9 research outputs found

    Data for "Fish lateral line innovation: insights into the evolutionary genomic dynamics of a unique mechanosensory organ"

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    <p>This zip file "Fish_lateral_line_comparative_genomics_data" contains two folders and two text files.</p> <p> </p> <p>The data contained in them pretains to the manuscript: </p> <p>Siby Philip, João Paulo Machado, Emanuel Maldonado, Vítor Vasconcelos, Stephen J O’Brien, Warren E Johnson, and Agostinho Antunes. Fish lateral line innovation: insights into the evolutionary genomic dynamics of a unique mechanosensory organ. Mol Biol Evol first published online July 27, 2012 doi:10.1093/molbev/mss194 </p> <p> </p> <p>The first folder "nexus_sequence_and_tree_file" contain "nexus" format files for all the 34 genes used in the study, the GBlocks filtered alignment followed by the corresponding phylogenetic tree. This file was used to carry out the HYPHY compartmentalization analysis (see the manuscript for details).</p> <p>The phylogenetic trees were built using PHYML and the best fit nucleotide substitution model was found using MrAIC, which is presented in the text file "MrAIC_AICc_models.txt".</p> <p>The second folder contains the phylogenetic trees used for the PAML analysis of the Postduplication branches, thus there are only 15 trees as specified in the manuscript.</p> <p>The text files contain the MrAIC chosen best fit substitution model (file 1) and the PyCogent Ensembl query script used (file 2; this same script is available in the PyCogent cookbook).</p> <p>any further request for data or detailed results should be addressed to Siby Philip (sibyphilips at gmail dot com).</p

    Western Ghats Barb Phylogenetics - Data

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    <p>This zip file contains data for the upcoming WG Barb phylogenetic revision paper. This file contains the alignment (phylip format) and the best ML tree by GARLI (methods obvious from the paper), the best ML tree with bootstrap probablities and bayesian posterior probablities. The zip file is currently locked (protected) but will be unlocked once the paper is accepted for publication.</p

    Data for "Morphological and genetic evidence for multiple evolutionary distinct lineages in the endangered and commercially exploited Red Lined Torpedo Barbs endemic to the Western Ghats of India" - Plos_one_June_2013

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    <p>Dataset for RLTB manuscript - "<strong><em>Morphological and genetic evidence for multiple evolutionary distinct lineages in the endangered and commercially exploited Red Lined Torpedo Barbs endemic to the Western Ghats of India</em></strong>". Data is submitted by Siby Philip. Authors for the paper are - Lijo John, Siby Philip, Neelesh Dahanukar, Anvar Ali PH, Josin Tharian, Rajeev Raghavan and Agostinho Antunes. (first and second authors are equal contributors, last and second last authors are both corresponding authors).</p> <p>The folder contains - Trace files (ABI files) for the sequences used for the study. The *BEAST xml file used to build the species tree and the ML distance matrix from the sequences.</p> <p>Any other details or help needed regarding the genetic methods/data should be sent to <em>sibyphilips</em> at_the_rate_of <em>gmail</em> DOT com.</p

    Morphological and Genetic Evidence for Multiple Evolutionary Distinct Lineages in the Endangered and Commercially Exploited Red Lined Torpedo Barbs Endemic to the Western Ghats of India

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    <div><p>Red lined torpedo barbs (RLTBs) (Cyprinidae: <i>Puntius</i>) endemic to the Western Ghats Hotspot of India, are popular and highly priced freshwater aquarium fishes. Two decades of indiscriminate exploitation for the pet trade, restricted range, fragmented populations and continuing decline in quality of habitats has resulted in their ‘Endangered’ listing. Here, we tested whether the isolated RLTB populations demonstrated considerable variation qualifying to be considered as distinct conservation targets. Multivariate morphometric analysis using 24 size-adjusted characters delineated all allopatric populations. Similarly, the species-tree highlighted a phylogeny with 12 distinct RLTB lineages corresponding to each of the different riverine populations. However, coalescence-based methods using mitochondrial DNA markers identified only eight evolutionarily distinct lineages. Divergence time analysis points to recent separation of the populations, owing to the geographical isolation, more than 5 million years ago, after the lineages were split into two ancestral stocks in the Paleocene, on north and south of a major geographical gap in the Western Ghats. Our results revealing the existence of eight evolutionarily distinct RLTB lineages calls for the re-determination of conservation targets for these cryptic and endangered taxa.</p></div

    Results of the DNA based species delimitation methods.

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    <p>Results of the DNA based species delimitation methods a) Heat-map showing the fixed distance threshold method and the clustering of the specimens; b) results of the GMYC method implemented on the cytb and cox1+ cytb ultrametric trees, the coloured blocks on the right side indicates the tips clustered together by the program as a same (putative) species; c) Result of the Bayesian method applied on the RLTB species tree, values at nodes are the speciation probabilities using three different prior settings (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069741#s4" target="_blank">materials and methods</a> for details); each evolutionarily distinct lineage (tip) is denoted with a distinct colour.</p

    Map showing distribution range of RLTBs and rivers from where samples were collected.

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    <p>Map showing distribution range of RLTBs and rivers from where samples were collected, the species-tree built in *BEAST is shown on the left side. Posterior probability values below 1 are shown at the nodes. Photograph of a specimen considered as <i>Puntius denisonii</i> is shown; notice the absence of a black spot on the dorsal fin which is the current diagnostic character for distinguishing it from its congener <i>Puntius chalakkudiensis</i> found at location CHD in the map, the tip label codes are explained in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069741#pone-0069741-t001" target="_blank">Table 1</a>. Note that according to the current taxonomy of RLTBs <i>P. denisonii</i> (most probably population PER-D), is nested within the different populations of <i>P. chalakkudiensis,</i> the other populations of <i>P.denisonii</i> are distributed above the palaghat gap. Here we show that each of these populations (labeled) qualify as evolutionarily distinct lineages.</p

    MANOVA/CVA discriminating different RLTB populations.

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    <p>MANOVA/CVA of 24 size adjusted biometric characters of 12 RLTB populations. (a) Clusters of all 12 populations on the first two canonical axis and (b) pair wise matrix of Fisher’s distances between the centroids of the clusters (upper diagonal) and P values for Fisher’s distances (lower diagonal). Percent discrimination by each canonical axis is shown in parenthesis.</p

    Micro-level distribution of the eight evolutionarily distinct lineages (EDL) including the two recognized species of RLTBs in the Western Ghats.

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    1<p>The precise type locality of <i>P. denisonii</i> is still unclear. Three river systems, Periyar, Pampa and Achankovil drain the larger landscape in and around from where Francis Day described <i>P. denisonii</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069741#pone.0069741-Day1" target="_blank">[89]</a>.</p><p>Lineages in bold represent the most heavily collected locations of RLTBs, see also <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069741#pone.0069741.s008" target="_blank">figure S8</a>. Voucher specimen of the specimens examined in our study are currently deposited at the museum of the Conservation Research Group (CRG), Department of.</p><p>Aquaculture, St. Albert’s College, Kochi, India.</p

    Results of Divergence time analysis.

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    <p>Timetree showing the divergence times of the major RLTB lineages, node bars denote the 95% credibility interval; values at nodes indicate the mean age in million years.</p
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