Molecular phylogeny of coleoid cephalopods (Mollusca: Cephalopoda) inferred from three mitochondrial and six nuclear loci: a comparison of alignment, implied alignment and analysis methods

Strugnell, Jan; Nishiguchi, Michelle K.. 2007 Molecular phylogeny of coleoid cephalopods (Mollusca: Cephalopoda) inferred from three mitochondrial and six nuclear loci: a comparison of alignment, implied alignment and analysis methods. Journal of Molluscan Studies, 73 (4). 399-410. 10.1093/mollus/eym038

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Abstract/Summary

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.

Item Type:	Publication - Article
Digital Object Identifier (DOI):	10.1093/mollus/eym038
Programmes:	BAS Programmes > Antarctic Funding Initiative Projects
ISSN:	0260-1230
NORA Subject Terms:	Marine Sciences Zoology Biology and Microbiology
Date made live:	25 Oct 2011 08:41 +0 (UTC)
URI:	https://nora.nerc.ac.uk/id/eprint/11969

Item Type:

Publication - Article

Digital Object Identifier (DOI):

10.1093/mollus/eym038

Programmes:

BAS Programmes > Antarctic Funding Initiative Projects

ISSN:

0260-1230

NORA Subject Terms:

Marine Sciences
Zoology
Biology and Microbiology

Date made live:

25 Oct 2011 08:41 +0 (UTC)