The Molecular Evolutionary Dynamics of Oxidative Phosphorylation (OXPHOS) Genes in Hymenoptera Yiyuan Li1,2, Rui Zhang3, Shanlin Liu4, Alexander Donath5, Ralph S
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Li et al. BMC Evolutionary Biology (2017) 17:269 DOI 10.1186/s12862-017-1111-z RESEARCH ARTICLE Open Access The molecular evolutionary dynamics of oxidative phosphorylation (OXPHOS) genes in Hymenoptera Yiyuan Li1,2, Rui Zhang3, Shanlin Liu4, Alexander Donath5, Ralph S. Peters6, Jessica Ware7, Bernhard Misof8, Oliver Niehuis9, Michael E. Pfrender1,2 and Xin Zhou10,11* Abstract Background: The primary energy-producing pathway in eukaryotic cells, the oxidative phosphorylation (OXPHOS) system, comprises proteins encoded by both mitochondrial and nuclear genes. To maintain the function of the OXPHOS system, the pattern of substitutions in mitochondrial and nuclear genes may not be completely independent. It has been suggested that slightly deleterious substitutions in mitochondrial genes are compensated by substitutions in the interacting nuclear genes due to positive selection. Among the four largest insect orders, Coleoptera (beetles), Hymenoptera (sawflies, wasps, ants, and bees), Diptera (midges, mosquitoes, and flies) and Lepidoptera (moths and butterflies), the mitochondrial genes of Hymenoptera exhibit an exceptionally high amino acid substitution rate while the evolution of nuclear OXPHOS genes is largely unknown. Therefore, Hymenoptera is an excellent model group for testing the hypothesis of positive selection driving the substitution rate of nuclear OXPHOS genes. In this study, we report the evolutionary rate of OXPHOS genes in Hymenoptera and test for evidence of positive selection in nuclear OXPHOS genes of Hymenoptera. Results: Our analyses revealed that the amino acid substitution rate of mitochondrial and nuclear OXPHOS genes in Hymenoptera is higher than that in other studied insect orders. In contrast, the amino acid substitution rate of non-OXPHOS genes in Hymenoptera is lower than the rate in other insect orders. Overall, we found the dN/dS ratio of the nuclear OXPHOS genes to be higher in Hymenoptera than in other insect orders. However, nuclear OXPHOS genes with high dN/dS ratio did not always exhibit a high amino acid substitution rate. Using branch-site and site model tests, we identified various codon sites that evolved under positive selection in nuclear OXPHOS genes. Conclusions: Our results showed that nuclear OXPHOS genes in Hymenoptera are evolving faster than the genes in other three insect orders. The branch test suggested that while some nuclear OXPHOS genes in Hymenoptera show a signature of positive selection, the pattern is not consistent across all nuclear OXPHOS genes. As only few codon sites were under positive selection, we suggested that positive selection might not be the only factor contributing to the rapid evolution of nuclear OXPHOS genes in Hymenoptera. Keywords: Molecular evolution, Positive selection, Mitochondrial-nuclear interaction, Insects * Correspondence: [email protected] Michael E. Pfrender and Xin Zhou share the co-senior authorship. 10Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing 100193, China 11Department of Entomology, China Agricultural University, Beijing 100193, China Full list of author information is available at the end of the article © The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Li et al. BMC Evolutionary Biology (2017) 17:269 Page 2 of 12 Background amino acid substitution rates in mitochondrial genes also Understanding the patterns and rates of molecular exhibit a high amino acid substitution rate and an elevated evolution requires consideration of the role of muta- dN/dS ratio (i.e., the ratio of the number of non- tion, drift, and selection acting on individual genes. In synonymous nucleotide substitutions per non-synonymous many cases, the effects of these forces are compli- site to the number of synonymous nucleotide substitutions cated due to physical and/or functional interaction of per synonymous site) in nuclear OXPHOS genes. This ob- the affected genes. A classic system of such interact- servation of an elevated substitution rate in nuclear ing genes represents the OXPHOS pathway [1–3]. OXPHOS genes is consistent with the idea of positive selec- The OXPHOS pathway is the primary ATP source in tion driving compensatory mutations in nuclear OXPHOS eukaryotic cells, generating 70–80% of the ATP de- genes in response to the elevated substitution rate in mito- mand of cells [4–6]. The OXPHOS pathway com- chondrial OXPHOS genes [2, 19, 20]. Beneficial mutations prises five enzyme complexes (complexes I-V), which in nuclear OXPHOS genes are likely to be fixed as they transport electrons to produce ATP. Complexes I, III, maintain the efficiency of the OXPHOS process. Consistent IV, and V are composed of polypeptides encoded by with the positive selection hypothesis, substitutions in nu- both the mitochondrial and the nuclear genes clear OXPHOS genes are over-represented in residues with (Table 1) [2, 7, 8]. Mitochondrial and nuclear critical functional importance, including mitochondrial- OXPHOS genes work together to maintain the ATP nuclear contacting residues [19], and regions in the nuclear production in the cell. Incompatible mitochondrial genome that are linked to hybrid breakdown [9]. and nuclear genes can reduce the efficiency of cellular While these previous studies have shown a pattern in ATP production and contribute to increased oxidative the rates of substitution in nuclear OXPHOS genes that stress, leading to a variety of physiological issues, in- is consistent with the positive selection hypothesis, and cluding developmental abnormalities [3, 9] and re- in some cases have identified sites under positive selec- duced hybrid fitness [10, 11]. Interestingly, the tion in nuclear OXPHOS genes, it remains unclear to mitochondrial genome of animals often show a 5–20 what extent the overall elevated amino acid substitution times higher substitution rate than the nuclear gen- rate of nuclear OXPHOS genes can be explained by ome [12–14] in large part due to fundamental differ- positive selection [19]. The signal of positive selection ences between mitochondrial and nuclear genomes in on nuclear OXPHOS genes is usually weak, with overall the mode of inheritance, ploidy level, effective popula- dN/dS ratios less than one [6] and with a small number tion size, and recombination [15–17]. A significant of sites under positive selection [19]. This weak signa- component of the elevated substitution rate in the ture of positive selection fuels an alternative hypothesis mitochondrial genome is the lack of recombination, that relaxed functional constraint on nuclear OXPHOS which makes it prone to the accumulation of slightly genes may lead to an elevated amino acid substitution deleterious mutations [14, 15, 18]. As a result of the rate and an elevated dN/dS ratio in lineages with ele- rapid rate of molecular evolution and accumulation of vated rates of mitochondrial evolution [6, 22]. Given the deleterious mutations in the mitochondrial genome, it has functional importance of the OXPHOS system, these been suggested that that nuclear OXPHOS genes should genes are likely to be under strong purifying selection, be exposed to positive selection for compensatory substi- resulting in low dN/dS ratios. Relaxed selection would tutions that maintain the functional properties of the partially release genes from this constraint and the interacting genes in the OXPHOS system. [2, 6, 19–21]. resulting elevation in dN/dS ratios that would be hard to A number of studies have examined the patterns of distinguish from an elevation due to positive selection. molecular evolution in the OXPHOSsystem(e.g.,[19,20]). To dissect the role of positive selection, we focus on an The general pattern that emerges is that species with a high order of insects, Hymenoptera, with notoriously high Table 1 Number of OXPHOS genes found in 1KITE data for each complex in this study Complex Function Number of Nuclear Number of Nuclear OXPHOS Number of Mitochondrial Number of Mitochondrial OXPHOS Genes Genes Used in This Study Genes Genes Used in This Study I NADH:ubiquinone 34 16 7 7 oxidoreductase II Succinate dehydrogenase 4 0 0 0 III Ubiquinol-cytochrome c 91 1 1 reductase IV Cytochrome c oxidase 8 1 3 3 V ATP synthase 13 5 2 2 Li et al. BMC Evolutionary Biology (2017) 17:269 Page 3 of 12 mitochondrial substitution rates [23]. In this lineage, the Table 2 Insect species used in this study effect of positive selection driving nuclear OXPHOS Order Species genes should be exaggerated compared to other insects. Hemiptera Acyrthosiphon pisum The rate of molecular evolution varies substantially Hymenoptera Acromyrmex echinatior across insect orders [24, 25]. Among the four largest in- Hymenoptera Apis mellifera sect orders (Coleoptera, Diptera, Lepidoptera and Hy- menoptera), the mitochondrial genes of Hymenoptera Hymenoptera Bombus terrestris show a significantly elevated amino acid substitution rate Hymenoptera Chrysis viridula compared to the rate of genes of other insect orders