Genetic diversity of each population of <i>S. ningshanensis</i>.

<p><i>S.D</i>., standard deviation.</p

Distributions of <i>Pachyhynobius shangchengensis</i>.

<p>Sampling sites for the present study are marked by red triangles and coded names (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078064#pone-0078064-t001" target="_blank">Table 1</a>). </p

Median-joining network of mtDNA haplotypes of <i>Pachyhynobius shangchengensis</i> on the Mount Dabieshan in China.

<p>Each haplotype is represented by a circle, with the area of the circle proportional to its frequency. Samples from Clade A to D were indicated by different colours. Median vector (mv1-mv14) is indicated by black.</p

Mismatch distribution analyses and neutrality test of <i>S. ningshanensis.</i>

<p><i>N</i>, number of sequences; <i>n</i>, number of haplotypes; <i>τ</i>, time in number of generations elapsed since the sudden expansion episode; <i>θ</i>₀, pre-expansion, and <i>θ</i>₁, post-expansion population size; <i>SSD</i>, sum of squared deviations; <i>R</i>, raggedness indexes.</p

Distribution of <i>s</i>-values from simulated genealogies constrained within the models of population divergence.

<p>Single-refugium hypothesis.</p

Maximum likelihood (ML) tree of the observed haplotypes of <i>Pachyhynobius shangchengensis</i>, with <i>Hynobius chinensis</i> and <i>Hynobius guabangshanensis</i> as outgroup.

<p>Numbers above the branches represent the bootstrap values.</p

Bayesian tree for the 67 sampled haplotypes of <i>S</i>. <i>ningshanensis</i> based on the combined mtDNA cyt b and COI sequences.

<p>The Bayesian posterior probabilities from Bayesian analyses are presented above or under the main branches. The scale bar represents substitutions per site.</p

Mismatch distribution analysis for the total population and the clades.

<p>Mismatch distribution analysis for the total population and the clades.</p

Demographic patterns of each clade and the total population as determined from the Bayesian skyline plot (BSP).

<p>The X-axis is in units of million years in the past and the Y-axis is <i>N</i>_e*µ (effective population size × mutation rate per site per generation). The median estimates for the log10 of the population size are shown as thick solid lines, and the 95% highest posterior density (HPD) limits are shown by the shaded areas.</p

Results of analysis of molecular variance (AMOVA) of <i>S. ningshanensis</i>.

<p><i>d.f.</i>, degrees of freedom.</p