Data from: Exploring the relationships between mutation rates, life history, genome size, environment and species richness in flowering plants

A new view is emerging of the interplay between mutation at the genomic level, substitution at the population level, and diversification at the lineage level. Many studies have suggested that rate of molecular evolution is linked to rate of diversification, but few have evaluated competing hypotheses. By analysing sequences from 130 families of angiosperms, we show that variation in the synonymous substitution rate is correlated among genes from the mitochondrial, chloroplast and nuclear genomes, and linked to differences in traits among families (average height and genome size). Within each genome, synonymous rates are correlated to nonsynomymous substitution rates, suggesting that increasing the mutation rate results in a faster rate of genome evolution. Substitution rates are correlated with species richness in protein-coding sequences from the chloroplast and nuclear genomes. These data suggest that species traits contribute to lineage-specific differences in the mutation rate which drive both synonymous and nonsynonymous rates of change across all three genomes, which in turn contribute to greater rates of divergence between populations, generating higher rates of diversification. These observations link mutation in individuals to population level processes and to patterns of lineage divergence. 28 pages, 3 tables, 3 figures; Supplement

学界正逐渐形成关于基因组层面突变、种群层面碱基替换以及支系层面分化三者间相互作用的全新认知。诸多研究已表明分子进化速率与支系分化速率存在关联，但鲜有研究对相互竞争的各类假说开展验证。本研究通过分析130个被子植物（angiosperms）科的序列数据，发现线粒体基因组（mitochondrial genome）、叶绿体基因组（chloroplast genome）与核基因组（nuclear genome）中各基因的同义替换速率（synonymous substitution rate）存在共变现象，且与各科的性状差异（平均株高与基因组大小）相关联。在每个基因组内部，同义替换速率与非同义替换速率（nonsynonymous substitution rate）均呈显著相关，这提示突变速率的提升会加快基因组的进化速率。叶绿体与核基因组的蛋白编码序列中，碱基替换速率与物种丰富度存在关联。上述数据表明，物种性状会导致不同支系间的突变速率产生差异，这种差异同时驱动三个基因组内的同义与非同义替换速率变化，进而加快种群间的分化速率，最终催生更高的支系分化率。本研究的这些发现将个体层面的突变事件、种群层面的演化过程与支系分化模式三者有机联系起来。全文共计28页，包含3张表格与3幅插图，另有补充材料。