The study of paleopolyploidies requ

The study of paleopolyploidies requires the comparison of multiple whole genome sequences. If the branches of a phylogeny
on which a whole-genome duplication (WGD) occurred could be identified before genome sequencing, taxa could be
selected that provided a better assessment of that genome duplication. Here, we describe a likelihood model in which the
number of chromosomes in a genome evolves according to a Markov process with one rate of chromosome duplication and
loss that is proportional to the number of chromosomes in the genome and another stochastic rate at which every
chromosome in the genome could duplicate in a single event. We compare the maximum likelihoods of a model in which the
genome duplication rate varies to one in which it is fixed at zero using the Akaike information criterion, to determine if
a model with WGDs is a good fit for the data. Once it has been determined that the data does fit the WGD model, we infer
the phylogenetic position of paleopolyploidies by calculating the posterior probability that a WGD occurred on each branch
of the taxon tree. Here, we apply this model to a molluscan tree represented by 124 taxa and infer three putative WGD
events. In the Gastropoda, we identify a single branch within the Hypsogastropoda and one of two branches at the base of
the Stylommatophora. We also identify one or two branches near the base of the Cephalopoda.