Chen Y.-Y.,Zhejiang University |
Chen Y.-Y.,State Conservation Center for Gene Resources of Endangered Wildlife |
Zhang Y.-Y.,Zhejiang University |
Zhang Y.-Y.,State Conservation Center for Gene Resources of Endangered Wildlife |
And 7 more authors.
Journal of Experimental Zoology Part B: Molecular and Developmental Evolution | Year: 2010
Ample variations of the major histocompatibility complex (MHC) genes are essential for vertebrates to adapt to various environmental conditions. In this study, we investigated the genetic variations and evolutionary patterns of seven functional MHC class II genes (one DRA, two DRB, two DQA, and two DQB) of the giant panda. The results showed the presence of two monomorphic loci (DRA and DQB2) and five polymorphic loci with different numbers of alleles (seven at DRB1, six at DRB3, seven at DQA1, four at DQA2, six at DQB1). The presence of balancing selection in the giant panda was supported by the following pieces of evidence: (1) The observed heterozygosity was higher than expected. (2) Amino acid heterozygosity was significantly higher at antigen-binding sites (ABS) compared with non-ABS sequences. (3) The selection parameter ω(dN/dS) was significantly higher at ABS compared with non-ABS sequences. (4) Approximately 95.45% of the positively selected codons (P>0.95) were located at or adjacent to an ABS. Furthermore, this study showed that (1) The Qinling subspecies exhibited high ωvalues across each locus (all >1), supporting its extensive positive selection. (2) The Sichuan subspecies displayed small ωat DRB1 (ω<0.72) and DQA2 (ω<0.48), suggesting that these sites underwent strong purifying selection. (3) Intragenic recombination was detected in DRB1, DQA1, and DQB1. The molecular diversity in classic Aime-MHC class II genes implies that the giant panda had evolved relatively abundant variations in its adaptive immunity along the history of host-pathogen co-evolution. Collectively, these findings indicate that natural selection accompanied by recombination drives the contrasting diversity patterns of the MHC class II genes between the two studied subspecies of giant panda. © 2009 WILEY-LISS, INC.
Yu J.,Chengdu Zoo |
Wang Q.,Chengdu Zoo |
Liu X.,Chengdu Zoo |
Deng J.,Chengdu Zoo |
And 4 more authors.
Acta Theriologica Sinica | Year: 2010
The hog deer (Axis porcinus) is a Class 1 National Key Protected Species in China ; the species has been extirpated within China. China has a captive population of only about 30, of which the Chengdu Zoo has 22. It is critical for captive management within China to identify paternity relationships and establish the pedigree of the hog deer population in the Chengdu Zoo. We used 7 microsatellites to genotype 22 live and 5 dead hog deer individuals from the Chengdu Zoo ; we identified potential 13 paternal relationships for animals in which maternity was already known. The exclusion method defined 8 of the 13 father - offspring pairs. The likelihood method determined the remaining 5 pairs with a confidence level of 95%. Combining the result of this paternity test with the breeding records of the Chengdu Zoo, we constructed the genetic pedigree for this hog deer population. Our result will serve as an important reference for the future artificial breeding strategy and management of the captive hog deer population in China.
Chen S.-C.,Tongji University |
Zhang L.,Tongji University |
Zeng J.,Tongji University |
Shi F.,Tongji University |
And 3 more authors.
Journal of Systematics and Evolution | Year: 2012
The monotypic genus Platycarya (Juglandaceae) is one of the most widespread temperate tree species in East Asia. In this research, we implemented a phylogeographical study using chloroplast DNA (cpDNA) (psbA-trnH and atpB-rbcL intergenic spacer) sequences on Platycarya strobilacea, in order to identify the locations of the species' main refugia and migration routes. A total of 180 individuals of P. stobilacea from 27 populations from China and Jeju Island (Korea) were collected. The results revealed that P. strobilacea had 35 haplotypes for the two intergenic spacers and high genetic diversity (h T = 0.926). This surprisingly high diversity of haplotypes indicates its long evolutionary history, which is in agreement with previous phylogenetic analyses and fossil records. Significant cpDNA population subdivision was detected (GST = 0.720; NST = 0.862), suggesting low levels of recurrent gene flow through seeds among populations and significant phylogeographical structure (NST > GST, P < 0.05). The construction of phylogenetic relationships of the 35 chlorotypes detected four major cpDNA clades. Divergence dating analyses using BEAST suggest that the divergence of the major cpDNA clades occurred before the Miocene. Demographic analysis indicated that the Eastern clade underwent localized demographic expansions. The molecular phylogenetic data, together with the geographic distribution of the haplotypes, suggest the existence of multiple glacial refugia in most of its current range in China through Quaternary climatic oscillations. © 2012 Institute of Botany, Chinese Academy of Sciences.
Guan B.-C.,Zhejiang University |
Fu C.-X.,Zhejiang University |
Fu C.-X.,State Conservation Center for Gene Resources of Endangered Wildlife |
Qiu Y.-X.,Zhejiang University |
And 3 more authors.
American Journal of Botany | Year: 2010
To evaluate the role of Quaternary refugial isolation in allopatric (incipient) speciation of East Asian temperate forest biotas, we analyzed amplified fragment length polymorphisms (AFLPs) and the breeding system in Dysosma versipellis. The study revealed that D. versipellis is mostly self-incompatible, genetically highly subdivided and depauperate at the population level (e.g., Φ ST =0.572/ H E = 0.083), and characterized by a low pollen-to-seed migration ratio (r ≈ 4.0). The latter outcome likely reflects limited pollen flow in a low-seed disperser whose hypothesized "sapromyophilous" flowers undergo scarce, inefficient, and likely specialized cross-pollination by small Anoplodera beetles, rather than carrion flies as assumed previously. In consequence, fruit set in D. versipellis was strongly pollen-limited. Our AFLP data support the hypothesis of a long-standing cessation of gene flow between western and central eastern populations, consistent with previous chloroplast DNA data. This phylogeographic pattern supports the role of the Sichuan Basin as a floristic boundary separating the Sino-Himalayan vs. Sino-Japanese Forest subkingdoms. Our genetic data of D. versipellis also imply that temperate deciduous forest elements to the west and the east of this basin responded differently to Quaternary climate change, which may have triggered or is leading to allopatric (incipient) speciation.