Testing heterogeneous base composition as potential cause for conflicting phylogenetic signal between mitochondrial and
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ORIGINAL ARTICLE
Testing heterogeneous base composition as potential cause for conflicting phylogenetic signal between mitochondrial and nuclear DNA in the land snail genus Theba Risso 1826 (Gastropoda: Stylommatophora: Helicoidea) Andre Böckers 1 & Carola Greve 2 & Rainer Hutterer 2 & Bernhard Misof 2 & Martin Haase 1
Received: 20 December 2015 / Accepted: 17 May 2016 # Gesellschaft für Biologische Systematik 2016
Abstract Several pitfalls can mislead phylogenetic analyses based on molecular data, including heterogeneous base composition. Previous work has revealed conflicting topologies in analyses of the land snail genus Theba Risso 1826 based on mitochondrial cytochrome oxidase subunit I (COI) and nuclear AFLP data, respectively. However, the third codon positions of COI had heterogeneous base composition, prompting the present investigation asking specifically if this was the cause for the mito-nuclear discordance. For a potentially better resolution of the mitochondrial data, we also sequenced a fragment of 16S rRNA, the loop sections of which proved to have inhomogeneous base frequencies as well. In partitioned phylogenetic analyses, we compared topologies generated from the original data to those based on alignments in which the heterogeneous partitions were RY-coded and to a LogDet transformed distance analysis. In addition, we tested whether conventional Bayesian analyses would reconstruct the original topology from inhomogeneous data simulated based on this original topology. All our analyses, regardless of whether we accounted for heterogeneous base frequencies or not, revealed very similar topologies, confirming previous findings. Thus, the phylogenetic signal of mtDNA in the land snail Electronic supplementary material The online version of this article (doi:10.1007/s13127-016-0288-0) contains supplementary material, which is available to authorized users. * Martin Haase [email protected] 1
Zoologisches Institut und Museum, Ernst-Moritz-Arndt—Universität Greifswald, Soldmannstraße 23, 17489 Greifswald, Germany
2
Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany
genus Theba appeared to be robust despite considerable inhomogeneity of base composition. Therefore, the discordance of mitochondrial and nuclear topologies is probably real and most likely a consequence of incomplete lineage sorting. Keywords Base composition . Conflicting phylogenetic signal . Heterogeneity . LogDet . Non-stationary evolution . RY-coding
Introduction Phylogenetic analyses based on molecular data can be misled by a variety of pitfalls such as model misspecification (Posada and Buckley 2004), long branch attraction (Felsenstein 1978), or heterogeneous base composition (Lockhart et al. 1994; Mooers and Holmes 2000; Jermiin et al. 2004) to name a few. Heterogeneous base composition may suggest relatedness of lineages which share similar nucleotide frequencies by chance and not by common descent. Compositional heterogeneity has been reported on different levels of phylogene
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