Abstract
Mitochondrial (mt) genome data have been proven to be informative for animal phylogenetic studies but may also suffer from systematic errors, due to the effects of accelerated substitution rate and compositional heterogeneity. We analyzed the mt genomes of 25 insect species from the four paraneopteran orders, aiming to better understand how accelerated substitution rate and compositional heterogeneity affect the inferences of the higher-level phylogeny of this diverse group of hemimetabolous insects. We found substantial heterogeneity in base composition and contrasting rates in nucleotide substitution among these paraneopteran insects, which complicate the inference of higher-level phylogeny. The phylogenies inferred with concatenated sequences of mt genes using maximum likelihood and Bayesian methods and homogeneous models failed to recover Psocodea and Hemiptera as monophyletic groups but grouped, instead, the taxa that had accelerated substitution rates together, including Sternorrhyncha (a suborder of Hemiptera), Thysanoptera, Phthiraptera and Liposcelididae (a family of Psocoptera). Bayesian inference with nucleotide sequences and heterogeneous models (CAT and CAT + GTR), however, recovered Psocodea, Thysanoptera and Hemiptera each as a monophyletic group. Within Psocodea, Liposcelididae is more closely related to Phthiraptera than to other species of Psocoptera. Furthermore, Thysanoptera was recovered as the sister group to Hemiptera.
Highlights
Mitochondrial genome data have been proven to be informative for animal phylogenetic studies but may suffer from systematic errors, due to the effects of accelerated substitution rate and compositional heterogeneity
We included a range of Paraneoptera species much broader than in previous studies and tested: 1) effects of compositional heterogeneity and accelerated substitution rates of mt genome sequences to phylogenetic reconstruction; 2) phylogenetic signals in nucleotide and amino acid datasets; and 3) whether there was a significant improvement in fit with the use of heterogeneous methods over homogeneous models in recovering the higher-level phylogeny of Paraneoptera with mt genome sequences
Phylogenies inferred with concatenated sequences of mt genes, failed to recover Psocodea as a monophyletic group but grouped Phthiraptera with Thysanoptera[13], and Sternorrhyncha with Thysanoptera, Liposcelididae and Phthiraptera in our maximum likelihood (ML) and Bayesian inference (BI) analyses with homogeneous models based on empirical frequencies of amino acid or nucleotide substitutions, like MtArt or GTR-based
Summary
Mitochondrial (mt) genome data have been proven to be informative for animal phylogenetic studies but may suffer from systematic errors, due to the effects of accelerated substitution rate and compositional heterogeneity. Insect mt genomes tend to have high percentage of A 1 T content, lineage-specific compositional heterogeneity and accelerated sequence evolution in some groups such as Thysanoptera, Psocodea, Sternorrhyncha (Hemiptera), Strepsiptera, and Hymenoptera[3,4,10,11,12,13,14] These potential biases limit the applicability of mt genome sequences in the reconstruction of higher-level phylogeny of insects, resulting in incongruence with morphological and nuclear data[3,13,15]. We included a range of Paraneoptera species much broader than in previous studies and tested: 1) effects of compositional heterogeneity and accelerated substitution rates of mt genome sequences to phylogenetic reconstruction; 2) phylogenetic signals in nucleotide and amino acid datasets; and 3) whether there was a significant improvement in fit with the use of heterogeneous methods over homogeneous models in recovering the higher-level phylogeny of Paraneoptera with mt genome sequences
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