The phylogeographical pattern of the Amur minnow Rhynchocypris lagowskii (Cypriniformes: Cyprinidae) in the Qinling Mountains

Abstract

In this study, the phylogeographical pattern of the Amur minnow (Rhynchocypris lagowskii) widely distributed in the cold freshwaters of the Qinling Mountains was examined. A total of 464 specimens from 48 localities were sequenced at a 540-bp region of the mitochondrial cytochrome b (Cytb) gene, and 69 haplotypes were obtained. The mean ratio of the number of synonymous and nonsynonymous substitutions per site (dN/dS) was 0.028 and indicated purifying selection. Haplotype diversity (h) and nucleotide diversity (π) of natural populations of R. lagowskii varied widely between distinct localities. Phylogenetic trees based on Bayesian inference (BI), maximum likelihood (ML), and maximum parsimony (MP) methods, and network analysis showed five well-differentiated lineages, but these did not completely correspond to localities and geographic distribution. Meanwhile, analysis of molecular variances (AMOVA) indicated the highest proportion of genetic variation was attributed to the differentiation between populations rather than by our defined lineages. In addition, there was no significant correlation between the pairwise Fst values and geographic distance (p > .05). Based on the molecular clock calibration, the time to the most recent common ancestor (TMRCA) was estimated to have emerged from the Late Miocene to the Early Pleistocene. Finally, the results of demographic history based on the neutrality test, mismatch distribution, and Bayesian skyline plot (BSP) analyses showed that collectively, the populations were stable during the Pleistocene while one lineage (lineage E) probably underwent a slight contraction during the Middle Pleistocene and a rapid expansion from the Middle to the Late Pleistocene. Therefore, the study suggests the current phylogeographical pattern of R. lagowskii was likely shaped by geological events that led to vicariance followed by dispersal and secondary contact, river capture, and climatic oscillation during the Late Miocene to the Early Pleistocene in the Qinling Mountains.

Keywords: Cytb; Qinling Mountains; Rhynchocypris lagowskii; phylogeographical pattern.

FIGURE 1

Amur minnow, Rhynchocypris lagowskii

FIGURE 2

Map of sampling localities for Rhynchocypris lagowskii populations. The map was downloaded from the National Geomatics Center of China with slight modification using Arcgis10.1. The locality codes are given in Table 1. The populations belonged to different lineages labelled red (a), yellow (b), blue (c), cyan (d), and purple (e), respectively

FIGURE 3

Bayesian inference tree between haplotypes based on Cytb sequences of Rhynchocypris lagowskii. The numbers above nodes are Bayesian posterior probabilities, maximum likelihood (ML), and maximum parsimony (MP) bootstrap values, respectively (above 50% are shown). The five lineages are differentiated by different colors (red, (a); yellow, (b); blue, (c); cyan, (d); purple, (e)). Estimated divergent dates in Mya are given in numbers down nodes with underline

FIGURE 4

Median‐joining network for all haplotypes of Rhynchocypris lagowskii based on the Cytb gene. Each cross‐hatched line represents one base‐pair difference between haplotypes, black dots are inferred missing haplotypes, and the haplotype frequency and proportion are relative to the size and split‐line of the circle. The five different colors correspond to lineages as in Figure 3

FIGURE 5

Plots of differentiation estimates of the pairwise Fst values against the geographic distance (km) between populations within the Cytb dataset of Rhynchocypris lagowskii. The linear regression overlays the scatter plots (R² = 0.00003154, p = .8520)

FIGURE 6

Mismatch distributions for each lineage and the total samples of Rhynchocypris lagowskii. The observed pairwise differences are shown as red bars and the simulated values under the sudden expansion model are blue solid lines

FIGURE 7

Bayesian skyline plots of historical demography for each lineage and the total samples of Rhynchocypris lagowskii. The solid line represents the median value of the population size and the dashed lines represent the 95% credible intervals. The X‐axis represents time using a mutation rate of 1% per million years ago (Mya), and the Y‐axis represents the effective population size