title: On gaps.
abstract: Gaps result from the alignment of sequences of unequal length during primary homology assessment. Viewed as character states originating from particular biological events (mutation), gaps contain historical information suitable for phylogenetic analysis. The effect of gaps as a source of phylogenetic data is explored via sensitivity analysis and character congruence among different data partitions. Example data sets are provided to show that gaps contain important phylogenetic information not recovered by those methods that omit gaps in their calculations. However, gap cost schemes are arbitrary (although they must be explicit) and thus data exploration is a necessity of molecular analyses, while character congruence is necessary as an external criterion for hypothesis decision.
authors.affiliation: Department of Invertebrates, American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024, USA.
authors.forename: G
authors.initials: G
authors.lastname: Giribet
authors.forename: W C
authors.initials: WC
authors.lastname: Wheeler
mesh_terms: D000818:Animals; D001097:Arachnida / Q000145:classification / Q000235:genetics; D001483:Base Sequence; D004247:DNA / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics; D016013:Likelihood Functions; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012313:RNA / Q000737:chemistry / Q000235:genetics; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid
chemical_list: D004275:DNA, Ribosomal; D012313:RNA; D004247:DNA