Chloroplast DNA (cpDNA) and isozyme data were used to reconstruct the evolutionary history of the 21 taxa comprising Helianthus sect Helianthus. Low levels of cpDNA and isozyme divergence suggest a recent origin, perhaps within the last 1-2 million years, with subsequent rapid evolution and diversification throughout North America. This, combined with evolutionary phenomena such as phylogenetic sorting and introgression, makes phylogenetic reconstruction difficult. A strict consensus tree derived from Wagner parsimony analysis of the isozyme data set showed almost complete lack of resolution. The three clades resolved were, however, largely consistent with previous phylogenetic hypotheses. The most parsimonious cpDNA-based Wagner tree was poorly resolved, but showed that sect. Helianthus as presently circumscribed is monophyletic. Surprisingly, the cpDNA-based phylogeny does not resemble any of the previous phylogenetic hypotheses for this group based on evidence from morphology, crossability, sesquiterpene lactone chemistry, and inferred chromosomal end arrangements. In general, species geographically most proximal are most closely related in terms of cpDNA, maternal inheritance of which is demonstrated herein. All four polytypic species in sect. Helianthus are polyphyletic in terms of cpDNA. Morphological classification and cpDNA genotype were discordant for populations or species of H. annuus, H. deblis subsp. cucumerifolius, H. neglectus, H. petiolaris subsp. fallax, H. petiolaris subsp. petiolaris, and H. anomalus. Cytoplasmic introgression appears to be the most parsimonius explanation for these discrepancies. The edaphic differentiation and generally allopatric distribution of most taxa in sect. Helianthus are consistent with an allopatric mode of speciation. Molecular and chromosomal evidence, however, suggest that allopatric, parapatric, and quantum speciation all operate. In addition, at least one geographic race may have been derived through introgression and three species appear to be derived via selection or random fixation of recombinant genotypes following interspecific hybridization. We also tested the hypothesis that levels of genetic polymorphism will be lower in geographically restricted species than in more widespread species. Eight of the 11 narrow endemics analyzed had lower levels of genetic diversity than any of their more widespread congeners.
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