Showing papers by "Michael F. Whiting published in 2010"

When phylogenetic assumptions are violated: base compositional heterogeneity and among-site rate variation in beetle mitochondrial phylogenomics

Abstract: The ability to generate large molecular datasets for phylogenetic studies benefits biologists, but such data expansion introduces numerous analytical problems. A typical molecular phylogenetic study implicitly assumes that sequences evolve under stationary, reversible and homogeneous conditions, but this assumption is often violated in real datasets. When an analysis of large molecular datasets results in unexpected relationships, it often reflects violation of phylogenetic assumptions, rather than a correct phylogeny. Molecular evolutionary phenomena such as base compositional heterogeneity and among-site rate variation are known to affect phylogenetic inference, resulting in incorrect phylogenetic relationships. The ability of methods to overcome such bias has not been measured on real and complex datasets. We investigated how base compositional heterogeneity and among-site rate variation affect phylogenetic inference in the context of a mitochondrial genome phylogeny of the insect order Coleoptera. We show statistically that our dataset is affected by base compositional heterogeneity regardless of how the data are partitioned or recoded. Among-site rate variation is shown by comparing topologies generated using models of evolution with and without a rate variation parameter in a Bayesian framework. When compared for their effectiveness in dealing with systematic bias, standard phylogenetic methods tend to perform poorly, and parsimony without any data transformation performs worst. Two methods designed specifically to overcome systematic bias, LogDet and a Bayesian method implementing variable composition vectors, can overcome some level of base compositional heterogeneity, but are still affected by among-site rate variation. A large degree of variation in both noise and phylogenetic signal among all three codon positions is observed. We caution and argue that more data exploration is imperative, especially when many genes are included in an analysis.

Assessing the effects of primer specificity on eliminating numt coamplification in DNA barcoding: a case study from Orthoptera (Arthropoda: Insecta).

Abstract: DNA barcoding is a diagnostic method of species identification based on sequencing a short mitochondrial DNA fragment of cytochrome oxidase I (COI), but its ability to correctly diagnose species is limited by the presence of nuclear mitochondrial pseudogenes (numts). Numts can be coamplified with the mitochondrial orthologue when using universal primers, which can lead to incorrect species identification and an overestimation of the number of species. Some researchers have proposed that using more specific primers may help eliminate numt coamplification, but the efficacy of this method has not been thoroughly tested. In this study, we investigate the taxonomic distribution of numts in 11 lineages within the insect order Orthoptera, by analysing cloned COI sequences and further test the effects of primer specificity on eliminating numt coamplification in four lineages. We find that numts are coamplified in all 11 taxa using universal (barcoding) primers, which suggests that numts may be widespread in other taxonomic groups as well. Increased primer specificity is only effective at reducing numt coamplification in some species tested, and only eliminates it in one species tested. Furthermore, we find that a number of numts do not have stop codons or indels, making it difficult to distinguish them from mitochondrial orthologues, thus putting the efficacy of barcoding quality control measures under question. Our findings suggest that numt coamplification is a serious problem for DNA barcoding and more quality control measures should be implemented to identify and eliminate numts prior to using mitochondrial barcodes for species diagnoses.

Mitochondrial genomics in Orthoptera using MOSAS.

Abstract: We present complete mitochondrial genomes (mitogenomes) for three orthopterans (Xyleus modestus, Physemacris variolosa, and Ellipes minuta) and describe MOSAS (manipulation, organization, storage, and analysis of sequences), software we developed to facilitate annotation and analysis. We analyze the base composition, start and stop codons, non-coding regions, and gene order among these and 18 other orthopteran mitogenomes from GenBank and reconstruct a phylogeny of Orthoptera. We propose a tetranucleotide start codon for cox1, and hypothesize that the tRNAAsp–tRNALys rearrangement is a synapomorphy for Acridomorpha, but not Caelifera. We further describe MOSAS, user-friendly software we used for this analysis. MOSAS streamlines sequence data storage, organization, annotation, and alignment, and provides convenient search tools for dataset construction and a robust annotation engine particularly suited to annotating mitogenomes (available at http://mosas.byu.edu).

One hundred years of instability in ensiferan relationships

Abstract: Although Ensifera is a major insect model group, its phylogenetic relationships have been understudied so far. Few phylogenetic hypotheses have been proposed, either with morphological or molecular data. The largest dataset ever used for phylogeny reconstruction on this group is molecular (16S rRNA, 18S rRNA and 28S rRNA sequences for 51 ensiferan species), which has been used twice with different resultant topologies. However, only one of these hypotheses has been adopted commonly as a reference classification. Here we re-analyse this molecular dataset with different methods and parameters to test the robustness and the stability of the adopted phylogeny. Our study reveals the instability of phylogenetic relationships derived from this dataset, especially for the deepest nodes of the group, and suggests some guidelines for future studies. The comparison between the different classifications proposed in the past 70 years for Ensifera and our results allows the identification of potential monophyletic clades (katydids, mole crickets, scaly crickets + Malgasia, true crickets, leaf roller crickets, cave crickets) and the remaining unresolved clades (wetas, Jerusalem crickets and most of the highest rank clades) in Ensifera phylogeny.

Phylogenetic analysis of the minute brown scavenger beetles (Coleoptera: Latridiidae), and recognition of a new beetle family, Akalyptoischiidae fam.n. (Coleoptera: Cucujoidea)

Abstract: We infer the first phylogenetic hypothesis for Latridiidae Erichson (Coleoptera: Cucujoidea). Portions of seven genes (18S ribosomal DNA, 28S ribosomal DNA, 12S ribosomal DNA, 16S ribosomal DNA, cytochrome c oxidase I and II and histone III) were analysed. Twenty-seven latridiid species were included, representing both subfamilies and more than half of the currently recognized genera. Eight outgroup taxa from other families of Cucujoidea were included. Parsimony and partitioned Bayesian analyses were performed on the combined dataset. In both phylogenetic analyses, the enigmatic Akalyptoischion Andrews (Latridiinae) was recovered outside of Latridiidae. The subfamilies Corticariinae and Latridiinae (without Akalyptoischion) were each recovered as monophyletic in both analyses. A new family, Akalyptoischiidae fam.n. is erected based on the results of the phylogenetic study and further support from adult morphology, key features of which are illustrated.

Polyphyly of the Pikeminnows (Teleostei: Cyprinidae) Inferred Using Mitochondrial DNA Sequences

Abstract: The phylogenetic relationships of the Colorado pikeminnow Ptychocheilus lucius, northern pikeminnow P. oregonensis, Sacramento pikeminnow P. grandis, Umpqua pikeminnow P. umpquae, and hardhead Mylopharodon conocephalus were examined by using molecular data to investigate monophyly of the genus Ptychocheilus. Phylogenies generated using DNA sequence data from the cytochrome b and 16S ribosomal DNA genes of the mitochondrial genome reveal that Ptychocheilus is a polyphyletic genus and suggest that the taxonomy of the group is in need of further revision. These data yield insights into the evolution of the pikeminnows and help place the significant evolutionary events in context with the geological history of parts of western North America (e.g., ancient drainage connections that may have allowed for dispersal, followed by speciation once those connections were broken).

Identification of a developmentally and hormonally regulated Delta-Class glutathione S-transferase in rice moth Corcyra cephalonica.

Abstract: Glutathione S-transferases (GSTs) are a large family of multifunctional enzymes, known for their role in cellular detoxification. Here we report a cytosolic GST with optimal activity at alkaline pH (8.3) from the visceral fat body of late-last instar (LLI) larvae of a lepidopteran insect rice moth Corcyra cephalonica. All previously known GSTs are active between pH 6.0 to 6.5. Purification and characterization revealed the Corcyra cephalonica GST (CcGST) as a 23-kDa protein. HPLC and 2D analysis showed a single isoform of the protein in the LLI visceral fat body. Degenerate primer based method identified a 701-nucleotide cDNA and the longest open reading frame contained 216 amino acids. Multiple sequence and structural alignment showed close similarity with delta-class GSTs. CcGST is present mainly in the fat body with highest activity at the late-last instar larval stage. Juvenile hormone (JH) negatively inhibits the CcGST activity both ex vivo and in vivo. We speculate that high expression and activity of CcGST in the fat body of the late-last instar larvae, when endogenous JH titer is low may have role in the insect post-embryonic development unrelated to their previously known function.