Nuclear and cytoplasmic variation within and between EurasianLarix(Pinaceae) species

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Abstract
The genetic variation in nuclear and cytoplasmic markers was investigated in 28 populations belonging to EurasianLarixspecies (L. decidua,L. sibirica,L. gmelinii,L. olgensis, andL. kaempferi). Nuclear genetic variation was assessed at 214 AFLP loci, and both PCR‐RFLP and four microsatellite loci were used to estimate variation of the chloroplast DNA. Variation of the mitochondrial genome was measured using RFLPs. Although population differentiation at both nuclear and chloroplast markers was much weaker than at mitochondrial DNA, it nonetheless corroborated the grouping observed with mitochondrial DNA. The AFLPs led to the same population grouping as mtDNA. Notably, the presence of two ancient western and eastern groups withinL. sibiricawas confirmed and possible postglacial routes inferred. The genetic composition of the northernmostL. sibiricapopulation in our sample established that it is located at the confluence of the eastern and western recolonization routes. The joint use of the three markers also indicated that populations around Lake Baikal are hybrids betweenL. gmeliniiandL. sibirica, withL. gmeliniiprimarily acting as the pollinator. Finally, AFLP‐based estimates of nucleotide variation were an order of magnitude larger than the strikingly low estimates of nucleotide variation recently reported inPinus sylvestris.