MOESM1 of Inferring ecological explanations for biogeographic boundaries of parapatric Asian mountain frogs

Additional file 1. Distributions for occurrence records of Feirana quadranus and F. taihangnica in environmental space (annual mean temperature versus total annual precipitation)

MOESM2 of Inferring ecological explanations for biogeographic boundaries of parapatric Asian mountain frogs

Additional file 2. Filtering environmental variables

Sampling information and haplotypes based on <i>ND2</i> gene for 34 sampled populations of <i>Feirana quadranus</i>.

<p>Sampling information and haplotypes based on <i>ND2</i> gene for 34 sampled populations of <i>Feirana quadranus</i>.</p

The classification of 200-m altitudinal intervals between 0 and 5000 m for spiny frogs.

<p>The Jaccard (1901) similarity measure is used. The between-groups method is used for the cluster analysis based on the similarity coefficient matrix.</p

Postglacial Colonization of the Qinling Mountains: Phylogeography of the Swelled Vent Frog (<em>Feirana quadranus</em>)

<div><h3>Background</h3><p>The influence of Pleistocene climatic fluctuations on intraspecific diversification in the Qinling–Daba Mountains of East Asia remains poorly investigated. We tested hypotheses concerning refugia during the last glacial maximum (LGM) in this region by examining the phylogeography of the swelled vent frog (<em>Feirana quadranus</em>; Dicroglossidae, Anura, Amphibia).</p> <h3>Methodology/Principal Findings</h3><p>We obtained complete mitochondrial <em>ND2</em> gene sequences of 224 individuals from 34 populations of <em>Feirana quadranus</em> for phylogeographic analyses. Additionally, we obtained nuclear tyrosinase gene sequences of 68 <em>F. quadranus</em>, one <em>F. kangxianensis</em> and three <em>F. taihangnica</em> samples to test for mitochondrial introgression among them. Phylogenetic analyses based on all genes revealed no introgression among them. Phylogenetic analyses based on <em>ND2</em> datasets revealed that <em>F. quadranus</em> was comprised of six lineages which were separated by deep valleys; the sole exception is that the Main Qinling and Micang–Western Qinling lineages overlap in distribution. Analyses of population structure indicated restricted gene flow among lineages. Coalescent simulations and divergence dating indicated that the basal diversification within <em>F. quadranus</em> may be associated with the dramatic uplifts of the Tibetan Plateau during the Pliocene. Coalescent simulations indicated that Wuling, Daba, and Western Qinling–Micang–Longmen Mountains were refugia for <em>F. quadranus</em> during the LGM. Demographic analyses indicated that the Daba lineage experienced population size increase prior to the LGM but the Main Qinling and the Micang–Western Qinling lineages expanded in population size and range after the LGM, and the other lineages almost have stable population size or slight slow population size decline.</p> <h3>Conclusions/Significance</h3><p>The Qinling–Daba Mountains hosted three refugia for <em>F. quadranus</em> during the LGM. Populations that originated in the Daba Mountains colonized the Main Qinling Mountains after the LGM. Recent sharp expansion of the Micang–Western Qinling and Main Qinling lineages probably contribute to their present-day secondary contact.</p> </div

Genetic diversity and neutrality tests for phylogenetic lineages of <i>Feirana quadranus</i>.

<p>Phylogenetic lineages were given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041579#pone-0041579-g003" target="_blank">Figure 3</a>. Mean ± standard deviation of <i>Hd</i> and <i>π</i> were given.</p>*<p>P<0.05</p>**<p>P<0.01.</p

Relationship between altitudinal range midpoints and body size of spiny frogs.

<p>Maximum snout to vent length (SVL) is used as an estimate of body size. The relationship is shown for (a) the subfamily Painae, (b) the tribe Paini and (c) the tribe Quasipaini respectively. The fitted line represents an ordinary least square (OLS) linear regression.</p

Bayesian tree for the 72 sampled haplotypes of <i>Feirana quadranus</i> based on <i>ND2</i> gene sequences.

<p>The bootstrap values calculated by Maximum Parsimony and Maximum Likelihood analyses and the Bayesian posterior probabilities from Bayesian analyses are presented above the main branches; the diamonds on branches mean that all support values are greater than 95%. The estimated divergence time (Ma, mean and 95% CI’s) for major nodes is below the branches. Ten major nodes (1–10) are indicated on the tree. Haplotypes (H1–H72) were given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041579#pone-0041579-t001" target="_blank">Table 1</a>.</p

Proportional likelihoods of the ancestral area for major lineages of <i>Feirana quadranus</i>.

<p>Nodes 1–10 were given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041579#pone-0041579-g003" target="_blank">Figure 3</a>. Mt. means Mountains.</p

Demographic patterns of each lineage and a combined pattern as determined from BSP.

<p>The central solid line represents the median value for the log of the population size (<i>N_ef</i> * τ) and the area between two thinner lines represent the 95% higher posterior density. The thicker dashed line represents the median of estimation time of the most recent common ancestor (MRCA), and the thinner is the lower limit of the 95% confidence interval. The combined figure shows the population size fluctuation after the lower limit of 95% CI’s of estimation time of the most recent common ancestor. Phylogenetic lineages correspond to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041579#pone-0041579-g003" target="_blank">Figure 3</a>.</p