Post K-Pg diversification of the mammalian order Eulipotyphla as suggested by phylogenomic analyses of ultra-conserved elements.,Molecular Phylogenetics and Evolution

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Post K-Pg diversification of the mammalian order Eulipotyphla as suggested by phylogenomic analyses of ultra-conserved elements.
Molecular Phylogenetics and Evolution ( IF 3.6 ) Pub Date : 2019-08-31 , DOI: 10.1016/j.ympev.2019.106605
Jun J Sato ₁ , Tessa M Bradford ₂ , Kyle N Armstrong ₂ , Stephen C Donnellan ₂ , Lazaro M Echenique-Diaz ₃ , Gerardo Begué-Quiala ₄ , Jorgelino Gámez-Díez ₅ , Nobuyuki Yamaguchi ₆ , Son Truong Nguyen ₇ , Masaki Kita ₈ , Satoshi D Ohdachi ₉

Affiliation

Laboratory of Animal Cell Technology, Faculty of Life Science and Technology, Fukuyama University, Higashimuracho, Aza, Sanzo, 985, Fukuyama 729-0292, Japan; School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia.
School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia; South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia.
Environmental Education Center, Miyagi University of Education, Aramaki Aza-Aoba, Aoba-ku, Sendai 980-0845, Japan.
Unidad Presupuestada Parque Nacional Alejandro de Humboldt (CITMA), Calle Abogado 14 e/12 y 13 Norte, Guantanamo 95200, Cuba.
Estación Ecológica La Melba, Unidad Presupuestada Parque Nacional Alejandro de Humboldt, CITMA-Guantánamo, Cuba.
Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, PO Box 2713, Doha, Qatar.
Institute of Ecology and Biological Resources and Graduate University of Science and Technology, Vietnam Academy of Sciences and Technology, 18 Hoang Quoc Viet, Hanoi, Viet Nam.
Graduate School of Bioagricultural Sciences, Nagoya University Furo-cho, Chikusa, Nagoya 464-8601, Japan.
Institute of Low Temperature Science, Hokkaido University, Kita-19 Nishi-8, Kita-ku, Sapporo 060-0819, Japan.

The origin of the mammalian order Eulipotyphla has been debated intensively with arguments around whether they began diversifying before or after the Cretaceous-Palaeogene (K-Pg) boundary at 66 Ma. Here, we used an in-solution nucleotide capture method and next generation DNA sequencing to determine the sequence of hundreds of ultra-conserved elements (UCEs), and conducted phylogenomic and molecular dating analyses for the four extant eulipotyphlan lineages-Erinaceidae, Solenodontidae, Soricidae, and Talpidae. Concatenated maximum-likelihood analyses with single or partitioned models and a coalescent species-tree analysis showed that divergences among the four major eulipotyphlan lineages occurred within a short period of evolutionary time, but did not resolve the interrelationships among them. Alternative suboptimal phylogenetic hypotheses received consistently the same amount of support from different UCE loci, and were not significantly different from the maximum likelihood tree topology, suggesting the prevalence of stochastic lineage sorting. Molecular dating analyses that incorporated among-lineage evolutionary rate differences supported a scenario where the four eulipotyphlan families diversified between 57.8 and 63.2 Ma. Given short branch lengths with low support values, traces of rampant genome-wide stochastic lineage sorting, and post K-Pg diversification, we concluded that the crown eulipotyphlan lineages arose through a rapid diversification after the K-Pg boundary when novel niches were created by the mass extinction of species.

中文翻译：

超保守元素的系统生物学分析表明，哺乳动物订单的Eulipotyphla后K-Pg多样化。

围绕哺乳动物是否在66 Ma的白垩纪-古近纪（K-Pg）边界之前或之后开始多样化的争论进行了激烈的辩论。在这里，我们使用溶液中核苷酸捕获方法和下一代DNA测序方法来确定数百个超保守元件（UCE）的序列，并针对四种现存的真脂质体谱系进行了系统生物学和分子测年分析-蛙科，茄科，茄科和塔皮科。结合最大似然分析的单一或分区模型和合并的物种树分析表明，四种主要的真脂虫谱系之间的分歧发生在进化时间的短时间内，但并没有解决它们之间的相互关系。备选的次优系统发育假说从不同的UCE基因座获得了相同数量的支持，并且与最大似然树拓扑没有显着差异，表明随机谱系排序的普遍性。整合了血统进化速率差异的分子测年分析支持了四个真脂质体家族在57.8 Ma和63.2 Ma之间多样化的情况。给定较短的分支长度和较低的支持值，在全基因组内随机谱系泛滥，并且在K-Pg多样化后，我们得出结论，当由K-Pg边界产生新的壁ni时，冠状真脂质体谱系是通过K-Pg边界后的快速多样化而产生的。物种的大灭绝。并且与最大似然树拓扑没有显着差异，表明随机谱系排序的普遍性。整合了血统进化速率差异的分子测年分析支持了四个真脂质体家族在57.8 Ma和63.2 Ma之间多样化的情况。给定较短的分支长度和较低的支持值，在全基因组内随机谱系泛滥，并且在K-Pg多样化后，我们得出结论，当由K-Pg边界产生新的壁ni时，冠状真脂质体谱系是通过K-Pg边界后的快速多样化而产生的。物种的大灭绝。并且与最大似然树拓扑没有显着差异，表明随机谱系排序的普遍性。整合了血统进化速率差异的分子测年分析支持了四个真脂质体家族在57.8 Ma和63.2 Ma之间多样化的情况。给定较短的分支长度和较低的支持值，在全基因组范围内随机谱系泛滥，并且在K-Pg多样化之后，我们得出结论，当K-Pg边界产生了新的壁ni时，冠状真脂质体谱系通过K-Pg边界后的快速多样化而产生。物种的大灭绝。整合了血统进化速率差异的分子测年分析支持了四个真脂质体家族在57.8 Ma和63.2 Ma之间多样化的情况。给定较短的分支长度和较低的支持值，在全基因组内随机谱系泛滥，并且在K-Pg多样化后，我们得出结论，当由K-Pg边界产生新的壁ni时，冠状真脂质体谱系是通过K-Pg边界后的快速多样化而产生的。物种的大灭绝。整合了血统进化速率差异的分子测年分析支持了四个真脂质体家族在57.8 Ma和63.2 Ma之间多样化的情况。给定较短的分支长度和较低的支持值，在全基因组内随机谱系泛滥，并且在K-Pg多样化后，我们得出结论，当由K-Pg边界产生新的壁ni时，冠状真脂质体谱系是通过K-Pg边界后的快速多样化而产生的。物种的大灭绝。

更新日期：2019-08-31

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