Improved characterisation of among-lineage rate variation in cetacean mitogenomes using codon-partitioned relaxed clocks
Improved characterisation of among-lineage rate variation in cetacean mitogenomes using codon-partitioned relaxed clocks
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DOI：
10.3109/19401736.2010.494727
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发表时间：
2010-06-01
影响因子：
--
通讯作者：
Lanfear, Robert
中科院分区：
文献类型：
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作者：
Ho, Simon Y. W.;Lanfear, Robert
背景和目标。后生动物线粒体基因组之间的替换率存在广泛的差异，包括谱系之间和位点之间的差异。在分子系统发育和年代测定分析中，通常会考虑谱系之间的替代率差异。然而，这是很少的情况下，在特定的谱系模式的速度变化之间的网站。材料和方法。我们使用分区松弛时钟方法分析了32个鲸类有丝分裂基因组的比对，其中将单独的松弛时钟模型应用于蛋白质编码基因的三个密码子位置中的每一个。通过比较贝叶斯因子，我们发现与严格时钟模型和包含较少放松时钟的较不复杂模型相比，该模型获得了压倒性的支持。我们的分析揭示了大量率之间的异质性鲸类动物的血统，这些模式的变化密码子位置之间的差异。然而，我们没有发现线粒体速率自相关的证据在整个鲸类的生殖。我们的研究证实了分区松弛时钟模型应用于有丝分裂基因组数据的可行性，并建议，分子系统发育和约会分析，可以通过这些模型的应用得到改善。
Background and aims. There is extensive variation in substitution rates among metazoan mitochondrial genomes, including differences among lineages and among sites. Differences in substitution rates among lineages are routinely taken into account in molecular phylogenetic and dating analyses. However, this is rarely the case for differences in the lineage-specific patterns of rate variation among sites.Materials and methods. We analysed an alignment of 32 cetacean mitogenomes using a partitioned relaxed-clock approach, in which a separate relaxed-clock model was applied to each of the three codon positions of the protein-coding genes.Results. By comparing Bayes factors, we found overwhelming support for this model compared with a strict-clock model and less-complex models comprising fewer relaxed clocks. Our analyses reveal the presence of substantial rate heterogeneity among cetacean lineages, and that these patterns of variation differ between codon positions. However, we find no evidence of mitochondrial rate autocorrelation throughout the cetacean phylogeny.Conclusions. Our study confirms the feasibility of applying a partitioned relaxed-clock model to mitogenomic data, and suggests that molecular phylogenetic and dating analyses may be improved by the application of these models.