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The impact of length‐variable data and alignment criterion on the phylogeny of Decapodiformes (Mollusca: Cephalopoda)
Author(s) -
Lindgren Annie R.,
Daly Marymegan
Publication year - 2007
Publication title -
cladistics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.323
H-Index - 92
eISSN - 1096-0031
pISSN - 0748-3007
DOI - 10.1111/j.1096-0031.2007.00160.x
Subject(s) - monophyly , phylogenetic tree , biology , phylogenetics , evolutionary biology , variable (mathematics) , topology (electrical circuits) , zoology , clade , mathematics , genetics , combinatorics , gene , mathematical analysis
In molecular phylogenetics, mode of analysis is typically the primary reason cited for obtaining different topologies. However, sequence alignment is as important in determining topology as analytical method or optimality criterion, particularly for length‐variable sequences. We investigate the effect of alignment strategy and parameters in an analysis of length‐variable 18S rDNA sequences from 41 oceanic squids (Decapodiformes), focusing particularly on the impact of including variable regions on the resulting topology. Decapodiformes are an enigmatic group of molluscs whose evolutionary relationships remain unclear because standard molecular analyses have continued to produce poorly supported or poorly resolved trees, possibly due to elevated levels of molecular evolution. We find that alignment strategy (Clustal X versus POY) has a greater affect on topology than does parameter choice. Some groups were robust to shifts in methodology, including cuttlefishes (Sepiidae), bobtail squids (Sepiolidae) and pygmy squids (Idiosepiidae). No alignment strategy supported the monophyly of Oegopsida, although Myopsida did consistently form a monophyletic group. The variable regions consistently provided more well‐supported and well‐resolved trees than the conserved regions alone, indicating the phylogenetic importance of including length‐variable data. © The Willi Hennig Society 2007.