The first mitogenomes of the superfamily Pamphilioidea (Hymenoptera: Symphyta): Mitogenome architecture and phylogenetic inference

Niu, Gengyun; Korkmaz, Ertan Mahir; Doğan, Özgül; Zhang, Yaoyao; Aydemir, Merve; Budak, Mahir; Du, Shiyu; Basibuyuk, Hasan H.; Wei, Meicai

doi:10.1016/j.ijbiomac.2018.11.129

Cited by 12 publications

(18 citation statements)

References 73 publications

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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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Section: Causes Of Mitonuclear Discordancementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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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“…Eight helices (H563, H1775, H1830, H1925, H2023, H2043, H2547 and H2588) were highly conserved. Furthermore, some helices (H837, H991, H1196 and H2347) were highly variable in terms of their sequence and secondary structure compared with other insects (Gillespie et al, 2006;Du et al, 2018;Niu et al. 2019;Castro and Dowton, 2005;Dowton et al, 2009).…”

Section: Ribosomal Rna Genesmentioning

confidence: 99%

“…Genomes from four species were also used as outgroups (Mecoptera, Diptera, Megaloptera, and Coleoptera) ( Table 1). The 27 species of Symphyta represented eight families: Tenthredinidae (Wei et al, 2014(Wei et al, , 2015Song et al, 2015Song et al, , 2016, Cimbicidae (Song et al, 2016;Doğan & Korkmaz, 2017;Yan et al, in press), Pergidae (Castro and Dowton, 2005), Orussidae (Dowton et al, 2009), Cephidae (Dowton et al, 2009;Korkmaz et al, 2015Korkmaz et al, , 2016Korkmaz et al, , 2017Korkmaz et al, , 2018, Argidae (Du et al, 2018), Megalodontesidae, and Pamphiliidae (Niu et al 2019). Phylogenetic relationships within the suborder Symphyta were reconstructed using both BI and ML analyses (Figure 9).…”

Section: Phylogenetic Relationshipsmentioning

confidence: 99%

Peer Review #2 of "Characterization of the mitochondrial genome of Analcellicampa xanthosoma gen. et sp. nov. (Hymenoptera: Tenthredinidae) (v0.1)"

2019

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A new genus with a new species of the tribe Hoplocampini of Hoplocampinae was described from China: Analcellicampa xanthosoma Wei & Niu, gen. et sp. nov. Hoplocampa danfengensis G. Xiao, 1994 was designated as the type species of the new genus. The characters of Analcellicampa danfengensis (G. Xiao) comb. nov. were briefly discussed. A key to the tribes and known genera of Hoplocampinae was provided. The nearly complete mitochondrial genome of A. xanthosoma was characterized as having a length of 15512 bp and containing 37 genes (22 tRNAs, 13 protein-coding genes (PCGs), and 2 rRNAs). The gene order of this new specimen was the same as that in the inferred insect ancestral mitochondrial genome. All PCGs were initiated by ATN codons and ended with TAA or T stop codons. All tRNAs had a typical cloverleaf secondary structure, except for trnS1. Remarkably, the helices H991 of rrnS and H47 of rrnL were redundant, while helix H563 of rrnL was highly conserved. A phylogeny based on previously reported symphytan mitochondrial genomes showed that A. xanthosoma is a sister group to Monocellicampa pruni, with high support values. We suggest that A. xanthosoma as well as M. pruni belongs to the tribe Hoplocampini of Hoplocampinae.

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The complete mitochondrial genome and novel gene arrangement in Nesodiprion zhejiangensis Zhou & Xiao (Hymenoptera: Diprionidae)

Bai

Merchant

et al. 2023

Funct Integr Genomics

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The first mitogenomes of the superfamily Pamphilioidea (Hymenoptera: Symphyta): Mitogenome architecture and phylogenetic inference

Cited by 12 publications

References 73 publications

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

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

Peer Review #2 of "Characterization of the mitochondrial genome of Analcellicampa xanthosoma gen. et sp. nov. (Hymenoptera: Tenthredinidae) (v0.1)"

The complete mitochondrial genome and novel gene arrangement in Nesodiprion zhejiangensis Zhou & Xiao (Hymenoptera: Diprionidae)

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