Dating the origins of polyploidy events
A general overview of all dated WGDs mapped on the green plant phylogeny is also presented in Figure 3. The gray and gold bars represent the distribution of the paranome and duplicated anchors identified with i-ADHo Re, respectively.Anchors and peak-based duplicates used as homeologs for absolute dating were extracted from between the WGD peak boundaries (see Table 1). (Nonvertical black solid line) Kernel density estimate of the dated homeologs; (vertical black solid line) its peak used as the WGD age estimate.
We argue that considering the evolutionary potential of polyploids in light of the environmental and ecological conditions present around the time of polyploidization could mitigate the stark contrast in the proposed evolutionary fates of polyploids.
First, we used positional information to select anchor pairs, i.e., homeologs located on duplicated segments generated through WGD, with ages corresponding to the WGD signature peak in the age distribution (Vanneste et al. Second, for species without positional information, or if fewer than 1000 orthogroups (see below) could be constructed based on anchors, we supplemented the anchor pairs with “peak-based” duplicates, which are non-anchor pairs that also map to the WGD signature peak in the age distribution and therefore are assumed to consist mainly of homeologs (Maere et al. The selection of homeologs for different plant species that experienced a WGD in the last ∼100 million years is illustrated in Figure 1 for a few exemplary species, and in Supplemental Figure S1 for all other species.
Next, all collected homeologs were combined with orthologs from other plant genomes to construct orthogroups (see Methods).
Much research has been dedicated to this topic, especially in the plant lineage because of the high frequency of WGD occurrence in plants, and studies have typically found ample support for both scenarios.
Recently formed polyploids frequently display increased meiotic and mitotic abnormalities through improper pairing of both subgenomes during cell division, resulting in genomic instability that has detrimental effects on plant fertility and fitness (Madlung et al. The study of mutant plants with higher ploidy levels exhibit more detrimental effects coupled with a strong drive to revert to lower ploidy levels via genomic reductions (Wang et al. Recently formed polyploid plants also need to cope with the minority cytotype disadvantage, a frequency-dependent reproductive disadvantage caused by ineffective matings of unreduced 2 gametes from the diploid progenitor majority cytotype, which results in the formation of less fit and fertile triploid hybrids (Levin 1975).
We include 38 full genome sequences and three transcriptome assemblies in a Bayesian evolutionary analysis framework that incorporates uncorrelated relaxed clock methods and fossil uncertainty.