Abstract
BackgroundSpecies complexes or aggregates consist of a set of closely related species often of different ploidy levels, whose relationships are difficult to reconstruct. The N Hemisphere Achillea millefolium aggregate exhibits complex morphological and genetic variation and a broad ecological amplitude. To understand its evolutionary history, we study sequence variation at two nuclear genes and three plastid loci across the natural distribution of this species complex and compare the patterns of such variations to the species tree inferred earlier from AFLP data.ResultsAmong the diploid species of A. millefolium agg., gene trees of the two nuclear loci, ncpGS and SBP, and the combined plastid fragments are incongruent with each other and with the AFLP tree likely due to incomplete lineage sorting or secondary introgression. In spite of the large distributional range, no isolation by distance is found. Furthermore, there is evidence for intragenic recombination in the ncpGS gene. An analysis using a probabilistic model for population demographic history indicates large ancestral effective population sizes and short intervals between speciation events. Such a scenario explains the incongruence of the gene trees and species tree we observe. The relationships are particularly complex in the polyploid members of A. millefolium agg.ConclusionsThe present study indicates that the diploid members of A. millefolium agg. share a large part of their molecular genetic variation. The findings of little lineage sorting and lack of isolation by distance is likely due to short intervals between speciation events and close proximity of ancestral populations. While previous AFLP data provide species trees congruent with earlier morphological classification and phylogeographic considerations, the present sequence data are not suited to recover the relationships of diploid species in A. millefolium agg. For the polyploid taxa many hybrid links and introgression from the diploids are suggested.
Highlights
Species complexes or aggregates consist of a set of closely related species often of different ploidy levels, whose relationships are difficult to reconstruct
After eliminating some sequences likely containing PCRrecombination, 303 sequences of the ncpGS and 313 of the SBP gene from broadly the same 70 individuals of 29 populations belonging to A. millefolium agg. were used for the data analyses (Table 1)
As the phylogenetic relationships of these three species indicated by the AFLP tree (Figure 1B) are in line with the morphological and biogeographical information, we suggest that the gene tree incongruence as well as their discordance with the inferred species tree are due to a lack of sorting of ancestral polymorphic alleles and/or due to introgression after the split of the species
Summary
Species complexes or aggregates consist of a set of closely related species often of different ploidy levels, whose relationships are difficult to reconstruct. By cultivation in experimental gardens, Clausen et al [6] documented local adaptation of A. millefolium populations to environments along an altitudinal transect in California from sea level to alpine regions. This has become a classic example of rapid adaptive divergence of plant populations [12,13,14,15,16,17,18]
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