Data from: Cladogenetic and anagenetic models of chromosome number evolution: a Bayesian model averaging approach

Chromosome number is a key feature of the higher-order organization of the
genome, and changes in chromosome number play a fundamental role in
evolution. Dysploid gains and losses in chromosome number, as well as
polyploidization events, may drive reproductive isolation and lineage
diversification. The recent development of probabilistic models of
chromosome number evolution in the groundbreaking work by Mayrose et al.
(2010, ChromEvol) have enabled the inference of ancestral chromosome
numbers over molecular phylogenies and generated new interest in studying
the role of chromosome changes in evolution. However, the ChromEvol
approach assumes all changes occur anagenetically (along branches), and
does not model events that are specifically cladogenetic. Cladogenetic
changes may be expected if chromosome changes result in reproductive
isolation. Here we present a new class of models of chromosome number
evolution (called ChromoSSE) that incorporate both anagenetic and
cladogenetic change. The ChromoSSE models allow us to determine the mode
of chromosome number evolution; is chromosome evolution occurring
primarily within lineages, primarily at lineage splitting, or in
clade-specific combinations of both? Furthermore, we can estimate the
location and timing of possible chromosome speciation events over the
phylogeny. We implemented ChromoSSE in a Bayesian statistical framework,
specifically in the software RevBayes, to accommodate uncertainty in
parameter estimates while leveraging the full power of likelihood based
methods. We tested ChromoSSE's accuracy with simulations and
re-examined chromosomal evolution in Aristolochia, Carex section
Spirostachyae, Helianthus, Mimulus sensu lato (s.l.), and Primula section
Aleuritia, finding evidence for clade-specific combinations of anagenetic
and cladogenetic dysploid and polyploid modes of chromosome evolution.