Molecualr evolutiona and genome biosiversity. Investigations involve five correlated areas: molecular phylogenetics; molecular ecology and conservation genetics; human genetics and evolution; origin of domestic animals and artificial selection; genome diversity and evolution.

1.    Molecular phylogenetics.— We use molecular data to reconstruct the evolutionary relationships of species, and maternal genealogies within species.  The phylogenies are used to explore changes in morphology, ecology, physiology, and behavior, as well as the mechanisms of speciation and macroevolutionary biogeography. The genealogies are used to recover the dispersal history of females, i.e. microevolutionary biogeography.

2.    iBOL.— China is taking part in the International Barcode of Life (iBOL) project at its highest level of organization, a Central Node, and we are participating as one of two sequencing facilities in China. These data will be used to discover where to focus more detailed evolutionary investigations, as a source of data for biological forensics, and for ecological assessments, such as the host species of mosquitoes.

3.    Molecular ecology and conservation genetics.— We are investigating the population genetic structure of selected endangered species. These investigations provide insight into their evolutionary history, and they provide scientific guidance in conservation biology. We test the prevailing hypothesis that low level of genetic diversity indicates that a species is endangered.

4.    Human genetics and evolution.— We use DNA sequence data to reconstruct the pre-history of modern humans. In addition, we probe the genetic causes underlying specific human traits and major diseases. As an application to human health, these investigations can identify individuals that may be prone to specific genetic diseases, and provide genetic clues for disease control and prevention.

5.    Origin of domestic animals and artificial selection.— Our studies into the origin and genetic diversity of economically important domestic animals identify their unrecorded history. Genomic comparisons elucidate the genetic bases of domestication, and discover changes in genes or genomic elements that contribute to domestication.

6.    Genome diversity and evolution.— Explore the fate of duplicate genes, how novel gene functions, new gene pathways, and gene networks evolved. Integrated with habitat and behavioral data, we investigate genomic variation, how (and why) the variations are selected , and the evolutionary forces underlying adaptation.

1.Yao Y.G, Kong QP, Bandelt HJ, Kivisild T, Zhang YP (2002) Phylogeographic differentiation of mitochondrial DNA in Han Chinese. Am. J. Hum. Genet. 70: 635-651.
2.Zhang JZ, Zhang YP, Rosenberg HF (2002) Adaptive Evolution of a Duplicated Pancreatic Ribonuclease Gene in a Leaf-Eating Monkey. Nature Genet. 30: 411-415.
3.Savolainen P, Zhang YP, Luo J, Lundeberg J, Leitner T (2002) Genetic evidence for an East Asian origin of domestic dogs. Science. 298: 1610-1613.
4.Shi P, Zhang JZ, Yang H, Zhang YP (2003) Adaptive diversification of bitter taste receptor genes in mammalian evolution. Mol. Biol. Evol. 20: 805-814.
5.Kong QP, Yao YG, Sun C, Bandelt HJ, Zhu CL, Zhang YP (2003) Phylogeny of East Asian mitochondrial DNA lineages inferred from complete sequences. Am. J. Hum. Genet. 73: 671-676.
6.Li HP, Meng S, Meng Z, Fu YX, Zhang YP (2003) Genetic Diversity and Population History of Golden Monkeys (Rhinopithecus roxellana). Genetics. 164: 269-275.
7.Yu L, Li QW, Ryder OA, Zhang YP (2004) Phylogenetic relationships within mammalian order Carnivora indicated by sequences of two nuclear DNA genes. Mol. Phylogenet. Evol. 33: 694-705.
8.Palanichamy MG, Sun C, Agrawal S, Bandelt HJ, Kong QP, Khan F, Wang CY, Chaudhuri TK, Palla V, Zhang YP (2004) Phylogeny of Mitochondrial DNA Macrohaplogroup N in India, Based on Complete Sequencing: Implications for the Peopling of South Asia. Am. J. Hum. Genet. 75: 966-978.
9.Li Y, Ye C, Shi P, Zou XJ, Xiao R, Gong YY and Zhang YP (2005) Independent origin of the growth hormone gene family in New World monkeys and Old World monkeys/hominoids. Journal of Molecular Endocrinology 35 (2): 399-409.
10.Chen SY, Su YH, Wu SF, Sha T and Zhang YP (2005) Mitochondrial diversity and phylogeographic structure of Chinese domestic goats. Mol. Phylogen.Evol. 37 (3): 804-814.
11.Shi P, Bielawski JP, Yang H, and Zhang YP (2005) Adaptive diversification of vomeronasal receptor 1 genes in rodents. JOURNAL OF MOLECULAR EVOLUTION 60: 566-576.
12.Yu L and Zhang YP (2006) The unusual adaptive expansion of pancreatic ribonuclease gene in Carnivora. Mol Biol Evol 23: 2326-2335.
13.Yu L, Li YW, Ryder OA, Zhang Y (2007) Analysis of complete mitochondrial genome sequences increases phylogenetic resolution of bears (Ursidae), a mammalian family that experienced rapid speciation. BMC Evolutionary Biology 7: 11.
14.Wu GS, Yao YG, Qu KX, Ding ZL, Li H, Palanichamy MG, Duan ZY, Li N, Chen YS, Zhang YP (2007) Population phylogenomic analysis of mitochondrial DNA in wild boars and domestic pigs revealed multiple domestication events in East Asia. Genome Biology 8: R245.
15.Wu DD, Irwin DM Zhang YP (2008) Molecular evolution of the keratin associated protein gene family in mammals, role in the evolution of mammalian hair. BMC Evolutionary Biology 8:241.
16.He F, Wu DD, Kong QP, Zhang YP (2008) Intriguing balancing selection on the intron 5 region of LMBR1 in human population. PLoS One 3: e2948.
17.Xie HB, Irwin DM, Zhang YP (2008) Evolution of conserved secondary structures and their function in transcriptional regulation networks BMC Genomics 9:520.
18.Wu DD, Wang GD, Irwin DM Zhang YP (2009) A profound role for the expansion of trypsin-like serine protease family in the evolution of hematophagy in mosquito. Mol Biol Evol.
19.Li H, Wang CY, Wang JX, Wu GS, Yu P, Yan XY, Chen YG, Zhao LH, Zhang YP (2009) Mutation analysis of a large Chinese pedigree with congenital preaxial polydactyly. Eur J Hum Genet 17: 604-10.
20.Che J, Hu JS, Zhou WW, Murphy RW, Papenfuss TJ, Chen MY, Rao DQ, Li PP, Zhang YP (2009) Phylogeny of the Asian spiny frog tribe Paini (Family Dicroglossidae) sensu Dubois. Mol Phylogenet Evol 50: 59-73.
21.Shen Y, Shi P, Sun YB, Zhang YP (2009) Relaxation of selective constraint on avian mitochondrial DNA following the degeneration of flight ability. Genome Res. 19:1760-5.
22.Yu L, Wang XY, Jin W, Luan PT, Ting N, Zhang YP. Adaptive evolution of digestive RNASE1 genes in leaf-eating monkeys revisited: new insights from 10 additional Colobines. Mol Biol Evol. [In press]