Population structure and demographic history of the chukar partridge Alectoris chukar in China

Pleistocene climate fluctuations have shaped the patterns of genetic diversity observed in extant species. Although the effects of recent glacial cycles on genetic diversity have been well studied on species in Europe and North America, genetic legacy of species in the Pleistocene in north and northwest of China where glaciations was not synchronous with the ice sheet development in the Northern Hemisphere or or had little or no ice cover during the glaciations＇ period, remains poorly understood. Here we used phylogeographic methods to investigate the genetic structure and population history of the chukar partridge Alec- toris chukar in north and northwest China. A 1,152 - 1,154 bp portion of the mtDNA CR were sequenced for all 279 specimens and a total number of 91 haplotypes were defined by 113 variable sites. High levels of gene flow were found and gene flow esti- mates were greater than 1 for most population pairs in our study. The AMOVA analysis showed that 81% and 16% of the total genetic variability was found within populations and among populations within groups, respectively. The demographic history of chukar was examined using neutrality tests and mismatch distribution analyses and results indicated Late Pleistocene popula- tion expansion. Results revealed that most populations of ehukar experienced population expansion during 0.027 - 0.06 Ma. These results are at odds with the results found in Europe and North America, where population expansions occurred after Last Glacial Maximum （LGM, 0.023 to 0.018 Ma）. Our results are not consistent with the results from avian species of Tibetan Plateau, either, where species experienced population expansion following the retreat of the extensive glaciation period （0.5 to 0.175 Ma）

Asymmetrical introgression patterns between rusty-necklaced partridge (Alectoris magna) and chukar partridge (Alectoris chukar) in China

The rusty-necklaced partridge(Alectoris magna)and the chukar partridge(Alectoris chukar)are the most com­mon gamebirds in northern China.Previous comparisons of mitochondrial DNA(mtDNA)have revealed an in­trogression phenomenon between 2 species of partridge in the Liupan Mountain region of China.mtDNA is ma­ternally inherited,making it difficult to determine the origin of parental genes.We assessed the genetic variation and gene flow between these 2 species of partridges using 8 microsatellite loci as neutral diagnostic markers in 171 samples from the hybrid zone.Our data revealed an extensive divergence of genetic structure between populations of rusty-necklaced partridges and chukar partridges.In this study,we found that 19 samples had been previously morphologically identified as rusty-necklaced partridge were genetically identified as hybrids through Bayesian analysis using STRUCTURE analysis.These hybrids exhibited a mosaic of alleles that were derived from both parental lineages.However,chukar partridges did not present the genotype of the rusty-neck­laced partridge.Thus,our findings demonstrate that the hybridization between the 2 species was the result of asymmetrical introgression,with gene flow occurring only from the chukar partridge to the rusty-necklaced par­tridge.In addition,we also note the high linkage disequilibrium in populations of the rusty-necklaced partridge.These results indicate that although unidirectional introgression did not reduce genetic diversity of the Alectoris partridges,it affected the balance of gene flow between populations.The data from microsatellite DNA prompt­ed our concern about the genetic integrity of the rusty-necklaced partridge.