Mueller Rachel Lockridge
Museum of Vertebrate Zoology, University of California, 3101 Valley Life Sciences Building Berkeley, California 94720-3160, USA.
Syst Biol. 2006 Apr;55(2):289-300. doi: 10.1080/10635150500541672.
The mitochondrial genome is one of the most frequently used loci in phylogenetic and phylogeographic analyses, and it is becoming increasingly possible to sequence and analyze this genome in its entirety from diverse taxa. However, sequencing the entire genome is not always desirable or feasible. Which genes should be selected to best infer the evolutionary history of the mitochondria within a group of organisms, and what properties of a gene determine its phylogenetic performance? The current study addresses these questions in a Bayesian phylogenetic framework with reference to a phylogeny of plethodontid and related salamanders derived from 27 complete mitochondrial genomes; this topology is corroborated by nuclear DNA and morphological data. Evolutionary rates for each mitochondrial gene and divergence dates for all nodes in the plethodontid mitochondrial genome phylogeny were estimated in both Bayesian and maximum likelihood frameworks using multiple fossil calibrations, multiple data partitions, and a clock-independent approach. Bayesian analyses of individual genes were performed, and the resulting trees compared against the reference topology. Ordinal logistic regression analysis of molecular evolution rate, gene length, and the G-shape parameter a demonstrated that slower rate of evolution and longer gene length both increased the probability that a gene would perform well phylogenetically. Estimated rates of molecular evolution vary 84-fold among different mitochondrial genes and different salamander lineages, and mean rates among genes vary 15-fold. Despite having conserved amino acid sequences, cox1, cox2, cox3, and cob have the fastest mean rates of nucleotide substitution, and the greatest variation in rates, whereas rrnS and rrnL have the slowest rates. Reasons underlying this rate variation are discussed, as is the extensive rate variation in cox1 in light of its proposed role in DNA barcoding.
线粒体基因组是系统发育和系统地理学分析中最常用的基因座之一，并且越来越有可能对来自不同分类群的整个基因组进行测序和分析。然而，对整个基因组进行测序并不总是可取或可行的。应该选择哪些基因来最好地推断一组生物中线粒体的进化历史，以及基因的哪些特性决定其系统发育性能？本研究在贝叶斯系统发育框架下解决了这些问题，参考了来自27个完整线粒体基因组的无肺螈科及相关蝾螈的系统发育；这一拓扑结构得到了核DNA和形态学数据的证实。在贝叶斯和最大似然框架下，使用多个化石校准、多个数据分区和一种不依赖分子钟的方法，估计了每个线粒体基因的进化速率以及无肺螈科线粒体基因组系统发育中所有节点的分歧日期。对单个基因进行了贝叶斯分析，并将得到的树与参考拓扑结构进行比较。对分子进化速率、基因长度和G形参数a进行的有序逻辑回归分析表明，进化速率较慢和基因长度较长都增加了一个基因在系统发育中表现良好的概率。估计的分子进化速率在不同的线粒体基因和不同的蝾螈谱系之间相差84倍，基因之间的平均速率相差15倍。尽管cox1、cox2、cox3和cob具有保守的氨基酸序列，但它们的核苷酸替换平均速率最快，速率变化最大，而rrnS和rrnL的速率最慢。本文讨论了这种速率变化的潜在原因，以及鉴于cox1在DNA条形码中的作用而产生的广泛速率变化。
