Data from: 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 to sequences? 3) Are models of the insertion/deletion process
essential, and if so at what phylogenetic depths? We report that there is
considerable information created by the indel (insertion/deletion) process
that is potentially available for phylogenetic inference. Ideally, we
should be able to independently obtain the same tree from both sequences
and from gaps; however there is still considerable variability in the
alignments produced by different programs. We predict that better and more
computationally tractable models of the indel process will be required
before the information in gaps can be fully exploited for phylogenetic
inference.