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

9303258克兰德尔在北美的小龙虾动物群中，至少有13个独立物种被提议在洞穴环境中定居；进化的分歧跨越了近6000万年。这些轮虫物种表现出视力丧失，缺乏色素，以及其他对地下环境的适应。这种分类群中的这些特征使得在分子水平上测试关于视力丧失影响的假说成为可能。研究人员将对13个物种对进行比较，以确定视觉色素视紫红质基因在分子水平上的变化。松弛的功能约束对视紫红质基因的分子进化的影响，从核苷酸替换、氨基酸替换和功能结构域的角度，将被检验。这种比较方法将受益于以前在放松功能约束的研究中所没有的强大的统计能力。此外，还将探索视紫红质基因在系统发育分析中的作用，以及对小龙虾亚科的10个属的亲缘关系的调查。%在这项研究中，将产生关于有和没有功能约束的DNA序列分子进化的比较数据，在没有功能约束的进化的情况下，预测到更高的遗传密码子替换率(混血物种)。在功能释放的条件下，在密码子内的每个核苷酸位置期望相等的替换率。这些突变事件将在视紫红质结晶蛋白的三级(三维)结构的背景下进行解释，该结构由15个可定义的结构域组成。然后，突变的“热点”就可以被检测到，并从遗传功能的角度进行解释。也许这项研究最有效的总体效果将是证明在分子遗传学水平上解决生物学问题时，通过采用系统发育方法可以获得的解释优势。***

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. ***