Departament de Biodiversitat i Conservació, Institut Mediterrani d'Estudis Avançats IMEDEA (CSIC-UIB), Miquel Marqués, 21, Esporles, 07190 Illes Balears, Spain.
Mol Phylogenet Evol. 2010 Aug;56(2):796-807. doi: 10.1016/j.ympev.2010.02.007. Epub 2010 Feb 10.
The ages of cladogenetic events in Coleoptera are frequently estimated with mitochondrial protein-coding genes (MPCGs) and the "standard" mitochondrial nucleotide substitution rate for arthropods. This rate has been used for different mitochondrial gene combinations and time scales despite it was estimated on short mitochondrial sequences from few comparisons of close related species. These shortcomings may cause greater impact at deep phylogenetic levels as errors in rates and ages increase with branch lengths. We use the full set of MPCGs of 15 species of beetles (two of them newly sequenced here) to estimate the nucleotide evolutionary rates in a reconstructed phylogeny among suborders, paying special attention to the effect of data partitioning and model choices on these estimations. The optimal strategy for nucleotide data, as measured with Bayes factors, was partitioning by codon position. This retrieved Adephaga as a sister group to Myxophaga with strong support (expected-likelihood weights test 0.94-1) and both sisters to Polyphaga, in contradiction with the most currently accepted views. The hypothesis of Archostemata being sister to the remaining Coleoptera, which is in agreement with morphology, was increasingly supported when third codon sites were recoded or completely removed, sequences were analyzed as AA, and heterogeneous models were implemented but the support levels remained low. Nucleotide substitution rates were strongly affected by the choice of data partitioning (codon position versus individual genes), with up to sixfold levels of variation, whereas differences in the molecular clock algorithm produced changes of only about 20%. The global mitochondrial protein coding rate using codon partitioning and an estimated age of 250 million years (MY) for the origin of the Coleoptera was 1.34% per branch per MY, which closely matches the 'standard' clock of 1.15% per MY. The estimation of the rates on alternative topologies gave similar results. Using local molecular clocks, the evolutionary rate in the Polyphaga and Archostemata was estimated to be nearly twice as fast as in the Adephaga and Myxophaga (1.03% versus 0.53% per MY). Rates across individual genes varied from 0.55% to 8.61% per MY. Our results suggest that cox1 might not be an optimal gene for implementing molecular clocks in deep phylogenies for beetles because it shows relatively slow rates at first and second codon positions but very fast rates at third ones. In contrast, nad5, nad4 and nad2 perform better, as they exhibit more homogeneous rates among codon positions.
鞘翅目动物的分支进化事件的年龄通常使用线粒体蛋白编码基因 (MPCG) 和节肢动物的“标准”线粒体核苷酸替代率来估计。尽管该替代率是基于少数近缘物种的短线粒体序列进行估计的，但它已被用于不同的线粒体基因组合和时间尺度。这些缺点在更深的系统发育水平上可能会产生更大的影响，因为随着分支长度的增加，速率和年龄的错误会增加。我们使用 15 种甲虫的 MPCG 全数据集（其中两种是新测序的）来估计亚目的重建系统发育中的核苷酸进化率，特别注意数据分区和模型选择对这些估计的影响。Bayes 因子衡量的最佳核苷酸数据策略是按密码子位置分区。这一策略将多食亚目恢复为与 Myxophaga 具有强烈支持的姐妹群（期望似然权重检验 0.94-1），而这两个姐妹群又与多足亚目一起，这与目前最被接受的观点相矛盾。与形态学一致的 Archostemata 是其余甲虫的姐妹群的假设，当第三个密码子位置被重新编码或完全去除、序列被分析为 AA 以及实施异质模型时，该假设得到了越来越多的支持，但支持水平仍然较低。核苷酸替代率受到数据分区选择（密码子位置与单个基因）的强烈影响，变化幅度高达六倍，而分子钟算法的差异仅产生约 20%的变化。使用密码子分区和甲虫起源于 2.5 亿年前的估计年龄（250 百万年）计算的全球线粒体蛋白质编码率为每分支每 MY 1.34%，与“标准”时钟 1.15%每 MY 非常接近。在替代拓扑结构上的估计得到了类似的结果。使用局部分子钟，在多食亚目和 Archostemata 中的进化率估计是多食亚目和 Myxophaga 的两倍快（1.03%与 0.53%每 MY）。个别基因的速率从 0.55%到 8.61%每 MY 不等。我们的结果表明，cox1 可能不是甲虫深系统发育中实施分子钟的最佳基因，因为它在第一和第二位密码子位置显示出相对较慢的速率，但在第三位密码子位置显示出非常快的速率。相比之下，nad5、nad4 和 nad2 表现更好，因为它们在密码子位置之间表现出更均匀的速率。
