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      A striking new genus and species of cave-dwelling frog (Amphibia: Anura: Microhylidae: Asterophryinae) from Thailand

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          Abstract

          We report on a discovery of Siamophryne troglodytes Gen. et sp. nov., a new troglophilous genus and species of microhylid frog from a limestone cave in the tropical forests of western Thailand. To assess its phylogenetic relationships we studied the 12S rRNA–16S rRNA mtDNA fragment with final alignment comprising up to 2,591 bp for 56 microhylid species. Morphological characterization of the new genus is based on examination of external morphology and analysis of osteological characteristics using microCT-scanning. Phylogenetic analyses place the new genus into the mainly Australasian subfamily Asterophryinae as a sister taxon to the genus Gastrophrynoides, the only member of the subfamily known from Sundaland. The new genus markedly differs from all other Asterophryinae members by a number of diagnostic morphological characters and demonstrates significant mtDNA sequence divergence. We provide a preliminary description of a tadpole of the new genus. Thus, it represents the only asterophryine taxon with documented free-living larval stage and troglophilous life style. Our work demonstrates that S. troglodytes Gen. et sp. nov. represents an old lineage of the initial radiation of Asterophryinae which took place in the mainland Southeast Asia. Our results strongly support the “out of Indo-Eurasia” biogeographic scenario for this group of frogs. To date, the new frog is only known from a single limestone cave system in Sai Yok District of Kanchanaburi Province of Thailand; its habitat is affected by illegal bat guano mining and other human activities. As such, S. troglodytes Gen. et sp. nov. is likely to be at high risk of habitat loss. Considering high ecological specialization and a small known range of the new taxon, we propose a IUCN Red List status of endangered for it.

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          Molecular Cloning : A Laboratory Manual

          <p>The first two editions of this manual have been mainstays of molecular biology for nearly twenty years, with an unrivalled reputation for reliability, accuracy, and clarity.<br>In this new edition, authors Joseph Sambrook and David Russell have completely updated the book, revising every protocol and adding a mass of new material, to broaden its scope and maintain its unbeatable value for studies in genetics, molecular cell biology, developmental biology, microbiology, neuroscience, and immunology.<br>Handsomely redesigned and presented in new bindings of proven durability, this three–volume work is essential for everyone using today’s biomolecular techniques.<br>The opening chapters describe essential techniques, some well–established, some new, that are used every day in the best laboratories for isolating, analyzing and cloning DNA molecules, both large and small.<br>These are followed by chapters on cDNA cloning and exon trapping, amplification of DNA, generation and use of nucleic acid probes, mutagenesis, and DNA sequencing.<br>The concluding chapters deal with methods to screen expression libraries, express cloned genes in both prokaryotes and eukaryotic cells, analyze transcripts and proteins, and detect protein–protein interactions.<br>The Appendix is a compendium of reagents, vectors, media, technical suppliers, kits, electronic resources and other essential information.<br>As in earlier editions, this is the only manual that explains how to achieve success in cloning and provides a wealth of information about why techniques work, how they were first developed, and how they have evolved. </p>
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            Vast underestimation of Madagascar's biodiversity evidenced by an integrative amphibian inventory.

            Amphibians are in decline worldwide. However, their patterns of diversity, especially in the tropics, are not well understood, mainly because of incomplete information on taxonomy and distribution. We assess morphological, bioacoustic, and genetic variation of Madagascar's amphibians, one of the first near-complete taxon samplings from a biodiversity hotspot. Based on DNA sequences of 2,850 specimens sampled from over 170 localities, our analyses reveal an extreme proportion of amphibian diversity, projecting an almost 2-fold increase in species numbers from the currently described 244 species to a minimum of 373 and up to 465. This diversity is widespread geographically and across most major phylogenetic lineages except in a few previously well-studied genera, and is not restricted to morphologically cryptic clades. We classify the genealogical lineages in confirmed and unconfirmed candidate species or deeply divergent conspecific lineages based on concordance of genetic divergences with other characters. This integrative approach may be widely applicable to improve estimates of organismal diversity. Our results suggest that in Madagascar the spatial pattern of amphibian richness and endemism must be revisited, and current habitat destruction may be affecting more species than previously thought, in amphibians as well as in other animal groups. This case study suggests that worldwide tropical amphibian diversity is probably underestimated at an unprecedented level and stresses the need for integrated taxonomic surveys as a basis for prioritizing conservation efforts within biodiversity hotspots.
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              TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics

              Background Most analysis programs for inferring molecular phylogenies are difficult to use, in particular for researchers with little programming experience. Results TREEFINDER is an easy-to-use integrative platform-independent analysis environment for molecular phylogenetics. In this paper the main features of TREEFINDER (version of April 2004) are described. TREEFINDER is written in ANSI C and Java and implements powerful statistical approaches for inferring gene tree and related analyzes. In addition, it provides a user-friendly graphical interface and a phylogenetic programming language. Conclusions TREEFINDER is a versatile framework for analyzing phylogenetic data across different platforms that is suited both for exploratory as well as advanced studies.
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                Author and article information

                Contributors
                Journal
                PeerJ
                PeerJ
                PeerJ
                PeerJ
                PeerJ
                PeerJ Inc. (San Francisco, USA )
                2167-8359
                23 February 2018
                2018
                : 6
                : e4422
                Affiliations
                [1 ] Division of Fishery, School of Agriculture and Natural Resources, University of Phayao , Phayao, Thailand
                [2 ] Department of Fishery, Ranong Marine Fisheries Station , Ranong, Thailand
                [3 ] Department of Ecology, Nakhon Pathom Rajabhat University , Nakhon Pathom Mueng, Nakhon Pathom, Thailand
                [4 ] Department of Zoology, Faculty of Science, Kasetsart University , Bangkok, Thailand
                [5 ] Geological Faculty, Petroleum Geology Department, Moscow State University , Moscow, Russia
                [6 ] Biological Faculty, Department of Vertebrate Zoology, Moscow State University , Moscow, Russia
                [7 ] Laboratory of Tropical Ecology, Joint Russian–Vietnamese Tropical Research and Technological Center , Hanoi, Vietnam
                Author information
                http://orcid.org/0000-0002-7576-2283
                Article
                4422
                10.7717/peerj.4422
                5828679
                29497587
                684a99cf-a65f-46cd-9534-1943a6f84db3
                © 2018 Suwannapoom 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
                : 21 December 2017
                : 7 February 2018
                Funding
                Funded by: Thailand Research Fund
                Award ID: DBG6180001
                Funded by: Russian Foundation for Basic Research
                Award ID: RFBR 15-29-02771
                Funded by: Russian Science Foundation
                Award ID: 14-50-00029
                This work was supported by the Thailand Research Fund (DBG6180001), and by the Russian Foundation for Basic Research (Grant No. RFBR 15-29-02771) (fieldwork, specimen examination). Molecular experiments, phylogenetic analyses, specimen storage, examination, and microCT-analysis were carried out with the financial support of Russian Science Foundation (RSF grant No. 14-50-00029). The funders had no role in the study design, data collection and analysis, decision to publish or preparation of the manuscript.
                Categories
                Biodiversity
                Biogeography
                Evolutionary Studies
                Taxonomy
                Zoology

                kanchanaburi province,siamophryne troglodytesgen. et sp. nov.,tadpole,troglophilous life style,tenasserim,sundaland,mtdna,biogeography,microct-scanning

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