Dating the origins of polyploidy events

Moreover, an estimated 15% and 31% of speciations in flowering plants and ferns, respectively, were accompanied by a ploidy increase (Wood et al. Most recent insights explaining the evolutionary success of polyploids have focused on their duplicated genome, which simultaneously provides thousands of novel genes for evolution to tinker with.

Even though the large majority of these duplicated genes are lost through pseudogenization (Lynch and Conery 2000), the remaining fraction can lead to novel and/or expanded functionality through Ohno’s classical models of neofunctionalization (the duplicated copy acquires a new function), subfunctionalization (the division and/or elaboration of preduplication functionality over the two daughter copies), and gene conservation due to dosage effects (the increased production of a beneficial gene product), and combinations thereof (Ohno 1970; Hahn 2009; Maere and Van de Peer 2010).

We interpret these results in the context of recent studies on invasive polyploid plant species, and suggest that polyploid establishment is promoted during times of environmental stress.

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.

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.

Two long-standing opposite views regard polyploidy either as an evolutionary dead end (Stebbins 1950; Wagner 1970) or as a road toward evolutionary success (Levin 1983).However, this study was limited in terms of taxonomic sampling due to the small number of plant genome sequences available at that time, and it relied on penalized likelihood inference methods that present inherent methodological challenges (Soltis and Burleigh 2009), such as, for instance, the assumption of an autocorrelated relaxed clock model that is most likely violated when taxon sampling is limited (Ho 2009).In the years since, the number of publicly available plant genomes has increased drastically, and the field of molecular dating has also progressed with the development of more powerful Bayesian methods of sequence divergence estimation that can incorporate advanced uncorrelated relaxed clock models and fossil age uncertainty (Drummond et al. Here, we revisit the previously proposed clustering of plant paleopolyploidizations around the K–Pg boundary using the latest genome sequence data sets and phylogenetic dating methods available.The omnipresence of whole-genome duplications (WGDs) in evolution is striking. In the vertebrate lineage, a third WGD occurred in the ancestor of the successful teleost fish (Panopoulou and Poustka 2005). WGDs have also been documented in other kingdoms, such as, for instance, three WGDs in the ciliate (Wolfe and Shields 1997).Both angiosperm and vertebrate ancestors have undergone at least two separate WGDs, therefore all of their descendants are in fact ancient polyploids (paleopolyploids) (Putnam et al. In the angiosperm lineage, subsequent and sometimes repeated WGDs have been reported in all major clades (Soltis et al. A systematic overview of WGD in invertebrates, amphibians, and reptiles is lacking, but several examples have been described, contradicting the classical notion that paleopolyploidies are absent in these lineages (Mable 2004; Song et al. Although the prevalence of WGDs has been firmly established (Van de Peer et al.

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Ancient whole-genome duplications (WGDs), also referred to as paleopolyploidizations, have been reported in most evolutionary lineages.

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