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