Methods for studying polyploid diversification and the dead end hypothesis: a reply to Soltis et al . (2014)

The fate of polyploid lineages has been of long-standing interest to evolutionary biologists. In our previous work (Mayrose et al., 2011a; reviewed in Arrigo & Barker, 2012), we used likelihood methods to estimate the effects of recent polyploidization events on diversification rates (speciation minus extinction). Our goal was to ask whether, across groups, there is a preponderance of evidence for or against the hypothesis that polyploid species diversify at different rates than diploid species. Our results demonstrated that polyploid lineages, when compared with their diploid relatives, tend to form new species more slowly and go extinct more quickly, for a combined effect of lower diversification rates. Soltis et al. (2014) recently called into question our conclusions and raised concerns about our analyses. Some of these concerns reflect open questions and limitations in the available data, but others are based on misinterpretations of the methods used and their implications. In the spirit of furthering the fascinating debate about the macroevolutionary consequences of polyploidization, we offer this response with the hope that it will clarify what has been shown, demonstrate the utility of the methods applied, and inspire future work. Soltis et al. (2014) frame their concerns as a series of arguments, and we follow their framework in responding to the points raised. Before embarking, it is worth reemphasizing what we defined as a ‘polyploid lineage’. Indeed, all angiosperms have one or more polyploidization events in their history if one looks back far enough (Jiao et al., 2011), and thus polyploidymust be definedwith respect to a reference time point. Because our focus was on the impacts on diversification of recent polyploidization events, we explicitly defined polyploids ‘as those lineages that underwent a polyploidization event since divergence from their generic ancestor’ (Mayrose et al., 2011a). This definition enabled us to perform a large-scale comparative study using chromosome number changes to infer polyploid transitions in 63 clades of plants. Thus, when asking whether polyploidization impacts subsequent diversification, it must be borne in mind that our analyses were conducted on rather short evolutionary timescales, comparing those taxa that had undergone fairly recent polyploidization (‘neopolyploids’) with those that had not. As we concluded in Mayrose et al. (2011a), it remains an interesting open question whether earlier polyploidy events had different impacts on speciation and extinction, as has been suggested, for example, in the context of mass extinction events (Fawcett et al., 2009; Vanneste et al., 2014).