Usually, offspring inherit one copy of each of their mom’s chromosomes and one copy of each of their dad’s chromosomes. This allows ploidy to be maintained over generations – that is I don’t have all of my ancestors chromosomes, otherwise my genome would be HUGE. However genome size does change over time, and sometimes it doubles (it can do this in a number of cool ways). This presents awesome opportunities and challenges. One challenge is pulling off meiosis at all – meiosis seems like a tough thing to do, but it gets even harder when my chromosome look very similar. An exciting opportunity associated with polyploidy is that different copies of the same gene are now free to evolve specialized functions, or to explore new functions (neo and subfunctionalization, [link]).
What is the ultimate evolutionary fate of polyploids? According to an exciting new paper in Science things usually don’t go so well. Using new methods (in the BiSSe family) that allow us to infer state dependent rates of speciation and extinction, Itay Mayrose and an impressive group of collaborators (Loren Rieseberg, Sally Otto, and my friend/coauthor Mike Barker) show that recent polyploids both speciate at lower rates and go extinct at higher rates than their diploid congeners. This makes sense, as if polyploidy was truly awesome we’d all be infaploids. Nonetheless, this paper did leave me asking many questions. I’m posting my criticisms below, a nice discussion in my comments section is welcome.
What I like
This is a cool implementation of bisse to a classic problem. This paper also included a nice bit of methods development in which the authors’ allowed for trait evolution to occur at the same time as speciation.
Mechanism: The authors do not clearly describe the biological underpinnings of this result. Since their methods is correlation based, they can’t really answer the question of underlying causes. Nonetheless, I would have appreciated some thoughtful hypotheses.
Latent variables: Polyploidy is often associated with the evolution of self-compatibility. Self compatibility is itself associated with elevated extinction rates. Similarly, the ranges of polyploids may differ from their diploid congers, and this too could influence speciation and extinction rates. I would be useful to extend BiSSe like models to address multivariate trait evolution. [update: since writing this draft I hear from emma goldberg and rich fitzjohn, who have already made much progress on the problem of correlated traits in isse models. Emma is now looking at speciation.extinction as a function of both mating system and ploidy… so we’ll find out more soon]
Ascertainment bias: To make this study tractable the authors define recent polyploidy by reference to to the ploidy level of their generic ancestor. This means that a case of polyploidy events so awesome that polyploids took the genus over, or so innovative that descendents earn their own generic status, will not count as successful polyploidizations.
Reference: Mayrose, I., S. H. Zhan, C. J. Rothfels, K. Magnuson-Ford, M. S. Barker, L. H. Rieseberg, and S. P. Otto. 2011. Recently-formed polyploid plants diversify at lower rates. Science 333: 1257