To fully understand the contemporary genetic structure of plants, both nuclear and plastid markers are needed. Three chloroplast DNA (cpDNA) lineages, which probably diverged before the major Pleistocene glaciations, have been identified in the circumpolar/circumboreal Vaccinium uliginosum. Here we investigate its nuclear DNA variation using nuclear ribosomal internal transcribed spacer (ITS) sequences, DNA ploidy level measurements and amplified fragment length polymorphisms (AFLPs). We also extend the cpDNA dataset. Two ITS lineages, corresponding to diploids and tetraploids, respectively, were identified. However, both main sequence types apparently occurred in most individual plants but showed ploidy-biased homogenization and possibly reflect paralogy predating the origin of V. uliginosum. The ploidy levels were largely consistent with the cpDNA lineages, suggesting that the initial cpDNA divergence followed early polyploidizations. Five main AFLP groups were identified, consistent with recent glacial refugia in Beringia, western Siberia, the southern European mountains and areas south/east of the Scandinavian and Laurentide ice sheets. Except from the southern European mountains, there has been extensive expansion from all refugia, resulting in several contact zones. Surprisingly, the presumably older ploidy and cpDNA patterns were partly inconsistent with the main AFLP groups and more consistent with AFLP subgroups. A likely major driver causing the inconsistencies is recent nuclear gene flow via unreduced pollen from diploids to tetraploids. This may prevent cytoplasmic introgression and result in overlayed patterns formed by processes dominating at different time scales. The data also suggest more recent polyploidizations, as well as several chloroplast capture events, further complicating this scenario. This study highlights the importance of combining different marker systems to unravel intraspecific histories.

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Author contributions: M.P. and C.B. designed research; M.P. and V.M. performed research; M.P. analyzed data; and M.P., V.M., and C.B. wrote the paper.The authors declare no conflict of interest.This article is a PNAS Direct Submission.

Biogeographers claimed for more than a century that arctic plants survived glaciations in ice-free refugia within the limits of the North European ice sheets. Molecular studies have, however, provided overwhelming support for postglacial immigration into northern Europe, even from the west across the Atlantic. For the first time we can here present molecular evidence strongly favouring in situ glacial persistence of two species, the rare arctic-alpine pioneer species Sagina caespitosa and Arenaria humifusa. Both belong to the 'west-arctic element' of amphi-Atlantic disjuncts, having their few and only European occurrences well within the limits of the last glaciation. Sequencing of non-coding regions of chloroplast DNA revealed only limited variation. However, two very distinct and partly diverse genetic groups, one East and one West Atlantic, were detected in each species based on amplified fragment length polymorphisms (AFLPs), excluding postglacial dispersal from North America as explanation for their European occurrences. Patterns of genetic diversity and distinctiveness indicate that glacial populations existed in East Greenland and/or Svalbard (A. humifusa) and in southern Scandinavia (S. caespitosa). Despite their presumed lack of long-distance dispersal adaptations, intermixed populations in several regions indicate postglacial contact zones. Both species are declining in Nordic countries, probably due to climate change-induced habitat loss. Little or no current connectivity between their highly fragmented and partly distinct populations call for conservation of several populations in each geographic region.

Minuartia biflora and Ranunculus pygmaeus are circumarctic plants with a few isolated occurrences in the European Alps. We analysed amplified fragment length polymorphism (AFLP) and chloroplast DNA sequence data to unravel the history of their immigration into the Alps and to provide data on their circumpolar phylogeography. In spite of the similar ecological requirements of the two species, they exhibit strikingly different immigration histories into the Alps. In M. biflora, the Alpine populations are most probably derived from source populations located between the Alpine and Scandinavian ice sheets, in accordance with the traditional biogeographic hypothesis. In contrast, the Alpine populations of R. pygmaeus cluster with those from the Tatra Mountains and the Taymyr region in northern Siberia, indicating that the distant Taymyr area served as source for the Alpine populations. Both species showed different levels of genetic diversity in formerly glaciated areas. In contrast to the considerable AFLP diversity observed in M. biflora, R. pygmaeus was virtually nonvariable over vast areas, with a single phenotype dominating all over the Alps and another, distantly related one dominating the North Atlantic area from Greenland over Svalbard to Scandinavia. The same pattern was observed in chloroplast DNA sequence data. Thus, postglacial colonization of R. pygmaeus was accompanied by extreme founder events.