Data from: Intraspecific haplotype diversity in Cherleria sedoides L. (Caryophyllaceae) is best explained by chloroplast capture from an extinct species

Cherleria sedoides, a plant species widespread in alpine areas of the major European mountain ranges and in Scotland, contains two highly divergent chloroplast haplotype groups, one widespread (WH) and one present only in some populations in the Alps (AH). We investigated whether this haplotype diversity is the result of (1) intraspecific differentiation, (2) retention of an ancestral polymorphism or (3) hybridisation. For this purpose, 106 matK sequences from throughout the Caryophyllaceae and 80 trnQ-rps16 and psbD-trnT sequences of C. sedoides (51) and other species of Cherleria (29) were used for the construction of phylogenies and haplotype networks. As the two haplotype groups were never each other’s closest relatives, haplotype diversity as a result of intraspecific differentiation is unlikely. Patterns of genetic differentiation within the WH and AH groups are very different. Whereas WH shows a radial pattern typical of rapid expansion, AH is divided into two divergent subgroups each containing more variation than the WH group. This suggests that the two haplotype groups have dissimilar histories and are therefore unlikely to represent an ancestral polymorphism. Instead, we conclude that the polymorphism is best interpreted as the result of hybridisation. As the WH and AH haplotype groups fall into Cherleria, but do not group with any extant species, we conclude that the rare AH group represents the original C. sedoides, and that the WH group was captured from another, now extinct, species of Cherleria.景天雪灵芝（Cherleria sedoides）是广泛分布于欧洲主要山脉阿尔卑斯山区及苏格兰的植物物种，其体内存在两个高度分化的叶绿体单倍型类群：其一为广布类群（WH），另一类群（AH）仅存在于阿尔卑斯山的部分种群中。本研究旨在探究该单倍型多样性的成因，具体包含三种假说：（1）种内分化；（2）祖先多态性的保留；（3）杂交事件。为此，研究人员采集了来自石竹科（Caryophyllaceae）各物种的106条matK序列，以及80条trnQ-rps16和psbD-trnT序列（其中51条来自景天雪灵芝，29条来自雪灵芝属其他物种），用于构建系统发育树与单倍型网络。由于两个单倍型类群从未互为姐妹群，因此种内分化导致单倍型多样性的可能性极低。WH与AH类群的遗传分化模式存在显著差异：WH呈现出快速扩张物种典型的放射状格局，而AH则被划分为两个分化程度较高的亚类群，且每个亚类群的遗传变异均高于WH类群。上述结果表明，两个单倍型类群的演化历史存在显著差异，因此不太可能由祖先多态性演化而来。与之相反，本研究认为该多态性更可能由杂交事件所导致。鉴于WH与AH单倍型类群均隶属于雪灵芝属，但未与任何现存物种聚为一支，研究人员推断稀有AH类群为原始的景天雪灵芝类群，而WH类群则是从另一种现已灭绝的雪灵芝属物种中捕获而来的。