What are the roles of taxon sampling and model fit in tests of cyto-nuclear discordance using avian mitogenomic data?
What are the roles of taxon sampling and model fit in tests of cyto-nuclear discordance using avian mitogenomic data?
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DOI：
10.1016/j.ympev.2018.10.008
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发表时间：
2019-01-01
影响因子：
4.1
通讯作者：
Kimball, Rebecca
中科院分区：
文献类型：
--
作者：
Tamashiro, Ryan;White, Noor;Kimball, Rebecca
核进化和线粒体进化之间的冲突导致了生命之树中某些关系的不确定性。这些冲突导致一些人质疑线粒体DNA在系统发育中的价值，因为现在可以很容易地获得基因组规模的核数据。然而，由于线粒体DNA是母系遗传的，不会重组，它的系统发育应该更接近物种树。此外，它的快速进化速度可能会导致突变沿着短节间积累，在那里来自核基因的相关信息可能是有限的。在这项研究中，我们研究了洞穴类的线粒体系统发育，以阐明它与最近发表的这类鸟类的核系统发育的一致性。洞穴包括斑嘴目(长臂鸟)、角嘴目(犀鸟)、珊瑚目(翠鸟及其盟友)和豌豆目(啄木鸟及其盟友)。我们假设，先前发表的线粒体树中稀疏的分类单元样本是导致明显的细胞-核不一致的原因。为了验证这一假设，我们组装了27个额外的洞穴有丝分裂基因组，并使用7种不同的分类群抽样方案估计了系统发育，范围从5到42个组内物种。我们还测试了划分和模型选择在观察到的不一致性中所起的作用。我们的分析表明，改进的分类群采样可以解决许多分歧。同样，划分在改善与核系统发育的拓扑学的一致性方面也很有价值，尽管用于生成线粒体系统发育的模型影响较小。总体而言，我们的结果表明，当分区与适当的分类单元采样一起使用时，线粒体树是可信的。
Conflicts between nuclear and mitochondrial phylogenies have led to uncertainty for some relationships within the tree of life. These conflicts have led some to question the value of mitochondrial DNA in phylogenetics now that genome-scale nuclear data can be readily obtained. However, since mitochondrial DNA is maternally inherited and does not recombine, its phylogeny should be closer to the species tree. Additionally, its rapid evolutionary rate may drive accumulation of mutations along short internodes where relevant information from nuclear loci may be limited. In this study, we examine the mitochondrial phylogeny of Cavitaves to elucidate its congruence with recently published nuclear phylogenies of this group of birds. Cavitaves includes the orders Trogoniformes (trogons), Bucerotiformes (hornbills), Coraciiformes (kingfishers and allies), and Piciformes (woodpeckers and allies). We hypothesized that sparse taxon sampling in previously published mitochondrial trees was responsible for apparent cyto-nuclear discordance. To test this hypothesis, we assembled 27 additional Cavitaves mitogenomes and estimated phylogenies using seven different taxon sampling schemes ranging from five to 42 ingroup species. We also tested the role that partitioning and model choice played in the observed discordance. Our analyses demonstrated that improved taxon sampling could resolve many of the disagreements. Similarly, partitioning was valuable in improving congruence with the topology from nuclear phylogenies, though the model used to generate the mitochondrial phylogenies had less influence. Overall, our results suggest that the mitochondrial tree is trustworthy when partitioning is used with suitable taxon sampling.