14 research outputs found

    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

    Bayesian phylogenetic tree of the mtDNA COI gene from <i>Corbicula</i> genus.

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    <p>Both Bayesian Inference posterior probabilities (BI) and Maximum Likelihood bootstrap values (ML) are indicated at the nodes.* Indicates the presence of monoflagellate sperm, ** indicates the presence of biflagellate sperm, <sup><b>α</b></sup> represents androgenetic lineages confirmed by cytological studies [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158108#pone.0158108.ref025" target="_blank">25</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158108#pone.0158108.ref032" target="_blank">32</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158108#pone.0158108.ref073" target="_blank">73</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158108#pone.0158108.ref074" target="_blank">74</a>].</p

    Hydrological data of the studied Portuguese rivers.

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    <p>Location of the sampled sites and additional information about length and area of the river and lake basins in Portuguese territory [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158108#pone.0158108.ref055" target="_blank">55</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158108#pone.0158108.ref056" target="_blank">56</a>].</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

    Dispersal routes of <i>Corbicula</i> spp. invasive lineages.

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    <p>Established <i>Corbicula</i> spp. dispersal routes are represented by continuous lines and dash lines correspond to other possible spread routes.</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

    Sperm morphology of <i>Corbicula fluminea</i> from Portugal.

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    <p>Biflagellate sperm of a specimen of <i>C</i>. <i>fluminea</i> from the Douro River (Microscopy photograph acquired by Olympus SZX10 microscope with an integrated Olympus D72 camera).</p
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