PAML branch-sie model A analysis to identify branches under episodic positive selection.

<p>lnL: log likelihood scores; -2ΔlnL: likelihood ratio test (LRT) to detect positive selection.</p><p>PAML branch-sie model A analysis to identify branches under episodic positive selection.</p

Der @Maler- und Lackierermeister : das deutsche Malermagzin

<div><p>Limestone Karst areas possess high levels of biodiversity and endemism. <i>Primulina</i> is a typical component of Karst endemic floras. The high species richness and wide distribution in various Karst microenvironments make the genus an idea model for studying speciation and local adaptation. In this study, we obtained 10 full-length sequences of the phytochrome <i>PHYE</i> from available transcriptome resources of <i>Primulina</i> and amplified partial sequences of <i>PHYE</i> from the genomic DNA of 74 <i>Primulina</i> species. Then, we used maximum-likelihood approaches to explore molecular evolution of <i>PHYE</i> in this Karst cave plant. The results showed that <i>PHYE</i> was dominated by purifying selection in both data sets, and two sites were identified as potentially under positive selection. Furthermore, the ω ratio varies greatly among different functional domains of <i>PHYE</i> and among different species lineages. These results suggest that potential positive selection in <i>PHYE</i> might have played an important role in the adaption of <i>Primulina</i> to heterogeneous light environments in Karst regions, and different species lineages might have been subjected to different selective pressures.</p></div

Bayesian phylogenetic tree of full-length <i>PHYE</i> sequences for 10 <i>Primulina</i> species.

<p>The tree was rooted at <i>P</i>. <i>swinglei</i>. Posterior probabilities were labeled at the nodes.</p

Sliding window analysis show variation of ω value along the <i>PHYE</i> gene from 74 partial sequences and 10 full-length sequences.

<p>The estimates were based on the Nei-Gojobori method. The window size was set at 30 bp and step size was set at 3 bp. Beneath the plot is a schematic of <i>PHYE</i>, which illustrates the distribution of the characteristic functional domains.</p

Bayesian phylogenetic tree of partial <i>PHYE</i> sequences for 74 <i>Primulina</i> species.

<p>Bayesian posterior probabilities above 0.5 were labeled at the nods. <i>Petrocodon dealbatus</i> and <i>Didymocarpus hancei</i> were used as outgroups. The species with full-length sequences are shaded.</p

Likelihood ratio test (LRT) stasticts for models of variable selective pressure among branches.

<p>M0 and M1 are one ratio model and free-ratio model, respectively.</p><p>lnL: log likelihood scores; -2ΔlnL: likelihood ratio test (LRT) to detect positive selection.</p><p>Likelihood ratio test (LRT) stasticts for models of variable selective pressure among branches.</p

Genotypes of 354 SSR loci

Genotypes of 354 SSR loc

SSR Flanking sequence

SSR Flanking sequenc

Genotypes of 795 SNP loci

Genotypes of 795 SNP loc

Fasta file of adaptive genes

Fasta file of adaptive gene