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Introgression frequently occurs between closely related plant species when there is incomplete reproductive isolation. However, few studies have been designed to examine the extent and direction of introgression from all three genomes, especially when they have different rates of gene flow. Conifers, in which chloroplast (cp), mitochondrial (mt) and nuclear (nr) genomes show contrasting rates of gene flow, provide a good model in which to carry out such a case study. Here we use data on sequence variation in 18 DNAs from three genomes for 311 individuals of 31 populations to investigate the extent and direction of introgressions between three spruce species in areas where they are sympatrically distributed. We found that one species seem to have introgressions derived from the other two species in areas of sympatric distribution; there were more introgressions from the maternally inherited mtDNA, which has the lowest rate of gene flow, and fewer introgressions from the bi-parentally inherited nrDNA. Further coalescent analysis of nrDNA population genetic data suggested that the species containing introgressions had experienced range expansion in the recent past while there was no such indication for the other two species. Our results support the hypotheses that introgressions occurred more frequently at genetic markers with lower rates of gene flow and that they usually took place from local species towards invading species that had undergone recent demographic expansion. [ABSTRACT FROM AUTHOR]

Species delimitation has been a major research focus in evolutionary biology. However, the genetic delimitation of recently diverged species varies depending on the markers examined. In this study, we aimed to examine genetic differentiation and delimitations between only two species of Pugionium Gaertn (Brassicaceae)- Pugionium cornutum (L.) Gaertn and Pugionium dolabratum Maxim-that occur in the desert habitats of central Asia and have parapatric distributions. We genotyped 169 individuals from 25 populations, using two chloroplast (cp) DNA fragments ( trnV- trnM and trnS- trnfM), seven simple repeated sequence (SSR) loci and the nuclear ribosomal internal transcribed spacer (ITS). Four cp haplotypes were identified, three of which commonly occur in the two species, suggesting incomplete species-specific lineage sorting. Between-species cpDNA differentiation ( F) was low, even lower than among populations of the same species. However, we found higher than average SSR F values, and both Bayesian clustering of SSR variables and maximum-likelihood genetic analyses divided all sampled individuals into two groups, agreeing well with morphological separation, although gene flow between species was obvious according to the SSR loci data. However, two types of ITS sequences were highly consistent with the morphological delimitation of the two species in all sampled individuals. These results together suggest that these two species shared numerous ancestral cpDNA polymorphisms and point to the importance of nuclear DNA (ITS or genetic accumulation at multiple loci) in delimiting recently diverged species. [ABSTRACT FROM AUTHOR]