Is recombination a problem for species-tree analyses?

As the field of phylogenetics transitions into phylogenomics it has spurred a shift in the general paradigm for data analysis whereby specific dataset attributes can now be considered in a model-based framework. Much effort has been put in to modeling the effects of nucleotide substitution within a genealogy (i.e., modeling mutations; Felsenstein 2005) and the sorting genes between lineages (i.e., coalescence; Knowles and Kubatko 2010), both of which are inherent properties of all species histories. Improvements in accuracy of species-tree estimation related to using models that account for these two sources of uncertainty have been well documented (Carstens and Knowles 2007; Edwards et al. 2007; Kubatko and Degnan 2007), but these are clearly not the only sources of gene tree species-tree discordance. As the field transitions towards using multilocus data, the role of other inherent dataset properties that may be sources of uncertainty, such as intralocus recombination needs to be exam...