57 research outputs found

    TableS2

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    Summary of mtDNA and microsatellite genetic variation for 52 a priori "sample groups". Note that this table also appears as an Excel file in online supplementary information associated with this article in Molecular Ecology

    Individual mtDNA sequences (n=1128)

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    Nexus file containing the 949 bp mtDNA ND5 sequences for each of the 1128 bobcat samples analyzed. Sequence name corresponds to the sample ID

    Unique mtDNA haplotypes (n=73)

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    Nexus file containing the sequences (949 bp) of the 73 unique ND5 mtDNA haplotypes discovered among 1128 bobcat samples. Also included in the file is the sequence "lynx" that was used as an outgroup (Canada lynx, Genbank accession AY598481)

    Microsatellite and Spatial Coordinate Data (n=1702)

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    Tab-delimited file containing microsatellite data, spatial coordinates, and other information for 1702 bobcat samples used in this study

    Phylogenetic depiction of the common-ancestry of invertebrate rhodopsins (<i>InRHO</i>) and melanopsin.

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    <p>The main opsin amino acid substitutions which are critical for the protein functional and structural innovations are color-coded. Maximum likelihood (ML) and Bayesian methods were used to build the phylogenetic tree and the support values of each method are shown for the main nodes (bootstrap and posterior probability, respectively). The grey amino acids are the maximum likelihood predicted motifs of the rhabdomeric photoreceptor ancestor.</p

    Site-specific selection models for the vertebrate melanopsin <i>OPN4m</i> and <i>OPN4x</i> genes.

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    <p>The likelihood values and the respective estimated parameters are shown for each model. The ω ratio is an average over all sites of the <i>OPN4m</i> and <i>OPN4x</i> paralogs. The asterisk (*) means that the alternative hypothesis is statistically significant at a 5% level, implementing the LRT (likelihood ratio test). Notes: <i>df</i> – degrees of freedom.</p

    Branch and site selective pressures during the <i>OPN4m/OPN4x</i> duplication event. A.

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    <p>Branch-site tests. Red lineages represent an inferred episode of positive selection. In those branches is represented the <i>p+</i> parameter (proportion of the positively selected sites). <b>B.</b> Representation of the positively selected and functional divergence sites (type I in yellow and type II in orange) in the three-dimensional structure of the <i>Gallus gallus</i> OPN4m protein. <b>C.</b> A detailed perspective of the retinal accommodation on the melanopsin molecule and the occurrence of the positively selected and type I and II functional divergence sites.</p

    Branch and site selective pressures during the teleost lineage-specific duplications: A. <i>OPN4m3/OPN4ma</i> and B. <i>OPN4x1/OPN4x2</i>.

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    <p>A punctual substitution (Y→C) was determined in the DRY motif in the OPN4m3 teleost melanopsin duplicant. Red lineages represent an episode of positive selection and the <i>p</i>+ parameter means the proportion of the positively selected sites. Black and grey circles represent the posterior probability level of G-protein coupling preference for each teleost fish amino acid sequence: 0.75–0.90 (grey circles) and >0.90 (black circles). The three-dimensional structure of the <i>Gallus gallus</i> OPN4m and OPN4x paralogs is also represented showing the occurrence of positive selection and functional divergence at the site level.</p

    Samples_information

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    Information of Lama guanicoe samples used in the analyses, including localities, geographic positions, type of sample, Haplotype and GenBank accessions numbers

    Melanopsin gene tree and the syntenic analyses in the melanopsin genomic paralogon.

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    <p>A. The phylogenetic analyses were retrieved with maximum likelihood and Bayesian methods and the support values for each method (bootstrap and posterior probability, respectively) are shown on the main nodes. The main duplication events that characterize melanopsin gene history are represented with yellow (2R) or green (3R) circles on the respective nodes. B. Paralogous genes are represented with the same color code (<i>LDB3</i>/<i>PDLIM5</i> and <i>BMPR1A</i>/<i>BMPR1B</i>). The red cross represents the gene loss in the mammalian <i>OPN4x</i>.</p
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