Polyploidy, an important factor in eukaryotic evolution, is especially abundant in angiosperms, where it often acts in concert with hybridization to produce allopolyploids. The application of molecular phylogenetic techniques has identified the origins of numerous allopolyploids, but little is known on genomic and chromosomal consequences of allopolyploidization, despite their important role in conferring divergence of allopolyploids from their parental species. Here, using several plastid and nuclear sequence markers, we clarify the origin of tetra-and hexaploids in a group of American daisies, allowing characterization of genome dynamics in polyploids compared to their diploid ancestors. All polyploid species are allopolyploids. Among the four diploid gene pools, the propensity for allopolyploidization is unevenly distributed phylogenetically with a few species apparently more prone to participate, but the underlying causes remain unclear. Polyploid genomes are characterized by differential loss of ribosomal DNA loci (5S and 35S rDNA), known hotspots of chromosomal evolution, but show genome size additivity, suggesting limited changes beyond those affecting rDNA loci or the presence of processes counterbalancing genome reduction. Patterns of rDNA sequence conversion and provenance of the lost loci are highly idiosyncratic and differ even between allopolyploids of identical parentage, indicating that allopolyploids deriving from the same lower-ploid parental species can follow different evolutionary trajectories.

Chromosome evolution (including polyploidy, dysploidy, and structural changes) as well as hybridization and introgression are recognized as important aspects in plant speciation. A suitable group for investigating the evolutionary role of chromosome number changes and reticulation is the medium-sized genus Melampodium (Millerieae, Asteraceae), which contains several chromosome base numbers (x=9, 10, 11, 12, 14) and a number of polyploid species, including putative allopolyploids. A molecular phylogenetic analysis employing both nuclear (ITS) and plastid (matK) DNA sequences, and including all species of the genus, suggests that chromosome base numbers are predictive of evolutionary lineages within Melampodium. Dysploidy, therefore, has clearly been important during evolution of the group. Reticulate evolution is evident with allopolyploids, which prevail over autopolyploids and several of which are confirmed here for the first time, and also (but less often) on the diploid level. Within sect. Melampodium, the complex pattern of bifurcating phylogenetic structure among diploid taxa overlain by reticulate relationships from allopolyploids has non-trivial implications for intrasectional classification.

Leontopodium is a genus of approximately 30 species with a conspicuous Asian-European disjunct distribution. In this study samples from the Himalayan/Tibetan centre of diversity of the genus, as well as from Europe, were analysed to infer a phylogeny of the genus using sequences of nuclear ribosomal (ITS and ETS) and plastid (matK and trnL/F) DNA. The Southeast Tibetan monotypic Sinoleontopodium [Leontopodium lingianum (Y.L.Chen) Dickoré, comb. nov.] falls into Leontopodium. Monophyly of Leontopodium, including Sinoleontopodium, is supported. Due to low rates of sequence divergence, intrageneric relationships in general are weakly supported, a pattern frequently observed in plant groups centred in the Tibetan Plateau. Three phylogenetic groups can be identified, however, and these are also supported by morphology. The low levels of nucleotide divergence suggest a young age for the group, which has been influenced by the turbulent geological history of the Tibetan Plateau. Leontopodium is a characteristic Sino-Himalayan element that appears to have found its way into the mountains of Europe in geologically recent times. The two European taxa, Leontopodium alpinum and L. nivale, form a genetically distinct group, which, considering the wide geographic disjunction, shows surprisingly little divergence from its Asian relatives.

The genus Melampodium consists of 40 species distributed throughout Mexico and Central America with extensions into the southwestern United States and Colombia and Brasil of South America. The genus reflects broad chromosomal evolution involving dysploidy and polyploidy withn = 9, 10, 11, 12, 14, 18, 20, 23, 24, 27, 28, 30, and 33 having been documented (x = 9, 10, 11, 12, and 14). The most recent classification of the genus, based primarily on morphology and chromosome num bers, recognized six taxonomic sections: Alcina, Bibractiaria, Melampodium, Rhizomaria, Serratura, and Zarabellia. Section Melampodium, which contains 22 species, was divided into five series: Cupulata, Leucantha, Longipila, Melampodium, and Sericea. This hypothesis had been tested by previous morphological phenetic and cladistic analyses, and several problem areas had been highlighted, especially involving section Alcina, but no modifications to the classification have been made. Recent molecular studies utilizing nrITS, 5S rDNA spacer and low‐copy nuclear PgiC gene, plus plastid matK and psbA‐trnH regions allow the classificatory hypothesis to be tested more precisely. Congruence between ITS and matK phylogenies for all species reveals sections Bibractiaria, Rhizomaria, and Serratura to be holophyletic. The largest section Melampodium is holophyletic with both plastid markers, but M. longipilum is shown as an outlier (tying to sect. Rhizomaria) in all nuclear marker phylogenies (ITS, PgiC and 5S rDNA spacer). Section Zarabellia appears holophyletic in matK but biphyletic with ITS, suggesting recogni tion of two distinct series. Section Alcina is the most problematic, being triphyletic in ITS and matK, and with the species not connecting to the same relatives. These insights recommend recognition of three sections from within section Alcina, one hous ing M. nutans (Nutantia Stuessy, sect. nov.) another M. glabrum (Glabrata Stuessy, sect. nov.) and a third M. perfoliatum (sect. Alcina (Cav.) DC.). These may represent ancient independent lines that have diverged from original x = 11 ancestors. Within section Melampodium, 5S rDNA NTS, PgiC and psbA‐trnH, in addition to ITS and matK, provide insights on relationships among taxonomic series. Series Leucantha and Longipila are holophyletic, and series Cupulata nearly so, with M. glabribracteatum deserving treatment in a series of its own. The most complex relationships are between series Melampodium, Cupulata, and Sericea, the latter comprising five exclusively polyploid taxa (4x and 6x). Molecular and cytogenetic data reveal allopolyploid origins for all of these polyploids, in some cases involving hybridization between the two series Cupulata and Melampodium / Sericea, such as with M. mayfieldii and M. longicorne, which exacerbates taxonomic circumscription.

Polyploids in M. cinereum and M. leucanthum are of recent autopolyploid origin in line with the lack of significant genomic changes. Hexaploid M. argophyllum also appears to be of autopolyploid origin against the previous hypothesis of an allopolyploid origin involving the other two species, but some gene flow with the other species in early phases of differentiation cannot be excluded.