Map showing the sampled populations of <i>T. shanjing</i>.

<p>Height is reflected by shading and populations are named as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056066#pone-0056066-t001" target="_blank">Table 1</a>.</p

Bayesian inference tree for <i>T. shanjing</i> based on the 58 haplotypes from cytochrome <i>b</i>, control region, tRNA-Phe, and 12S rRNA sequences.

<p>The nodal numbers are BPP and MP bootstrap value, respectively.</p

Estimation of the empirical theta values and effective population size.

<p>Estimation of the empirical theta values and effective population size.</p

Mismatch distributions for total samples and some major lineages of <i>B. pleuraden</i>.

<p>Mismatch distributions for total samples and some major lineages of <i>B. pleuraden</i>.</p

Networks of the 63 haplotypes detected from cyt <i>b</i> and COI sequences of <i>B. pleuraden</i>.

<p>The sizes of the circles are proportional to haplotype frequencies and black dots represent missing haplotypes (not sampled or extinct).</p

The results of SAMOVA for grouping of all populations and AMOVA for grouping of populations within lineage D.

*<p><i>P</i>>0.05;</p>**<p><i>P</i><0.001.</p

Models of coalescent simulation used to test refugial hypotheses.

<p>(a) Hypothesis of single refugium at the end of the Last Glacial Maximum (T = 18 000 years BP); (b) Hypothesis of two refugia at the end of the Last Glacial Maximum (T1 = 18 000 years BP, T = 830 000 years BP); (c) Hypothesis of three refugia at the end of the Last Glacial Maximum (T1 = 18 000 years BP, T2 = 760 000 years BP, T = 830 000 years BP); (d) Hypothesis of four refugia at the end of the Last Glacial Maximum (T1 = 18 000 years BP, T2 = 710 000 years BP, T3 = 760 000 years BP, T = 830 000 years BP); (e) Hypothesis of four refugia before the Last Glacial Maximum (T1 = 250 000 years BP, T2 = 290 000 years BP, T3 = 70 000 years BP, T4 = 530 000 years BP, T5 = 710 000 years BP, T6 = 760 000 years BP, T = 830 000 years BP). The detail interpretation for these models is given in the text.</p

Results of neutrality tests and mismatch analyses.

<p>Results of neutrality tests and mismatch analyses.</p

Bayesian skyline plots showing the demographic history of each lineage of <i>T. shanjing</i>.

<p>Dark lines represent median values for the log₁₀ of the population size, and blue lines represent the 95% highest probability density (HPD) intervals.</p

Sampling localities, phylogroup, sample sizes (<i>N</i>), haplotypes and their frequencies, gene diversity, nucleotide diversity, and the probability of being the population of origin of the lineage (MRCA %).

<p>Sampling localities, phylogroup, sample sizes (<i>N</i>), haplotypes and their frequencies, gene diversity, nucleotide diversity, and the probability of being the population of origin of the lineage (MRCA %).</p