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

我们项目的目的是通过野外生态学家和统计学家的密切合作，为保护遗传学开发有效的野外调查和数据分析方法。主要研究成果包括：a)微生物风险分析中的群体遗传学方法：我们建立了一种部分似然方法来推断宿主内病毒序列的有效群体大小和分子进化速率，并研究了病毒序列的最佳采样设计，用于推断宿主内的适应性进化。HIV-1 env基因分析显示两者呈负相关。b)报春花作为濒危植物群体：建立了近交群体QTL定位方法，并进行了不同花型结构的杂交实验，估算了报春花相关性状的QTL。通过微卫星标记的父系分析，研究了基因流的程度。c)大毒按蚊作为疟疾的传播媒介…更多：样本采集自整个东南亚地区。线粒体COI和CoII基因的群体遗传分析揭示了物种边界上基因渗入的证据。对微卫星标记数量的实验设计和基因型的分类进行了研究，以推断种群结构。用半参数聚结模型对这些基因进行分析表明，在大约0.2MYA左右出现瓶颈，随后是种群扩张。d)西班牙蝗虫杂交带：在西班牙北部的杂交带采集褐蝗（Chorthippus brunneus）和雅可布蝗（C jacobsi）样本，进行杂交实验。开发了一种软件来测量歌曲的遗传背景，这是一个重要的特征，有助于前合子分离。同时开发了AFLP标记自动分型软件进行QTL分析。e)种群增强中的保护遗传学：为了研究种群增强计划对野生种群遗传结构的影响，采用经验贝叶斯方法估计了种群分化程度，并分析了日本红鲷（Pagrurs major）的线粒体DNA数据。同时检测连锁不平衡和细分群体遗传分化的层次模型。通过数值模拟、同工酶数据分析和人群SNP数据分析，验证了其有效性。少

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