Finally our paper on Bayesian species tree estimation is published in Systematic Biology, although it has been available (advance access) there since 2014. This is a very nice method implemented by Leo Martins in the software Guenomu, in which a species tree can be build from multiple gene-family alignments. It is based on a Bayesian hierarchical statistical model of the incongruence between gene trees and species trees that ignores the evolutionary process responsible for it, inspired by Steel and Rodrigo (2008) ML supertree approach. This method does not require the identification of orthologs and can use information from multiple individuals from the same species.
This paper is part of a special issue based on the Systematic Biology symposium that I organized in 2013 Evolution meetings at Snowbird. The introduction to this symposium is also available here.
Martins LO, Mallo D, Posada D. 2016. A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction. Systematic Biology 65: 397-416.
Posada D. 2016. Phylogenomics for Systematic Biology. Systematic Biology 65: 353-356.