In 2008–2011, he was the Changjiang Chair Professor at Sun Yat-sen University, with an award from the Ministry of Education of China.
[4] Yang developed a number of statistical models and methods in the 1990s, which have been implemented in maximum likelihood and Bayesian software programs for phylogenetic analysis of DNA and protein sequence data.
[5][6] However, the assumed model of character change was simple and, for example, does not account for variable rates among sites in the sequence.
Yang developed a maximum likelihood model of gamma-distributed evolutionary rate variation among sites in the sequence in 1993–4.
A stream of papers followed this to extend the original model to accommodate variable selection pressures (measured by the dN/dS ratio) among evolutionary lineages or among sites in the protein sequence.
[13][14][15] And the branch-site models attempt to detect positive selection that affects only a few amino acid sites along pre-specific lineages.
[24] Yang and Rannala also developed the multispecies coalescent model,[25] which has emerged as the natural framework for comparative analysis of genomic sequence data from multiple species, incorporating the coalescent process in both modern species and extinct ancestors.
He was a co-organizer of the Royal Society Discussion Meeting on "Statistical and computational challenges in molecular phylogenetics and evolution" on 28–29 April 2008,[37] and the Royal Society Discussion Meeting on "Dating species divergence using rocks and clocks", on 9–10 November 2015.