14 research outputs found

    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

    Type I and type II divergence between the OPN4 paralogs and the teleost lineage-specific duplications.

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    <p>θ<sub>I</sub> and θ<sub>II</sub> are the coefficients of type I and II functional divergence. Asterisks (*) mark results with statistical significance at 5% level of confidence and <i>se</i> denotes the standard error.</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

    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

    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

    Additional file 3: Figure S1. of Adaptive genomic evolution of opsins reveals that early mammals flourished in nocturnal environments

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    Species-specific evolutionary rate for mammalian opsins. ω-lineages were standardized subtracting the median and divided by the interquartile range. Coloured circles correspond to the species subjected to branch selection tests and significant results are indicated with an asterisk (*). (PDF 501 kb

    Additional file 4: Table S3. of Adaptive genomic evolution of opsins reveals that early mammals flourished in nocturnal environments

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    Species-specific branch selection tests. The one-ratio model (H0) was tested against the two-ratios model considering the alternative hypotheses (H1) of verifying differentiated ω-ratio in the indicated branch. lnL is the logarithm of the model likelihood and the LRT is the likelihood ratio test. All the LRT comparisons were performed with 1 degree of freedom. Significant alternative hypothesis are marked with an asterisk (*) considering a Bonferroni corrected p-value of 0.002 (24 test comparisons). (PDF 278 kb

    Additional file 10: Table S7. of Adaptive genomic evolution of opsins reveals that early mammals flourished in nocturnal environments

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    Dataset of the eco-morphological variables for the studied mammalian species. Variables: activity pattern (nocturnal, cathemeral and diurnal), VS and UVS OPN1sw1 sensitivity, orbit convergence (degrees, °) and visual acuity (cycle per degree, cpd). OPN1sw1 inactive copies were indicated with an asterisk (*) in the column of the sw1 86 site. Data retrieved from the references [5, 11, 65–72]. (XLSX 22 kb
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