| Summary: | <p>Abstract</p> <p>Background</p> <p>Revealing the past and present demographic history of populations is of high importance to evaluate the conservation status of species. Demographic data can be obtained by direct monitoring or by analysing data of historical and recent collections. Although these methods provide the most detailed information they are very time consuming. Another alternative way is to make use of the information accumulated in the species' DNA over its history. Recent development of the coalescent theory makes it possible to reconstruct the demographic history of species using nucleotide polymorphism data. To separate the effect of natural selection and demography, multilocus analysis is needed because these two forces can produce similar patterns of polymorphisms. In this study we investigated the amount and pattern of sequence variability of a Europe wide sample set of two peat moss species (<it>Sphagnum fimbriatum </it>and <it>S. squarrosum</it>) with similar distributions and mating systems but presumably contrasting historical demographies using 3 regions of the nuclear genome (appr. 3000 bps). We aimed to draw inferences concerning demographic, and phylogeographic histories of the species.</p> <p>Results</p> <p>All three nuclear regions supported the presence of an Atlantic and Non-Atlantic clade of <it>S. fimbriatum </it>suggesting glacial survival of the species along the Atlantic coast of Europe. Contrarily, <it>S. squarrosum </it>haplotypes showed three clades but no geographic structure at all. Maximum likelihood, mismatch and Bayesian analyses supported a severe historical bottleneck and a relatively recent demographic expansion of the Non-Atlantic clade of <it>S. fimbriatum</it>, whereas size of <it>S. squarrosum </it>populations has probably decreased in the past. Species wide molecular diversity of the two species was nearly the same with an excess of replacement mutations in <it>S. fimbriatum</it>. Similar levels of molecular diversity, contrasting phylogeographic patterns and excess of replacement mutations in <it>S. fimbriatum </it>compared to <it>S. squarrosum </it>mirror unexpected differences in the demography and population history of the species.</p> <p>Conclusion</p> <p>This study represents the first detailed European wide phylodemographic investigation on bryophytes and shows how pattern of nucleotide polymorphism can reveal unexpected differences in the population history of haploid plants with seemingly similar characteristics.</p>
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