Phylogenomic Relationships of Diploids and the Origins of Allotetraploids in Dactylorhiza (Orchidaceae)
Phylogenomic Relationships of Diploids and the Origins of Allotetraploids in Dactylorhiza (Orchidaceae)
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DOI：
10.1093/sysbio/syz035
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发表时间：
2020-01-01
影响因子：
6.5
通讯作者：
Paun, Ovidiu
中科院分区：
文献类型：
--
作者：
Brandrud, Marie K.;Baar, Juliane;Paun, Ovidiu
解开系统发育关系证明具有挑战性的群体最近进化，特别是如果有持续的网状。虽然它们在大多数情况下是立即从二倍体亲属中分离出来的，但同胞异源多倍体的集合经常彼此杂交，从而增加了已经具有挑战性的情况的复杂性。鸭茅属（兰科：兰科）是一个受异源多倍体物种形成和网状系统发育关系影响很大的属。在这里，我们使用成千上万个基因组位置的遗传变异来解开Dactylorhiza复杂的进化历史。我们首先调查的界限和二倍体物种的关系，在该属中使用合并和最大似然方法，然后组16异源四倍体的最大隶属关系，他们假定的父母二倍体，实施基于基因型的可能性的方法。使用来自母系遗传质体RADseq基因座的信息推断每个异源四倍体的杂交方向。从父母类群的年龄估计开始，这些异源四倍体实体的相对年龄通过量化其与二倍体的遗传相似性和与同胞异源四倍体相比的私有等位基因的数量来推断。欧洲西北部主要是冰川期后起源的年轻异源四倍体，而相对较老的异源四倍体分布在更南部，那里的气候条件在更新世冰期期间保持相对稳定。我们的生物信息学方法应该证明是有效的其他自然发生的，非模式，多倍体植物复合体的研究。
Disentangling phylogenetic relationships proves challenging for groups that have evolved recently, especially if there is ongoing reticulation. Although they are in most cases immediately isolated from diploid relatives, sets of sibling allopolyploids often hybridize with each other, thereby increasing the complexity of an already challenging situation. Dactylorhiza (Orchidaceae: Orchidinae) is a genus much affected by allopolyploid speciation and reticulate phylogenetic relationships. Here, we use genetic variation at tens of thousands of genomic positions to unravel the convoluted evolutionary history of Dactylorhiza. We first investigate circumscription and relationships of diploid species in the genus using coalescent and maximum likelihood methods, and then group 16 allotetraploids by maximum affiliation to their putative parental diploids, implementing a method based on genotype likelihoods. The direction of hybrid crosses is inferred for each allotetraploid using information from maternally inherited plastid RADseq loci. Starting from age estimates of parental taxa, the relative ages of these allotetraploid entities are inferred by quantifying their genetic similarity to the diploids and numbers of private alleles compared with sibling allotetraploids. Whereas northwestern Europe is dominated by young allotetraploids of postglacial origins, comparatively older allotetraploids are distributed further south, where climatic conditions remained relatively stable during the Pleistocene glaciations. Our bioinformatics approach should prove effective for the study of other naturally occurring, nonmodel, polyploid plant complexes.