Fig 1.
Locations of sampling sites in this study.
Site numbers and river systems are listed in Table 1. a, southern mainland China sampling sites for Aphyocypris normalis (solid red circles); b, Hainan Island sampling sites for A. normalis (solid red circles). Three major river systems of Hainan Island are identified by different colors: white–the Nandu River; blue–the Wanquan River; yellow–the Changhua River; c, Taiwan sampling sites for A. moltrechti as the outgroup (solid blue triangles).
Table 1.
Sample locations and haplotype distributions of Aphyocypris samples used in this study.
Fig 2.
Bayesian tree of 1091-bp-long haplotypes inferred from partial cytb gene.
Branch lengths are proportional to the scale given in nucleotide substitutions per site. Numbers at internal nodes are Bayesian inferences (only value >0.90 are shown) and bootstrap values (>70%) for NJ and ML analyses. Only the values for major clades or sub-clades are shown. Solid circles at internal nodes indicate they were supported by all three analyses; open circles indicate they were supported by Bayesian and NJ analyses; and solid triangles indicate they were supported by Bayesian analysis only. Abbreviations beside clades or sub-clades correspond to the clades listed in Table 1. * indicates the haplotypes from the Zhoushui River, which were assigned to Aphyocypris amnis by Liao et al. [71].
Fig 3.
Phylogenetic analysis of Aphyocypris normalis and its closely related species derived by the Bayesian method under the HKY+I+G model.
Numbers at internal nodes are Bayesian posterior probabilities and only value >90% are shown.
Table 2.
Estimates of evolutionary divergence (K2P) between sequence pairs between clades/sub-clades (below) and standard errors (above).
Fig 4.
Statistical parsimony haplotype network for haplotypes constructed by TCS 1.21.
Numbers inside circles are haplotype codes. Circle size reflects the number of individuals having the corresponding haplotype. Small solid dots signify possible missing haplotypes. A line connecting two haplotypes represents one nucleotide substitution. White circles: haplotypes collected from Hainan Island; grey circles: haplotypes collected from southern mainland China. The red broken line separates the two major clusters in this analysis.
Table 3.
Estimates of time since the most recent common ancestor (tMRCA; time scale in millions of years; standard errors are presented in parentheses) and 95% HPD estimates for clades/sub-clades for the main internal nodes of Aphyocypris normalis phylogeny (Fig 2) obtained using the cytb sequences based on a constant population model.
Table 4.
Results from the analysis of molecular variance (AMOVA) used to evaluate two a priori biogeographical hypotheses.
Table 5.
Sources of variation calculated with SAMOVA under K = 3.
Fig 5.
a, Climate ranges of Hainan Island, based on He and Zhang [36]; b, eight phylogeographic ranges inferred from this study’s cytb dataset analyses, modified by climate characteristics; c, haplotype distribution in the continental area. Sampling site locations and haplotypes at each collection site are also marked. The yellow areas in Hainan maps (a, b) indicate mountainous regions more than 750 m ASL. Red triangle: Wuzhishan Mountain. Green triangle: Yinggeling Mountain.