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      Multilocus genetic and morphological phylogenetic analysis reveals a radiation of shiny South Asian jumping spiders (Araneae, Salticidae)

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          Abstract

          Abstract

          This study presents a systematic revision of South Asian members of the Tribe Chrysillini Simon, 1901. Genetic and morphological variations were analysed of a “similar-looking” group of species that were initially identified as members of the jumping spider genera Chrysilla Thorell, 1887 and Phintella Strand, in Bösenberg and Strand 1906 to determine their phylogenetic relationships. Results suggest that the assessed morphospecies complex constitute of three evolutionary lineages, two previously unrecognised, which are described and diagnosed as two new genera: Phintelloides gen. n. and Proszynskia gen. n. The third lineage, Phintella , is sister to these proposed genera. The following new species are described: Phintelloides alborea sp. n., P. brunne sp. n., P. flavoviri sp. n., P. flavumi sp. n., P. orbisa sp. n., Phintella argentea sp. n., and P. jaleeli sp. n. Sri Lanka is rich in biodiversity but currently has one of the highest rates of deforestation. Lack of clarity on diversity and distribution of the islands’ biodiversity can lead to underestimations during threat assessments and thus downgrading of conservation needs of individual species.

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          SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information

          We present SequenceMatrix, software that is designed to facilitate the assembly and analysis of multi-gene datasets. Genes are concatenated by dragging and dropping FASTA, NEXUS, or TNT files with aligned sequences into the program window. A multi-gene dataset is concatenated and displayed in a spreadsheet; each sequence is represented by a cell that provides information on sequence length, number of indels, the number of ambiguous bases ("Ns"), and the availability of codon information. Alternatively, GenBank numbers for the sequences can be displayed and exported. Matrices with hundreds of genes and taxa can be concatenated within minutes and exported in TNT, NEXUS, or PHYLIP formats, preserving both character set and codon information for TNT and NEXUS files. SequenceMatrix also creates taxon sets listing taxa with a minimum number of characters or gene fragments, which helps assess preliminary datasets. Entire taxa, whole gene fragments, or individual sequences for a particular gene and species can be excluded from export. Data matrices can be re-split into their component genes and the gene fragments can be exported as individual gene files. SequenceMatrix also includes two tools that help to identify sequences that may have been compromised through laboratory contamination or data management error. One tool lists identical or near-identical sequences within genes, while the other compares the pairwise distance pattern of one gene against the pattern for all remaining genes combined. SequenceMatrix is Java-based and compatible with the Microsoft Windows, Apple MacOS X and Linux operating systems. The software is freely available from http://code.google.com/p/sequencematrix/. © The Willi Hennig Society 2010.
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            Enzyme clearing of alcian blue stained whole small vertebrates for demonstration of cartilage.

            Preparation of small vertebrates cleared after alcian blue staining of cartilage is facilitated by trypsin digestion. Specimens are fixed in formation, washed, skinned, and eviscerated. After staining in a solution of alcian blue in acetic acid-alcohol for 24-48 hours, they are transferred to water through graded alcohols. Excess alcian blue is removed over a period of up to three weeks by changes every 2-3 days of 1% trypsin in approximately one-third-saturated sodium borate. Bony tissues may be stained after this in a solution of alizarin red S in 0.5% KOH. Specimens are bleached if necessary and dehydrated through graded KOH-glycerine mixtures for storage in glycerine. Since alcohol treatment in addition to formalin fixation does not affect results with this method, it should be useful to researchers who want to study the cartilage or cartilaginous skeletons in museum specimens, which are routinely fixed in formalin and stored in alcohol.
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              T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks

              T-REX (Tree and reticulogram REConstruction) is a web server dedicated to the reconstruction of phylogenetic trees, reticulation networks and to the inference of horizontal gene transfer (HGT) events. T-REX includes several popular bioinformatics applications such as MUSCLE, MAFFT, Neighbor Joining, NINJA, BioNJ, PhyML, RAxML, random phylogenetic tree generator and some well-known sequence-to-distance transformation models. It also comprises fast and effective methods for inferring phylogenetic trees from complete and incomplete distance matrices as well as for reconstructing reticulograms and HGT networks, including the detection and validation of complete and partial gene transfers, inference of consensus HGT scenarios and interactive HGT identification, developed by the authors. The included methods allows for validating and visualizing phylogenetic trees and networks which can be built from distance or sequence data. The web server is available at: www.trex.uqam.ca.
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                Author and article information

                Contributors
                Journal
                Zookeys
                Zookeys
                2
                urn:lsid:arphahub.com:pub:45048d35-bb1d-5ce8-9668-537e44bd4c7e
                urn:lsid:zoobank.org:pub:91BD42D4-90F1-4B45-9350-EEF175B1727A
                ZooKeys
                Pensoft Publishers
                1313-2989
                1313-2970
                2019
                16 January 2019
                : 839
                : 1-81
                Affiliations
                [1 ] National Institute of Fundamental Studies, Hantana Road, Kandy, Sri Lanka National Institute of Fundamental Studies Kandy Sri Lanka
                [2 ] Department of Zoology, Faculty of Science, Eastern University, Vantharumoolai, Sri Lanka Eastern University Vantharumoolai Sri Lanka
                Author notes
                Corresponding author: Suresh P. Benjamin ( suresh.benjamin@ 123456gmail.com )

                Academic editor: J. Miller

                Article
                28312 urn:lsid:arphahub.com:pub:01aa5bf3-f296-57f8-9e2f-3a7743fd1927 urn:lsid:zoobank.org:pub:43089010-13EB-43A7-9FDE-AFA9E52AC431
                10.3897/zookeys.839.28312
                6482596
                31065224
                9769cde0-1c4e-4330-ac9e-5c255502bcdd
                Nilani Kanesharatnam, Suresh P. Benjamin

                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
                : 12 July 2018
                : 20 December 2018
                Categories
                Research Article
                Araneae
                Salticidae
                Systematics
                Asia

                Animal science & Zoology
                chrysillini ,cryptic species,ecomorphs,india,monophyly,new genera,parsimony,synapomorphies,animalia,araneae,salticidae

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