Meeting Abstract

1.1  Jan. 4  Issues in DNA sequence alignment and its affect on topology: the evolution of Decapodiformes (Mollusca: Cephalopoda) LINDGREN, AR*; DALY, M; The Ohio State University; The Ohio State University lindgren.11@osu.edu

In molecular phylogenetics, mode of analysis is typically the primary reason for obtaining different topologies. However, sequence alignment is likely to be as important in determining topology as analytical method or optimality criterion. The impact of alignment method or parameter parameters is most significant for length-variable sequences. We investigate the effect of alignment strategy and parameters an analysis of length-variable 18S rDNA sequences from 41 oceanic squids (Decapodiformes), focusing particularly on the impact of including hypervariable regions on the resulting topology. Decapodiforms are an enigmatic group of mollusc whose evolutionary relationships remain unclear because standard molecular analyses have continued to produce poorly-supported or resolved trees, due potentially to elevated levels of molecular evolution. We find that alignment strategy (ClustalX versus POY) has a greater affect on topology than does parameter choice. However, some groups are highly robust to shifts in methodology, including cuttlefishes (Sepiidae), bobtail squids (Sepiolidae) and pygmy squids (Idiosepiidae). No alignment strategy supported the monophyly of Oegopsida, although the Myopsida did consistently form a monophyletic group. The hypervariable regions consistently provided more well-supported and well-resolved trees than the conserved regions alone, indicating the importance of including hypervariable data.