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      Mitochondrial phylogenomics of Hemiptera reveals adaptive innovations driving the diversification of true bugs

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          Abstract

          Hemiptera, the largest non-holometabolous order of insects, represents approximately 7% of metazoan diversity. With extraordinary life histories and highly specialized morphological adaptations, hemipterans have exploited diverse habitats and food sources through approximately 300 Myr of evolution. To elucidate the phylogeny and evolutionary history of Hemiptera, we carried out the most comprehensive mitogenomics analysis on the richest taxon sampling to date covering all the suborders and infraorders, including 34 newly sequenced and 94 published mitogenomes. With optimized branch length and sequence heterogeneity, Bayesian analyses using a site-heterogeneous mixture model resolved the higher-level hemipteran phylogeny as (Sternorrhyncha, (Auchenorrhyncha, (Coleorrhyncha, Heteroptera))). Ancestral character state reconstruction and divergence time estimation suggest that the success of true bugs (Heteroptera) is probably due to angiosperm coevolution, but key adaptive innovations (e.g. prognathous mouthpart, predatory behaviour, and haemelytron) facilitated multiple independent shifts among diverse feeding habits and multiple independent colonizations of aquatic habitats.

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          Most cited references41

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          TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations

          We present TranslatorX, a web server designed to align protein-coding nucleotide sequences based on their corresponding amino acid translations. Many comparisons between biological sequences (nucleic acids and proteins) involve the construction of multiple alignments. Alignments represent a statement regarding the homology between individual nucleotides or amino acids within homologous genes. As protein-coding DNA sequences evolve as triplets of nucleotides (codons) and it is known that sequence similarity degrades more rapidly at the DNA than at the amino acid level, alignments are generally more accurate when based on amino acids than on their corresponding nucleotides. TranslatorX novelties include: (i) use of all documented genetic codes and the possibility of assigning different genetic codes for each sequence; (ii) a battery of different multiple alignment programs; (iii) translation of ambiguous codons when possible; (iv) an innovative criterion to clean nucleotide alignments with GBlocks based on protein information; and (v) a rich output, including Jalview-powered graphical visualization of the alignments, codon-based alignments coloured according to the corresponding amino acids, measures of compositional bias and first, second and third codon position specific alignments. The TranslatorX server is freely available at http://translatorx.co.uk.
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            A comprehensive phylogeny of beetles reveals the evolutionary origins of a superradiation.

            Beetles represent almost one-fourth of all described species, and knowledge about their relationships and evolution adds to our understanding of biodiversity. We performed a comprehensive phylogenetic analysis of Coleoptera inferred from three genes and nearly 1900 species, representing more than 80% of the world's recognized beetle families. We defined basal relationships in the Polyphaga supergroup, which contains over 300,000 species, and established five families as the earliest branching lineages. By dating the phylogeny, we found that the success of beetles is explained neither by exceptional net diversification rates nor by a predominant role of herbivory and the Cretaceous rise of angiosperms. Instead, the pre-Cretaceous origin of more than 100 present-day lineages suggests that beetle species richness is due to high survival of lineages and sustained diversification in a variety of niches.
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              A general comparison of relaxed molecular clock models.

              Several models have been proposed to relax the molecular clock in order to estimate divergence times. However, it is unclear which model has the best fit to real data and should therefore be used to perform molecular dating. In particular, we do not know whether rate autocorrelation should be considered or which prior on divergence times should be used. In this work, we propose a general bench mark of alternative relaxed clock models. We have reimplemented most of the already existing models, including the popular lognormal model, as well as various prior choices for divergence times (birth-death, Dirichlet, uniform), in a common Bayesian statistical framework. We also propose a new autocorrelated model, called the "CIR" process, with well-defined stationary properties. We assess the relative fitness of these models and priors, when applied to 3 different protein data sets from eukaryotes, vertebrates, and mammals, by computing Bayes factors using a numerical method called thermodynamic integration. We find that the 2 autocorrelated models, CIR and lognormal, have a similar fit and clearly outperform uncorrelated models on all 3 data sets. In contrast, the optimal choice for the divergence time prior is more dependent on the data investigated. Altogether, our results provide useful guidelines for model choice in the field of molecular dating while opening the way to more extensive model comparisons.
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                Author and article information

                Journal
                Proc Biol Sci
                Proc. Biol. Sci
                RSPB
                royprsb
                Proceedings of the Royal Society B: Biological Sciences
                The Royal Society
                0962-8452
                1471-2954
                13 September 2017
                6 September 2017
                6 September 2017
                : 284
                : 1862
                : 20171223
                Affiliations
                [1 ]Key Laboratory of Pest Monitoring and Green Management, Ministry of Agriculture, Department of Entomology, China Agricultural University , Beijing 100193, People's Republic of China
                [2 ]Department of Entomology, University of Kentucky , Lexington, KY 40546, USA
                [3 ]Naturhistorisches Museum , Augustinergasse 2, 4001 Basel, Switzerland
                [4 ]Markey Cancer Center, University of Kentucky , Lexington, KY 40536, USA
                Author notes

                Electronic supplementary material is available online at https://dx.doi.org/10.6084/m9.figshare.c.3849793.

                Author information
                http://orcid.org/0000-0002-2385-8224
                Article
                rspb20171223
                10.1098/rspb.2017.1223
                5597834
                28878063
                a4b331f3-58a5-4c5d-b4d8-50f231be8212
                © 2017 The Authors.

                Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.

                History
                : 31 May 2017
                : 25 July 2017
                Funding
                Funded by: National Basic Research Program of China;
                Award ID: 2013CB127600
                Funded by: Chinese Universities Scientific Fund, http://dx.doi.org/10.13039/501100005236;
                Award ID: 2017QC066
                Award ID: 2017QC100
                Award ID: 2017ZB002
                Funded by: National Natural Science Foundation of China, http://dx.doi.org/10.13039/501100001809;
                Award ID: 31372229
                Award ID: 31401991
                Award ID: 31420103902
                Categories
                1001
                70
                183
                Evolution
                Research Article
                Custom metadata
                September 13, 2017

                Life sciences
                hemiptera,phylogeny,evolutionary history,ancestral character state reconstruction,mitochondrial genome

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