Phylogenetic inference from genome-wide data.
The unprecedented amount of data resulting from next-generation sequencing has opened a new era in phylogenomics. However, although large datasets should in theory increase resolution, multilocus data has also uncovered a great deal of phylogenetic incongruence among different genomic regions, due both to stochastic error and to the action of different evolutionary process like incomplete lineage sorting, gene duplication and loss and horizontal gene transfer. In this talk I will explain some of the most important challenges we will have to face to reconstruct the history of species. I will also describe different strategies for the phylogenetic analysis of genome-wide data that we have recently developed, including a new species tree approach that offers a very good compromise between model complexity and computational feasibility.