Mitochondrial phylogenomics of the Hymenoptera

Tang, Pu; Zhu, Jiachen; Zheng, Bo-yin; Wei, Shu‐Jun; Sharkey, Michael J.; Chen, Xue-Xin; Vogler, Alfried P.

doi:10.1016/j.ympev.2018.10.040

Cited by 103 publications

(93 citation statements)

References 62 publications

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“…The overall base composition of the mitogenome was estimated to be A 42.9%, T 43.3%, C 7.6%, and G 6.2%, with a high AT content of 86.2%. Compared with the ancestral insect mitochondrial genome, the mitogenome of T. acutissimae exhibits dramatic mitochondrial gene rearrangement, which is usually found in Cynipoidea species (Mao et al 2015;Tang et al 2019). Most PCGs of T. acutissimae had the conventional start codons ATN (five ATG, five ATT, and two ATA), with the exception of nad4L (TTG).…”

Section: Cynipidae; Mitochondrial Genome; Trichagalma Acutissimae; Phmentioning

confidence: 99%

Mitochondrial genome of Trichagalma acutissimae (Hymenoptera: Cynipoidea: Cynipidae) and phylogenetic analysis

Xue

Zhang

Gao

et al. 2020

Mitochondrial DNA Part B

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Trichagalma acutissimae (Monzen) (Hymenoptera: Cynipidae) is a major pest of Quercus variabilis Blume in the Taihang Mountains in China. In this study, we sequenced and analyzed the mitochondrial genome (mitogenome) of T. acutissimae . This mitogenome was 16,078 bp long and encoded 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and 2 ribosomal RNA unit genes (rRNAs). The whole mitogenome exhibited heavy AT nucleotide bias (86.2%). Except for nad4L that started with TTG, all other PCGs started with the standard ATN codon. All 13 PCGs terminate with the stop codon TAA. Phylogenetic analysis showed that T. acutissimae got together with Synergus sp. with high support value, indicating the close relationship of these two genus. All five Cynipoidea species constituted a major clade and formed a sister group to Proctotrupoidea and Chalcidoidea.

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Section: Cynipidae; Mitochondrial Genome; Trichagalma Acutissimae; Phmentioning

confidence: 99%

Mitochondrial genome of Trichagalma acutissimae (Hymenoptera: Cynipoidea: Cynipidae) and phylogenetic analysis

Xue

Zhang

Gao

et al. 2020

Mitochondrial DNA Part B

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“…One other factor that might influence rate of mitochondrial introgression is its mutation rate, lower rates making introgression more probable than higher rates, latter of which should more likely lead to compensatory co-evolution and mitonuclear incompatibilities (see Table 3 in Sloan et al, 2017). As mitochondrial genomes of basal hymenopterans do evolve significantly slower compared to Apocrita (particularly Xyeloidea, Pamphilioidea, and Tenthredionoidea; Niu et al, 2019;Tang et al, 2019), the combination of haplodiploidy and slow rate of mitochondrial evolution might better explain widespread mitonuclear discordance in some (many?) species rich groups of sawflies rather than just haplodiploidy.…”

Section: Causes Of Mitonuclear Discordancementioning

confidence: 99%

“…Sloan et al (2017) suggested that lower mutation rates promote adaptive mitochondrial introgression while higher rates lead more likely to compensatory co-evolution and mitonuclear incompatibilities. As mitochondrial genomes of Apocrita (the bulk of hymenopteran species) evolve faster than those of basal hymenopterans (Kaltenpoth et al, 2012;Ma et al, 2019;Niu et al, 2019;Tang et al, 2019), mitochondrial introgression might be less common in Apocrita compared to sawflies. Within the sawflies, Xyeloidea, Pamphilioidea, and Tenthredinoidea have the slowest evolving mtDNA, while Cephoidea, Orussoidea, Siricoidea, and possibly Anaxyleoidea (which are more closely related to Apocrita), have intermediate or fast evolutionary rate (Ma et al, 2019;Niu et al, 2019;Tang et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

“…As mitochondrial genomes of Apocrita (the bulk of hymenopteran species) evolve faster than those of basal hymenopterans (Kaltenpoth et al, 2012;Ma et al, 2019;Niu et al, 2019;Tang et al, 2019), mitochondrial introgression might be less common in Apocrita compared to sawflies. Within the sawflies, Xyeloidea, Pamphilioidea, and Tenthredinoidea have the slowest evolving mtDNA, while Cephoidea, Orussoidea, Siricoidea, and possibly Anaxyleoidea (which are more closely related to Apocrita), have intermediate or fast evolutionary rate (Ma et al, 2019;Niu et al, 2019;Tang et al, 2019). While we are not aware of cases of large-scale discordance between mitochondrial barcodes and species boundaries in Apocrita, there are several such cases among sawflies, particularly among Tenthredinoidea (Linnen and Farrell, 2007;Schmidt et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

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Detection of cross-contamination and strong mitonuclear discordance in two species groups of sawfly genus Empria (Hymenoptera, Tenthredinidae)

Prous

Lee

Mutanen

2019

Preprint

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In several sawfly taxa strong mitonuclear discordance has been observed, with nuclear genes supporting species assignments based on morphology, whereas the barcode region of the mitochondrial COI gene suggesting different relationships. As previous studies were based on only few nuclear genes, the causes and the degree of mitonuclear discordance remain ambiguous. Here, we obtain genomic-scale ddRAD data together with Sanger sequencing of mitochondrial COI and two to three nuclear protein coding genes to investigate species limits and mitonuclear discordance in two closely related species groups within the sawfly genus Empria. As found previously based on nuclear ITS and mitochondrial COI sequences, species are in most cases supported as monophyletic based on previous and new nuclear data reported here, but not based on mitochondrial COI. This mitonuclear discordance can be explained by occasional mitochondrial introgression with little or no nuclear gene flow, a pattern that might be common in haplodiploid taxa with slowly evolving mitochondrial genomes. Some species in E. immersa group are not recovered as monophyletic also based on nuclear data, but this could partly be because of unresolved taxonomy. Preliminary analyses of ddRAD data did not recover monophyly of E. japonica within E. longicornis group (three Sanger sequenced nuclear genes strongly supported monophyly), but closer examination of the data and additional Sanger sequencing suggested that both specimens were substantially (possibly 10-20% of recovered loci) cross-contaminated. A reason could be due to specimen identification tag jumps during sequencing library preparation of pooled specimens that in previous studies have been shown to affect up to 2.5% of the sequenced reads. We provide an R script to examine patterns of identical loci among the specimens and estimate that cross-contamination rate is not unusually high for our ddRAD dataset as a whole (based on counting identical sequences between immersa and longicornis groups that are well separated from each other and probably do not hybridise). The high rate of cross-contamination for both E. japonica specimens might be explained by small number of recovered loci (~1000) compared to most other specimens (>10 000 in some cases) because of poor sequencing results. We caution drawing unexpected biological conclusions when closely related specimens are pooled before sequencing and tagged only at one end of the molecule or at both ends using unique combination of limited number of tags (less than the number of specimens).

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“…Mitochondrial genomes are considered powerful markers for resolving different levels of phylogenetics that include deep divergent lineages (Condamine, Nabholz, Clamens, Dupuis, & Sperling, 2018;Tang et al, 2018) or recently radiated groups (Jacobsen et al, 2012;Stokkan et al, 2018), due to their maternal inheritance, relatively high evolutionary rate and rare recombination (Barr, Neiman, & Taylor, 2005;Boore, 1999;Cameron, 2014;Curole & Kocher, 1999). In addition to the information on nucleotide sequences, the significance of mitochondrial gene rearrangement to support relationships of taxa that are inferred from the phylogenetic context have been proposed since the mid-1980s (Brown, 1985) and have been elucidated by some previous studies (Cameron, 2014;Galaska, Li, Kocot, Mahon, & Halanych, 2018;Rokas & Holland, 2000).…”

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confidence: 99%

Integrative taxonomy uncovers hidden species diversity in the rheophilic genus Potamometra (Hemiptera: Gerridae)

Zheng

Zhu

et al. 2019

Zoologica Scripta

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The genus Potamometra Bianchi, 1896 represents big rheophilic semi‐aquatic bugs that typically inhabit middle‐altitude mountainous streams. Here, we integrated molecular and morphological data for delimiting species boundaries and understanding the evolutionary history of the genus Potamometra. Twenty‐seven complete mitochondrial genomes of Potamometra were sequenced, with samples representing most of the known geographically distributed locations around the Sichuan Basin. The results of different species delimitation methods (ABGD, bPTP, GMYC and BPP) based on the monolocus or multilocus data strongly supported the existence of two cryptic new species (Potamometra anderseni Zheng, Ye & Bu, sp. nov. and Potamometra zhengi Zheng, Ye & Bu, sp. nov.) although more entities were found in the tree‐based delimitation methods. The two new species were successfully validated using morphological characters within a detailed taxonomic framework. Phylogenetic analyses supported the reciprocal monophyly of the seven highly node‐supported clades, which were matched with the five known species and two new taxa. A novel gene arrangement pattern that two trnF (trnF1 and trnF2) genes separated by an intergenic spacer (IGS) were found in all the species except the sister group of Potamometra berezowskii Bianchi, 1896 and Potamometra linnavuorii Chen, Nieser & Bu, 2016. This gene rearrangement event could be explained by the tandem duplication and random loss (TDRL) model. Our study emphasized that the combination of molecular sequence data, morphological characters and mitochondrial structural information could improve the accuracy of species delimitation.

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Mitochondrial phylogenomics of the Hymenoptera

Cited by 103 publications

References 62 publications

Mitochondrial genome of Trichagalma acutissimae (Hymenoptera: Cynipoidea: Cynipidae) and phylogenetic analysis

Mitochondrial genome of Trichagalma acutissimae (Hymenoptera: Cynipoidea: Cynipidae) and phylogenetic analysis

Detection of cross-contamination and strong mitonuclear discordance in two species groups of sawfly genus Empria (Hymenoptera, Tenthredinidae)

Integrative taxonomy uncovers hidden species diversity in the rheophilic genus Potamometra (Hemiptera: Gerridae)

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