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How well do multispecies coalescent methods perform with mitochondrial genomic data? A case study of butterflies and moths (Insecta: Lepidoptera)
Systematic Entomology ( IF 4.8 ) Pub Date : 2020-04-01 , DOI: 10.1111/syen.12431
Min Jee Kim 1 , Iksoo Kim 1 , Stephen L. Cameron 2
Affiliation  

Despite the broad adoption of multispecies coalescent (MSC) methods for nuclear phylogenomics, they have yet to be applied to mitochondrial (mt) genomic data. As the potential sources of phylogenomic bias that MSC methods can address, such as incomplete lineage sorting, horizontal gene transfer and gene tree heterogeneity, have been found in mt genomic data, these approaches may improve the accuracy of phylogenetic inference with these data. In the present study, we examined the behaviour of MSC methods in reconstructing the phylogeny of Lepidoptera (butterflies and moths), a group for which mt genomic data are known to have strong resolving power. Traditional concatenation methods of analysing mt genomes for Lepidoptera infer topologies highly congruent with those generated from independent nuclear datasets. Individual mt gene trees performed poorly in recovering consensus relationships at deep levels (i.e. superfamily monophyly and inter‐relationships) and only moderately well for shallow relationships (i.e. within Papilionoidea). In contrast, MSC analyses with ASTRAL performed strongly with almost complete concordance to both concatenated mt genome analyses and independent nuclear analyses at both deep and shallow phylogenetic scales. Outgroup choice had a limited impact on tree accuracy, with even phylogenetically distant outgroups still resulting in topologies highly congruent with results from nuclear datasets, although MSC analyses appeared to be marginally more affected by outgroup choice than concatenation analyses. In general, discordance between concatenation and MSC analyses was found at nodes whose resolution varied between previous nuclear phylogenomic studies. The sensitivity of individual relationships to analysis with MSC vs concatenation can thus be used to test the robustness of phylogenetic hypotheses. For insect phylogenetics, MSC is a reliable inference method for mt genomic data and is thus a useful complement to the already widely used concatenation approaches.

中文翻译:

多物种聚结方法对线粒体基因组数据的表现如何?蝴蝶和飞蛾的案例研究(昆虫纲:鳞翅目)

尽管核系统基因组学广泛采用了多物种聚结 (MSC) 方法,但它们尚未应用于线粒体 (mt) 基因组数据。由于在 mt 基因组数据中发现了 MSC 方法可以解决的系统发育偏差的潜在来源,例如不完整的谱系排序、水平基因转移和基因树异质性,这些方法可能会提高这些数据的系统发育推断的准确性。在本研究中,我们检查了 MSC 方法在重建鳞翅目(蝴蝶和飞蛾)系统发育方面的行为,鳞翅目昆虫基因组数据已知具有很强的分辨能力。分析鳞翅目 mt 基因组的传统串联方法推断拓扑与从独立核数据集生成的拓扑高度一致。单个 mt 基因树在恢复深层(即超家族单系和相互关系)的共识关系方面表现不佳,而在浅层关系(即在凤蝶总科内)中表现不佳。相比之下,使用 ASTRAL 的 MSC 分析表现强劲,在深层和浅层系统发育尺度上与串联 mt 基因组分析和独立核分析几乎完全一致。外群选择对树的准确性影响有限,即使在系统发育上遥远的外群仍然导致拓扑与核数据集的结果高度一致,尽管与串联分析相比,MSC 分析似乎更受外群选择的影响。一般来说,在之前的核系统发育研究之间分辨率不同的节点上发现了串联和 MSC 分析之间的不一致。因此,个体关系对 MSC 与串联分析的敏感性可用于测试系统发育假设的稳健性。对于昆虫系统发育,MSC 是一种可靠的 mt 基因组数据推断方法,因此是对已经广泛使用的串联方法的有用补充。
更新日期:2020-04-01
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