Gaps, an elusive source of phylogenetic information

Morrison (2009) raises a very fundamental question, “Why would phylogeneticists ignore computerized sequence alignment?” While well aware of the difficulties, he considers the whole issue is a ‘gaping hole that needs to be filled’. Particularly with the expansion of genomic-scale data there are many advantages to using automated alignment for phylogenetic analyses, the most obvious being that it is much more efficient and potentially less prone to experimenter bias. So yes, it is obviously desirable to automate data preparation as far as possible, but the question remains whether we are yet at the stage that automated sequence alignment can obtain the full and correct phylogenetic information in the data. In this paper we use an example shorebird dataset to explore three related questions regarding the interplay between alignment and phylogeny estimation: 1) are gap-rich alignments reliable for phylogenetic inference? 2) How much phylogenetic information is contained in gaps as compared...