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Liu J, Chen J, Cai X, Yang D, Li X, Liu X. Comparative Analysis of the Mitochondrial Genomes of Chloropidae and Their Implications for the Phylogeny of the Family. Int J Mol Sci 2024; 25:2920. [PMID: 38474171 DOI: 10.3390/ijms25052920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
Chloropidae, commonly known as grass flies, represent the most taxonomically diverse family of Diptera Carnoidea, comprising over 3000 described species worldwide. Previous phylogenetic studies of this family have predominantly relied on morphological characters, with mitochondrial genomes being reported in a few species. This study presents 11 newly sequenced mitochondrial genomes (10 Chloropidae and 1 Milichiidae) and provides the first comprehensive comparative analysis of mitochondrial genomes for Chloropidae. Apart from 37 standard genes and the control region, three conserved intergenic sequences across Diptera Cyclorrhapha were identified in all available chloropid mitochondrial genomes. Evolutionary rates within Chloropidae exhibit significant variation across subfamilies, with Chloropinae displaying higher rates than the other three subfamilies. Phylogenetic relationships based on mitochondrial genomes were inferred using maximum likelihood and Bayesian methods. The monophyly of Chloropidae and all four subfamilies is consistently strongly supported, while subfamily relationships within Chloropidae remain poorly resolved, possibly due to rapid evolution.
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Affiliation(s)
- Jiuzhou Liu
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Jiajia Chen
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaodong Cai
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Ding Yang
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Xuankun Li
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Xiaoyan Liu
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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Pei W, Xu W, Li H, Yan L, Gai Y, Yang N, Yang J, Chen J, Peng H, Pape T, Zhang D, Zhang C. Unusual rearrangements of mitogenomes in Diptera revealed by comparative analysis of 135 tachinid species (Insecta, Diptera, Tachinidae). Int J Biol Macromol 2024; 258:128997. [PMID: 38154713 DOI: 10.1016/j.ijbiomac.2023.128997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 12/30/2023]
Abstract
The Tachinidae is one of the most speciose families in Diptera, and the exclusively parasitoid species play an important role in regulating populations of many herbivorous insects in ecosystems, including many agricultural pests. To better comprehend the characteristics and evolution of the mitochondrial genome for the Tachinidae, we are adding a massive amount of new molecular data by assembling the mitogenomes for 71 genera and 135 species from all four tachinid subfamilies through next-generation sequencing, and we are presenting the most comprehensive mitogenomic phylogenetic analysis of this family so far. Extensive rearrangements observed in the mitogenome of Admontia podomyia (Exoristinae) are unique for the entire suborder Cyclorrhapha. The rearrangement pattern suggests that the process involved a tandem duplication of the complete mitogenome, followed by both random and nonrandom loss of one copy of each gene. Additionally, five minor mitogenome rearrangements are discovered and described in three subfamilies. We present the largest species-level phylogenetic hypothesis for Tachinidae to date, based on mitogenomes of 152 species of Tachinidae, representing all four subfamilies and with five non-tachinid outgroups. Our analyses support the monophyly of the Tachinidae and most tribes and genera were recovered with good support, but the higher-level phylogenetic relationships within Tachinidae were poorly resolved, indicating that mitogenome data alone are not enough to unambiguously resolve the deeper phylogenetic relationships within Tachinidae.
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Affiliation(s)
- Wenya Pei
- School of Ecology and Nature Conservation, Beijing Forestry University, Qinghua East Road 35, Beijing 10083, China
| | - Wentian Xu
- School of Ecology and Nature Conservation, Beijing Forestry University, Qinghua East Road 35, Beijing 10083, China
| | - Henan Li
- School of Ecology and Nature Conservation, Beijing Forestry University, Qinghua East Road 35, Beijing 10083, China
| | - Liping Yan
- School of Ecology and Nature Conservation, Beijing Forestry University, Qinghua East Road 35, Beijing 10083, China
| | - Yi Gai
- School of Ecology and Nature Conservation, Beijing Forestry University, Qinghua East Road 35, Beijing 10083, China
| | - Nan Yang
- Serving Officer in Administration Department of Baihua Mountain Reserve, Beijing 10083, China
| | - Jun Yang
- Serving Officer in Administration Department of Baihua Mountain Reserve, Beijing 10083, China
| | - Jinliang Chen
- Dalaoling Nature Reserve Administration of Yichang Three Gorges, Yichang 443000, China
| | - Honglin Peng
- Dalaoling Nature Reserve Administration of Yichang Three Gorges, Yichang 443000, China
| | - Thomas Pape
- Natural History Museum of Denmark, Science Faculty, University of Copenhagen, Copenhagen, Denmark
| | - Dong Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Qinghua East Road 35, Beijing 10083, China.
| | - Chuntian Zhang
- College of Life Science, Shenyang Normal University, Shenyang 110034, China.
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Cao JJ, Wang Y, Murányi D, Cui JX, Li WH. Mitochondrial genomes provide insights into the Euholognatha (Insecta: Plecoptera). BMC Ecol Evol 2024; 24:16. [PMID: 38297210 PMCID: PMC10832105 DOI: 10.1186/s12862-024-02205-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/22/2024] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND Euholognatha is a monophyletic group within stoneflies comprised by a superfamily Nemouroidea and a family Scopuridae. Based on morphological data, the family-level phylogenetic relationships within Euholognatha are widely accepted, but there is still controversy among different molecular studies. To better understand the phylogeny of all six extant euholognathan families, we sequenced and analyzed seven euholognathan mitogenomes. RESULTS The sequence heterogeneity analysis observed a low degree of compositional heterogeneity in euholognathan mitogenomes. Meanwhile, leuctrid mitogenomes were more heterogeneous than other euholognathan families, which may affect the phylogenetic reconstruction. Phylogenetic analyses with various datasets generated three topologies. The Leuctridae was recovered as the earliest branching lineage, and the sister relationship of Capniidae and Taeniopterygidae was supported by most tree topologies and FcLM analyses. When separately excluding sparsely sampled Scopuridae or high heterogeneity leuctrid taxa, phylogenetic analyses under the same methods generated more stable and consistent tree topologies. Finally, based on the results of this study, we reconstructed the relationships within Euholognatha as: Leuctridae + (Scopuridae + ((Taeniopterygidae + Capniidae) + (Nemouridae + Notonemouridae))). CONCLUSION Our research shows the potential of data optimizing strategies in reconstructing phylogeny within Euholognatha and provides new insight into the phylogeny of this group.
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Affiliation(s)
- Jin-Jun Cao
- Henan International Joint Laboratory of Taxonomy and Systematic Evolution of Insecta, Henan Institute of Science and Technology, Henan, 453003, China
| | - Ying Wang
- Henan International Joint Laboratory of Taxonomy and Systematic Evolution of Insecta, Henan Institute of Science and Technology, Henan, 453003, China.
| | - Dávid Murányi
- Department of Zoology, Eszterházy Károly Catholic University, Leányka u. 6, Eger, H-3300, Hungary.
| | - Jian-Xin Cui
- Henan International Joint Laboratory of Taxonomy and Systematic Evolution of Insecta, Henan Institute of Science and Technology, Henan, 453003, China
| | - Wei-Hai Li
- Henan International Joint Laboratory of Taxonomy and Systematic Evolution of Insecta, Henan Institute of Science and Technology, Henan, 453003, China.
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Liu Q, Cai YD, Ma L, Liu H, Linghu T, Guo S, Wei S, Song F, Tian L, Cai W, Li H. Relaxed purifying selection pressure drives accelerated and dynamic gene rearrangements in thrips (Insecta: Thysanoptera) mitochondrial genomes. Int J Biol Macromol 2023; 253:126742. [PMID: 37689283 DOI: 10.1016/j.ijbiomac.2023.126742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/06/2023] [Accepted: 08/26/2023] [Indexed: 09/11/2023]
Abstract
Insect mitochondrial genomes (mitogenome) generally present a typical gene order, which is considered as the ancestral arrangement. All sequenced mitogenomes in the Thysanoptera display high levels of gene rearrangement. Due to limited number of thrips mitogenomes sequenced, how gene rearrangement may be shaped by evolution remain unclear. Here, we analyzed 33 thrips mitogenomes, including 14 newly sequenced. These mitogenomes were diverse in organization, nucleotides substitution and gene arrangements. We found 28 highly rearranged gene orders with the breakpoints of gene rearrangements from 25 to 33. Reconstruction of the ancestors mitochondrial gene arrangements states indicated that Tubulifera have more complex pathways than Terebrantia in the gene order evolution. Molecular calibration estimated that divergence of two suborders occurred in the middle Triassic while the radiation of thrips was associated with the arose and flourish of angiosperm. Our evolutionary hypothesis testing suggests that relaxation of selection pressure enabled the early phase of Thysanoptera evolution, followed by a stronger selective pressure fixed diversification. Our analyses found gene inversion increases the nonsynonymous substitution rates and provide an evolutionary hypothesis driving the diverse gene orders.
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Affiliation(s)
- Qiaoqiao Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Yao D Cai
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Ling Ma
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Hangrui Liu
- Department of Physics and Astronomy, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Tianye Linghu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Shaokun Guo
- Key Laboratory of Surveillance and Management for Plant Quarantine Pests of Ministry of Agriculture and Rural Affairs, Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Shujun Wei
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Fan Song
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Li Tian
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Wanzhi Cai
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China.
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Marques-Neto JC, de Lima GM, Maciel CMT, Maciel BR, Abrunhosa FA, Sampaio I, Maciel CR. In silico prospecting of the mtDNA of Macrobrachium amazonicum from transcriptome data. BMC Genomics 2023; 24:677. [PMID: 37950193 PMCID: PMC10637016 DOI: 10.1186/s12864-023-09770-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Macrobrachium amazonicum is a freshwater prawn widely distributed in South America that is undergoing speciation, so the denomination "M. amazonicum complex" is used for it. The mitochondrial cytochrome c oxidase subunit I (COI) gene has been used to elucidate this speciation, but heteroplasmies and pseudogenes have been recorded, making separation difficult. Obtaining genes from cDNA (RNA) rather than genomic DNA is an effective tool to mitigate those two types of occurrences. The aim of this study was to assemble in silico the mitochondrial DNA (mtDNA) of the Amazonian coastal population of M. amazonicum inhabiting the state of Pará. RESULTS Sequences were obtained from the prawn's transcriptome using the de novo approach. Six libraries of cDNA from the androgen gland, hepatopancreas, and muscle tissue were used. The mtDNA of M. amazonicum was 14,960 bp in length. It contained 13 protein-coding genes, 21 complete transfer RNAs, and the 12S and 16S subunits of ribosomal RNA. All regions were found on the light strand except tRNAGln, which was on the heavy strand. The control region (D-loop) was not recovered, making for a gap of 793 bp. The cladogram showed the formation of the well-defined Macrobrachium clade, with high support value in the established branches (91-100). The three-dimensional spatial conformation of the mtDNA-encoded proteins showed that most of them were mainly composed of major α-helices that typically shows in those proteins inserted in the membrane (mitochondrial). CONCLUSIONS It was possible to assemble a large part of the mitochondrial genome of M. amazonicum in silico using data from other genomes deposited in GenBank and to validate it through the similarities between its COI and 16S genes and those from animals of the same region deposited in GenBank. Depositing the M. amazonicum mtDNA sequences in GenBank may help solve the taxonomic problems recorded for the species, in addition to providing complete sequences of candidate coding genes for use as biomarkers in ecological studies.
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Affiliation(s)
- Jerônimo Costa Marques-Neto
- Laboratory of Aquaculture, Coastal Studies Institute, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
| | - Gabriel Monteiro de Lima
- Laboratory of Aquaculture, Coastal Studies Institute, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
| | - Carlos Murilo Tenório Maciel
- Laboratory of Aquaculture, Coastal Studies Institute, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
- Coastal Studies Institute, School of Biological Sciences, Laboratory of Aquaculture/BioDatta, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
| | - Bruna Ramalho Maciel
- Coastal Studies Institute, School of Biological Sciences, Laboratory of Aquaculture/BioDatta, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
| | - Fernando Araujo Abrunhosa
- Coastal Studies Institute, School of Biological Sciences, Laboratory of Carcinology, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
| | - Iracilda Sampaio
- Coastal Studies Institute, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
| | - Cristiana Ramalho Maciel
- Laboratory of Aquaculture, Coastal Studies Institute, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil.
- Coastal Studies Institute, School of Biological Sciences, Laboratory of Aquaculture/BioDatta, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil.
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Xiong Z, He D, Guang X, Li Q. Novel tRNA Gene Rearrangements in the Mitochondrial Genomes of Poneroid Ants and Phylogenetic Implication of Paraponerinae (Hymenoptera: Formicidae). Life (Basel) 2023; 13:2068. [PMID: 37895449 PMCID: PMC10608118 DOI: 10.3390/life13102068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/04/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
Ants (Formicidae) are the most diverse eusocial insects in Hymenoptera, distributed across 17 extant subfamilies grouped into 3 major clades, the Formicoid, Leptanilloid, and Poneroid. While the mitogenomes of Formicoid ants have been well studied, there is a lack of published data on the mitogenomes of Poneroid ants, which requires further characterization. In this study, we first present three complete mitogenomes of Poneroid ants: Paraponera clavata, the only extant species from the subfamily Paraponerinae, and two species (Harpegnathos venator and Buniapone amblyops) from the Ponerinae subfamily. Notable novel gene rearrangements were observed in the new mitogenomes, located in the gene blocks CR-trnM-trnI-trnQ-ND2, COX1-trnK-trnD-ATP8, and ND3-trnA-trnR-trnN-trnS1-trnE-trnF-ND5. We reported the duplication of tRNA genes for the first time in Formicidae. An extra trnQ gene was identified in H. venator. These gene rearrangements could be explained by the tandem duplication/random loss (TDRL) model and the slipped-strand mispairing model. Additionally, one large duplicated region containing tandem repeats was identified in the control region of P. clavata. Phylogenetic analyses based on protein-coding genes and rRNA genes via maximum likelihood and Bayes methods supported the monophyly of the Poneroid clade and the sister group relationship between the subfamilies Paraponerinae and Amblyoponinae. However, caution is advised in interpreting the positions of Paraponerinae due to the potential artifact of long-branch attraction.
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Affiliation(s)
- Zijun Xiong
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China;
- BGI Research, Wuhan 430074, China
| | - Ding He
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark;
| | | | - Qiye Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China;
- BGI Research, Wuhan 430074, China
- BGI Research, Shenzhen 518083, China;
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Haran J, Li X, Allio R, Shin S, Benoit L, Oberprieler RG, Farrell BD, Brown SDJ, Leschen RAB, Kergoat GJ, McKenna DD. Phylogenomics illuminates the phylogeny of flower weevils (Curculioninae) and reveals ten independent origins of brood-site pollination mutualism in true weevils. Proc Biol Sci 2023; 290:20230889. [PMID: 37817603 PMCID: PMC10565390 DOI: 10.1098/rspb.2023.0889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 09/11/2023] [Indexed: 10/12/2023] Open
Abstract
Weevils are an unusually species-rich group of phytophagous insects for which there is increasing evidence of frequent involvement in brood-site pollination. This study examines phylogenetic patterns in the emergence of brood-site pollination mutualism among one of the most speciose beetle groups, the flower weevils (subfamily Curculioninae). We analysed a novel phylogenomic dataset consisting of 214 nuclear loci for 202 weevil species, with a sampling that mainly includes flower weevils as well as representatives of all major lineages of true weevils (Curculionidae). Our phylogenomic analyses establish a uniquely comprehensive phylogenetic framework for Curculioninae and provide new insights into the relationships among lineages of true weevils. Based on this phylogeny, statistical reconstruction of ancestral character states revealed at least 10 independent origins of brood-site pollination in higher weevils through transitions from ancestral associations with reproductive structures in the larval stage. Broadly, our results illuminate the unexpected frequency with which true weevils-typically specialized phytophages and hence antagonists of plants-have evolved mutualistic interactions of ecological significance that are key to both weevil and plant evolutionary fitness and thus a component of their deeply intertwined macroevolutionary success.
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Affiliation(s)
- J. Haran
- CBGP, CIRAD, INRAE, IRD, Institut Agro, Univ. Montpellier, Montpellier, France
| | - X. Li
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, People's Republic of China
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, USA
- Center for Biodiversity Research, University of Memphis, Memphis, TN 38152, USA
| | - R. Allio
- CBGP, INRAE, IRD, CIRAD, Institut Agro, Univ. Montpellier, Montpellier, France
| | - S. Shin
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, USA
- Center for Biodiversity Research, University of Memphis, Memphis, TN 38152, USA
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - L. Benoit
- CBGP, CIRAD, INRAE, IRD, Institut Agro, Univ. Montpellier, Montpellier, France
| | - R. G. Oberprieler
- CSIRO, Australian National Insect Collection, GPO Box 1700, Canberra, Australian Capital Territory 2601, Australia
| | - B. D. Farrell
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - S. D. J. Brown
- Bio-Protection Research Centre, Lincoln University, P.O. Box 85084, Lincoln 7647, New Zealand
| | | | - G. J. Kergoat
- CBGP, INRAE, IRD, CIRAD, Institut Agro, Univ. Montpellier, Montpellier, France
| | - D. D. McKenna
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, USA
- Center for Biodiversity Research, University of Memphis, Memphis, TN 38152, USA
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Li YD, Engel MS, Tihelka E, Cai C. Phylogenomics of weevils revisited: data curation and modelling compositional heterogeneity. Biol Lett 2023; 19:20230307. [PMID: 37727076 PMCID: PMC10509570 DOI: 10.1098/rsbl.2023.0307] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 08/29/2023] [Indexed: 09/21/2023] Open
Abstract
Weevils represent one of the most prolific radiations of beetles and the most diverse group of herbivores on land. The phylogeny of weevils (Curculionoidea) has received extensive attention, and a largely satisfactory framework for their interfamilial relationships has been established. However, a recent phylogenomic study of Curculionoidea based on anchored hybrid enrichment (AHE) data yielded an abnormal placement for the family Belidae (strongly supported as sister to Nemonychidae + Anthribidae). Here we reanalyse the genome-scale AHE data for Curculionoidea using various models of molecular evolution and data filtering methods to mitigate anticipated systematic errors and reduce compositional heterogeneity. When analysed with the infinite mixture model CAT-GTR or using appropriately filtered datasets, Belidae are always recovered as sister to the clade (Attelabidae, (Caridae, (Brentidae, Curculionidae))), which is congruent with studies based on morphology and other sources of molecular data. Although the relationships of the 'higher Curculionidae' remain challenging to resolve, we provide a consistent and robust backbone phylogeny of weevils. Our extensive analyses emphasize the significance of data curation and modelling across-site compositional heterogeneity in phylogenomic studies.
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Affiliation(s)
- Yan-Da Li
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Michael S. Engel
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024-5192, USA
| | - Erik Tihelka
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Chenyang Cai
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
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9
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Du Z, Zhao Q, Wang X, Sota T, Tian L, Song F, Cai W, Zhao P, Li H. Climatic oscillation promoted diversification of spinous assassin bugs during Pleistocene glaciation. Evol Appl 2023; 16:880-894. [PMID: 37124089 PMCID: PMC10130555 DOI: 10.1111/eva.13543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/28/2023] Open
Abstract
Insect speciation is among the most fascinating topics in evolutionary biology; however, its underlying mechanisms remain unclear. Allopatric speciation represents one of the major types of speciation and is believed to have frequently occurred during glaciation periods, when climatic oscillation may have caused suitable habitats to be fragmented repeatedly, creating geographical isolation among populations. However, supporting evidence for allopatric speciation of insects in East Asia during the Pleistocene glaciation remains lacking. We aim to investigate the effect of climatic oscillation during the Pleistocene glaciation on the diversification pattern and evolutionary history of hemipteran insects and to test the hypothesis of Pleistocene species stability using spinous assassin bugs Sclomina (Hemiptera: Reduviidae), a small genus widely distributed in southern China but was later found to have cryptic species diversity. Here, using the whole mitochondrial genome (mitogenome) and nuclear ribosomal RNA genes, we investigated both interspecific and intraspecific diversification patterns of spinous assassin bugs. Approximate Bayesian computation, ecological niche modeling, and demographic history analyses were also applied to understand the diversification process and driven factors. Our data suggest that the five species of Sclomina are highly diverged, despite three of them currently being cryptic. Speciation occurred during the Pleistocene when suitable distribution areas were possibly fragmented. Six phylogeographic groups in the type species S. erinacea were identified, among which two groups underwent expansion during the early Last Glacial Period and after Last Glacier Maximum. Our analyses suggest that this genus may have experienced climate-driven habitat fragmentation and postglacial expansion in the Pleistocene, promoting allopatric speciation and intraspecific diversification. Our results reveal underestimated species diversity in a small insect group and illustrate a remarkable example of allopatric speciation of insects in East Asia promoted by Pleistocene climatic oscillations. These findings provide important insights into the speciation processes and aid the conservation of insect species diversity.
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Affiliation(s)
- Zhenyong Du
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant ProtectionChina Agricultural UniversityBeijingChina
- Sanya Institute of China Agricultural UniversitySanyaChina
| | - Qian Zhao
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant ProtectionChina Agricultural UniversityBeijingChina
- Sanya Institute of China Agricultural UniversitySanyaChina
| | - Xuan Wang
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant ProtectionChina Agricultural UniversityBeijingChina
- Sanya Institute of China Agricultural UniversitySanyaChina
| | - Teiji Sota
- Department of Zoology, Graduate School of ScienceKyoto University, SakyoKyotoJapan
| | - Li Tian
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant ProtectionChina Agricultural UniversityBeijingChina
- Sanya Institute of China Agricultural UniversitySanyaChina
| | - Fan Song
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant ProtectionChina Agricultural UniversityBeijingChina
- Sanya Institute of China Agricultural UniversitySanyaChina
| | - Wanzhi Cai
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant ProtectionChina Agricultural UniversityBeijingChina
- Sanya Institute of China Agricultural UniversitySanyaChina
| | - Ping Zhao
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf (Ministry of Education) and Guangxi Key Laboratory of Earth Surface Processes and Intelligent SimulationNanning Normal UniversityNanningChina
| | - Hu Li
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant ProtectionChina Agricultural UniversityBeijingChina
- Sanya Institute of China Agricultural UniversitySanyaChina
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Tsz Long Wong D, Norman H, Creedy TJ, Jordaens K, Moran KM, Young A, Mengual X, Skevington JH, Vogler AP. The phylogeny and evolutionary ecology of hoverflies (Diptera: Syrphidae) inferred from mitochondrial genomes. Mol Phylogenet Evol 2023; 184:107759. [PMID: 36921697 DOI: 10.1016/j.ympev.2023.107759] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 03/01/2023] [Accepted: 03/08/2023] [Indexed: 03/16/2023]
Abstract
Hoverflies (Diptera: Syrphidae) are a diverse group of pollinators and a major research focus in ecology, but their phylogenetic relationships remain incompletely known. Using a genome skimming approach we generated mitochondrial genomes for 91 species, capturing a wide taxonomic diversity of the family. To reduce the required amount of input DNA and overall cost of the library construction, sequencing and assembly was conducted on mixtures of specimens, which raises the problem of chimera formation of mitogenomes. We present a novel chimera detection test based on gene tree incongruence, but identified only a single mitogenome of chimeric origin. Together with existing data for a final set of 127 taxa, phylogenetic analysis on nucleotide and amino acid sequences using Maximum Likelihood and Bayesian Inference revealed a basal split of Microdontinae from all other syrphids. The remainder consists of several deep clades assigned to the subfamily Eristalinae in the current classification, including a clade comprising the subfamily Syrphinae (plus Pipizinae). These findings call for a re-definition of subfamilies, but basal nodes had insufficient support to allow such action. Molecular-clock dating placed the origin of the Syrphidae crown group in the mid-Cretaceous while the Eristalinae-Syrphinae clade likely originated near the K/Pg boundary. Transformation of larval life history characters on the tree suggests that Syrphidae initially had sap feeding larvae, which diversified greatly in diet and habitat association during the Eocene and Oligocene, coinciding with the diversification of angiosperms and the evolution of various insect groups used as larval host, prey, or mimicry models. Mitogenomes proved to be a powerful phylogenetic marker for studies of Syrphidae at subfamily and tribe levels, allowing dense taxon sampling that provided insight into the great ecological diversity and rapid evolution of larval life history traits of the hoverflies.
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Affiliation(s)
- Daniel Tsz Long Wong
- Department of Life Sciences, Imperial College London, Exhibition Road, London, SW7 2BX, U.K; Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, U.K.
| | - Hannah Norman
- Department of Life Sciences, Imperial College London, Exhibition Road, London, SW7 2BX, U.K; Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, U.K.
| | - Thomas J Creedy
- Department of Life Sciences, Imperial College London, Exhibition Road, London, SW7 2BX, U.K; Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, U.K.
| | - Kurt Jordaens
- Department of Biology-Invertebrates Unit, Royal Museum for Central Africa, Joint Experimental Molecular Unit Leuvensesteenweg 13, B-3080 Tervuren, Belgium.
| | - Kevin M Moran
- Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri-Food Canada, K.W. Neatby Building, 960 Carling Avenue, Ottawa, Ontario, ON K1A 0C6, Canada; Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, ON K1S 5B6, Canada.
| | - Andrew Young
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, ON N1G 2W1, Canada.
| | - Ximo Mengual
- Zoologisches Forschungsmuseum Alexander Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Adenauerallee 127, 53113 Bonn, Germany.
| | - Jeffrey H Skevington
- Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri-Food Canada, K.W. Neatby Building, 960 Carling Avenue, Ottawa, Ontario, ON K1A 0C6, Canada; Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, ON K1S 5B6, Canada.
| | - Alfried P Vogler
- Department of Life Sciences, Imperial College London, Exhibition Road, London, SW7 2BX, U.K; Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, U.K.
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11
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Palacios-Barreto P, Mar-Silva AF, Bayona-Vasquez NJ, Adams DH, Díaz-Jaimes P. Characterization of the complete mitochondrial genome of the brazilian cownose ray Rhinoptera brasiliensis (Myliobatiformes, Rhinopteridae) in the western Atlantic and its phylogenetic implications. Mol Biol Rep 2023; 50:4083-4095. [PMID: 36877343 DOI: 10.1007/s11033-023-08272-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 01/11/2023] [Indexed: 03/07/2023]
Abstract
BACKGROUND The Brazilian cownose ray, Rhinoptera brasiliensis has undergone a global population reduction and is currently classified by IUCN as Vulnerable. This species is sometimes confused with Rhinoptera bonasus, the only external diagnostic characteristic to distinguish between both species is the number of rows of tooth plates. Both cownose rays overlap geographically from Rio de Janeiro to the western North Atlantic. This calls for a more comprehensive phylogenetic assessment using mitochondria DNA genomes to better understand the relationships and delimitation of these two species. METHODS AND RESULTS The mitochondrial genome sequences of R. brasiliensis was obtained by next-generation sequencing. The length of the mitochondrial genome was 17,759 bp containing 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a non-coding control region (D-loop). Each PCG was initiated by an authoritative ATG codon, except for COX1 initiated by a GTG codon. Most of the PCGs were terminated by a complete codon (TAA/TAG), while an incomplete termination codon (TA/T) was found in five out of the 13 PCGs. The phylogenetic analysis showed that R. brasiliensis was closely related to R. steindachneri whereas the reported mitogenome as R. steindachneri (GenBank accession number KM364982), differs from multiple mitocondrial DNA sequences of R. steindachneri and is nearly identical to that of R. javanica. CONCLUSION The new mitogenome determined in this study provides new insight into the phylogenetic relationships in Rhinoptera, while providing new molecular data that can be applied to population genetic studies.
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Affiliation(s)
- Paola Palacios-Barreto
- Posgrado en Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Av. Ciudad Universitaria 3000, C.P. 04510, Coyoacán, Ciudad de México, México.,Fundación colombiana para la investigación y conservación de Tiburones y Rayas, SQUALUS, Cali, Colombia
| | - Adán Fernando Mar-Silva
- Posgrado en Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Av. Ciudad Universitaria 3000, C.P. 04510, Coyoacán, Ciudad de México, México
| | - Natalia J Bayona-Vasquez
- Division of Natural Science and Mathematics, Oxford College, Emory University, 30054, Oxford, GA, USA
| | - Douglas H Adams
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, Indian River Field Laboratory, 32901, Melbourne, FL, USA
| | - Píndaro Díaz-Jaimes
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Ciudad de México, México.
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12
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Yu G, Lai S, Liao S, Cao Y, Li W, Long C, Tarno H, Wang J. Complete Mitochondrial Genome of Scolytoplatypodini Species (Coleoptera: Curculionidae: Scolytinae) and Phylogenetic Implications. Genes (Basel) 2023; 14:162. [PMID: 36672903 PMCID: PMC9859420 DOI: 10.3390/genes14010162] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/02/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
The complete mitochondrial genomes (mitogenomes) of beetles in the tribe Scolytoplatypodini (genus Scolytoplatypus) were sequenced and annotated. These included Scolytoplatypus raja (15,324 bp), Scolytoplatypus sinensis (15,394 bp), Scolytoplatypus skyliuae (15,167 bp), and Scolytoplatypus wugongshanensis (15,267 bp). The four mitogenomes contained 37 typical genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and 2 ribosomal RNA genes (rRNAs). The gene orientation and arrangement of the four mitogenomes were similar to other Coleoptera mitogenomes. PCGs mostly started with ATN and terminated with TAA. The Ka/Ks ratio of 13 PCGs in the four species revealed that cox1 had the slowest evolutionary rate and atp8 and nad6 had a higher evolutionary rate. All tRNAs had typical cloverleaf secondary structures, but trnS1 lacked dihydrouridine arm. Partial tRNAs lost the discriminator nucleotide. The trnY did not possess the discriminator nucleotide and also lost three bases, showing a special amino-acyl arm. Bayesian inference (BI) and maximum likelihood (ML) methods were conducted for phylogenetic analyses using 13 PCGs. Scolytoplatypodini was clustered with Hylurgini and Hylastini, and the monophyly of Scolytoplatypodini was supported. The four newly sequenced mitogenomes increase understanding of the evolutionary relationships of Scolytoplatypodini and other Scolytinae species.
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Affiliation(s)
- Guangyu Yu
- Laboratory of Invasion Biology, School of Agricultural Sciences, Jiangxi Agricultural University, Nanchang 340045, China
| | - Shengchang Lai
- Laboratory of Invasion Biology, School of Agricultural Sciences, Jiangxi Agricultural University, Nanchang 340045, China
- Forest Protection, Forestry College, Nanjing Forest University, Nanjing 210036, China
| | - Song Liao
- Laboratory of Invasion Biology, School of Agricultural Sciences, Jiangxi Agricultural University, Nanchang 340045, China
| | - Yufeng Cao
- Laboratory of Invasion Biology, School of Agricultural Sciences, Jiangxi Agricultural University, Nanchang 340045, China
| | - Weijun Li
- Laboratory of Invasion Biology, School of Agricultural Sciences, Jiangxi Agricultural University, Nanchang 340045, China
| | - Chengpeng Long
- College of Forestry and Biotechnology, Zhejiang Agricultural and Forestry University, Lin’an 311300, China
| | - Hagus Tarno
- Laboratory of Invasion Biology, School of Agricultural Sciences, Jiangxi Agricultural University, Nanchang 340045, China
- Department of Plant Pests and Diseases, Faculty of Agriculture, Universitas Brawijaya, Jl. Veteran, Malang 65145, Indonesia
| | - Jianguo Wang
- Laboratory of Invasion Biology, School of Agricultural Sciences, Jiangxi Agricultural University, Nanchang 340045, China
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Fossil History of Ambrosia Beetles (Coleoptera; Platypodidae) with Description of a New Genus from Dominican Amber. DIVERSITY 2022. [DOI: 10.3390/d15010045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The fossil record of ambrosia beetles is summarized and a new genus and species in the subfamily Mecopelminae, Gongyloceria dominicana gen. et sp. nov. is described. The new genus differs from the extant genus Mecopelmus Blackman, 1944, possessing weakly elongated tarsi, finely faceted eyes, a scape not reaching the posterior margin of the eye, coarsely sculptured pronotum and elytra, and a larger body size. It is the first Miocene record of the Mecopelminae. The genus Xyleborites Wickham, 1913, placem. n. is transferred from the Scolytidae to the Platypodidae. A list of the fossil Platypodidae, including a key to the subfamilies and tribes of ambrosia beetles, is presented. Xyleborites longipennis Wickham, 1913 and Gongyloceria dominicana sp. nov. may have been related to Paullinieae recorded from the late Eocene and the early Miocene of North and Central America. Distribution maps with fossil records for ambrosia beetles are included.
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Zhang LJ, Li YJ, Ge XY, Li XY, Yang YX, Bai M, Ge SQ. Mitochondrial genomes of Sternochetus species (Coleoptera: Curculionidae) and the phylogenetic implications. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2022; 111:e21898. [PMID: 35434835 DOI: 10.1002/arch.21898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 02/25/2022] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
The three weevil species, Sternochetus gravis, S. mangiferae, and S. olivieri, have all been reported to be serious pests of mango fruits. Morphology, biology, and various management approaches of these economically important weevils have been well studied. However, no mitochondrial genomes have been reported from the genus Sternochetus. Herein, we assembled mitogenomes of all the three Sternochetus species to reveal their mitogenomic characteristics. A DNA library of 350 bp insert size was constructed and sequenced in Illumina's HiSeq 6000 platform with a pair-end 150 bp sequencing strategy by Novogene. The sequence reads were assembled using GetOrganelle v1.7.1 and the genes were annotated by Geneious Prime 2021.0.3 and MITOS Web Server. Coupled with 61 published mitogenomes from 13 subfamilies of Curculionidae, we reconstructed phylogenetic trees to resolve evolutionary relationships of these closely related species and also examined subfamily-level classification among Curculionidae. All three mitogenomes are double-stranded circular molecules with 22 transfer RNA genes, 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 1 noncoding control region as in other insects. Higher interspecific nucleotide divergence (about 10%) of 13 PCGs indicated these three Sternochetus species diverged a long time ago. Phylogenetic analyses using both maximum likelihood and Bayesian inference methods showed that Sternochetus falls into the basal clade of Cryptorhynchini, a tribe in the subfamily Molytinae. The relationship of S. olivieri as a sister species to S. gravis + S. mangiferae was strongly supported. The monophyly of Cryptorhynchini was also well supported whereas Molytinae was suggested to be a polyphyletic group.
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Affiliation(s)
- Li-Jie Zhang
- Institute of plant quarantine, Science and Technical Research Center of China Customs, Beijing, China
| | - Yu-Jie Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xue-Ying Ge
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Xue-Yan Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yu-Xia Yang
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Ming Bai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Si-Qin Ge
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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Mitogenomics of the Olive Seed Weevil, Anchonocranus oleae Marshall and Implications for Its Phylogenetic Position in Curculionidae. INSECTS 2022; 13:insects13070607. [PMID: 35886783 PMCID: PMC9321040 DOI: 10.3390/insects13070607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 11/29/2022]
Abstract
Simple Summary Anchonocranus oleae is a southern African weevil that feeds on the seeds of the African Wild Olive, a close relative of the European cultivated olive tree. The species is known to occur in the Western Cape of South Africa, the main region of olive production in Southern Africa. We generated reference DNA barcodes and the complete mitogenome of A. oleae as part of our ongoing genetic cataloguing of insects associated with wild and cultivated olives in South Africa. The phylogenetic position of A. oleae in the family Curculionidae was inferred to be in the Curculioninae, Conoderinae, Cossoninae, Molytinae, and Scolytinae (CCCMS) clade but could not be precisely determined due to the paucity of genetic data for adequate taxonomic context, highlighting the need for further coverage of related tribes and genera. Nevertheless, the data generated in this study contribute to the enrichment of baseline information on olive-associated insects, in general, and on the genus Anchonocranus, in particular. Abstract Anchonocranus oleae Marshall (Coleoptera: Curculionidae) is a seed-feeding weevil native to southern Africa; its larvae are known to develop in the fruits of the African Wild Olive and, more rarely, cultivated olives. The species has been mainly found in the Western Cape province of South Africa, but it has remained in relative obscurity because it does not seem to represent a current threat to commercial olive production. As part of an ongoing effort to produce baseline genetic data for olive-associated entomofauna in South Africa, we generated reference DNA barcodes for A. oleae collected from wild and cultivated olives and sequenced its mitogenome for assessment of the phylogenetic position of the species in the family Curculionidae. The mitochondrial phylogeny estimate indicated that A. oleae shares a common ancestor with Elaidobius (tribe Derelomini), but a definite and close relationship to this tribe and the precise tribal placement of A. oleae in the subfamily Curculioninae could not be inferred due to the lack of representative mitogenomes of other relevant curculionine tribes and genera. This study will assist future work on the DNA-based species identification, genetic diversity, and phylogenetic position of the genus Anchonocranus and related taxa.
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Qilemoge, Yang D. The mitochondrial genome of Gymnopternus bomiensis (Diptera: Dolichopodidae). Mitochondrial DNA B Resour 2022; 7:1201-1202. [PMID: 35814172 PMCID: PMC9267409 DOI: 10.1080/23802359.2022.2090294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The mitochondrial genome of Gymnopternus bomiensis (Yang, 1996) (Diptera: Dolichopodidae) has been reported in this study. This is the first mitogenome representative of Gymnopternus. The sequenced region is determined to be 15,212 bp, including 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a partial A-T rich region. The nucleotide composition biased toward A and T, and the overall A + T% was up to 74.0%. Additionally, we reconstructed the phylogeny of relative species using 13 PCRs and two rRNAs. Bayesian inference analysis strongly supported the monophyly of Dolichopodinae. It also suggested that Gymnopternus is the sister group of Dolichopus.
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Affiliation(s)
- Qilemoge
- School of Biological Science and Technology, Baotou Teachers’ College, Baotou, China
| | - Ding Yang
- College of Plant Protection, China Agricultural University, Beijing, China
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Liu Q, He J, Song F, Tian L, Cai W, Li H. Positive Correlation of the Gene Rearrangements and Evolutionary Rates in the Mitochondrial Genomes of Thrips (Insecta: Thysanoptera). INSECTS 2022; 13:insects13070585. [PMID: 35886761 PMCID: PMC9321049 DOI: 10.3390/insects13070585] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/24/2022] [Accepted: 06/24/2022] [Indexed: 01/04/2023]
Abstract
Simple Summary Aeolothrips, commonly known as banded thrips, is the largest genus of the family Aeolothripidae (predatory thrips). In the current study, we sequenced the mitochondrial genome (mitogenome) of the banded thrip species Aeolothrips xinjiangensis. We found a novel gene arrangement in this mitogenome that has not been reported in Thysanoptera. By comparing the gene order and rearrangement patterns, we found seven identical gene blocks and three identical rearrangement events in two mitogenomes of banded thrips. There was marked variation in the mitochondrial gene order across thrip species, with only two conserved gene blocks shared by all 14 thrips. In addition, we found a positive correlation between the degree of gene rearrangement and evolutionary rate. Our results suggested that the mitogenomes of thrips have tended to be stable since their massive rearrangement. Abstract Extensive gene rearrangement is characteristic in the mitogenomes of thrips (Thysanoptera), but the historical process giving rise to the contemporary gene rearrangement pattern remains unclear. To better understand the evolutionary processes of gene rearrangement in the mitogenomes of thrips, we sequenced the mitogenome of the banded thrip species Aeolothrips xinjiangensis. First, we found a novel mitochondrial gene order in this species. This mitogenome is 16,947 bp in length and encodes the typical 37 coding genes (13 protein-coding genes, 22 tRNA genes, and two rRNA genes) of insects. The gene arrangement was dramatically different from the putative ancestral mitogenome, with 26 genes being translocated, eight of which were inverted. Moreover, we found a novel, conserved gene block, trnC-trnY, which has not been previously reported in the mitogenomes of thrips. With this newly assembled mitogenome, we compared mitogenome sequences across Thysanoptera to assess the evolutionary processes giving rise to the current gene rearrangement pattern in thrips. Seven identical gene blocks were shared by two sequenced banded thrip mitogenomes, while the reversal of ND2 combined with TDRL events resulted in the different gene orders of these two species. In phylogenetic analysis, the monophyly of the suborders and families of Thysanoptera was well supported. Across the gene orders of 14 thrips, only two conserved gene blocks, ATP8-ATP6 and ND4-ND4L, could be found. Correlation analysis showed that the degree of gene rearrangement was positively correlated with the non-synonymous substitution rate in thrips. Our study suggests that the mitogenomes of thrips remain stable over long evolutionary timescales after massive rearrangement during early diversification.
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Affiliation(s)
- Qiaoqiao Liu
- MOA Key Lab of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (Q.L.); (J.H.); (F.S.); (L.T.); (W.C.)
| | - Jia He
- MOA Key Lab of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (Q.L.); (J.H.); (F.S.); (L.T.); (W.C.)
- Institute of Plant Protection, Academy of Ningxia Agriculture and Forestry Science, Yinchuan 750002, China
| | - Fan Song
- MOA Key Lab of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (Q.L.); (J.H.); (F.S.); (L.T.); (W.C.)
| | - Li Tian
- MOA Key Lab of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (Q.L.); (J.H.); (F.S.); (L.T.); (W.C.)
| | - Wanzhi Cai
- MOA Key Lab of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (Q.L.); (J.H.); (F.S.); (L.T.); (W.C.)
| | - Hu Li
- MOA Key Lab of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (Q.L.); (J.H.); (F.S.); (L.T.); (W.C.)
- Correspondence:
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Lalonde MML, Marcus JM. A global molecular phylogeny yields insights into the dispersal and invasion history of Junonia, a butterfly genus with remarkable dispersal abilities. Proc Biol Sci 2022; 289:20212801. [PMID: 35673860 PMCID: PMC9174730 DOI: 10.1098/rspb.2021.2801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The nymphalid butterfly genus Junonia has remarkable dispersal abilities. Occurring on every continent except Europe and Antarctica, Junonia are often among the only butterflies on remote oceanic islands. The biogeography of Junonia has been controversial, plagued by taxonomic disputes, small phylogenetic datasets, incomplete taxon sampling, and shared interspecific mitochondrial haplotypes. Junonia originated in Africa but its route into the New World remains unknown. Presented here is, to our knowledge, the most comprehensive Junonia phylogeny to date, using full mitogenomes and nuclear ribosomal RNA repeats from 40 of 47 described species. Junonia is monophyletic and the genus Salamis is its probable sister clade. Genetic exchange between Indo-Pacific Junonia villida and New World Junonia vestina is evident, suggesting a trans-Pacific route into the New World. However, in both phylogenies, the sister clades to most New World Junonia contain both African and Asian species. Multiple trans-Atlantic or trans-Pacificinvasions could have contributed to New World diversification. Hybridization and lateral transfer of mitogenomes, already well-documented in New World Junonia, also occurs in at least two Old World lineages (Junonia orithya/Junonia hierta and Junonia iphita/Junonia hedonia). Variation associated with reticulate evolution creates challenges for phylogenetic reconstruction, but also may have contributed to patterns of speciation and diversification in this genus.
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Affiliation(s)
- Melanie M. L. Lalonde
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Jeffrey M. Marcus
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
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Paula DP, Barros SKA, Pitta RM, Barreto MR, Togawa RC, Andow DA. Metabarcoding versus mapping unassembled shotgun reads for identification of prey consumed by arthropod epigeal predators. Gigascience 2022; 11:6554098. [PMID: 35333301 PMCID: PMC8952265 DOI: 10.1093/gigascience/giac020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 12/07/2021] [Accepted: 02/09/2022] [Indexed: 12/19/2022] Open
Abstract
Background A central challenge of DNA gut content analysis is to identify prey in a highly degraded DNA community. In this study, we evaluated prey detection using metabarcoding and a method of mapping unassembled shotgun reads (Lazaro). Results In a mock prey community, metabarcoding did not detect any prey, probably owing to primer choice and/or preferential predator DNA amplification, while Lazaro detected prey with accuracy 43–71%. Gut content analysis of field-collected arthropod epigeal predators (3 ants, 1 dermapteran, and 1 carabid) from agricultural habitats in Brazil (27 samples, 46–273 individuals per sample) revealed that 64% of the prey species detections by either method were not confirmed by melting curve analysis and 87% of the true prey were detected in common. We hypothesized that Lazaro would detect fewer true- and false-positive and more false-negative prey with greater taxonomic resolution than metabarcoding but found that the methods were similar in sensitivity, specificity, false discovery rate, false omission rate, and accuracy. There was a positive correlation between the relative prey DNA concentration in the samples and the number of prey reads detected by Lazaro, while this was inconsistent for metabarcoding. Conclusions Metabarcoding and Lazaro had similar, but partially complementary, detection of prey in arthropod predator guts. However, while Lazaro was almost 2× more expensive, the number of reads was related to the amount of prey DNA, suggesting that Lazaro may provide quantitative prey information while metabarcoding did not.
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Affiliation(s)
- Débora Pires Paula
- Embrapa Genetic Resources and Biotechnology, Brasília-DF, 70770-917, Brazil
| | | | | | | | | | - David A Andow
- Department of Entomology, University of Minnesota, MN, 55108, St. Paul, USA
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Hui-Yun T, Chiba H, Lohman DJ, Yen SH, Aduse-Poku K, Ohshima Y, Wu LW. Out of Asia: Intercontinental dispersals after the Eocene-Oligocene transition shaped the zoogeography of Limenitidinae butterflies (Lepidoptera: Nymphalidae). Mol Phylogenet Evol 2022; 170:107444. [DOI: 10.1016/j.ympev.2022.107444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/15/2022] [Accepted: 02/15/2022] [Indexed: 11/29/2022]
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Zhang H, Song N, Yin X. Higher-level phylogeny of Chrysomelidae based on expanded sampling of mitogenomes. PLoS One 2022; 17:e0258587. [PMID: 35061698 PMCID: PMC8782406 DOI: 10.1371/journal.pone.0258587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 09/30/2021] [Indexed: 11/24/2022] Open
Abstract
Chrysomelidae is one of the most diverse lineages of beetles. The classification and phylogeny of Chrysomelidae have been contentious. In this study, we obtained 16 new mitogenome sequences by using next-generation sequencing. Combined with the published mitogenomes, we inferred the phylogenetic relationships of Chrysomelidae. Different data recoding strategies and substitution models were applied to phylogenetic reconstruction. In the Maximum likelihood analyses under the homogeneous model, Dayhoff recoding allowed for the improved phylogenetic resolution due to the decreased level of heterogeneous sequence divergence. Bayesian inference under the heterogeneous model yielded generally well resolved subfamily relationships. The present mitogenome data strongly supported Chrysomelidae as a monophyletic group. Consistent with previous work, we found three major subfamily clades within Chrysomelidae. However, the pattern of the "sagrine" clade plus the "eumolpine" clade being sister to the "chrysomeline" clade contrasted with the prior study. The placement of the genus Syneta with regards to these three clades was ambiguous. Relationships recovered suggested several major chrysomelid lineages, including: (1) Bruchinae in the "sagrine" clade; (2) Donaciinae + Criocerinae; (3) Spilopyrinae + (Cassidinae + (Eumolpinae + (Lamprosomatinae + Cryptocephalinae))); (4) Chrysomelinae + (Alticinae + Galerucinae). Results also suggested the placement of Timarcha outside the major Chrysomelinae.
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Affiliation(s)
- Heng Zhang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Nan Song
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Xinming Yin
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
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22
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Jiang M, Xu SF, Tang TS, Miao L, Luo BZ, Ni Y, Kong FD, Liu C. Development and evaluation of a meat mitochondrial metagenomic (3MG) method for composition determination of meat from fifteen mammalian and avian species. BMC Genomics 2022; 23:36. [PMID: 34996352 PMCID: PMC8742424 DOI: 10.1186/s12864-021-08263-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 12/17/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Bioassessment and biomonitoring of meat products are aimed at identifying and quantifying adulterants and contaminants, such as meat from unexpected sources and microbes. Several methods for determining the biological composition of mixed samples have been used, including metabarcoding, metagenomics and mitochondrial metagenomics. In this study, we aimed to develop a method based on next-generation DNA sequencing to estimate samples that might contain meat from 15 mammalian and avian species that are commonly related to meat bioassessment and biomonitoring. RESULTS In this project, we found the meat composition from 15 species could not be identified with the metabarcoding approach because of the lack of universal primers or insufficient discrimination power. Consequently, we developed and evaluated a meat mitochondrial metagenomics (3MG) method. The 3MG method has four steps: (1) extraction of sequencing reads from mitochondrial genomes (mitogenomes); (2) assembly of mitogenomes; (3) mapping of mitochondrial reads to the assembled mitogenomes; and (4) biomass estimation based on the number of uniquely mapped reads. The method was implemented in a python script called 3MG. The analysis of simulated datasets showed that the method can determine contaminant composition at a proportion of 2% and the relative error was < 5%. To evaluate the performance of 3MG, we constructed and analysed mixed samples derived from 15 animal species in equal mass. Then, we constructed and analysed mixed samples derived from two animal species (pork and chicken) in different ratios. DNAs were extracted and used in constructing 21 libraries for next-generation sequencing. The analysis of the 15 species mix with the method showed the successful identification of 12 of the 15 (80%) animal species tested. The analysis of the mixed samples of the two species revealed correlation coefficients of 0.98 for pork and 0.98 for chicken between the number of uniquely mapped reads and the mass proportion. CONCLUSION To the best of our knowledge, this study is the first to demonstrate the potential of the non-targeted 3MG method as a tool for accurately estimating biomass in meat mix samples. The method has potential broad applications in meat product safety.
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Affiliation(s)
- Mei Jiang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, 100193 Beijing, PR China
| | - Shu-Fei Xu
- Technology Center of Xiamen Entry-exit Inspection and Quarantine Bureau, Xiamen, Fujian 361026 PR China
| | - Tai-Shan Tang
- Technology Center of Jiangsu Entry-exit Inspection and Quarantine Bureau, Nanjing, Jiangsu 210009 PR China
| | - Li Miao
- Technology Center of Henan Entry-exit Inspection and Quarantine Bureau, Zhengzhou, Henan 450003 PR China
| | - Bao-Zheng Luo
- Technology Center of Zhuhai Entry-exit Inspection and Quarantine Bureau, Zhuhai, Guangdong 519000 PR China
| | - Yang Ni
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province 350002 PR China
| | - Fan-De Kong
- Technology Center of Xiamen Entry-exit Inspection and Quarantine Bureau, Xiamen, Fujian 361026 PR China
| | - Chang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, 100193 Beijing, PR China
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23
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OUP accepted manuscript. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlab125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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24
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Lin C, Gao S, Yang D. The mitochondrial genome of Calohilara tibetensis Ding, He, Lin, and Yang, 2020 (Diptera: Empididae). Mitochondrial DNA B Resour 2021; 6:2613-2614. [PMID: 34409155 PMCID: PMC8366656 DOI: 10.1080/23802359.2021.1962212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The dance fly Calohilara tibetensis Ding, He, Lin and Yang, 2020 belongs to the subfamily Empidinae of Empididae. The mitochondrial genome of C. tibetensis was sequenced as the new representative of the subfamily Empidinae. The nearly complete mitogenome was 15,354 bp, consisting of 13 protein-coding genes, two rRNAs, and 22 tRNAs. All genes have the similar locations and strands with that of other published species of Empididae. The nucleotide composition biases toward A and T is 77.4% of the entirety. All PCGs start with ATN codons except COI and NAD1, and end with TAA or incomplete stop codon. Bayesian inference (BI) analysis strongly supported the monophyly of both Empididae and Dolichopodidae and the monophyly of subfamily Empidinae. It suggested that Calohilara is the sister group of Hilara.
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Affiliation(s)
- Chen Lin
- Institute of Life Science and Technology, Inner Mongolia Normal University, Huhhot, PR China
- College of Plant Protection, China Agricultural University, Beijing, PR China
| | - Shang Gao
- College of Plant Protection, China Agricultural University, Beijing, PR China
| | - Ding Yang
- College of Plant Protection, China Agricultural University, Beijing, PR China
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Xu S, Wu Y, Liu Y, Zhao P, Chen Z, Song F, Li H, Cai W. Comparative Mitogenomics and Phylogenetic Analyses of Pentatomoidea (Hemiptera: Heteroptera). Genes (Basel) 2021; 12:1306. [PMID: 34573288 PMCID: PMC8471585 DOI: 10.3390/genes12091306] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 01/04/2023] Open
Abstract
Pentatomoidea is the largest superfamily of Pentatomomorpha; however, the phylogenetic relationships among pentatomoid families have been debated for a long time. In the present study, we gathered the mitogenomes of 55 species from eight common families (Acanthosomatidae, Cydnidae, Dinidoridae, Scutelleridae, Tessaratomidae, Plataspidae, Urostylididae and Pentatomidae), including 20 newly sequenced mitogenomes, and conducted comparative mitogenomic studies with an emphasis on the structures of non-coding regions. Heterogeneity in the base composition, and contrasting evolutionary rates were encountered among the mitogenomes in Pentatomoidea, especially in Urostylididae, which may lead to unstable phylogenetic topologies. When the family Urostylididae is excluded in taxa sampling or the third codon positions of protein coding genes are removed, phylogenetic analyses under site-homogenous models could provide more stable tree topologies. However, the relationships between families remained the same in all PhyloBayes analyses under the site-heterogeneous mixture model CAT + GTR with different datasets and were recovered as (Cydnidae + (((Tessaratomidae + Dinidoridae) + (Plataspidae + Scutelleridae)) + ((Acanthosomatidae + Urostylididae) + Pentatomidae)))). Our study showed that data optimizing strategies after heterogeneity assessments based on denser sampling and the use of site-heterogeneous mixture models are essential for further analysis of the phylogenetic relationships of Pentatomoidea.
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Affiliation(s)
- Shiwen Xu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; (S.X.); (Y.W.); (Y.L.); (Z.C.); (F.S.); (H.L.)
| | - Yunfei Wu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; (S.X.); (Y.W.); (Y.L.); (Z.C.); (F.S.); (H.L.)
| | - Yingqi Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; (S.X.); (Y.W.); (Y.L.); (Z.C.); (F.S.); (H.L.)
| | - Ping Zhao
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf (Ministry of Education) and Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning 530001, China;
| | - Zhuo Chen
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; (S.X.); (Y.W.); (Y.L.); (Z.C.); (F.S.); (H.L.)
| | - Fan Song
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; (S.X.); (Y.W.); (Y.L.); (Z.C.); (F.S.); (H.L.)
| | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; (S.X.); (Y.W.); (Y.L.); (Z.C.); (F.S.); (H.L.)
| | - Wanzhi Cai
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; (S.X.); (Y.W.); (Y.L.); (Z.C.); (F.S.); (H.L.)
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Wang L, Ding S, Cameron SL, Li X, Liu Y, Yao G, Yang D. Middle Jurassic origin in India: a new look at evolution of Vermileonidae and time-scaled relationships of lower brachyceran flies. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Vermileonidae (wormlions) comprises 61 described species in 12 genera and is one of the oddest and most rarely collected dipteran families. Larvae of Vermileonidae are famous for their pitfall prey behaviour, whereas the adults are rarely seen. Here we report, for the first time, the complete mitochondrial genome from members of Vermileonidae. Phylogenetic reconstruction based on a representative sampling of the order reveals new insights into relationships between the Vermileonidae and other members of lower brachyceran flies. A sister-group relationship between Vermileonidae and Xylophagidae is supported, and the higher-level clade relationships are Tabanomorpha + (Muscomorpha + (Xylophagomorpha + Stratiomyomorpha)). Combining mitochondrial genome data with a morphological phylogeny, geographical distribution and geological history, we propose that the Vermileonidae originated in India during the Middle Jurassic, spreading to Africa via land bridges during the Late Jurassic, to the Palaearctic after the collision of India with Laurasia in the Late Oligocene, and to the Nearctic in the Early Miocene, via either North Atlantic or Beringian land bridges. Wet forested regions have proved to be barriers to their dispersal, explaining their absence from Central Africa, South America and eastern North America.
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Affiliation(s)
- Liang Wang
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Shuangmei Ding
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Stephen L Cameron
- Department of Entomology, Purdue University, West Layfayette, IN, USA
| | - Xin Li
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Yue Liu
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Gang Yao
- Jinhua Polytechnic, Jinhua, Zhejiang, China
| | - Ding Yang
- College of Plant Protection, China Agricultural University, Beijing, China
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27
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Mello CADA, Amorim IC, Silva AFD, Medeiros GRD, Wallau GL, Moura RDCD. Mitogenome of Coprophanaeus ensifer and phylogenetic analysis of the Scarabaeidae family (Coleoptera). Genet Mol Biol 2021; 44:e20200417. [PMID: 34387299 PMCID: PMC8361247 DOI: 10.1590/1678-4685-gmb-2020-0417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 05/02/2021] [Indexed: 12/02/2022] Open
Abstract
Several studies about the phylogenetic relationships of the Scarabaeinae subfamily (Coleoptera: Scarabaeidae) have been performed, but some phylogenetic uncertainties persist including the relationship and monophyly of different tribes and some genera. The aim of this study was to characterize the mitogenome of Coprophanaeus ensifer in order to establish its position within the Scarabaeidae family and to contribute to the resolution of some phylogenetic uncertainties. The mitogenome was sequenced on the Illumina HiSeq 4000, assembled using the Mitobim software and annotated in MITOS WebServer. The phylogenetic trees were reconstructed by Bayesian inference. The C. ensifer mitogenome is a molecule of 14,964 bp that contains the number and organization of the genes similar to those of most Coleoptera species. Phylogenetic reconstruction suggests monophyly of the tribe Phanaeini and supports the hypothesis that Coprini is a sister group of Phanaeini. The results also revealed the position of the tribe Oniticellini which is grouped with Onthophagini and Onitini. The geographic distribution of these species that form the most ancestral clade suggests with Scarabaeinae originated in Africa.
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Affiliation(s)
| | - Igor Costa Amorim
- Universidade de Pernambuco, Instituto de Ciências Biológicas, Laboratório de Biodiversidade e Genética de Insetos, Recife, PE, Brazil
| | | | - Giuliene Rocha de Medeiros
- Universidade de Pernambuco, Instituto de Ciências Biológicas, Laboratório de Biodiversidade e Genética de Insetos, Recife, PE, Brazil
| | - Gabriel Luz Wallau
- Departamento de Entomologia, Instituto Aggeu Magalhães - FIOCRUZ, Recife, Pernambuco, Brazil
| | - Rita de Cássia de Moura
- Universidade de Pernambuco, Instituto de Ciências Biológicas, Laboratório de Biodiversidade e Genética de Insetos, Recife, PE, Brazil
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28
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Lin C, Yang D. The mitochondrial genome of Lichtwardtia dentalis Zhang, Masunaga et Yang, 2009 (Diptera: Dolichopodidae). Mitochondrial DNA B Resour 2021; 6:2266-2268. [PMID: 34286094 PMCID: PMC8266247 DOI: 10.1080/23802359.2021.1948369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The long-legged fly Lichtwardtia dentalis Zhang, Masunaga et Yang, 2009 belongs to the subfamily Dolichopodinae of Dolichopodidae. The newly sequenced mitogenome of L. dentalis is a new representative of the subfamily. The nearly complete mitogenome is 15,124 bp in length, consisting of 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), and 22 transfer RNA genes (tRNAs). All genes have similar locations and encoding directions with that of other published mitogenomes of Dolichopodidae. The nucleotide composition biases toward A and T with the overall A + T % is 73.9%. All protein-coding genes initiate with standard start codon ATN except COI and NAD1, and TAA/TAG are conventionally used as stop codons. All tRNAs, ranging from 62 to 71 bp, have a clover-leaf structure. Based on the result of the phylogenetic analysis, Dolichopodidae and Empididae were monophyletic, and the relationships among subfamilies of Dolichopodidae were Diaphorinae + (Peloropeodinae + (Xanthochlorinae + (Medeterinae + Dolichopodinae))). The monophyly of the subfamily Dolichopodinae and the sister relationship between Dolichopus and Lichtwardtia were also strongly supported.
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Affiliation(s)
- Chen Lin
- Institute of Life Science and Technology, Inner Mongolia Normal University, Hohhot, PR China
- College of Plant Protection, China Agricultural University, Beijing, PR China
| | - Ding Yang
- College of Plant Protection, China Agricultural University, Beijing, PR China
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29
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Peris D, Delclòs X, Jordal B. Origin and evolution of fungus farming in wood-boring Coleoptera - a palaeontological perspective. Biol Rev Camb Philos Soc 2021; 96:2476-2488. [PMID: 34159702 DOI: 10.1111/brv.12763] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 12/11/2022]
Abstract
Insect-fungus mutualism is one of the better-studied symbiotic interactions in nature. Ambrosia fungi are an ecological assemblage of unrelated fungi that are cultivated by ambrosia beetles in their galleries as obligate food for larvae. Despite recently increased research interest, it remains unclear which ecological factors facilitated the origin of fungus farming, and how it transformed into a symbiotic relationship with obligate dependency. It is clear from phylogenetic analyses that this symbiosis evolved independently many times in several beetle and fungus lineages. However, there is a mismatch between palaeontological and phylogenetic data. Herein we review, for the first time, the ambrosia system from a palaeontological perspective. Although largely ignored, families such as Lymexylidae and Bostrichidae should be included in the list of ambrosia beetles because some of their species cultivate ambrosia fungi. The estimated origin for some groups of ambrosia fungi during the Cretaceous concurs with a known high diversity of Lymexylidae and Bostrichidae at that time. Although potentially older, the greatest radiation of various ambrosia beetle lineages occurred in the weevil subfamilies Scolytinae and Platypodinae during the Eocene. In this review we explore the evolutionary relationship between ambrosia beetles, fungi and their host trees, which is likely to have persisted for longer than previously supposed.
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Affiliation(s)
- David Peris
- Institute of Geosciences, University of Bonn, Nussallee 8, Bonn, 53115, Germany.,Department of Earth and Ocean Dynamics, Faculty of Earth Sciences, University of Barcelona, Martí i Franquès s/n, Barcelona, 08028, Spain
| | - Xavier Delclòs
- Department of Earth and Ocean Dynamics, Faculty of Earth Sciences, University of Barcelona, Martí i Franquès s/n, Barcelona, 08028, Spain.,Biodiversity Research Institute (IRBio), University of Barcelona, Avinguda Diagonal 643, Barcelona, 08028, Spain
| | - Bjarte Jordal
- Museum of Natural History, University Museum of Bergen, University of Bergen, Haakon Sheteligs plass 10, Bergen, N-5007, Norway
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Liu Y, Wang J, Yang D. The mitochondrial genome of Desmomyia sinensis (Diptera: Rhagionidae). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:1837-1839. [PMID: 34124361 PMCID: PMC8183545 DOI: 10.1080/23802359.2021.1934166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The mitochondrial genome of Desmomyia sinensis Yang et Yang, 1997 was sequenced, the new representative of the family Rhagionidae. The complete mitochondrial genome is 16,430 bp totally, which consists of 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and one non-coding control region. The nucleotide composition is biased toward A and T, accounting for 77.9% of the total. All genes have the conservational arrangement like other published species of Rhagionidae. Bayesian inference analysis strongly supported the monophyly of Rhagionidae and sister relationship between Coenomyiidae and Xylophagidae. The phylogenetic relationship among families of Tabanomorpha is very clear: (Athericidae + Tabanidae) + (Rhagionidae + (Coenomyiinae + Xylophagidae)).
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Affiliation(s)
- Yue Liu
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Jingyu Wang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Ding Yang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
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Liu J, Xiao J, Hao X, Yuan X. Unique Duplication of trnN in Odontoptilum angulatum (Lepidoptera: Pyrginae) and Phylogeny within Hesperiidae. INSECTS 2021; 12:insects12040348. [PMID: 33919713 PMCID: PMC8070526 DOI: 10.3390/insects12040348] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/08/2021] [Accepted: 04/12/2021] [Indexed: 12/11/2022]
Abstract
To explore the variation and relationship between gene rearrangement and phylogenetic effectiveness of mitogenomes among lineages of the diversification of the tribe Tagiadini in the subfamily Pyrginae, we sequenced the complete mitogenome of Odontoptilum angulatum. The genome is 15,361 bp with the typical 37 genes, a large AT-rich region and an additional trnN (trnN2), which is completely identical to trnN (sequence similarity: 100%). The gene order differs from the typical Lepidoptera-specific arrangement and is unique to Hesperiidae. The presence of a "pseudo-trnS1" in the non-coding region between trnN1 and trnN2 supports the hypothesis that the presence of an extra trnN can be explained by the tandem duplication-random loss (TDRL) model. Regarding the phylogenetic analyses, we found that the dataset comprising all 37 genes produced the highest node support, as well as a monophyly of Pyrginae, indicating that the inclusion of RNAs improves the phylogenetic signal. Relationships among the subfamilies in Hesperiidae were also in general agreement with the results of previous studies. The monophyly of Tagiadini is strongly supported. Our study provides a new orientation for application of compositional and mutational biases of mitogenomes in phylogenetic analysis of Tagiadini and even all Hesperiidae based on larger taxon sampling in the future.
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Affiliation(s)
- Jiaqi Liu
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, Entomological Museum, College of Plant Protection, Northwest A&F University, Yangling 712100, China; (J.L.); (J.X.)
| | - Jintian Xiao
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, Entomological Museum, College of Plant Protection, Northwest A&F University, Yangling 712100, China; (J.L.); (J.X.)
| | - Xiangyu Hao
- College of Life Sciences, Northwest A&F University, Yangling 712100, China;
| | - Xiangqun Yuan
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, Entomological Museum, College of Plant Protection, Northwest A&F University, Yangling 712100, China; (J.L.); (J.X.)
- Correspondence: ; Tel.: +86-1375-998-5152
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Du Z, Wu Y, Chen Z, Cao L, Ishikawa T, Kamitani S, Sota T, Song F, Tian L, Cai W, Li H. Global phylogeography and invasion history of the spotted lanternfly revealed by mitochondrial phylogenomics. Evol Appl 2021; 14:915-930. [PMID: 33897812 PMCID: PMC8061274 DOI: 10.1111/eva.13170] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 12/12/2022] Open
Abstract
Biological invasion has been a serious global threat due to increasing international trade and population movements. Tracking the source and route of invasive species and evaluating the genetic differences in their native regions have great significance for the effective monitoring and management, and further resolving the invasive mechanism. The spotted lanternfly Lycorma delicatula is native to China and invaded South Korea, Japan, and the United States during the last decade, causing severe damages to the fruits and timber industries. However, its global phylogeographic pattern and invasion history are not clearly understood. We applied high-throughput sequencing to obtain 392 whole mitochondrial genome sequences from four countries to ascertain the origin, dispersal, and invasion history of the spotted lanternfly. Phylogenomic analyses revealed that the spotted lanternfly originated from southwestern China, diverged into six phylogeographic lineages, and experienced northward expansion across the Yangtze River in the late Pleistocene. South Korea populations were derived from multiple invasions from eastern China and Japan with two different genetic sources of northwestern (Loess Plateau) and eastern (East Plain) lineages in China, whereas the each of Japan and the United States had only one. The United States populations originated through single invasive event from South Korea, which served as a bridgehead of invasion. The environmental conditions, especially the distribution of host Ailanthus trees, and adaptability possibly account for the rapid spread of the spotted lanternfly in the native and introduced regions.
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Affiliation(s)
- Zhenyong Du
- Department of EntomologyMOA Key Lab of Pest Monitoring and Green ManagementCollege of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Yunfei Wu
- Department of EntomologyMOA Key Lab of Pest Monitoring and Green ManagementCollege of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Zhuo Chen
- Department of EntomologyMOA Key Lab of Pest Monitoring and Green ManagementCollege of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Liangming Cao
- The Key Laboratory of Forest ProtectionNational Forestry and Grassland AdministrationResearch Institute of Forest Ecology, Environment and ProtectionChinese Academy of ForestryBeijingChina
| | - Tadashi Ishikawa
- Laboratory of EntomologyFaculty of AgricultureTokyo University of AgricultureAtsugiJapan
| | - Satoshi Kamitani
- Entomological LaboratoryGraduate School of Bioresource and Bioenvironmental SciencesKyushu UniversityFukuokaJapan
| | - Teiji Sota
- Department of ZoologyGraduate School of ScienceKyoto UniversitySakyoJapan
| | - Fan Song
- Department of EntomologyMOA Key Lab of Pest Monitoring and Green ManagementCollege of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Li Tian
- Department of EntomologyMOA Key Lab of Pest Monitoring and Green ManagementCollege of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Wanzhi Cai
- Department of EntomologyMOA Key Lab of Pest Monitoring and Green ManagementCollege of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Hu Li
- Department of EntomologyMOA Key Lab of Pest Monitoring and Green ManagementCollege of Plant ProtectionChina Agricultural UniversityBeijingChina
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Liu J, Li X, Cai X, Du B, Liu X, Yang D. The complete mitochondrial genome of Dicraeus orientalis Becker, 1911 (Diptera: Chloropidae). Mitochondrial DNA B Resour 2021; 6:951-952. [PMID: 33796695 PMCID: PMC7995912 DOI: 10.1080/23802359.2021.1889414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dicraeus orientalis feeds on the seeds of Poaceae. The complete mitochondrial genome of D. orientalis was sequenced and annotated as the first representative of the family Chloropidae. The full length of mitogenome was 16,188 bp, consisting of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs). The nucleotide composition was highly A + T biased, accounting for 79.1% of the whole mitogenome. All PCGs start with ATN codons except COI, which end with TAN or incomplete stop codon. ML analysis revealed that Carnoidea was closely related to Ephydroidea and the phylogenetic relationship within Acalyptratae was Tephritoidea + ((Carnoidea + Ephydroidea) + Opomyzoidea).
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Affiliation(s)
- Jiuzhou Liu
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xin Li
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Xiaodong Cai
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Bintao Du
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiaoyan Liu
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ding Yang
- College of Plant Protection, China Agricultural University, Beijing, China
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Chamorro ML, de Medeiros BAS, Farrell BD. First phylogenetic analysis of Dryophthorinae (Coleoptera, Curculionidae) based on structural alignment of ribosomal DNA reveals Cenozoic diversification. Ecol Evol 2021; 11:1984-1998. [PMID: 33717436 PMCID: PMC7920784 DOI: 10.1002/ece3.7131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 11/10/2020] [Accepted: 11/12/2020] [Indexed: 01/09/2023] Open
Abstract
Dryophthorinae is an economically important, ecologically distinct, and ubiquitous monophyletic group of pantropical weevils with more than 1,200 species in 153 genera. This study provides the first comprehensive phylogeny of the group with the aim to provide insights into the process and timing of diversification of phytophagous insects, inform classification and facilitate predictions. The taxon sampling is the most extensive to date and includes representatives of all five dryophthorine tribes and all but one subtribe. The phylogeny is based on secondary structural alignment of 18S and 28S rRNA totaling 3,764 nucleotides analyzed under Bayesian and maximum likelihood inference. We used a fossil-calibrated relaxed clock model with two approaches, node-dating and fossilized birth-death models, to estimate divergence times for the subfamily. All tribes except the species-rich Rhynchophorini were found to be monophyletic, but higher support is required to ascertain the paraphyly of Rhynchophorini with more confidence. Nephius is closely related to Dryophthorini and Stromboscerini, and there is strong evidence for paraphyly of Sphenophorina. We find a large gap between the divergence of Dryophthorinae from their sister group Platypodinae in the Jurassic-Cretaceous boundary and the diversification of extant species in the Cenozoic, highlighting the role of coevolution with angiosperms in this group.
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Affiliation(s)
- Maria Lourdes Chamorro
- Systematic Entomology LaboratoryARS, USDA, c/o National Museum of Natural HistoryWashingtonDCUSA
| | | | - Brian D. Farrell
- Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeMAUSA
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35
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Song N, Zhai Q, Zhang Y. Higher-level phylogenetic relationships of rove beetles (Coleoptera, Staphylinidae) inferred from mitochondrial genome sequences. Mitochondrial DNA A DNA Mapp Seq Anal 2021; 32:98-105. [PMID: 33570440 DOI: 10.1080/24701394.2021.1882444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Rove beetles (Staphylinidae) and allied families constitute a huge radiation of Coleoptera, but basal relationships in this group remain controversial. In this study, we newly sequenced eight mitogenomes of representatives of Staphylinidae by using next-generation sequencing method. Together with 99 existing mitogenomes of Staphyliniformia, (sub)family relationships were investigated with ML and Bayesian searches under various substitution models and data recoding schemes. The results consistently supported Scydmaenidae and Silphidae to be subordinate groups of Staphylinidae. Within the monophyletic Staphylinidae (including Scydmaenidae and Silphidae), the hypothesis of four major subfamily groups cannot be confirmed. Bayesian inferences under the site-heterogeneous mixture model generally supported the basal position of major clades corresponding to the Omaliine group. At the subfamily level, the monophyly of Pselaphinae, Oxytelinae, Scaphidiinae, Steninae and Staphylininae was supported. However, the subfamilies Omaliinae, Tachyporinae, Aleocharinae and Paederinae were each non-monophyletic.
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Affiliation(s)
- Nan Song
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Qing Zhai
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Yaling Zhang
- Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa, China
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36
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Zhao C, Kang Z, Xu Y, Zhang X. Tanyptera (Tanyptera) hebeiensis Yang et Yang (Diptera: Tipulidae) newly recorded from Shandong, China: sequencing and phylogenetic analysis of the mitochondrial genome. Mitochondrial DNA B Resour 2021; 6:115-118. [PMID: 33521282 PMCID: PMC7819113 DOI: 10.1080/23802359.2020.1848478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 11/04/2020] [Indexed: 11/25/2022] Open
Abstract
The genus Tanyptera Latreille, 1804 is recorded from Shandong Province, China for the first time with T. (T.) hebeiensis Yang et Yang, 1988 found in Mount Kunyu, Shandong. In this study, we report the complete mitochondrial genome sequence of T. (T.) hebeiensis, representing the first mitochondrial genome of the subfamily Ctenophorinae (Diptera: Tipulidae), which is a circular molecule of 15,888 bp with an AT content of 77.6%. The mitochondrial genome contains 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a non-coding region. Gene overlaps are found at nine gene junctions, ranging from 1 to 8 bp in length. The canonical mitochondrial start codons for invertebrate mitochondrial genomes are found in 12 PCGs, except for COI which uses the uncanonical start codons TCG. Stop codons of 10 PCGs are invariably complete TAA and TAG, while COII, ND4, and ND5 end with a single thymine stop codon. Phylogenetic analysis reveals that the Pediciidae is a sister group to the remaining Tipuloidea, the Cylindrotomidae has a sister-group relationship with the Tipulidae, and the Limoniidae is not a monophyletic clade.
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Affiliation(s)
- Chuande Zhao
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Zehui Kang
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Yuanyuan Xu
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Xiao Zhang
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
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Arribas P, Andújar C, Moraza ML, Linard B, Emerson BC, Vogler AP. Mitochondrial Metagenomics Reveals the Ancient Origin and Phylodiversity of Soil Mites and Provides a Phylogeny of the Acari. Mol Biol Evol 2020; 37:683-694. [PMID: 31670799 DOI: 10.1093/molbev/msz255] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
High-throughput DNA methods hold great promise for phylogenetic analysis of lineages that are difficult to study with conventional molecular and morphological approaches. The mites (Acari), and in particular the highly diverse soil-dwelling lineages, are among the least known branches of the metazoan Tree-of-Life. We extracted numerous minute mites from soils in an area of mixed forest and grassland in southern Iberia. Selected specimens representing the full morphological diversity were shotgun sequenced in bulk, followed by genome assembly of short reads from the mixture, which produced >100 mitochondrial genomes representing diverse acarine lineages. Phylogenetic analyses in combination with taxonomically limited mitogenomes available publicly resulted in plausible trees defining basal relationships of the Acari. Several critical nodes were supported by ancestral-state reconstructions of mitochondrial gene rearrangements. Molecular calibration placed the minimum age for the common ancestor of the superorder Acariformes, which includes most soil-dwelling mites, to the Cambrian-Ordovician (likely within 455-552 Ma), whereas the origin of the superorder Parasitiformes was placed later in the Carboniferous-Permian. Most family-level taxa within the Acariformes were dated to the Jurassic and Triassic. The ancient origin of Acariformes and the early diversification of major extant lineages linked to the soil are consistent with a pioneering role for mites in building the earliest terrestrial ecosystems.
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Affiliation(s)
- Paula Arribas
- Island Ecology and Evolution Research Group, IPNA-CSIC, La Laguna, Tenerife, Spain.,Department of Life Sciences, Natural History Museum, London, United Kingdom.,Department of Life Sciences, Imperial College London, Ascot, United Kingdom
| | - Carmelo Andújar
- Island Ecology and Evolution Research Group, IPNA-CSIC, La Laguna, Tenerife, Spain.,Department of Life Sciences, Natural History Museum, London, United Kingdom.,Department of Life Sciences, Imperial College London, Ascot, United Kingdom
| | - María Lourdes Moraza
- Departamento de Biología Ambiental, Universidad de Navarra, Facultad de Ciencias, Pamplona, Spain
| | - Benjamin Linard
- Department of Life Sciences, Natural History Museum, London, United Kingdom.,LIRMM, Université de Montpellier, CNRS, Montpellier, France.,ISEM, Université de Montpellier, CNRS, IRD, EPHE, CIRAD, INRAP, Montpellier, France
| | - Brent C Emerson
- Island Ecology and Evolution Research Group, IPNA-CSIC, La Laguna, Tenerife, Spain
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, United Kingdom.,Department of Life Sciences, Imperial College London, Ascot, United Kingdom
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38
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Salazar K, Nattier R. New Light on Historical Specimens Reveals a New Species of Ladybird (Coleoptera: Coccinellidae): Morphological, Museomic, and Phylogenetic Analyses. INSECTS 2020; 11:E766. [PMID: 33172182 PMCID: PMC7694756 DOI: 10.3390/insects11110766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/24/2020] [Accepted: 10/27/2020] [Indexed: 11/22/2022]
Abstract
Natural history collections house an important source of genetic data from yet unexplored biological diversity. Molecular data from museum specimens remain underexploited, which is mainly due to the degradation of DNA from specimens over time. However, Next-Generation Sequencing (NGS) technology can now be used to sequence "old" specimens. Indeed, many of these specimens are unique samples of nomenclatural types and can be crucial for resolving systematic or biogeographic scientific questions. Two ladybird beetle specimens from Patagonia corresponding to a new species of the genus Eriopis Mulsant were found in the collections of the Muséum national d'Histoire naturelle (MNHN), Paris. Here, we describe Eriopis patagonia Salazar, sp. nov. Total DNA of one of the two specimens was sequenced by NGS using a paired-end Illumina approach. We reconstruct and characterize the mitochondrial genome of this species (16,194 bp). Then, the protein-coding genes (PCGs) and ribosomal RNAs (rRNAs) were used to infer by maximum likelihood and Bayesian Inference the phylogenetic position of E. patagonia among 27 representatives of Coccinellidae. Phylogenetic analysis confirmed the position of Eriopis as sister group to Cycloneda Crotch. Hence, we highlight the high potential of sequencing technology for extracting molecular information from old specimens, which are used here for the systematic study of a genus, while demonstrating the importance of preserving biological collections.
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Affiliation(s)
- Karen Salazar
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005 Paris, France;
- Grupo de Investigación Insectos de Colombia, Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Ciudad Universitaria, Bogotá 111321, Colombia
| | - Romain Nattier
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005 Paris, France;
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Lei G, Fu Y, Wu WJ. Type and distribution of sensilla in the antennae of Euplatypus parallelus (F.) (Coleoptera: Curculionidea, Platypodinae). PLoS One 2020; 15:e0241275. [PMID: 33108376 PMCID: PMC7591032 DOI: 10.1371/journal.pone.0241275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/12/2020] [Indexed: 11/18/2022] Open
Abstract
Euplatypus parallelus (F.) (Coleoptera: Curculionidea) is the most destructive cosmopolitan insect pest of the Platypodinae. Pheromone-based luring agents are used currently in controlling bark beetle. Antennae are the primary insect organs sensing volatiles of host trees and pheromones of pioneer males. We studied the external morphology of antennae and the type, distribution, and the number of the beetle sensilla. Our results show E. parallelus have a geniculate antenna composed of 6 segments, namely the scape, 4-segmented funicle and club. Ninety-seven percent of the antennal sensors were distributed in the club, and 3% were distributed in the scape and funicle. 6 types of sensilla on the antennae were found, including sensilla trichodea (subtypes: STI, STII and STIII), sensilla basiconica (subtypes: SBI, SBII, SBIII and SBIV), sensilla chaetica (subtypes: SChI, SChII and SChIII), as well as sensilla coeloconica, sensilla campaniform and sensilla furcatea. There was no significant difference in the type, distribution and number of sensilla in males and females. No significant difference in the shape and distribution of antennae was found between sexes, but the length of antennae and the number of SChI, SChII, STI, SBI, SBIII and SBIV were significantly larger in females than males. We revealed the external cuticular structure of the antennae in E. parallelus, which can be used to guide future electrophysiological investigations to understand the ability of this beetle to detect semiochemicals.
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Affiliation(s)
- Gaoke Lei
- Laboratory of Insect Ecology, South China Agricultural University, Guangzhou, China
| | - Yueguan Fu
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Science, Haikou, China
| | - Wei-Jian Wu
- Laboratory of Insect Ecology, South China Agricultural University, Guangzhou, China
- * E-mail:
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40
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Chen Z, Liu Y, Wu Y, Song F, Cai W, Li H. Novel tRNA gene rearrangements in the mitochondrial genome of Camarochiloides weiweii (Hemiptera: Pachynomidae). Int J Biol Macromol 2020; 165:1738-1744. [PMID: 33069822 DOI: 10.1016/j.ijbiomac.2020.10.051] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 09/19/2020] [Accepted: 10/07/2020] [Indexed: 12/13/2022]
Abstract
Pachynomidae is a poorly known heteropteran group currently considered as a distinct family closely related to Reduviidae. Taxonomic position of Pachynomidae has been debated for a long time. Knowledge about mitochondrial genome (mitogenome) of this family also remain limited. In the present study, we describe the complete mitogenome of Camarochiloides weiweii, the first mitogenome sequenced for this family. This mitogenome consists of 13 protein-coding genes, two rRNA genes and 21 tRNA genes. Two tRNA gene rearrangements in this genome, including the translocation of trnA and trnR as well as the transposition of trnH, were observed and could be explained by the tandem duplication-random loss (TDRL) model. Bayesian and maximum likelihood analyses based on sequences of three different mitogenomic datasets recovered the monophyly of Reduvioidea, and the sister relationship between Reduvioidea and the remaining Cimicomorpha lineages. This study enlightens the future application of mitogenomic data in the phylogenetic study of Cimicomorpha based on the large-scale sampling.
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Affiliation(s)
- Zhuo Chen
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Yingqi Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Yunfei Wu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Fan Song
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Wanzhi Cai
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China.
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Narakusumo RP, Riedel A, Pons J. Mitochondrial genomes of twelve species of hyperdiverse Trigonopterus weevils. PeerJ 2020; 8:e10017. [PMID: 33083123 PMCID: PMC7566755 DOI: 10.7717/peerj.10017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 09/01/2020] [Indexed: 11/20/2022] Open
Abstract
Mitochondrial genomes of twelve species of Trigonopterus weevils are presented, ten of them complete. We describe their gene order and molecular features and test their potential for reconstructing the phylogeny of this hyperdiverse genus comprising > 1,000 species. The complete mitochondrial genomes examined herein ranged from 16,501 bp to 21,007 bp in length, with an average AT content of 64.2% to 69.7%. Composition frequencies and skews were generally lower across species for atp6, cox1-3, and cob genes, while atp8 and genes coded on the minus strand showed much higher divergence at both nucleotide and amino acid levels. Most variation within genes was found at the codon level with high variation at third codon sites across species, and with lesser degree at the coding strand level. Two large non-coding regions were found, CR1 (between rrnS and trnI genes) and CR2 (between trnI and trnQ), but both with large variability in length; this peculiar structure of the non-coding region may be a derived character of Curculionoidea. The nad1 and cob genes exhibited an unusually high interspecific length variation of up to 24 bp near the 3' end. This pattern was probably caused by a single evolutionary event since both genes are only separated by trnS2 and length variation is extremely rare in mitochondrial protein coding genes. We inferred phylogenetic trees using protein coding gene sequences implementing both maximum likelihood and Bayesian approaches, each for both nucleotide and amino acid sequences. While some clades could be retrieved from all reconstructions with high confidence, there were also a number of differences and relatively low support for some basal nodes. The best partition scheme of the 13 protein coding sequences obtained by IQTREE suggested that phylogenetic signal is more accurate by splitting sequence variation at the codon site level as well as coding strand, rather than at the gene level. This result corroborated the different patterns found in Trigonopterus regarding to A+T frequencies and AT and GC skews that also greatly diverge at the codon site and coding strand levels.
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Affiliation(s)
- Raden Pramesa Narakusumo
- State Museum of Natural History Karlsruhe, Karlsruhe, Germany.,Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | | | - Joan Pons
- Diversidad Animal y Microbiana, Instituto Mediterráneo de Estudios Avanzados IMEDEA (CSIC-UIB), Esporles, Balearic Islands, Spain
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Mitochondrial genomes of stick insects (Phasmatodea) and phylogenetic considerations. PLoS One 2020; 15:e0240186. [PMID: 33021991 PMCID: PMC7537864 DOI: 10.1371/journal.pone.0240186] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 09/22/2020] [Indexed: 11/24/2022] Open
Abstract
Phasmatodea represents an order of hemimetabolous insects. This group includes species with extreme forms of masquerade crypsis, whereby they imitate twigs, bark, lichen, moss, and leaves. In this study, we sequenced and annotated three mitochondrial genomes (mitogenomes) from Phasmatodea. The lengths of the novel mitogenomes range from 14,162 bp to 15,879 bp. The gene content and organization correspond to those inferred for the ancestral insect. We conducted phylogenetic analyses together with the existing mitogenomes of polyneopterans and mayflies. In most cases, the Phasmatodea was non-monophyletic, with Embioptera and Zoraptera nested inside. The mitogenome sequences from Embioptera and Zoraptera suffered from high substitution rates and displayed very long branches in phylogenetic trees. The monophyletic Phasmatodea was recovered only when the analysis employed the site-heterogeneous CAT-GTR model in PhyloBayes and used the nucleotide dataset PCG_nt. The Euphasmatodea was well established by various data types and inference methods. In addition, the clade Heteropterygidae and the subfamilies Lonchodinae and Necrosciinae were strongly supported. The Australasian clade Lanceocercata was recovered across analyses. However, the Clitumninae was non-monophyletic.
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Gillett CPDT, Toussaint EFA. Macroevolution and shifts in the feeding biology of the New World scarab beetle tribe Phanaeini (Coleoptera: Scarabaeidae: Scarabaeinae). Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa058] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The New World scarab beetle tribe Phanaeini contains coprophagous, necrophagous, mycetophagous and suspected myrmecophilous species. We analyse the largest tribal molecular dataset assembled, incorporating, for the first time, the enigmatic monobasic genus Megatharsis, the thalassinus group of the subgenus Coprophanaeus (Metallophanaeus), and the subgenus Dendropaemon (Eurypodea) (formerly Tetramereia), unveiling their macroevolutionary and biogeographical history in light of Cenozoic abiotic changes and inferring shifts in feeding biology through time. We recover the contentious genus Gromphas outside an otherwise monophyletic Phanaeini. We infer Megatharsis in a clade containing the apparent myrmecophilous genus Dendropaemon, within the Coprophanaeus clade, and demonstrate that the subgenus Coprophanaeus (Metallophanaeus) is polyphyletic, whilst species groups within the subgenus Coprophanaeus (Coprophanaeus) are monophyletic. Our divergence time analyses and ancestral range estimation indicate an eastern South American origin for Phanaeini in the early Eocene, with subsequent colonization of Central America and the Nearctic during the Oligocene, long before a Panamanian land bridge. A shift to necrophagy in Coprophanaeus is possibly linked to increasing Neotropical small vertebrate diversity since the Eocene and, astonishingly, myrmecophily evolved from necrophagy 35 Mya. These drastic shifts in lifestyle are not concordant with variations in diversification rates and appear unlinked to Quaternary extinction of large mammals.
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Affiliation(s)
- Conrad P D T Gillett
- University of Hawaiʻi Insect Museum, College of Tropical Agriculture and Human Resources, University of Hawaiʻi at Mānoa, Maile Way, Honolulu, HI, USA
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Feng Z, Wu Y, Yang C, Gu X, Wilson JJ, Li H, Cai W, Yang H, Song F. Evolution of tRNA gene rearrangement in the mitochondrial genome of ichneumonoid wasps (Hymenoptera: Ichneumonoidea). Int J Biol Macromol 2020; 164:540-547. [PMID: 32693134 DOI: 10.1016/j.ijbiomac.2020.07.149] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/10/2020] [Accepted: 07/13/2020] [Indexed: 12/21/2022]
Abstract
Gene rearrangements in the mitochondrial genome (mt genome) are common in certain insect groups and can be an informative character for phylogenetic reconstruction. However, knowledge of the mechanism and biases of gene rearrangement in insect mt genomes is still limited. With an accelerated rate of gene rearrangements, Hymenoptera is an important group for mt genome rearrangements diversity and for understanding the gene rearrangement evolution in mt genomes. Here, we sequenced the complete mt genome of Aphidius gifuensis and analyzed the evolution of tRNA gene rearrangements in the mt genomes of ichneumonoid wasps. Two control regions were detected in A. gifuensis and most of the tRNA rearrangement events occurred around these control regions. tRNA gene rearrangements occurred in almost all of the sequenced mt genomes of Ichneumonoidea and the gene block CR-trnI-trnQ-trnM-ND2-trnW-trnC-trnY was the main hot spot of gene rearrangement. Mapped over the backbone phylogeny of Ichneumonoidea, we found that the inversion and translocation of both trnI and trnM is likely a synapomorphic rearrangement in Braconidae. Our study also demonstrated that the gene block CR-trnI-trnQ-trnM-ND2-trnW-trnC-trnY was important for inferring the gene rearrangement dynamics in Ichneumonoidea.
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Affiliation(s)
- Zengbei Feng
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Yunfei Wu
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Chun Yang
- Tobacco Company, Yuxi 653100, Yunnan, China
| | - Xinghui Gu
- Tobacco Company, Yuxi 653100, Yunnan, China
| | - John James Wilson
- Vertebrate Zoology at World Museum, National Museums Liverpool, Liverpool, UK; Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Hu Li
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Wanzhi Cai
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Hailin Yang
- Tobacco Company, Yuxi 653100, Yunnan, China.
| | - Fan Song
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China.
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45
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Ma S, Kang Z. Sequence analysis of mitochondrial genome of the false and phantom crane-fly Ptychoptera qinggouensis Kang, Yao and Yang, 2013 (Diptera, Ptychopteridae). Mitochondrial DNA B Resour 2020; 5:2767-2769. [PMID: 33457942 PMCID: PMC7782171 DOI: 10.1080/23802359.2020.1788452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 06/20/2020] [Indexed: 11/25/2022] Open
Abstract
The genus Ptychoptera Meigen, 1803 is the largest genus of the family Ptychopteridae with 78 known species. In this study, we report a nearly complete mitochondrial (mt) genome of this genus, which is a circular molecule of more than 15,028 bp. The mt genome contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a non-coding region. The overall base composition is A (38.1%), T (36.7%), C (14.9%), and G (10.4%), with an AT content of 74.8%. The AT content of N-strand genes (75.7%) is higher than that of the J-strand genes (71.7%). Phylogenetic analysis reveals that the monophyly of Ptychopteridae, Bibiomorpha, Tipulomorpha and Brachycera are strongly supported, and the sister group relationship between Tanyderidae and Ptychopteridae is not supported.
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Affiliation(s)
- Shuo Ma
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Zehui Kang
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
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Zhao C, Wang J, Zhang B, Han J, Zhang J, Zhang D, Wang L. The mitochondrial genome of Paralimna (Paralimna) concors (Diptera: Ephydridae). Mitochondrial DNA B Resour 2020; 5:3717-3718. [PMID: 33367073 PMCID: PMC7655072 DOI: 10.1080/23802359.2020.1833374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
The mitogenome of Paralimna (Paralimna) concors was sequenced. The mitogenome was 16,155 bp totally, consisting of 13 protein-coding genes (PCGs), two rRNAs, and 22 transfer RNAs. The nucleotide composition biases toward A and T is 78.6% of the entirety. All PCGs start with ATN codons except COI and ND1, and end with TAA or incomplete stop codon. Phylogenetic analyses based on 11 dipteran species supported the monophyly of Ephydroidea and the relationship of Opomyzoidea + (Ephydroidea + (Lauxanioidea + (Sphaeroceroidea + (Sciomyzoidea + Tephritoidea)))).
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Affiliation(s)
- Chenjing Zhao
- Department of Biology, Taiyuan Normal University, Jinzhong, PR China
| | - Jiaojie Wang
- College of Plant Protection, China Agricultural University, Beijing, PR China
| | - Bing Zhang
- College of Plant Protection, China Agricultural University, Beijing, PR China
| | - Jiangwan Han
- Forestry Technology Comprehensive Service Station of Diebu, Diebu, PR China
| | - Junhua Zhang
- Institute of Animal and Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, PR China
| | - Danli Zhang
- Department of Biology, Taiyuan Normal University, Jinzhong, PR China
| | - Liang Wang
- College of Plant Protection, China Agricultural University, Beijing, PR China
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Ding S, Yang D. Complete mitochondrial genome of Coenomyia ferruginea (Scopoli). (Diptera, Coenomyiidae). Mitochondrial DNA B Resour 2020; 5:2711-2712. [PMID: 33457916 PMCID: PMC7782303 DOI: 10.1080/23802359.2020.1787889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The dipteran family Coenomyiidae was firstly separated from the Xylophagidae by Akrira Nagatomi in 1975. We sequenced and annotated the mitochondrial genome of Coenomyia ferruginea, the first representative of genera Coenomyia with complete mitochondrial data. This mitogenome is 17,283 bp totally, which consists of 22 transfer RNAs, 13 protein-coding genes, 2 ribosomal RNAs, and 1 non-coding control region. All genes have the conservational arrangement like other published species of brachyceran flies. The nucleotide composition biases toward A and T, the overall A + T% was up to 75.4% of the entire mitogenome. Both Bayesian inference and ML analysis strongly supported the sister relationship between Coenomyiidae and Xylophagidae. Our results also suggested that Xylophagomorpha is the sister group to Stratiomyomorpha.
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Affiliation(s)
- Shuangmei Ding
- College of Plant Protection, China Agriculture University, Beijing, China
| | - Ding Yang
- College of Plant Protection, China Agriculture University, Beijing, China
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Bohmann K, Mirarab S, Bafna V, Gilbert MTP. Beyond DNA barcoding: The unrealized potential of genome skim data in sample identification. Mol Ecol 2020; 29:2521-2534. [PMID: 32542933 PMCID: PMC7496323 DOI: 10.1111/mec.15507] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 06/03/2020] [Accepted: 06/05/2020] [Indexed: 02/06/2023]
Abstract
Genetic tools are increasingly used to identify and discriminate between species. One key transition in this process was the recognition of the potential of the ca 658bp fragment of the organelle cytochrome c oxidase I (COI) as a barcode region, which revolutionized animal bioidentification and lead, among others, to the instigation of the Barcode of Life Database (BOLD), containing currently barcodes from >7.9 million specimens. Following this discovery, suggestions for other organellar regions and markers, and the primers with which to amplify them, have been continuously proposed. Most recently, the field has taken the leap from PCR-based generation of DNA references into shotgun sequencing-based "genome skimming" alternatives, with the ultimate goal of assembling organellar reference genomes. Unfortunately, in genome skimming approaches, much of the nuclear genome (as much as 99% of the sequence data) is discarded, which is not only wasteful, but can also limit the power of discrimination at, or below, the species level. Here, we advocate that the full shotgun sequence data can be used to assign an identity (that we term for convenience its "DNA-mark") for both voucher and query samples, without requiring any computationally intensive pretreatment (e.g. assembly) of reads. We argue that if reference databases are populated with such "DNA-marks," it will enable future DNA-based taxonomic identification to complement, or even replace PCR of barcodes with genome skimming, and we discuss how such methodology ultimately could enable identification to population, or even individual, level.
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Affiliation(s)
- Kristine Bohmann
- Section for Evolutionary GenomicsThe GLOBE InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Siavash Mirarab
- Department of Electrical and Computer EngineeringUniversity of CaliforniaSan DiegoCAUSA
| | - Vineet Bafna
- Department of Computer Science and EngineeringUniversity of CaliforniaSan DiegoCAUSA
| | - M. Thomas P. Gilbert
- Section for Evolutionary GenomicsThe GLOBE InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary HologenomicsThe GLOBE InstituteUniversity of CopenhagenCopenhagenDenmark
- NTNU University MuseumTrondheimNorway
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Fu Y, Yu J, Fang X, Shen M, Fu J, Xiao Y. Complete mitochondrial genome of Niphades castanea (Coleoptera: Curculionidae). Mitochondrial DNA B Resour 2020; 5:2403-2405. [PMID: 33457806 PMCID: PMC7781971 DOI: 10.1080/23802359.2020.1772683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 05/16/2020] [Indexed: 11/24/2022] Open
Abstract
Niphades castanea Chao is an important insect pest on many plants which belong to genus Castanea. The complete mitochondrial genome of N. castanea was sequenced and analyzed. The phylogenetic relationships between N. castanea and other 41 species in the family Curculionidae were reconstructed using maximum likelihood (ML) methods based on the concatenated nucleotide sequences, the phylogenetic analysis showed that N. castanea is closely related to Hylobitelus xiaoi, which is in accordance with the traditional morphological classification.
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Affiliation(s)
- Yue Fu
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, China
- Hubei Zhongke Research Institute of Industrial Technology, Huanggang, China
| | - Jiaojun Yu
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, China
- Hubei Zhongke Research Institute of Industrial Technology, Huanggang, China
| | - Xiangliang Fang
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, China
- Hubei Zhongke Research Institute of Industrial Technology, Huanggang, China
| | - Mi Shen
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, China
- Hubei Zhongke Research Institute of Industrial Technology, Huanggang, China
| | - Jun Fu
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, China
- Hubei Zhongke Research Institute of Industrial Technology, Huanggang, China
| | - Yunli Xiao
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, China
- Hubei Zhongke Research Institute of Industrial Technology, Huanggang, China
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Canty R, Ruzzier E, Cronk Q, Percy D. Salix transect of Europe: records of willow-associated weevils (Coleoptera: Curculionoidea) from Greece to Arctic Norway, with insights from DNA barcoding. Biodivers Data J 2020; 8:e52881. [PMID: 32549748 PMCID: PMC7286951 DOI: 10.3897/bdj.8.e52881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 06/01/2020] [Indexed: 11/12/2022] Open
Abstract
Background Curculionid beetles associated with willow (Salix spp.) were surveyed at 42 sites across Europe, from Greece (lat. 38.8 °N) to arctic Norway (lat. 69.7 °N). DNA sequence data provide additional verification of identifications and geographic clustering. New information In all, 73 curculionid species were collected from willows, of which seven were particularly abundant. The most widespread species were: Acalyptuscarpini Fabricius, 1793 at 15 sites; Tachyergesstigma Germar, 1821 at 13 sites; Phyllobiusoblongus (Linnaeus, 1758) at 11 sites; Phyllobiusmaculicornis Germar, 1824 at 10 sites; and Archariussalicivorus (Paykull, 1792), Melanapionminimum (Herbst, 1797), and Phyllobiuscf.pyri (Linnaeus, 1758) all at nine sites. The mean number of curculionid species collected on willow at each site was 5.5 (range 0-14). Compared to chrysomelids, curculionids were richer in species but the species had relatively low average abundance. Widespread curculionid species appear to have scattered and patchy observed distributions with limited geographical structuring in our data. However, deeper sampling (e.g. over multiple seasons and years), would give a better indication of distribution, and may increase apparent geographical structuring. There is some site-to-site variation in colour in a few taxa, but little notable size variation. DNA barcoding, performed on some of the more common species, provides clear species clusters and definitive separation of the taxonomically more challenging species, as well as some interesting geographic insights. Our northernmost sample of Phyllobiusoblongus is unique in clustering with Canadian samples of this species. On the other hand, our samples of Acalyptuscarpini cluster with European samples and are distinct from a separate Canadian cluster of this species. We provide the first available DNA sequences for Phyllobiusthalassinus Gyllenhal, 1834 (Hungary).
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