Factors affecting diversity within species at 4-fold degenerate sites for unpreferred codons using intervals with conserved recombination rate.

A generalized linear model with quasibinomial distribution for the fine-scale intervals on chromosome 2 with conserved recombination rates between D. pseudoobscura Flagstaff, D. pseudoobscura Pikes Peak, and D. miranda after correction for the global modifier. This model illustrates the relationship of average pairwise D. pseudoobscura diversity for 4-fold degenerate sites of unpreferred codons to various factors. Windows that were nonsignificant when analyzed with a rare events logistic regression and had an Odds Ratio between (0.62 to 1.615) across maps were considered “conserved.” For this analysis, the “neutral mutation rate” was set as the average pairwise D. lowei–D. persimilis divergence at 4-fold degenerate sites for unpreferred codons. For consistency between models, if an interaction term was significant in any of the models (see Tables 3, S9, S10, and S11), it was kept in all. Results from uncondensed chromosome 2, XL, and XR exhibit similar relationships (Tables S9, S10, and S11). An asterisk indicates significance at an α of 0.05.本研究针对2号染色体（chromosome 2）上的精细区间构建了准二项分布（quasibinomial distribution）广义线性模型（generalized linear model），该区间内拟暗果蝇（D. pseudoobscura）弗拉格斯塔夫品系、拟暗果蝇派克峰品系与米兰达果蝇（D. miranda）之间的重组率已通过全局修饰因子（global modifier）完成校正。该模型阐释了非偏好密码子（unpreferred codons）4倍简并位点（4-fold degenerate sites）的平均拟暗果蝇成对多样性与多种影响因子之间的关联。经稀有事件logistic回归（rare events logistic regression）分析无统计学显著性，且在各遗传图谱中比值比（Odds Ratio）处于0.62至1.615区间的基因组窗口被认定为"保守区间"。本分析中，中性突变率（neutral mutation rate）设定为洛氏果蝇（D. lowei）与拟斯氏果蝇（D. persimilis）非偏好密码子4倍简并位点的平均成对分化水平。为保证各模型间的分析一致性，若任意模型中存在显著性交互项（interaction term，参见表3、表S9、表S10及表S11），则所有模型均保留该交互项。完整的2号染色体、XL染色体及XR染色体的分析结果呈现出相似的关联模式（参见表S9、表S10及表S11）。文中星号代表在显著性水平α=0.05下具有统计学显著性。