The gap character matrix was generated using SeqState [43], which implements the simple indel coding method of Simmons and Ochoterena [19]. This method codes gaps as binary characters with ³´ corresponding to presence of a gap (tKHDEVHQFHRIQXFOHRWLGHVDQG³´ corresponding to absence of a gap (the presence of nucleotides). Gaps with different start and/or end positions are coded separately, and any gap that is enclosed within a lRQJHUJDSLVFRGHGDVPLVVLQJ³"´) for taxa with the longer gap. Three gap matrices were generated, one based upon all indels, a second with gap characters based on indels longer than 1 bp and a third with gap characters based on indels longer than 2 bp. All data matrices are available from the Early Bird web site [44].
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