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Journal Molluscan Studies Advance Access published online on November 7, 2007
Journal of Molluscan Studies, doi:10.1093/mollus/eym038
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© The Author 2007. Published by Oxford University Press on behalf of The Malacological Society of London, all rights reserved

MOLECULAR PHYLOGENY OF COLEOID CEPHALOPODS (MOLLUSCA: CEPHALOPODA) INFERRED FROM THREE MITOCHONDRIAL AND SIX NUCLEAR LOCI: A COMPARISON OF ALIGNMENT, IMPLIED ALIGNMENT AND ANALYSIS METHODS

Jan Strugnell1,2, and Michele K. Nishiguchi3

1School of Biology and Biochemistry, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; 2 British Antarctic Survey, Natural Environmental Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK; and 3Department of Biology, New Mexico State University, Box 30001, MSC 3AF, Las Cruces, NM 88003-8001, USA

Correspondence: J. Strugnell; e-mail: jmst{at}bas.ac.uk


  Abstract

Recent molecular studies investigating higher-level phylogenetics of coleoid cephalopods (octopuses, squids and cuttlefishes) have produced conflicting results. A wide range of sequence alignment and analysis methods are used in cephalopod phylogenetic studies. The present study investigated the effect of commonly used alignment and analysis methods on higher-level cephalopod phylogenetics. Two sequence homology methods: (1) eye alignment, (2) implied alignment, and three analysis methods: (1) parsimony, (2) maximum likelihood, (3) Bayesian methodologies, were employed on the longest sequence dataset available for the coleoid cephalopods, comprising three mitochondrial and six nuclear loci. The data were also tested for base composition heterogeneity, which was detected in three genes and resolved using RY coding. The Octopoda, Argonautoidea, Oegopsida and Ommastrephidae are monophyletic in the phylogenies resulting from each of the alignment and analysis combinations. Furthermore, the Bathyteuthidae are the sister taxon of the Oegopsida in each case. However many relationships within the Coleoidea differed depending upon the alignment and analysis method used. This study demonstrates how differences in alignment and analysis methods commonly used in cephalopod phylogenetics can lead to different, but often highly supported, relationships.

(Received 15 December 2006; accepted 1 September 2007)


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