Molecular Ecolog OF The Rusty-Necklaced Patridge(Alectoris Magna)Implicated By Mitochodrial DNA And Microsateiiitc Makcrs

The rusty-necklaced partridge (Alectoris magna) is an endemic species of birds in China belonging to Aves, Galliformes, Phasianidae, Alectoris with two described subspecies A.m.magna and A.m.lanzhouensis. In this study, the molecular ecology of A.magna was studied from12populations across the entire distributional ranges based on mitochondrial DNA (CR+Cytb) and microsatellite markers. Introgression between A.magna and Alectoris chukar was also studied using mtDNA (CR+Cytb) and microsatellite markers. The aims of this study are to:(1) examine the effects of environmental factors on population genetic diversity of the12A.magna populations;(2) reconstruct the phylogeographic relationship of A.magan and detect whether there exists obvious phylogeographic differentiation in this species;(3) compare the phylogeographic structures based on different molecular markers;(4) demonstrate the roles of Pleistocene glaciation and climate oscillation played in the population structure, based on the analyses of genetic differentiation and population demography;(5) detect the effects of hybridization on the genetic diversity of A.magna;(6)confirm the geographic ranges of hybridization and speculate the time when the hybridization happened;(7)discuss the genetic conservation of A.magna.In this study, partial mtDNA CR sequences (1127bp) of173specimens, partial mtDNA Cytb sequences(807bp) of230specimens, and eight microsatellite loci for257specimens from12populations were used to analyze the molecular ecology of A.magna. Partial mtDNA CR sequences(473bp)of287specimens and Partial mtDNA Cytb sequences(807bp)of267specimens from15populations of A.magna, as well as partial sequences (473bp) of285specimens from25populations of Alectoris chukar and partial sequences (807bp) of48specimens from eight populations of A. chukar, were used to analyze the hybridization. The main results include:1. There were significant differences in base composition among12A.magna populations. The value of A+T preponderated over a half of the total base content, which was consistent with mtDNA control—region including abundance A and T. Forty-four haplotypes were defined by34variable sites with the mean haplotype diversity of0.916and the nucleotide diversity of0.00449based on mtDNA CR. Fourteen haplotypes were defined by14variable sites with the mean haplotype diversity of0.738and the nucleotide diversity of0.00216based on mtDNA Cytb. The average expected and observed heterozygosity was0.90and0.88, respectively. The genetic diversity of A.magna was lower than other birds distributed on Tibetan Plateau and Loess Plateau.2. A significantly negtive correlation was observed between nucleotide diversity of mtDNA CR and rainfall, indicating the more abundant the precipitation, the lower the genetic diversity. Precipitation played an important role in genetic diversity of A.magna. A significantly positive correlation was observed between expeted heterozygosity (HE) and variation coefficients of annual mean relative humidity (VCH), indicating the more unstable the climate, the higher the genetic diversity.3. For mtDNA CR, Cytb and combined sequences, all of the haplotypes formed three paraphyletic groups without evident spatial clustering. The similar results was also observed in the analysis based on microsatellites markers, indicating the lack of phylogeographic structure in A.magna.4. AMOVA analyses suggested that the variation among individuals within populations (ΦST) was maximized and the variation among regional groups(ΦCT) was minimized. However, ΦST,ΦCT and the variation among populations (ΦSC) were all statistically significant. Most of populations pairwise Fst-value was also statistically significant. Only one haplotype was shared by the specimens from Qaidam Basin and the other regional groups, indicating the low genetic differentiation between the populations from Qaidam Basin and the other regional groups. The populations in Qaidam Basin might be isolated from the other populations by the glaciation occurred in Pleistocene glacial period. However, the glacial ablation in the following interglacial period resulted in the disappearance of barriers. Extensive gene flow occurred between all populations of A.magna, decreasing the genetic differentiation among populations.5. For the CR and combined data set, the specimens from Qaidam Basin were distributed in both ends of the networks. The Qaidam specimens distributed in the right end have no shared haplotype with specimens from the other regional groups in all of the networks based on CR, Cytb and combined sequences. They might be native to Qaidam Basin. However, the Qaidam specimens distributed in the left ends have shared haplotypes with specimens from the other regional groups in all of the three haplotype network. They might be derived from the specimens from the other regioanl groups and be isolated more recently than the specimens native to Qaidam Basin. Thus, they showed lower genetic differentiation with specimens from other regional groups. 6. The analysis of mismatch distribution and test of selective neutrality indicated that subspecies A.m.lanzhouensis had experienced population expansion at0.23-0.18Mya, co-occurring with the Penultimate Glaciation(0.33-0.13Mya) and the fifth cold period (0.24-0.15Mya), when the climate was dry and cold and the desert-steppe extended.7. The A.chukar's mitochondrial genotype could be found in A.magna, but A.magna's mitochondrial genotype could not be found in A.chukar. Thus, we can confirm that there existed introgression hybridization between A.magna and A.chukar. The introgression hybridization was only found in the surronding of the Liupan Mountains to Lixian County. Only A.chukar's mitochondrial genotype and A.magna's nuclear genotype could be observed in the hybrids. High level of introgression was observed in populations near to Liupan Mountains. The hybrid rate have reached100%in Longde. The asymmetrical introgression may result in the extinction of the population of A.magna distrubuted near to Liupan Mountains. The time when hybridization happened was about0.049-0.062Myr, which is consistent with the population expansion time of A.chukar (0.027-0.060Mya).8. Bayes analysis based on CR and Cytb revealed limited phylogenetic distinction between geographically distant populations of the rusty-necklaced partridge, and tentative support for a single evolutionarily significant unit (ESU) range. AMOVA revealed that the most genetic variation was distributed within populations. However, the genetic variations among groups and poulations were also statistically significant. The population pairwise Fst-value was not statistically significant among Minghe(MH), Jingyuan(JY), Huining(HN), Li country(LX) and Haiyuan(HY), but statistically significant among the other populations. According to the criteria of Mus, MH, JY, HN, LX and HY should be treated as a MU and the other populations should be treated as independent MUs.