Many hypotheses exist for the relative diversity of seed plant taxa. We discuss one of them: how the relative dearth of cycad diversity throughout their 300 million year history may be a result of a lack of duplication of their entire nuclear genome, often termed polyploidy. We show theoretically how polyploidy causes speciation via cryptic reproductive isolation. Polyploidy can also cause radiations via epigenetically induced heterochrony and plasticity. Most cycads have only a few large chromosomes because of a lack of whole genome duplication or, except possibly in the genus Zamia, chromosomal fission. Large chromosomes and extremely small effective population sizes result in substantial linkage disequilibrium, genetic hitchhiking and genetic drift in cycads. By contrast, other seed plants have higher incidences of polyploidy and may therefore have been more prone to radiations.

Zamia is unique among Cycadales in its diversity of morphology, ecology and chromosome numbers. The chromosome numbers in Zamia range from 16 to 28, excluding 20, manifest as both interspecific and intraspecific series. It has long been recognized that Robertsonian transformations (chromosomal fission or fusion) probably dominate karyotype evolution in Zamiaceae, although it has been debated whether chromosome numbers are increasing or decreasing. We re-analyse published karyotypes of Zamia spp., relating both chromosome forms and sizes to recent phylogenetic data. We show that karyotype evolution is most probably moving towards increased asymmetry, with higher numbers of smaller chromosomes, thus supporting chromosomal fission. We also address additional hypotheses for increasing chromosome numbers, namely pericentric inversions and unequal translocations. Finally, we discuss the role of these chromosomal changes in evolutionary radiations.

There are two ways eukaryotes double number of chromosomes: (1) whole genome duplication (polyploidy), in which all nuclear DNA is replicated, and (2) karyotypic fission (pseudopolyploidy), in which all chromosomes are physically bifurcated. We contrast polyploidy with pseudopolyploidy, highlighting when it is crucial to look at genetic vs. genomic levels. We review history of pseudopolyploidy, including recent mechanisms by which chromosomal bifurcation may occur and outline methods for detecting such genomic changes. We then delve into the evolutionary implications, with particular focus on adaptive potential, of these two forms of doubling chromosome numbers. We address the common assertion that polyploidy induces adaptive radiations, which contains three fallacies. First, while polyploidy causes quantum speciation, evolutionary theory implies that these radiations should be non-adaptive. Polyploidy causes reproductive isolation, minute effective population sizes, and increased mutation rates, which all imply a diminished role for selection. Second, due to lack of karyotyping in recent decades and lack of distinction between genomic and genetic effects, it is usually impossible to detect pseudopolyploids. Third, pseudopolyploids lack minority cytotype exclusion because they readily backcross with their progenitors, which thereby means no reproductive isolation for newly formed pseudopolyploids. Pseudopolyploidy will thereby not result in radiations until pseudopolyploid descendants undergo subsequent chromosome rearrangements or grow new centromeres. Pseudopolyploids may have a modest selective advantage over their progenitors due to diminished linkage disequilibrium. Thus, pseudopolyploidy may induce adaptive non-radiations. We encourage a renaissance of karyotyping to distinguish between these two mechanisms and a renaissance in genomic perspectives in evolution.