The marginal posterior probability distributions of migration rates between Central <i>sinicus</i> and <i>septentrionalis</i>.

<p>The IM analysis was performed for mtDNA, combined nuclear gene sequences, combined mtDNA and nuclear gene sequences and microsatellites, respectively.</p

Summary of the number and sampling locality of individuals used in the molecular analyses.

<p>Summary of the number and sampling locality of individuals used in the molecular analyses.</p

Clustering of <i>R. sinicus</i> individuals in STRUCTURE based on microsatellite genotypes.

<p>Clusters are shown for values of K = 2 to 5 inclusive. The mtDNA clade relationships are shown above the four cluster plots.</p

IM estimates of posterior mode and 90% credible intervals for directional migration rates (<i>m₁</i> and <i>m₂</i>).

<p>IM estimates of posterior mode and 90% credible intervals for directional migration rates (<i>m₁</i> and <i>m₂</i>).</p

Maximum parsimony tree and statistical parsimony network based on concatenated mtDNA sequences.

<p>(a) The phylogenetic tree. Node support is indicated with MP, NJ and ML bootstrap values and Bayesian posterior probabilities (given above and below the branch, respectively). (b) The network with a 95% connection limit. Each circle represents a single haplotype and the circle size is scaled by the haplotype frequency. Filled black circles represent missing or unsampled haplotypes. The numbers in the network represent mutational steps between haplotypes.</p

Details of primers used in this study.

<p>Details of primers used in this study.</p

Mean estimates of TMRCA with 95% credible intervals for each clade or group of clades based on <i>Cytb</i> data.

<p>Mean estimates of TMRCA with 95% credible intervals for each clade or group of clades based on <i>Cytb</i> data.</p

Morphological and echolocation data for bats with corresponding membership in mtDNA clades and microsatellite clusters.

<p>(a) Forearm (mm) and body mass (g) data measured for 396 individuals. Open and filled triangles correspond to female and male bats, respectively. (b) Boxplots of the echolocation call frequency (kHz) recorded from 130 individuals. (c) Map showing the sample sites of <i>R. sinicus</i> in this study. Forty-one sampling localities were classified into eight regions, depicted by dashed lines. These regions were further divided into four groups coded by colours (East: green; Central: purple; Hainan Island (HND): blue; Yunnan (YN): orange). Populations are presented as pie charts in which individuals are coloured based on the membership of mtDNA clades (I, II, III and IV). The relationships between clades are shown on the left side of the map (see details in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056786#pone-0056786-g002" target="_blank">Figure 2</a>). (d) Populations are presented as pie charts in which individuals are coloured based on the membership of microsatellite clusters (I, II, III, IV and mixed, see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056786#pone-0056786-g004" target="_blank">Figure 4</a>).</p

Map showing the distributions of the member species of the <i>R. rouxii</i>-group, and the ranges of the focal subspecies of <i>Rhinolophus sinicus</i>.

<p>Map showing the distributions of the member species of the <i>R. rouxii</i>-group, and the ranges of the focal subspecies of <i>Rhinolophus sinicus</i>.</p

Summary of genetic diversity for five gene sequences and eight microsatellite loci in eight regions of <i>R. sinicus</i>.

<p>N1–N6, sample sizes for genes and microsatellite loci; n, number of haplotypes observed; h, haplotype diversity; π(%), nucleotide diversity; mean π(%), mean nucleotide diversity of four nuclear genes. A, mean number of alleles per locus; H_E, expected heterozygosity; H_O, observed heterozygosity; Rs, allele richness standardized by three individuals. The numbers of private alleles with >10% frequency are shown in parentheses.</p