Molecular Phylogeny Of The Alpine Partridges In China

The alpine partridges in China consist of 5 genera,11 species and 29 subspecies of Galliformes taxonomic groups distributing mainly on and around Qingzang plateau. The samples we collected are composed of 4 genera,9 species and 23 subspecies of it, i.e.4 subspecies of Tetraogallus himalayensis,3 subspecies of T. tibetanus,5 subspecies of Alectoris chukar,2 subspecies of A. magna,1 subspecies of Perdix perdix,3 subspecies of P. dauuricae,3 subspecies of P. hodgsoniae,1 of Tetraophasis obscures and T. szechenyii. Together with other Phasianidae samples and the categories from Genebank, Taxa studied herein include 41 Phasianidae species and 20 of 21 phasianidae genera in China and 67 species and 30 genera in the world. The nuclear gene and several mitochondrial genes sequences, representing these Galliformes groups, were analyzed to (1) ascertain the evolutionary relationship between the alpine partridges and other related phasianid genera, (2) produce a molecular phylogeny of the extant species of the alpine partridges, and (3) correlate the inferred molecular phylogeny and extent of interspecific genetic divergence with Pliocene/Pleistocene biogeographical scenarios in the Qinghai-Tibet Plateau region to suggest speciational patterns in these alpine partridges.The different gene segments were separated and concatenated for analysis simultaneously. Congruence among the different DNA data sets was evaluated using the incongruence-length-difference (ILD) test. Each data set was subjected to maximum parsimony (MP) using PAUP*4.0b10 and Bayesian analyses using MrBayes 3.0. Bayesian analysis of combined data (c-mos+CYT B+ND2) and D-loop data were also used separately to estimate the divergence times for clades of these alpine partridges by software BEAST 1.4.8.We obtained the nucleotide sequences including partial c-mos gene (613bp), ND2 gene(1023bp), control region (1056bp) and complete CYT B gene (1143bp). The ILD test of different combined dataset were acceptable(>0.05). Among the alpine partridge genera, CYT B and ND2 showed similar composition of nucleotide pair and similar rates and types of nucleotide substitutions. The percentage of nonsynonymous substitution is comparatively higher in genus Tetraophasis on CYT B nucleotide sequences, but not on ND2. The transition to transversion ratio (Ti/Tv) is also higher in genus Tetraophasis.The genera of Phasianidae in China should be classified into 4 clades:(1) Tetraogallus/Alectoris/Coturnix, (2) Phasianus/Chrysolophus/Lophura/Syrmaticus/ Crossoptilon/Tetraophasis and Lophophorus, also including Ithaginis/Tragopan/ Pucrasia/Perdix, (3) Gallus/Bambusicola/Francolinus, (4)Pavo and Polyplectron.Blood Pheasant (genus Ithaginis) and Tragopan had uncertain positions in traditional classification but should been placed in tribe Phasianini in molecular phylogenetic analysis. Genus Arborophila was basal in whole Phasianidae clade, indicated it's age-old phylogenetic position.Tetraophasis was sister to genus Lophophorus doubtlessly and the clade should also been placed in pheasants. The divergence time between them indicated that the clade Tetraophasis and the clade Lophophorus had been formed in the region of Hengduan Mountains before the uplift of the Tibetan Plateau, and the ancestor populations of Tetraophasis had been segregated into two partitions by the early Pleistocene glaciation and then formed the two species of Tetraophasis.All three species of genus Perdix were grouped into a monophyletic cluster and should be placed into the pheasant group in our analyses. Tibetan partridges(Perdix hodgsoniae) were consistently placed basal to other Perdix species, and P. dauuricae przewalskii and P. hodgsoniae hodgsoniae, the subspecies distributed in main land of Tibet plateau, were basal to the other two subspecies in their own clade, respectively. These phylogenetic relationships suggested that the Perdix were originated from Tibet region. Divergence time estimates indicated that the Tibetan partridge split from the ancestor of Daurian partridge and gray partridge about 3.63 myr ago, we consider that the grassland-adapted ancestor of the typical partridges spread to the plateau during the middle Pliocene (4.52-2.75 myr ago). Throughout the course of the Qingzang Movement and the Pleistocene glaciations, some populations of the ancestor stayed in some basins, survived the glaciations and gave rise to Tibetan partridge. Other groups were forced to move north by rapid ascension of the Plateau, whereafter the big second glacier (approximately 2.05-1.28 myr ago) in central China compelled them to split into west and east branches, which now form the prey partridge in the west and the Daurian partridge in the east.The three subspecies of Tetraogallus tibetanus studied herein showed no significant phylogeographic structure, we suggested that it's resulted from the adaptation to the climatic conditions and glacial cycles on the Qinghai-Tibetan Plateau. The phylogeny of 4 subspecies within Tetraogallus himalayensis indicated their eastward dispersal course along the south margin of Tarim Basin during the medium-term uplift (approximately 0.88 myr ago) of Qingzang plateau. Our studies also suggested that divergence between T. tibetanus and T. himalayensis took place before the sudden uplift of the Plateau.Divergence time estimates between Alectoris chukar and A. magna indicated that the two species split away about 2.76 myr ago, and the molecular phylogenetic analysis showed no phylogeographic partitions among the 5 subspecies of A. chukar.