PRF/J: Loss of Functional Constraints: Implications for Molecular Evolution and Phylogenetics

小行星9303258 在北美的小龙虾动物群中，至少有13种独立的物种在洞穴环境中定居;进化分歧跨越了近6000万年。 这些穴居物种表现出视力丧失，缺乏色素，以及对地下环境的其他适应。 这分类群中的这些特征使得有可能在分子水平上测试关于视力丧失的影响的假设。 13个物种对，包括一个troglobitic（盲）和一个epigean（不盲）物种，将比较分子水平的变化，在基因的视觉色素视紫红质。 放松功能约束的影响，视紫红质基因的分子进化，在核苷酸取代，氨基酸取代，和功能结构域，将被检查。 这种比较的方法将受益于大量的统计力量，以前没有在放松功能约束的研究。 此外，视紫红质基因在系统发育分析中的实用性有待探索，沿着的是对螯虾亚科10个属的关系的调查。在这项研究中，将产生有和没有功能限制的DNA序列的分子进化的比较数据，预测在没有功能限制的进化情况下（troglobitic物种），遗传密码子替换的速率更高。 在功能释放的条件下，预期在密码子内的每个核苷酸位置处具有相等的取代速率。 这些突变事件将在视紫红质的结晶蛋白的三级（3维）结构的背景下解释，其由15个可定义的结构域组成。 然后可以检测突变的“热点”，并根据遗传功能进行解释。 也许这项研究的最有力的一般效果将是展示解释的优势，可以通过采用系统发育的方法时，在分子遗传水平上攻击生物学问题。***

9303258 CRANDALL Within the North American crayfish fauna there are at least 13 proposed independent species colonizations of the cave environment; the evolutionary divergences span nearly 60 million years. These troglobitic species exhibit loss of vision, lack of pigment, and other aptations to the subterranean environment. Such characters in this taxon make it possible to test hypotheses about effects of vision loss at the molecular level. Thirteen species pairs, consisting of one troglobitic (blind) and one epigean (not blind) species, will be compared for molecular level changes in the gene for the visual pigment rhodopsin. Effects of relaxed functional constraint on the molecular evolution of the rhodopsin gene, in terms of nucleotide substitutions, amino acid substitutions, and functional domains, will be examined. This comparative approach will benefit from substantial statistical power not previously available in studies of relaxed functional constraint. In addition the utility of the rhodopsin gene in phylogenetic analyses is to be explored, along with investigation of relationships of the ten genera of the crayfish subfamily Cambarinae. %%% In this study that will generate comparative data on the molecular evolution of DNA sequences both with and without functional constraint, higher rates of genetic codon substitution are predicted in the case of evolution without functional constraints (troglobitic species). Under cond ition of functional release, equal rates of substitution are expected at each nucleotide position within a codon. These mutational events will be interpreted in a context of tertiary (3 dimensional) structure of the crystallized protein of rhodopsin, which is comprised of 15 definable domains. Mutational "hotspots" can then be detected and interpreted in terms of genetic function. Perhaps the most potent general effect of this research will be to demonstrate the interpretive advantage which can be derived by adopting the phylogenetic approach when attacking biological questions at the molecular genetic level. ***