DOI: 10.5061/dryad.sm95d
title: Data from: Intraspecific haplotype diversity in Cherleria sedoides L. (Caryophyllaceae) is best explained by chloroplast capture from an extinct species

description: 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.
description: Caryophyllaceae_matK_AligmentThe Caryophyllaceae-wide matK alignment, used to produce the trees in Fig. 2 and Online Resource 2. The names correspond to those in Voucher_Table.txt. For our sequences, DNA numbers follow the names, while for sequences downloaded from GenBank, GB follows the names.Caryophyllaceae_matK-ConT_Fig_2The consensus tree from the BEAST analysis of matK data, shown in Fig. 2 and Online Resource 2. The names correspond to those in Voucher_Table.txt. For our sequences, DNA numbers follow the names, while for sequences downloaded from GenBank, GB follows the names.Cherleria_cpDNA_MatrixThe Cherleria-wide alignment from the chloroplast trnQ-rps16 and psbD-trnT regions, used to produce the tree in Fig. 3. The names correspond to those in Voucher_Table.txt. DNA numbers follow the names.Cherleria_cpDNA_GapsThe coded indels from the Cherleria-wide alignment from the chloroplast trnQ-rps16 and psbD-trnT regions, used to produce the tree in Fig. 3. The names correspond to those in Voucher_Table.txt. DNA numbers follow the names.Cherleria_cpDNA+Indels_ConT_Fig_3The consensus tree from the BEAST analysis of the trnQ-rps16 and psbD-trnT data, shown in Fig. 3. The names correspond to those in Voucher_Table.txt. DNA numbers follow the names.Cherleria_cpDNA_SNPs+Gaps_TCS.nexThe Cherleria-wide alignment from the chloroplast trnQ-rps16 and psbD-trnT regions for the TCS analysis shown in Fig. 4. The names correspond to those in Voucher_Table.txt. DNA numbers follow the names.Voucher_TableThe voucher table as a tab-delimitted text file including the full species name with authorities, the name in the tree, the DNA number (when we extracted the DNA sample), the voucher and country where it was collected (again, only for our samples), and the GenBank numbers for the sequences that are included in these alignments.