| Squalidus argentatus, belonging to Squalidus Dybowsky, Gobioninae,Cyprinidae, which is a small-sized freshwater fish distributed in MainlandChina, Hainan Island and Taiwan. The paper analysed the Populationgenetic structure and phylogeography of Squalidus argentatus based onmicrosatellite markers and rpS7:1.11pairs of microsatellite loci amplify primers were designed. And11pairs of polymorphic and stable primers were developed on43individuals collected from Yangtze River and Qiantang River. The numberof alleles, observed and expected heterozygosity per locus in twopopulations ranged from3to14, from0.333to0.954and from0.480to0.928, respectively. MISA10and MISA10are significantly deviated fromHardy–Weinberg expectations due to the heterozygote deficiency.2. So, we selected9pairs of polymorphic and stable primers weretested for nine populations (Amur River, Yangtze River, QiantangjiangRiver, Oujiang, Minjiang River, JiuLongjiang River, Hanjiang River, PearlRiver, Changhuajiang River). A total of111different alleles were observedacross all loci for all samples. The average number of alleles perpopulation was8.0. The mean expected heterozygosity per populationranged from0.56to0.68. These results suggest that S. argentatuspopulations were polymorphic. High positive FIS might be caused by inbreeding. The pattern of genetic differentiation among populationsobserved from pair-wise FST and RST tests, based on the microsatellitedata. Both showed that the tested populations of S. argentatus weresignificantly (P<0.05) differentiated. Pair-wise FST values ranged from0.0012to0.1677, with a mean value of0.068, and RST values rangedfrom-0.0270to0.4455, with a mean value of0.354. There are small buthighly significant values of pairwise FST, which showed there was geneticdifferentiation among populations. According to the Mantel test, there wasno significant correlation between genetic and geographic distance in thesampled locations (R2=-0.000004; P=0.45). Spatial analysis ofmolecular variance (SAMOVA) indicated the value of FCT was highestwhen K=4(FCT=0.086, P=0.16): HL, LY and SK; AH; CH; and the rest.Most of the remaining variation was within populations (77.09%) withsome among populations within groups (14.22%). All variancecomponents were significant (P <0.000)(Table5). In the STRUCTUREanalysis, a value of K=5resulted in the highest log-likelihood value. Thisresult suggests that there were probably one original population, fromwhich the216individuals in the current9populations were derived, andthere were no strong differentiation existed among the populations of S.argentatus. Bottleneck tests were performed under both the stepwisemutation model (SMM) and the two-phase model (TPM). For theWilcoxon’s sign rank test, six populations (AH, KH, JY, SC, SG and CH)had significant heterozygosity excess (P<0.05) under the TPM, suggestinga recent population size reduction. Under population analyzed，Three maingroups were identified: The first major cluster included population SG.The second cluster included populations HL, JY, CH, SC and KH. Thethird included SK, LY and AH.3.We invested the genetic structure and demographic history of156 individuals of Squalidus argentatus using rpS7, Genetic diversity: weobtained391variable sites of960base pairs and137haplotype, Averagebase frequencies for S7were as follows, A=30.6%, T=33.1%, C=16.1%,G=19.7%, The haplotype diversity was from0.890to1.000, average was0.997, we investigated nucleotide diversity on the value of θ and π, theaverage θ and π of all populations were0.089and0.027. Phylogenyreconstruction, Network estimation and nested clade analysis: we usedMEGA5.0to rebuild relationship among individuals based onNeighbor-joining, the results showed all individuals present lineage A andlineage B, lineage A consist of all individuals, but lineage B only consistof Yangtze River, Qiantang River, Oujiang, Min River, JiuLong River andHanjiang based on haplotype and geographical distribution. Geneticstructuring: FST of all populations was0.271, and pairwise FST was from0.005to0.658, which showed the populations have a high geneticdifferentiation. The index of genetic differentiation was high0.317between lineage A and lineage B. AMOVA analysis showed71.96%ofdifferentiation within populations, only29.12%among populations, and-1.08%among geographical. ΦCT among individuals among geographicalwas-0.01078(p=0.481), ΦCT among individuals within geographical was0.288(p=0.00000), ΦCT among individuals among populations was0.280(p=0.00000). The results showed there was not apparentgeographical differentiation based on rpS7. Historical demographicanalysis: we analysis mismatch distribution and neutrality test usingDNASP5.0, which showed the population ever experience expansion.And Beast1.6analysis showed the population expansion may happenbefore125000-250000, on the base of lineage, the population of lineage Amay happen before200000and the population of lineage B may happenbefore250000. The study constructed the database of genetic structure, and reconstructedthe phylogenetic relationship of squalidus argentatus among differentdrainage. These results will enable us to study the evolution of fresh watersystem, Geography, and conservation genetics of this species in the future. |
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