TEST OF NEUTRAL MOLECULAR EVOLUTION

描述：这是一项修订后的提案，旨在确定 力量会影响蛋白质的进化。提出了四个实验；都是 基于从密切相关的DNA序列数据收集 种黑腹果蝇和拟果蝇，以及种 对D.Yakuba-D.teissieri和D.erecta-D.Orena。严格中立 进化与种群大小无关，但固定的概率 轻微有害等位基因的数量与种群大小成反比 优势等位基因的固定概率直接 与人口规模成正比。因此，如果有效人口 大小对于不同的谱系是已知的，在 可以对这些谱系进行分析，以确定是否存在替换 平均严格中性，略微有害或有利。Dr。 Kreitman认为，该物种的有效种群规模。 黑腹潜蝇比拟态金丝猴小，因为它们的 密码子偏好率前者高于后者。此外，遗传变异 与低重组率的基因组区域相比，物种内的重组率降低 高重组率的区域。对此有两种不同的解释 观察-与选定的有害物质有关的中性变化的损失 突变(背景选择)和中性遗传变异的丧失 与肯定选择的优势突变(选择性扫描)相关联- 两者都意味着在人口减少的地区有效人口规模较小 重组。 鉴于这些先验推断的人口规模对比，以下数据 将被收集以测试进化的替代是否主要是 中性(零假设)，略微有害或略有适应。 1.氨基酸替换取代的数量很好地确定 约25个同源基因在黑腹金龟子、拟态金龟子和 Outgroup，D.Yakuba。将选择已在D中进行测序的基因座。 它编码大量的蛋白质，这些蛋白质位于高密度区 和不在(3R)a中的重组，D之间的固定反转。 Simans和黑腹金丝猴D.这些基因座将从拟态盘藻中获得。 和D.Yakuba通过根据黑素胃泌素序列设计的引物进行聚合酶链式反应 以及来自其他同源物的保守区的知识；并进行了测序。这个 黑腹葡萄球菌和拟态葡萄球菌的替换替换数量将 通过将每个物种与外群物种进行比较来确定。测试，测试 系统性世系效应(例如，在一种 物种)，内含子序列中的替换(假定是中性的)将是 下定决心。D.编码区氨基酸替换率。 根据血统效应进行调整的黑色鬼和拟态金丝虫将被 与确定取代是否主要是中性的(比率相等)相比较， 略具危害性(黑腹金龟子发病率较高)，或略有 有利的(拟单胞菌较高的比率)。2.实验1将是 在两个基因的低重组区对25个基因进行重复 物种。这里的假设是，两者的有效人口规模 低重组率地区的物种几乎相等，预测 这些生物的替代率不会有世系差异 基因。3.在(3R)中，a是一个固定的倒位(84F-93F) 和拟人掌。拟态石杉具有祖先的基因序列。重组 染色体3在着丝粒附近被抑制(从81-84)，所以基因 在这种反转的断点附近将改变重组 环境。倒位内12个近端基因和12个远端基因 将被测序，以及相同基因的氨基酸替换率 在这两个地区经历了不同的有效人口规模 我们将对物种进行比较。在略微有害的模式下， 黑腹盘藻近端断裂点基因的替换 比拟单胞菌中相同的基因更大，并且替换率 来自黑腹金龟子远端断裂点的基因将少于 在拟态金黄色葡萄球菌中有相同的基因。相反的预测将适用于 有利的替代方案。4.D。 Blackogaster和D.Simans比较了同义词的比率 替换、相对密码子偏向和氨基酸替换率将 使用种对D.Yakuba-D.teissieri和D.erecta-进行测试- D·奥瑞娜。同样的25个高重组区基因在 第一个实验将在另外三个物种中进行测序。费率 将确定这些同义词和氨基酸的替代 物种对，并检查与观察到的模式的一致性 黑腹小卷蛾和拟黑腹小卷蛾。

DESCRIPTION: This is a revised proposal to determine what evolutionary forces affect protein evolution. Four experiments are proposed; all are based on the collection of DNA sequence data from the closely related species Drosophila melanogaster and D. simulans, as well as the species pairs D. yakuba - D. teissieri and D. erecta - D. orena. Strictly neutral evolution is independent of population size, but the probability of fixation of slightly deleterious alleles is inversely proportional to population size and the probability of fixation of advantageous alleles is directly proportional to population size. Therefore, if the effective population sizes are known for different lineages, the patterns of substitutions in these lineages can be analyzed to determine whether substitutions are on average strictly neutral, slightly deleterious or advantageous. Dr. Kreitman argues that the species effective population size of D. melanogaster is smaller than that of D. simulans, because there is less codon bias in the former than the latter. Furthermore, genetic variation within species is reduced in genomic regions of low recombination compared to regions of high recombination. Two alternative explanations for these observations - loss of neutral variation linked to selected deleterious mutations (background selection), and loss of neutral genetic variation linked to positively selected advantageous mutations (selective sweeps) - both imply smaller effective population sizes in regions of reduced recombination. Given these a priori inferred population size contrasts, the following data will be collected to test whether evolutionary substitutions are primarily neutral (the null hypothesis), slightly deleterious or slightly adaptive. 1. Numbers of amino acid replacement substitutions well be determined for approximately 25 homologous genes in D. melanogaster, D. simulans and the outgroup, D. yakuba. Loci will be chosen that have been sequenced in D. melanogaster, that encode large proteins, that are in regions of high recombination and that are not in In(3R)a, a fixed inversion between D. simulans and D. melanogaster. The loci will be obtained from D. simulans and D. yakuba by PCR using primers designed from the melanogaster sequence and knowledge of conserved regions from other homologs; and sequenced. The number of replacement substitutions in D. melanogaster and D. simulans will be determined by comparing each to the outgroup species. To test for systematic lineage effects (e.g., high mutation rates in one of the species), substitutions in intron sequences (presumed to be neutral) will be determined. Rates of amino acid replacement in the coding regions of D. melanogaster and D. simulans, adjusted for lineage effects, will then be compared to determine if substitutions are primarily neutral (rates equal), slightly deleterious (higher rates in D. melanogaster), or slightly advantageous (higher rates in D. simulans). 2. Experiment 1 will be repeated for a sample of 25 genes in regions of low recombination in both species. Here the assumption is that the effective population size of both species in regions of low recombination are nearly equal, and the prediction is that there will be no lineage differences in substitution rates of these genes. 3. In(3R)a is a fixed inversion (84F-93F) between D. melanogaster and D. simulans. D. simulans has the ancestral gene order. Recombination on chromosome 3 is suppressed near the centromere (from 81-84), so genes near the breakpoints of this inversion will have changed recombinational environments. 12 proximal genes and 12 distal genes within the inversion will be sequenced, and rates of amino acid substitution of the same genes that have experienced different effective population sizes in the two species will be compared. Under the slightly deleterious model, rates of substitution of genes from the proximal breakpoint in D. melanogaster will be greater than the same genes in D. simulans, and rates of substitution of genes from the distal breakpoints in D. melanogaster will be less than the same genes in D. simulans. The opposite predictions would be true for advantageous substitutions. 4. The generality of the inferences from D. melanogaster and D. simulans comparisons of rates of synonymous substitutions, relative codon bias and rates of amino acid replacement will be tested using the species pairs D. yakuba - D. teissieri and D. erecta - D. orena. The same 25 high recombination region genes sequenced in the first experiment will be sequenced in the three additional species. Rates of synonymous and amino acid substitutions will be determined for these species pairs, and examined for consistency with the patterns observed for D. melanogaster and D. simulans.