timetrees. Also added is a Bayesian method for estimating neutral evolutionary probabilities of alleles in a species using multispecies sequence alignments and a machine learning method to test for the autocorrelation of evolutionary rates in phylogenies. The computer memory requirements for the maximum likelihood analysis are reduced significantly through reprogramming, and the graphical user interface has been made more responsive and interactive for very big data sets. These enhancements will improve the user experience, quality of results, and the pace of biological discovery. Natively compiled graphical user interface and command-line versions of MEGA11 are available for Microsoft Windows, Linux, and macOS from www.megasoftware.net .
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              UFBoot2: Improving the Ultrafast Bootstrap Approximation

              Abstract The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has been steadily adopted as an efficient alternative to SBS and other bootstrap approaches. Here, we present UFBoot2, which substantially accelerates UFBoot and reduces the risk of overestimating branch supports due to polytomies or severe model violations. Additionally, UFBoot2 provides suitable bootstrap resampling strategies for phylogenomic data. UFBoot2 is 778 times (median) faster than SBS and 8.4 times (median) faster than RAxML rapid bootstrap on tested data sets. UFBoot2 is implemented in the IQ-TREE software package version 1.6 and freely available at http://www.iqtree.org.
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                Author and article information

                Contributors
                Journal
                Biodivers Data J
                Biodivers Data J
                1
                urn:lsid:arphahub.com:pub:F9B2E808-C883-5F47-B276-6D62129E4FF4
                urn:lsid:zoobank.org:pub:245B00E9-BFE5-4B4F-B76E-15C30BA74C02
                Biodiversity Data Journal
                Pensoft Publishers
                1314-2836
                1314-2828
                2024
                04 November 2024
                : 12
                : e136491
                Affiliations
                [1 ] Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi, Vietnam Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology Hanoi Vietnam
                [2 ] Forest Resources and Environment Center, Forest Inventory and Planning Institute, Hanoi, Vietnam Forest Resources and Environment Center, Forest Inventory and Planning Institute Hanoi Vietnam
                [3 ] Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam Graduate University of Science and Technology, Vietnam Academy of Science and Technology Hanoi Vietnam
                [4 ] Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam Institute of Genome Research, Vietnam Academy of Science and Technology Hanoi Vietnam
                [5 ] Zoological Garden, Cologne, Germany Zoological Garden Cologne Germany
                [6 ] Institute of Zoology, University of Cologne, Cologne, Germany Institute of Zoology, University of Cologne Cologne Germany
                Author notes
                Corresponding author: Cuong The Pham ( cuongiebr@ 123456gmail.com ).

                Academic editor: Bin Wang

                Author information
                https://orcid.org/0000-0002-0709-974X
                https://orcid.org/0000-0002-6601-0880
                https://orcid.org/0000-0002-5640-4536
                Article
                136491 25957
                10.3897/BDJ.12.e136491
                11555430
                df502f69-457b-4965-8679-ab6c9ee39f44
                Chung Van Hoang, Anh Mai Luong, Truong Quang Nguyen, Tao Thien Nguyen, Hoa Thi Ninh, Linh Hoang Tu Le, Thomas Ziegler, Cuong The Pham

                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
                : 06 September 2024
                : 31 October 2024
                Page count
                Figures: 5, Tables: 1, References: 34
                Categories
                Taxonomy & Inventories
                Chordata
                Megophryidae
                Amphibia
                Anura
                Vertebrata
                Animalia
                Taxonomy
                Phylogeny
                Systematics
                Vietnam
                Far East
                Asia

                leptobrachellahuynhi sp. nov.,sin ho,hoang lien range,molecular phylogeny,taxonomy

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