Development of methods of sampling survey and analysis for field conservation genetics

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The purpose of our project is to develop efficient methods of field survey and data analysis for conservation genetics by close collaboration between field ecologists and statisticians. The achievement is summarized as :a)Population genetics approach in risk analysis of micro-organism : We developed a partial likelihood procedure to infer the effective population sizes and rates of molecular evolutions of viral sequences within hosts, and investigated an optimal sampling design of viral sequences for the inference of adaptive evolution within a host. Analysis of HIV-1 env gene showed a negative correlation between them.b)Primula as an endangered plant population : Method of QTL mapping for outbreeding populations was developed, and crossing experiments of different types of floral architectures were conducted to estimate the QTLs of the related traits. By paternity analysis of microsattelite markers, the extent of gene flow was studied.c)Anopheles dirus mosquitoes as vectors of malaria … More : Samples were collected from the whole area of Southeast Asia. Population genetic analysis of COI and CoII genes in mitochondria revealed evidence of introgression over the species boundary. Experimental design of the number of microsattelite markers and categorization of genotypes were studied for the inference of population structure. Analysis of these genes with a semiparametric coalescent model implied a bottleneck around some 0.2MYA followed by population expansion.d)Hybrid zone of grasshoppers in Spain : Samples of Chorthippus brunneus and C jacobsi were collected from the hybrid zone in northern Spain and crossing experiment was conducted. Software was developed to measure the genetic background of the song, an important character contributing to prezygotic isolation. Software of automatic typing of AFLP markers was also developed for QTL analysis.e)Conservation genetics in stock enhancement : To study how stock enhancement program may have affected the genetic structure in the wild population, an empirical Bayes procedure was developed to estimate the extent of population differentiation and mitochondrial DNA data of Pagrurs major (Japanese red sea bream) was analyzed. A hierarchical model for simultaneous detection of linkage disequilibrium and genetic differentiation of subdivided populations. Its efficacy was examined by numerical simulation and the analyses of isozyme data Plecoglossus altivelis altivelis (ayu) and SNP data from human populations. Less