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首页> 外文期刊>Genome Biology and Evolution >Mitochondrial Architecture Rearrangements Produce Asymmetrical Nonadaptive Mutational Pressures That Subvert the Phylogenetic Reconstruction in Isopoda
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Mitochondrial Architecture Rearrangements Produce Asymmetrical Nonadaptive Mutational Pressures That Subvert the Phylogenetic Reconstruction in Isopoda

机译：线粒体结构重排产生不对称的非适应性突变压力，颠覆了等位基因的系统发育重建。

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The phylogeny of Isopoda, a speciose order of crustaceans, remains unresolved, with different data sets (morphological, nuclear, mitochondrial) often producing starkly incongruent phylogenetic hypotheses. We hypothesized that extreme diversity in their life histories might be causing compositional heterogeneity/heterotachy in their mitochondrial genomes, and compromising the phylogenetic reconstruction. We tested the effects of different data sets (mitochondrial, nuclear, nucleotides, amino acids, concatenated genes, individual genes, gene orders), phylogenetic algorithms (assuming data homogeneity, heterogeneity, and heterotachy), and partitioning; and found that almost all of them produced unique topologies. As we also found that mitogenomes of Asellota and two Cymothoida families (Cymothoidae and Corallanidae) possess inversed base (GC) skew patterns in comparison to other isopods, we concluded that inverted skews cause long-branch attraction phylogenetic artifacts between these taxa. These asymmetrical skews are most likely driven by multiple independent inversions of origin of replication (i.e., nonadaptive mutational pressures). Although the PhyloBayes CAT-GTR algorithm managed to attenuate some of these artifacts (and outperform partitioning), mitochondrial data have limited applicability for reconstructing the phylogeny of Isopoda. Regardless of this, our analyses allowed us to propose solutions to some unresolved phylogenetic debates, and support Asellota are the most likely candidate for the basal isopod branch. As our findings show that architectural rearrangements might produce major compositional biases even on relatively short evolutionary timescales, the implications are that proving the suitability of data via composition skew analyses should be a prerequisite for every study that aims to use mitochondrial data for phylogenetic reconstruction, even among closely related taxa.
机译：Isopoda的系统发育（甲壳类动物的一个特定顺序）仍未解决，具有不同的数据集（形态，核，线粒体）通常会产生完全不一致的系统发育假说。我们假设他们生活史中的极端多样性可能会导致线粒体基因组中的组成异质性/异质性，并损害系统发育重建。我们测试了不同数据集（线粒体，核，核苷酸，氨基酸，级联基因，单个基因，基因顺序），系统进化算法（假设数据同质，异质性和异质性）和分区的影响;并且发现它们几乎都产生了独特的拓扑。由于我们还发现Asellota和两个葫芦科（Cymothoidaae）（Cymothoidae和Corallanidae）的有丝分裂基因组与其他等足类动物相比具有反向碱基（GC）倾斜模式，因此得出结论，反向倾斜导致这些类群之间的长分支吸引系统发生伪像。这些不对称的偏斜很可能是由复制起点的多个独立反转（即非自适应突变压力）驱动的。尽管PhyloBayes CAT-GTR算法成功地减弱了其中的一些伪影（并优于分区），但线粒体数据在重建等足目系统发育方面的适用性有限。无论如何，我们的分析使我们能够为一些尚未解决的系统发育争论提出解决方案，并支持Asellota是最基本的等足类动物分支候选者。正如我们的发现表明，即使在相对较短的进化时间尺度上，架构重排也可能会产生主要的成分偏差，其含义是，通过成分偏斜分析分析证明数据的适用性应该是每项旨在将线粒体数据用于系统发育重建的研究的前提，甚至在密切相关的分类单元中。

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