Molecular Ecology And Phylogeography Of Chukar Partridge (Alectoris Chukar)

The chukar (Alectoris chukar) is a kind of widely distributed wildfowls belonging to Aves, Galliformes, Phasianidae, Alectoris whose distribution is throughout Mediter-ranean islands, central Asia and the northeastern of China that. Currently, up to 16 subspecies have been identified. In this study, I addressed the phylogeny of 15 subspecies of chukars based on mitochondrial DNA control region (mtDNA CR), as well as the molecular ecology and phylogeography from 25 populations of five Chinese chukar subspecies based on mtDNA CR and microsatellite markers. The aims of this study are to:(1) explore the origin of chukars by molecular phylogenetic analysis of 15 subspecies of chukar; (2) examine the effects of environmental factors on population genetic diversity of the 25 chukar populations distributed in China; (3) reconstruct the phylogeographic relationship of Chinese chukars under the background of Pleistocene climate oscillation; (4) demonstrate the roles of either sex played in the population expansion, based on both the maternal and bi-parental inherited markers; (5) infer the geological or past demographic events that may probably have determined the current population structures; (6) offer the rational protect proposals of the chukars from the prospective of population genetics. In this study, we obtained mtDNA CR sequences of 427 specimens from 15 chukar subspecies, and sequences of mtDNA CR, as well as eight microsatellite loci, for 288 specimens from 25 Chinese chukar populations. The main results include:1. The base compositions of mtDNA CR of chukar are T 32.1%, C 27.3%, A 26.4% and G 14.2%. Totally,139 haplotypes were defined by 127 variable sites that were detected in the 427 specimens from 15 chukar subspecies, with the mean haplotype diversity of 0.961 and the nucleotide diversity of 0.0054. The average expected and observed heterozygosity was 0.8624 and 0.7847, implying a relatively high genetic diversity of chukars.2. The 15 subspecies and 25 Chinese populations of chukars mainly showed the same pattern of "high haplotype diversity while low nucleotide diversity", which, in addition to the unimodal of mismatch distribution and the test of selective neutrality, all indicated that Chinese chukar populations had experienced population expansion at late Pleistocene. Most populations experienced expansion at the metaphase of Late Pleistocene (0.027-0.06 Ma), co-occurring with the fifth cold period, with the exception of populations from Honghui (HH), Wudu (WD), Dongdashan (DSH), Jingtai (JT) and Wuhai (WH) that experienced expandsion at 0.063-0.144 Ma ago, consistent with the forth warm period.3. The nucleotide diversity was significantly negative-correlated with the latitude. Genetic diversity showed a positive correlation with varying environmental factors, whereas other index of genetic diversity such as haplotype diversity, expected heterozygosity and observed heterozygosity had statistically non-significant correlation with environmental factors. Such a relationship that the more unstable the climate was, the higher the genetic diversity we observed was, may be caused by wide sampling sites, remarkable climatic differences and high adaptative ability of chukars.4. The gene flow detected from mtDNA CR is higher than that from micro satellite, indicating that female chukars played a dominating role in population expansion. It thus provided molecular evidence to the assumption that it's the female that spreads out of their natal territories in Phasianidae species.5. The phylogenetic tree based on the mtDNA CR and the nucleotide diversity of 15 chukar subspecies indicated that chukars might originate from the region of western Himalayas-Pamirs-western Tianshan, which is consistent with the previous conclusion that chukar originated from central Asia based on the plumage features and the subspecies'distribution. On the phylogenetic tree, the 15 chukar subspecies clustered into two subspecies groups, of which the divergence time was about 0.45 Ma (calculated by mtDNA CR genetic distance and MDIV methods) that is consistent with Gablah interglacial period (0.30-0.73 Ma) on the Tibet Plateau or the interglacial period (0.030-0.047 Ma) after the Gaowangfeng Glaciation in late Mid-Pleistocene at the Tianshan Mountains. Thereafter, the climate became cold and dry so that the two groups spreaded out of their original habitats and differentiated separately into the current distribution pattern. The divergence time between 15 subspecies is equivalent to the Gunz-Mindel interglacial (0.30-0.69 Ma) and Mindel-Riss interglacial (0.125-0.20 Ma) at Europe or the third warm period (0.24-0.36 Ma) and the fourth warm period (0.06-0.15 Ma) in China, showing that the chukar is a kind of bird that expanded in glacial but was isolated in interglacial. Both the MP and Bayesian trees constructed by mtDNA CR sequences were same to the 15 subspecies phylogeny tree constructed based on the genetic distance of mtDNA CR.6. The nucleotide diversity and phylogenetic tree of Chinese chukars supported the idea that Chinese chukars originated from two regions, the western Himalayans-Pamirs and the western Tianshan-Tarbagatay, with the predominant regions concentrated at the arid and semi-arid area of western Tianshan-Tarbagatay in central Asia. Then, they dispersed eastward and formed the subspecies with the same morphological characters.7. Chinese chukar populations showed no unambiguous phylogeographic structure based on both the mtDNA CR and microsatellite markers. The reasons may be that i) the distributed area of chukars had little or no ice cover during the glacial period; ii) the climate fluctuations had no or little influence on the habitats of chukar during glacial-interglacial of Pleistocene; and iii) the mountains did not form physical barriers to chukar populations. Mantel test based on mtDNA CR and microsatellite suggested that there were no significant positive-correlations between FST/(1-FST) and geographic distances, which showed that the genetic differences were not simply resulted from geographical distances. The Analysis of Molecular Variance (AMOVA) showed that 69.07%(mtDNA CR) and 81.03% (microsatellite) of the total genetic variability were distributed within population.8. Phylogeographic analysis of intraspecific genetic variation provides valuable information on how to identify management units (MUs) and evolutionarily significant units (ESUs) for endangered species. According to the criteria of MUs and ESUs, we suggest that the chukars who distribute Longdong Loess Plateau, Helanshan Mountains, Qilianshan Mountains and western Tianshan mountains should be treated as ESU, respectively. And the six Chinese chukar subspecies should be treated as separate MUs. As for populations, the populations of Huoerguosi (HEG), Akesai (AKS), Subei (SB), Tongchuan (TC) and Wudu (WD) should be treated as MUs, especially the WD population, because it belongs to the Oriental realm, where the climate is more moderate and humidity than other locations of chukar populations.