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dc.contributor.authorTimmermans, Martijn J.T.N.en
dc.contributor.authorBarton, Christopheren
dc.contributor.authorHaran, Julienen
dc.contributor.authorAhrens, Dirken
dc.contributor.authorCulverwell, C. Lornaen
dc.contributor.authorOllikainen, Alisonen
dc.contributor.authorDodsworth, Stevenen
dc.contributor.authorFoster, Peter G.en
dc.contributor.authorBocak, Ladislaven
dc.contributor.authorVogler, Alfried P.en
dc.date.accessioned2019-02-11T12:35:45Z
dc.date.available2019-02-11T12:35:45Z
dc.date.issued2015-12-08
dc.identifier.citationTimmermans M., Barton C., Haran J., Ahrens D., Culverwell C., Ollikainen A., Dodsworth S., Foster P., Bocak L., Vogler A. (2016) 'Family-level sampling of mitochondrial genomes in Coleoptera: Compositional heterogeneity and phylogenetics', Genome Biology and Evolution, 8 (1), pp.161-175.en
dc.identifier.issn1759-6653
dc.identifier.pmid26645679
dc.identifier.doi10.1093/gbe/evv241
dc.identifier.urihttp://hdl.handle.net/10547/623129
dc.description.abstractMitochondrial genomes are readily sequenced with recent technology and thus evolutionary lineages can be sampled more densely. This permits better phylogenetic estimates and assessment of potential biases resulting from heterogeneity in nucleotide composition and rate of change. We gathered 245 mitochondrial sequences for the Coleoptera representing all 4 suborders, 15 superfamilies of Polyphaga, and altogether 97 families, including 159 newly sequenced full or partial mitogenomes. Compositional heterogeneity greatly affected 3rd codon positions, and to a lesser extent the 1st and 2nd positions, even after RY coding. Heterogeneity also affected the encoded protein sequence, in particular in the nad2, nad4, nad5 and nad6 genes. Credible tree topologies were obtained with the nhPhyML (‘non-homogeneous’) algorithm implementing a model for branch-specific equilibrium frequencies. Likelihood searches using RAxML were improved by data partitioning by gene and codon position. Finally, the PhyloBayes software, which allows different substitution processes for amino acid replacement at various sites, produced a tree that best matched known higher-level taxa and defined basal relationships in Coleoptera. After rooting with Neuropterida outgroups, suborder relationships were resolved as (Polyphaga (Myxophaga (Archostemata + Adephaga))). The infraorder relationships in Polyphaga were (Scirtiformia (Elateriformia (Staphyliniformia + Scarabaeiformia) (Bostrichiformia (Cucujiformia)))). Polyphagan superfamilies were recovered as monophyla except Staphylinoidea (paraphyletic for Scarabaeiformia) and Cucujoidea, which can no longer be considered a valid taxon. The study shows that, whilst compositional heterogeneity is not universal, it cannot be eliminated for some mitochondrial genes, but dense taxon sampling and the use of appropriate Bayesian analyses can still produce robust phylogenetic trees.
dc.description.sponsorshipThis work was supported by a grant from the Leverhulme Trust to A.P.V., C.B., D.A., and L.B. (grant F/00969/H). M.T.J.N. was supported by an NERC Postdoctoral Fellowship (NE/I021578/1).en
dc.language.isoenen
dc.publisherOxford University Pressen
dc.relation.urlhttps://academic.oup.com/gbe/article/8/1/161/2574155en
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/*
dc.subjectmitogenomesen
dc.subjectrogue taxaen
dc.subjectlong-range PCRen
dc.subjectRY codingen
dc.subjectPhyloBayesen
dc.subjectmixture modelsen
dc.subjectC400 Geneticsen
dc.titleFamily-level sampling of mitochondrial genomes in Coleoptera: compositional heterogeneity and phylogeneticsen
dc.typeArticleen
dc.identifier.journalGenome Biology and Evolutionen
dc.identifier.pmcidPMC4758238
dc.date.updated2019-02-11T12:04:25Z
dc.description.noteOA article Creative Commons CC-BY-NC
html.description.abstractMitochondrial genomes are readily sequenced with recent technology and thus evolutionary lineages can be sampled more densely. This permits better phylogenetic estimates and assessment of potential biases resulting from heterogeneity in nucleotide composition and rate of change. We gathered 245 mitochondrial sequences for the Coleoptera representing all 4 suborders, 15 superfamilies of Polyphaga, and altogether 97 families, including 159 newly sequenced full or partial mitogenomes. Compositional heterogeneity greatly affected 3rd codon positions, and to a lesser extent the 1st and 2nd positions, even after RY coding. Heterogeneity also affected the encoded protein sequence, in particular in the nad2, nad4, nad5 and nad6 genes. Credible tree topologies were obtained with the nhPhyML (‘non-homogeneous’) algorithm implementing a model for branch-specific equilibrium frequencies. Likelihood searches using RAxML were improved by data partitioning by gene and codon position. Finally, the PhyloBayes software, which allows different substitution processes for amino acid replacement at various sites, produced a tree that best matched known higher-level taxa and defined basal relationships in Coleoptera. After rooting with Neuropterida outgroups, suborder relationships were resolved as (Polyphaga (Myxophaga (Archostemata + Adephaga))). The infraorder relationships in Polyphaga were (Scirtiformia (Elateriformia (Staphyliniformia + Scarabaeiformia) (Bostrichiformia (Cucujiformia)))). Polyphagan superfamilies were recovered as monophyla except Staphylinoidea (paraphyletic for Scarabaeiformia) and Cucujoidea, which can no longer be considered a valid taxon. The study shows that, whilst compositional heterogeneity is not universal, it cannot be eliminated for some mitochondrial genes, but dense taxon sampling and the use of appropriate Bayesian analyses can still produce robust phylogenetic trees.


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