Center for Evolutionary Medicine and Informatics, The Biodesign Institute, Arizona State University, AZ, USA.
Mol Biol Evol. 2011 Jun;28(6):1927-42. doi: 10.1093/molbev/msr014. Epub 2011 Jan 17.
Mitochondrial (mt) genes and genomes are among the major sources of data for evolutionary studies in birds. This places mitogenomic studies in birds at the core of intense debates in avian evolutionary biology. Indeed, complete mt genomes are actively been used to unveil the phylogenetic relationships among major orders, whereas single genes (e.g., cytochrome c oxidase I [COX1]) are considered standard for species identification and defining species boundaries (DNA barcoding). In this investigation, we study the time of origin and evolutionary relationships among Neoaves orders using complete mt genomes. First, we were able to solve polytomies previously observed at the deep nodes of the Neoaves phylogeny by analyzing 80 mt genomes, including 17 new sequences reported in this investigation. As an example, we found evidence indicating that columbiforms and charadriforms are sister groups. Overall, our analyses indicate that by improving the taxonomic sampling, complete mt genomes can solve the evolutionary relationships among major bird groups. Second, we used our phylogenetic hypotheses to estimate the time of origin of major avian orders as a way to test if their diversification took place prior to the Cretaceous/Tertiary (K/T) boundary. Such timetrees were estimated using several molecular dating approaches and conservative calibration points. Whereas we found time estimates slightly younger than those reported by others, most of the major orders originated prior to the K/T boundary. Finally, we used our timetrees to estimate the rate of evolution of each mt gene. We found great variation on the mutation rates among mt genes and within different bird groups. COX1 was the gene with less variation among Neoaves orders and the one with the least amount of rate heterogeneity across lineages. Such findings support the choice of COX 1 among mt genes as target for developing DNA barcoding approaches in birds.
线粒体（mt）基因和基因组是鸟类进化研究的主要数据来源之一。这使得鸟类的线粒体基因组研究成为鸟类进化生物学中激烈争论的核心。事实上，完整的 mt 基因组被积极用于揭示主要目之间的系统发育关系，而单个基因（例如细胞色素 c 氧化酶 I [COX1]）则被认为是物种鉴定和定义物种界限的标准（DNA 条形码）。在这项研究中，我们使用完整的 mt 基因组研究新鸟类目之间的起源时间和进化关系。首先，我们通过分析 80 个 mt 基因组，包括本研究中报告的 17 个新序列，解决了新鸟类系统发育中深节点以前观察到的多系问题。例如，我们发现有证据表明，鸽形目和鸻形目是姐妹群。总的来说，我们的分析表明，通过改进分类学采样，完整的 mt 基因组可以解决主要鸟类群体之间的进化关系。其次，我们使用我们的系统发育假设来估计主要鸟类目起源的时间，以检验它们的多样化是否发生在白垩纪/第三纪（K/T）边界之前。使用几种分子定年方法和保守的校准点来估计这些时间树。虽然我们发现的时间估计值比其他人报告的稍年轻，但大多数主要目都起源于 K/T 边界之前。最后，我们使用我们的时间树来估计每个 mt 基因的进化率。我们发现 mt 基因之间以及不同鸟类群体内部的突变率存在很大差异。COX1 是新鸟类目之间变异最小的基因，也是谱系间变异最小的基因。这些发现支持在鸟类中选择 COX1 作为开发 DNA 条形码方法的目标。
