Huttley Gavin A, Wakefield Matthew J, Easteal Simon
John Curtin School of Medical Research, The Australian National University, Canberra, Australia.
Mol Biol Evol. 2007 Aug;24(8):1722-30. doi: 10.1093/molbev/msm094. Epub 2007 May 9.
Accurate estimation of any phylogeny is important as a framework for evolutionary analysis of form and function at all levels of organization from sequence to whole organism. Using alignments of nonrepetitive components of opossum, human, mouse, rat, and dog genomes we evaluated two alternative tree topologies for eutherian evolution. We show with very high confidence that there is a basal split between rodents (as represented by the mouse and rat) and a branch joining primates (as represented by humans) and carnivores (as represented by dogs), consistent with some but not the most widely accepted mammalian phylogenies. The result was robust to substitution model choice with equivalent inference returned from a spectrum of models ranging from a general time reversible model, a model that treated nucleotides as either purines and pyrimidines, and variants of these that incorporated rate heterogeneity among sites. By determining this particular branching order we are able to show that the rate of molecular evolution is almost identical in rodent and carnivore lineages and that sequences evolve approximately 11%-14% faster in these lineages than in the primate lineage. In addition by applying the chicken as outgroup the analyses suggested that the rate of evolution in all eutherian lineages is approximately 30% slower than in the opossum lineage. This pattern of relative rates is inconsistent with the hypothesis that generation time is an important determinant of substitution rates and, by implication, mutation rates. Possible factors causing rate differences between the lineages include differences in DNA repair and replication enzymology, and shifts in nucleotide pools. Our analysis demonstrates the importance of using multiple sequences from across the genome to estimate phylogeny and relative evolutionary rate in order to reduce the influence of distorting local effects evident even in relatively long sequences.
准确估计任何系统发育对于从序列到整个生物体的各级组织的形态和功能进化分析框架而言都很重要。利用负鼠、人类、小鼠、大鼠和狗基因组的非重复成分比对，我们评估了真兽类进化的两种替代树形拓扑结构。我们非常有信心地表明，啮齿动物（以小鼠和大鼠为代表）与连接灵长类动物（以人类为代表）和食肉动物（以狗为代表）的分支之间存在基部分裂，这与一些但并非最广泛接受的哺乳动物系统发育一致。该结果对于替代模型的选择具有稳健性，从一般时间可逆模型、将核苷酸视为嘌呤和嘧啶的模型以及纳入位点间速率异质性的这些模型的变体等一系列模型都返回了等效推断。通过确定这个特定的分支顺序，我们能够表明啮齿动物和食肉动物谱系中的分子进化速率几乎相同，并且这些谱系中的序列进化速度比灵长类谱系快约11% - 14%。此外，通过将鸡作为外类群，分析表明所有真兽类谱系的进化速率比负鼠谱系慢约30%。这种相对速率模式与世代时间是替代速率以及隐含的突变速率的重要决定因素这一假设不一致。导致谱系间速率差异的可能因素包括DNA修复和复制酶学的差异以及核苷酸库的变化。我们的分析证明了使用来自全基因组的多个序列来估计系统发育和相对进化速率的重要性，以便减少即使在相对较长序列中也明显存在的扭曲局部效应的影响。
