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      A new species of Phrynoglossus Peters, 1867; Dicroglossidae) from southeastern Bangladesh, with comments on the genera Occidozyga and Phrynoglossus

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          Abstract

          We describe a new cryptic species of Phrynoglossus from Chattogram Division, Bangladesh based on an integrative taxonomic analysis based on morphology, phylogenetics, and bioacoustics which unambiguously support the placement of the species in the genus Phrynoglossus. We also present a compilation of published morphological characters for all twelve Phrynoglossus species and two species of Occidozyga as well as comments on taxonomy, morphology, and geographic distribution for the two genera. The new species is found to be most morphologically similar to P. martensii, however a provided set of character states visibly differentiates these two species. Finally, habitat for Phrynoglossus swanbornorum sp. nov. is highly fragmented and faces imminent threats from development and agriculture, and although it is confirmed to occur within government protected areas in the southeastern region of Bangladesh, few wildlife regulations are enforced within them. Thus, following IUCN criteria, we consider the new species as Endangered based on criteria B1ab(i,ii,iii,iv) + 2ab(i,ii,iii,iv).

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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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            MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

            Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d N /d S rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
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              RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.

              RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML). Low-level technical optimizations, a modification of the search algorithm, and the use of the GTR+CAT approximation as replacement for GTR+Gamma yield a program that is between 2.7 and 52 times faster than the previous version of RAxML. A large-scale performance comparison with GARLI, PHYML, IQPNNI and MrBayes on real data containing 1000 up to 6722 taxa shows that RAxML requires at least 5.6 times less main memory and yields better trees in similar times than the best competing program (GARLI) on datasets up to 2500 taxa. On datasets > or =4000 taxa it also runs 2-3 times faster than GARLI. RAxML has been parallelized with MPI to conduct parallel multiple bootstraps and inferences on distinct starting trees. The program has been used to compute ML trees on two of the largest alignments to date containing 25,057 (1463 bp) and 2182 (51,089 bp) taxa, respectively. icwww.epfl.ch/~stamatak
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                Author and article information

                Contributors
                Journal
                PeerJ
                PeerJ
                peerj
                peerj
                PeerJ
                PeerJ Inc. (San Diego, USA )
                2167-8359
                19 August 2021
                2021
                : 9
                : e11998
                Affiliations
                [1 ]Creative Conservation Alliance , Dhaka, Dhaka District, Bangladesh
                [2 ]Department of Zoology, Jagannath University , Dhaka, Dhaka District, Bangladesh
                Article
                11998
                10.7717/peerj.11998
                8380431
                3d72ec98-b93f-4f89-9c21-11488f3c5b28
                ©2021 Trageser et al.

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.

                History
                : 14 January 2021
                : 27 July 2021
                Funding
                Funded by: Whitley Fund for Nature
                Field work and laboratory costs for this study was supported by the Creative Conservation Alliance with funding from the Whitley Fund for Nature. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Biodiversity
                Conservation Biology
                Ecology
                Taxonomy
                Zoology

                amphibia,systematics,phylogeny,puddle frog,conservation,species complex,bioacoustic,morphology,anura

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