Title
Searching for the optimal data partitioning strategy in mitochondrial phylogenomics: A phylogeny of Acridoidea (Insecta: Orthoptera: Caelifera) as a case study
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
Recommended Citation
"Searching for the optimal data partitioning strategy in mitochondrial phylogenomics: A phylogeny of Acridoidea (Insecta: Orthoptera: Caelifera) as a case study" (2013). Faculty Bibliography 2010s. 4270.
https://stars.library.ucf.edu/facultybib2010/4270
Comments
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