Polyploidy, the possession of more than 2 complete genomes, is a major force in plant evolution known to affect the genetic and genomic constitution and the phenotype of an organism, which will have consequences for its ecology and geography as well as for lineage diversification and speciation. In this review, we discuss phylogenetic patterns in the incidence of polyploidy including possible underlying causes, the role of polyploidy for diversification, the effects of polyploidy on geographical and ecological patterns, and putative underlying mechanisms as well as chromosome evolution and evolution of repetitive DNA following polyploidization. Spurred by technological advances, a lot has been learned about these aspects both in model and increasingly also in nonmodel species. Despite this enormous progress, long-standing questions about polyploidy still cannot be unambiguously answered, due to frequently idiosyncratic outcomes and insufficient integration of different organizational levels (from genes to ecology), but likely this will change in the near future. See also the sister article focusing on animals by Choleva and Janko in this themed issue.

A large proportion of genomic information, particularly repetitive elements, is usually ignored when researchers are using next-generation sequencing. Here we demonstrate the usefulness of this repetitive fraction in phylogenetic analyses, utilizing comparative graph-based clustering of next-generation sequence reads, which results in abundance estimates of different classes of genomic repeats. Phylogenetic trees are then inferred based on the genome-wide abundance of different repeat types treated as continuously varying characters; such repeats are scattered across chromosomes and in angiosperms can constitute a majority of nuclear genomic DNA. In six diverse examples, five angiosperms and one insect, this method provides generally well-supported relationships at interspecific and intergeneric levels that agree with results from more standard phylogenetic analyses of commonly used markers. We propose that this methodology may prove especially useful in groups where there is little genetic differentiation in standard phylogenetic markers. At the same time as providing data for phylogenetic inference, this method additionally yields a wealth of data for comparative studies of genome evolution.

DNA ploidy levels were estimated using DAPI‐flow cytometry of silica‐dried specimens of the European mountain plant Senecio carniolicus (Asteraceae), covering its entire distribution area in the Eastern Alps (77 populations, 380 individuals) and the Carpathians (five populations, 22 individuals). A complex pattern of ploidy level variation (2x, 4x, 5x, 6x, and 7x cytotypes) was found in this species, which has been considered uniformly hexaploid. Hexaploids predominated in the Eastern Alps and was the only cytotype found in the Carpathians, while odd ploidy levels (5x, 7x) constituted a small fraction of the samples (<1.3%). Tetraploids occurred in two disjunct areas, which correspond with putative Pleistocene refugia for silicicolous alpine plants. Diploids occurred in large portions of the Alps but were absent from areas most extensively glaciated in the past. Intrapopulational cytotype mixture was detected in 22 populations—the majority involving diploids and hexaploids—with intermediate ploidy levels mostly lacking, suggesting limited gene flow and the evolution of reproductive isolation. Significant and reproducible intracytotype variation in nuclear DNA content was observed. Higher genome size in western diploids might be due to ancient introgression with the closely related S. incanus or to different evolutionary pathways in the geographically separated diploids.

Genome size was estimated using Feulgen densitometry for 76 accessions of 40 taxa of Orobanche and two taxa each of the related genera Phelypaea and Cistanche, providing the first data set for any group of nonphotosynthetic angiosperms. The 2C‐values were 16.8–19.9 pg in Cistanche, 2.9–11.6 pg in Orobanche sect. Orobanche, 6.8–10.8 pg in sect. Trionychon, 4.3–5.1 pg in sect. Myzorrhiza, and 4.9–5.8 pg and 10.5 pg in the two diploid species Phelypaea coccinea and P. tournefortii, respectively. Distribution of genome size is congruent with phylogenetic lineages identified by analyses of nuclear ITS sequence data, in particular regarding the distinctness of O. anatolica from the rest of sect. Orobanche. With the exception of tetraploid O. transcaucasica, polyploid taxa of sect. Orobanche are among those with the smallest C‐values, suggesting substantial genome downsizing after polyploidization (as in other angiosperm groups). In O. sect. Orobanche, genome size evolved more rapidly in earlier stages of its evolution than in later stages. This might be indicative of adaptive radiation, but this hypothesis requires corroboration in the form of genome size estimates on more taxa and accessions.