| Summary: | <p>Abstract</p> <p>Background</p> <p>Effects of polyploidisation on gene flow between natural populations are little known. Central European diploid and tetraploid populations of <it>Arabidopsis arenosa </it>and <it>A. lyrata </it>are here used to study interspecific and interploidal gene flow, using a combination of nuclear and plastid markers.</p> <p>Results</p> <p>Ploidal levels were confirmed by flow cytometry. Network analyses clearly separated diploids according to species. Tetraploids and diploids were highly intermingled within species, and some tetraploids intermingled with the other species, as well. Isolation with migration analyses suggested interspecific introgression from tetraploid <it>A. arenosa </it>to tetraploid <it>A. lyrata </it>and vice versa, and some interploidal gene flow, which was unidirectional from diploid to tetraploid in <it>A. arenosa </it>and bidirectional in <it>A. lyrata</it>.</p> <p>Conclusions</p> <p>Interspecific genetic isolation at diploid level combined with introgression at tetraploid level indicates that polyploidy may buffer against negative consequences of interspecific hybridisation. The role of introgression in polyploid systems may, however, differ between plant species, and even within the small genus <it>Arabidopsis</it>, we find very different evolutionary fates when it comes to introgression.</p>
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