Glacial history of the alpine herb Rumex Nivalis (Polygonaceae): a comparison of common phylogeographic methods with nested clade analysis

Abstract

The glacial history of the alpine herb Rumex nivalis was investigated using amplified fragment length polymorphisms (AFLPs) and restriction fragment length polymorphisms with polymerase chain reaction (PCR-RFLPs) of cpDNA. Both traditional statistical methods widely applied in phylogeographic research and nested clade analysis were used. The AFLPs indicated little geographic structure probably due to the wind-pollinated reproductive system of the dioecious R. nivalis. Because cpDNA haplotypes exhibited distinct distributional patterns, correlation between AFLPs and PCR-RFLPs was low. The results of common statistical methods and of nested clade analysis were largely congruent. Both supported in situ survival of one group of common haplotypes in the Central Alps. For another group of common haplotypes, classical phylogeographic analyses gave strong evidence for survival in peripheral refugia at the northern alpine border, whereas this conclusion was not as clearly supported in the nested clade analysis. Nested clade analysis provided several detailed insights on past and ongoing populational demographic processes. Thus, it is a valuable tool in the phylogeographical analysis of haplotype data, but it should preferably be combined with other statistical analyses. In situations with low genetic variation in cpDNA, classical phylogeographic analytical tools on nuclear DNA will still be the methods of choice.

Sex-specific SCAR markers in the dioecious plant Rumex nivalis (Polygonaceae) and implications for the evolution of sex chromosomes

“…Thus, AFLPs indeed proved to be a powerful method to detect male-specific fragments in this sexually heterogametic and heteromorphic species and, at the same time, they were a useful starting point for the development of SCAR primers. The potential of AFLPs to produce a high number of fragments (Vos et al 1995) and, therefore, an increased chance to detect character-linked markers, is reflected in the fact that the source of the present development of male-specific markers in R. nivalis was a side-product of its phylogeographic investigation (Stehlik 2002).…”

“…in Central and southeastern Europe (Wagenitz 1981). In a previous AFLP analysis (Stehlik 2002), some fragments were tentatively identified as sex-specific. One of these fragments was especially intense and present in all male plants (N=80).…”

“…(Stehlik 2002), male-specific fragments were found using amplified fragment-length polymorphisms (AFLP; Vos et al 1995). R. nivalis belongs to the section Acetosa (Wagenitz 1981) for which sex determination is outlined above.…”

The phylogeography of an alpine leaf beetle: Divergence within Oreina elongata spans several ice ages

“…Climate cycles may therefore have led currently isolated populations to have come repeatedly into contact during cold periods as their suitable habitat expanded. For the alpine flora, long-term refugia within the Alps and at their northern, southern and eastern borders have been proposed on the basis of recent molecular studies (Stehlik et al, 2001;Stehlik, 2002;Schönswetter et al, 2005). Such results have important implications for the community ecology of montane habitats.…”

Consequences of Geographical Habitats on Population Structure and Genetic Diversity in Campanula spp.

“…Results were similar for Hypericum nummularium L. populations in the Alps, which were not true in the Pyrenees, 19 Also, in Eryngium alpestris Schultes populations, no significant correlation was found at a geographical distance of 250 km, 47 while in a study on Rumex nivalis Hegetschw, a correlation was found only in a large region of Switzerland. 48 Results from cluster analysis of single data sets were less related to geographical distribution. In fact, we found that the myb marker was more adept at differentiating species while NBS markers were best for discriminating populations.…”