Data from: Comparative analyses of plastid and AFLP data suggest different colonization history and asymmetric hybridisation between Betula pubescens and B. nana

Birches (Betula spp.) hybridize readily, confounding genetic signatures of refugial isolation and postglacial migration. We aimed to distinguish hybridization from range-shift processes in the two widespread and cold-adapted species B. nana and B. pubescens, previously shown to share a similarly east–west-structured variation in plastid DNA (pDNA). We sampled the two species throughout their ranges and included reference samples of five other Betula species and putative hybrids. We analysed 901 individual plants using mainly nuclear high-resolution markers (amplified fragment length polymorphisms; AFLPs); a subset of 64 plants was also sequenced for two pDNA regions. Whereas the pDNA variation as expected was largely shared between B. nana and B. pubescens, the two species were distinctly differentiated at AFLP loci. In B. nana, both the AFLP and pDNA results corroborated the former pDNA-based hypothesis that it expanded from at least two major refugia in Eurasia, one south of and one east of the North European ice sheets. In contrast, B. pubescens showed a striking lack of geographic structuring of its AFLP variation. We identified a weak but significant increase in nuclear (AFLP) gene flow from B. nana into B. pubescens with increasing latitude, suggesting hybridization has been most frequent at the postglacial expansion front of B. pubescens and that hybrids mainly backcrossed to B. pubescens. Incongruence between pDNA and AFLP variation in B. pubescens can be explained by efficient expansion from a single large refugium combined with leading-edge hybridization and plastid capture from B. nana during colonization of new territory already occupied by this more cold-tolerant species.AFLPmatrix_original_B_nanaBinary AFLP matrix with 119 markers, 570 individuals of Betula nana and B. glandulosa generated by 3 primer combinationsBN_BG_570_119.txtAFLPmatrix_orginal_Betula_pub_alle_332_155Binary AFLP matrix with 155 markers, 332 individuals of mainly Betula pubescens, but also including reference species and hybrids generated by 3 primer combinationsBP_alle_332_155.txtAFLPmatrix_Betula_all_901ind_104_markers_1primerAFLP matrix based on the combined scoring of on primer in common among the original data sets for B. nana and B. pubescens and reference speciesB_all_901_104.txtAFLPmatrix_Betula_nana_only_528_115Subset of the original AFLP matrix (3primers)nwithout populations of B. glandulosa, 115 polymorphic markers and 528 indBN_kun_528_115.txtAFLP_matrix_Betula_pub_only_303_132Subset of the original aflp matrix of B. pubescens, without reference populations-only including 303 individuals of B. pubescens, 3 primer combinations, 132 markersBP_kun_303_132.txtBetula_901_104structure-inputInput-file to STRUCTURE software based on the combined AFLP matrix with 901 individuals, 104 markers (one primer combination)B_all_901_104structure-input.txtBetula_pubescens_only_303_132_structure-inputInput file to the software program structure based on the aflp matrix only including populations of B. pubescens, 3 primers, 303 ind and 132 markersBP_kun_structure-input.txtBetula_nana_only_structure-inputInput file to the software program STRUCTURE based on the AFLP matrix only including B.nana ind(528) and 115 markers, 3 primer combinationsBN_kun_structure.txtB_nana_only_pairwise_geographical_distanceGeographical distances among B. nana populations used for Mantel testBN_kun_pairwise_geographical_distance.txtB_pubescens_only_pairwise_geographical_distanceGeographical distances among B. pubescens populations used for Mantel testBP_kun_pairwise_geographical_distance.txtBetula_ssp_pop_marker_frq__1primerAFLP marker frequencies per population based on the combined AFLP matrix . Used as inputfile for NJ-analyses among populationsB_all_pop_marker_frq__1primer.txtBetula_pubescens_and ref_pop_marker_frq__3primersAFLP marker frequencies per population based on the original B pubescens AFLP matrix (3 primers). Used as inputfile for NJ-analyses among populationsBP_pop_marker_frq__3primers.txttrnS_trnG_Alignment_58seqAlignment file for trnS-trnG region based on plastid sequences used to generate haplotypestrnQ-rsp16_AlignmentAlignment of plastid sequences trmQ-rsp16AlignmentQtrntrimmet.fa