[Molecular evolution of MHC DQA genes. II. Phylogenetic analysis based on nucleotide substitution and SCU bias]

Phylogenetics of 23 alleles at MHC DQA loci in 7 mammalian species was studied based on their nucleotide (NT) substitution and synonymous codon usage (SCU) bias. (1) It was demonstrated that the NT substitution rates are 1.0 x 10(-9) NT/site/yr for exon2 and 1.3 x 10(-9) NT/site/yr for exon2-4 in a large time scale, which is similar to other nuclear genes, while for mouse and rat the rates are nearly twice as high as above mentioned. (2) The DQA locus diversity and their interallelic diversity developed long after the radiation of mammalian 80Mya (million years ago). The bovine counterpart, of, and with the same recent ancestor of ovine DQA2, remains to be discovered. HLA-DQA2 locus split from HLA-DQA1 ancestor at the time between 12 approximately 20 Mya while allele diversity of HLA-DQA1 emerged and developed from 24 Mya to less than 1 Mya. (3) The phylogenetic trees based on SCU divergence reflect the phylogenetics of MHC DQA genes quite well generally in a new respect and reveal that HLA-DQA2 has a distinctive SCU bias different from all other MHC DQA locianalyzed. It indicates that SCU statistics plays an important and unique role in phylogenetic analysis of orthologous genes. The method to estimate the SCU divergence and SCU similarity was improved in this research.