Using Genomic Location and Coalescent Simulation to identify Paralogy, Hybridisation and Incomplete Lineage Sorting in nuclear loci. paralogy hybridisation and genomic location

Here we propose a model by which paralogy, hybridisation and incomplete lineage sorting can be successfully identified using genomic location information coupled with the coalescent model. The potential of the model is evaluated on simulated data derived from a species network with nine species, of which one is of hybrid origin, and a single gene duplication that leads to paralogous comparisons. On a first step, putative paralogous genes are identified and excluded and, on a second step, blocks of linked genes are grouped according to their hybrid history. Existing multispecies coalescent software can then be applied to recover the species tree without violating the underlying model. As an empirical case study, the model is also applied to a set 12 genes from seven species belonging to the plant genus Medicago. We demonstrate that the information derived from specific genomic locations can be used to reduce the effect of paralogous genes and to sort genes when hybridisation is present.