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      An integrative taxonomic revision of lesser gymnures (Eulipotyphla: Hylomys) reveals five new species and emerging patterns of local endemism in Tropical East Asia

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          Abstract

          We here present a comprehensive integrative taxonomic review of the genus Hylomys, using molecular (mitochondrial genomes and up to five nuclear loci) and morphological data from museum specimens across its distribution, resulting in the description of two new species and the elevation of three subspecies to specific status. This revision significantly increases the known diversity of Hylomys from two to seven extant species, challenging the traditional view of species-level diversity within gymnures. We discuss the implications of the taxonomic findings for conservation, particularly in relation to the restricted distribution ranges of several species that may be threatened by habitat loss and/or climate change. Our research emphasizes the importance of scientific collections and underscores the potential of museum genomics and additional field sampling to identify new species and improve our understanding of species diversity in poorly studied regions. Speciation events within Hylomys occurred during the Late Miocene and Early Pliocene, possibly driven by shifting climate conditions such as the strengthening of the Indian monsoon and the expansion of seasonally dry conditions. This study supports northern Sumatra and the southern Annamites as centres of localized endemicity and suggests the need for additional small mammal surveys across Sumatra’s Barisan Range.

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          The Sequence Alignment/Map format and SAMtools

          Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk
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            ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates

            Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates. The improvement is achieved by incorporating a model of rate-heterogeneity across sites not previously considered in this context, and by allowing concurrent searches of model-space and tree-space.
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              MultiQC: summarize analysis results for multiple tools and samples in a single report

              Motivation: Fast and accurate quality control is essential for studies involving next-generation sequencing data. Whilst numerous tools exist to quantify QC metrics, there is no common approach to flexibly integrate these across tools and large sample sets. Assessing analysis results across an entire project can be time consuming and error prone; batch effects and outlier samples can easily be missed in the early stages of analysis. Results: We present MultiQC, a tool to create a single report visualising output from multiple tools across many samples, enabling global trends and biases to be quickly identified. MultiQC can plot data from many common bioinformatics tools and is built to allow easy extension and customization. Availability and implementation: MultiQC is available with an GNU GPLv3 license on GitHub, the Python Package Index and Bioconda. Documentation and example reports are available at http://multiqc.info Contact: phil.ewels@scilifelab.se
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                Journal
                Zoological Journal of the Linnean Society
                Oxford University Press (OUP)
                0024-4082
                1096-3642
                December 21 2023
                December 21 2023
                Article
                10.1093/zoolinnean/zlad177
                2ab52d16-2bfb-435d-9b3d-814b38b8c004
                © 2023

                https://creativecommons.org/licenses/by-nc-nd/4.0/

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