68 research outputs found
Result of the Bayesian coalescent-based estimation of divergence time among different evolutionary clades/subclades and the time to the most recent common ancestor (<i>t</i><sub>MRCA</sub>) of different evolutionary clades/subclades.
<p>Results based on non-partition and partitioned by each codon were shown (two partitions: pos1+pos2, pos3; three partitions: pos1, pos2, pos3). Mean values are shown in bold and 95% HPD are shown in brackets.</p
Table <b>5.</b> Results of hierarchical analyses of molecular variance (AMOVA) conducted using different grouping options.
*<p>Populations contain only one sample are exclude in all the analyses Main evolutionary clades and subclades in clade 1 are observed in our phylogenetic trees.</p><p># Jiajin Moutain, Erlang Moutain, Gongga Mountain, Hongya county.</p
Table <b>4.</b> Pairwise <i>F</i><sub>ST</sub> values among the 13 populations surveyed of <i>Apodemus draco</i>.
<p>Populations contain only one sample are exclude in this analyses.</p><p>Numbers in bold indicate statistically significant genetic differentiation (<i>P</i><0.05). Populations are numbered as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038184#pone-0038184-t001" target="_blank">Table 1</a>.</p
Median-joining network of all cyt <i>b</i> haplotypes found in <i>Apodemus draco</i>.
<p>The missing haplotypes in the network are represented by gray dots. Circle sizes are proportional to the number of individuals sharing the same haplotypes. Each mutation step is shown as a short line connecting neighboring haplotypes, and numbers of mutations between haplotypes are indicated near branches if it is greater than one. Haplotype designations can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038184#pone-0038184-t001" target="_blank">Table 1</a>. Evolutionary clades correspond to the five major clades and three subclades in Fig. 2. Haplotypes from different populations are marked as *.</p
The result of McDonald-Kreitman test for cyt <i>b</i> gene of <i>Apodemus draco</i> (N = 126) and <i>A. latronum</i> (N = 68).
<p>Values corrected by Jukes and Cantor (1969) are given in parentheses.</p
Sampling information of <i>Apodemus draco</i>.
<p>We did not have the coordinates of the individuals in the first five populations because their sequences are from GenBank. Their references and GenBank accession numbers can be found in text.</p
Fifty percent majority rule consensus tree from Bayesian analysis of <i>Apodemus draco</i> based on all the haplotypes of cyt <i>b</i> data.
<p>Numbers represent node supports inferred from Bayesian posterior probability of non-partitioned data and partitioned data, and maximum parsimony bootstrap analyses, respectively. Only values of the main evolutionary clades are shown. The haplotype names can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038184#pone-0038184-t001" target="_blank">Table 1</a>.</p
Genetic diversity indices and demographical analyses for cyt <i>b</i> sequences in <i>Apodemus draco</i>.
<p>Number of individuals (<i>n</i>), number of haplotypes (<i>H</i>), haplotype diversity (<i>h</i>), nucleotide diversity (π), Fu’s <i>Fs</i>, Ramos-Onsins and Rozas’s R<sub>2</sub> statistics (R<sub>2</sub>), the shape of mismatch distribution, the sum of squared deviations (SSD) and raggedness indexes (<i>r</i>) are shown. Numbers in bold indicate statistically significant genetic differentiation (<i>P</i><0.05).</p
Results of spatial autocorrelation analyses of cyt <i>b</i> sequences in <i>Apodemus draco</i>.
<p>Analyses were performed using different distance classes (5, 10 and 15). Only the results of z = 10 and 15 distance classes were shown. Black circles represent values significantly different (<i>p</i><0.05) from the mean <i>Ay</i>. (a) All individuals. (b) Exclude all the GenBank sequences due to we did not have their coordinates. (c) Individuals in clade 1.</p
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