Phylogenies from concatenated data: Is the end nigh?

Abstract

Gene trees from independent molecular markers often differ. Simple data matrix concatenation cannot represent the various biologically meaningful processes that underlie these differences, and in an age of high-throughput DNA sequencing and coalescent-based species tree inference methods, the approach seems increasingly quaint. I argue that concatenation still has its place in our suite of approaches, but that care should be taken when deciding which data might be combined under what circumstances. I present recommendations for avoiding the worst pitfalls of the approach.