Searching for the optimal data partitioning strategy in mitochondrial phylogenomics: A phylogeny of Acridoidea (Insecta: Orthoptera: Caelifera) as a case study

    Authors

    J. R. Leavitt; K. D. Hiatt; M. F. Whiting;H. J. Song

    Comments

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    Abbreviated Journal Title

    Signal Image Video Process.

    Keywords

    Phylogeny; Mitochondria; Phylogenomics; Data partition; Orthoptera; Caelifera; TRANSFER-RNA GENES; MULTIPLE SEQUENCE ALIGNMENT; COMPOSITIONAL; HETEROGENEITY; MAXIMUM-LIKELIHOOD; ARTHROPODA INSECTA; GENOME PHYLOGENY; HIGH-THROUGHPUT; BAYES FACTORS; DNA; REARRANGEMENTS; Biochemistry & Molecular Biology; Evolutionary Biology; Genetics &; Heredity

    Abstract

    One of the main challenges in analyzing multi-locus phylogenomic data is to find an optimal data partitioning strategy to account for variable evolutionary histories of different loci for any given dataset. Although a number of studies have addressed the issue of data partitioning in a Bayesian phylogenetic framework, such studies in a maximum likelihood framework are comparatively lacking. Furthermore, a rigorous statistical exploration of possible data partitioning schemes has not been applied to mitochondrial genome (mtgenome) data, which provide a complex, but manageable platform for addressing various challenges in analyzing phylogenomic data. In this study, we investigate the issue of data partitioning in the maximum likelihood framework in the context of the mitochondrial phylogenomics of an orthopteran superfamily Acridoidea (Orthoptera: Caelifera). The present study analyzes 34 terminals representing all 8 superfamilies within Caelifera, which includes newly sequenced partial or complete mtgenomes for 11 families. Using a new partition-selection method implemented in the software PartitionFinder, we compare a large number of data partitioning schemes in an attempt to identify the most effective method of analyzing the mtgenome data. We find that the best-fit partitioning scheme selected by PartitionFinder is superior to any a priori schemes commonly utilized in mitochondrial phylogenomics. We also show that over-partitioning is often detrimental to phylogenetic reconstruction. A comparative analysis of mtgenome structures finds that the tRNA gene rearrangement between cytochrome c oxidase subunit II and ATP synthase protein 8 does not occur in the most basal caeliferan lineage Tridactyloidea, suggesting that this gene rearrangement must have evolved at least in the common ancestor of Tetrigoidea and Acridomorpha. We find that mtgenome data contain sufficient phylogenetic information to broadly resolve the relationships across Acridomorpha and Acridoidea. (C) 2013 Elsevier Inc. All rights reserved.

    Journal Title

    Molecular Phylogenetics and Evolution

    Volume

    Mol. Phylogenet. Evol.

    Issue/Number

    2

    Publication Date

    1-1-2013

    Document Type

    Article

    Language

    English

    First Page

    494

    Last Page

    508

    WOS Identifier

    67

    ISSN

    1055-7903

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