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Lis JA, Domagała PJ. Inconsistencies in the Classification of the Family Cydnidae (Hemiptera: Heteroptera: Pentatomoidea) Revealed by Molecular Apomorphies in the Secondary and Tertiary Structures of 18S rRNA Length-Variable Region L (LVR L). Int J Mol Sci 2024; 25:939. [PMID: 38256014 PMCID: PMC10815949 DOI: 10.3390/ijms25020939] [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: 11/26/2023] [Revised: 01/02/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
The SSU nuclear rDNA (encoding 18S ribosomal RNA) is one of the most frequently sequenced genes in the molecular analysis of insects. Molecular apomorphies in the secondary and tertiary structures of several 18S rRNA length-variable regions (LVRs) located within the V2, V4, and V7 hypervariable regions can be good indicators for recovering monophyletic groups within some heteropteran families. Among the LVRs that have been analysed, the LVR L in the V4 hypervariable region is the longest and most crucial for such assessments. We analysed the 18S rRNA V4 hypervariable region sequences of 45 species from the family Cydnidae, including all 6 subfamilies (Amaurocorinae, Amnestinae, Cephalocteinae, Cydninae, Garsauriinae, and Sehirinae) and three pentatomoid families (Parastrachiidae, Thaumastellidae, and Thyreocoridae), which have often been included in the broadly defined Cydnidae family. This is the first time that representatives of all Cydnidae subfamilies have been included in a molecular analysis. Only taxa from two subfamilies, Sehirinae and Cydninae, have been used in previous molecular studies. The secondary and tertiary structures of the LVR L were predicted for each species using the two-step procedure already accepted for such analyses to recover any molecular apomorphy essential for determining monophyly. The results of our comparative studies contradict the current understanding of the relationships among burrowing bugs and the current family classification.
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Affiliation(s)
- Jerzy A. Lis
- Institute of Biology, University of Opole, Oleska 22, 45-052 Opole, Poland;
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Lis B, Domagała PJ, Lis JA. Tribe Acalyptaini ( Hemiptera: Tingidae: Tinginae) Revisited: Can Apomorphies in Secondary and Tertiary Structures of 18S rRNA Length-Variable Regions (LVRs) Support Tribe Validity? INSECTS 2023; 14:600. [PMID: 37504606 PMCID: PMC10380217 DOI: 10.3390/insects14070600] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/25/2023] [Accepted: 06/28/2023] [Indexed: 07/29/2023]
Abstract
The lace bug tribe Acalyptaini (Tingidae: Tinginae) includes five genera, Acalypta, Derephysia, Dictyonota, Kalama, and Recaredus, and it was recently resurrected based on morphological and karyological characters. We aimed to validate the distinctiveness of this tribe using 18S rDNA sequences, which have not been used in previous Tingidae phylogenomic studies. Our results confirmed the monophyly of the tribe. Moreover, the monophyly of the subfamily Cantacaderinae and its basal position within the family Tingidae were indicated, as well as the position of the tribe Litadeini as sister to all other Tinginae. In addition, we attempted to determine the apomorphic morpho-molecular characters in the secondary and tertiary structures of length-variable regions of the 18S rRNA sequences of the analysed species. The results showed that two LVRs (LVR X and LVR L) of the hypervariable region V4 exhibited significant variability in the number of nucleotides and could be considered for apomorphic recognition.
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Affiliation(s)
- Barbara Lis
- Institute of Biology, University of Opole, 45-052 Opole, Oleska 22, Poland
| | - Paweł J Domagała
- Institute of Biology, University of Opole, 45-052 Opole, Oleska 22, Poland
| | - Jerzy A Lis
- Institute of Biology, University of Opole, 45-052 Opole, Oleska 22, Poland
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Lis JA. Molecular Apomorphies in the Secondary and Tertiary Structures of Length-Variable Regions (LVRs) of 18S rRNA Shed Light on the Systematic Position of the Family Thaumastellidae (Hemiptera: Heteroptera: Pentatomoidea). Int J Mol Sci 2023; 24:ijms24097758. [PMID: 37175465 PMCID: PMC10178826 DOI: 10.3390/ijms24097758] [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: 04/02/2023] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 05/15/2023] Open
Abstract
The SSU nrDNA, a small subunit of the nuclear ribosomal DNA (coding 18S rRNA), is one of the most frequently sequenced genes in molecular studies in Hexapoda. In insects, including true bugs (Hemiptera: Heteroptera), only its primary structures (i.e., aligned sequences) are predominantly used in phylogenetic reconstructions. It is known that including RNA secondary structures in the alignment procedure is essential for improving accuracy and robustness in phylogenetic tree reconstruction. Moreover, local plasticity in rRNAs might impact their tertiary structures and corresponding functions. To determine the systematic position of Thaumastellidae within the superfamily Pentatomoidea, the secondary and-for the first time among all Hexapoda-tertiary structures of 18S rRNAs in twelve pentatomoid families were compared and analysed. Results indicate that the shapes of the secondary and tertiary structures of the length-variable regions (LVRs) in the 18S rRNA are phylogenetically highly informative. Based on these results, it is suggested that the Thaumastellidae is maintained as an independent family within the superfamily Pentatomoidea, rather than as a part of the family Cydnidae. Moreover, the analyses indicate a close relationship between Sehirinae and Parastrachiidae, expressed in morpho-molecular synapomorphies in the predicted secondary and tertiary structures of the length-variable region L (LVR L).
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Affiliation(s)
- Jerzy A Lis
- Institute of Biology, University of Opole, Oleska 22, 45-052 Opole, Poland
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Duan Y, Fu S, Ye Z, Bu W. Phylogeny of Urostylididae (Heteroptera: Pentatomoidea) reveals rapid radiation and challenges traditional classification. ZOOL SCR 2023. [DOI: 10.1111/zsc.12582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Yujie Duan
- Institute of Entomology, College of Life Sciences Nankai University Tianjin China
| | - Siying Fu
- Institute of Entomology, College of Life Sciences Nankai University Tianjin China
| | - Zhen Ye
- Institute of Entomology, College of Life Sciences Nankai University Tianjin China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences Nankai University Tianjin China
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Grozeva S, Stoianova D, Konstantinov F, Simov N, Kuznetsova VG. A synopsis of the numbers of testicular follicles and ovarioles in true bugs (Heteroptera, Hemiptera) - sixty-five years of progress after J. Pendergrast's review. Zookeys 2022; 1136:71-123. [PMID: 36762052 PMCID: PMC9836485 DOI: 10.3897/zookeys.1136.96431] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
The structure of testes and ovaries can be described in its simplest form by the number of follicles and ovarioles they contain. Sixty-five years after the last review of the internal reproductive systems in true bugs (Heteroptera), the data accumulated today on the number of testicular follicles and ovarioles in their gonads are summarized. In addition, data on the number and type (mesadenia/ectadenia) of accessory glands are given. The hemipteran suborder Heteroptera constitutes one of the most diverse groups of non-homometabolous ('Hemimetabola') insects, comprising more than 40,000 described species worldwide and approximately 100 families, classified into seven infraorders. Data are available for all infraorders; however, more than 90% of studied species belong to the largest and most evolutionarily derived infraorders Cimicomorpha and Pentatomomorpha. In true bugs, in general, the number of follicles varies from one to nine (in a testis), and the number of ovarioles varies from two to 24 (in an ovary). Seven follicles per testis and seven ovarioles per ovary prevail being found in approximately 43.5% (307 species) and 24.4% (367 species) of studied species, respectively. Such a structure of testes and ovaries is considered an ancestral character state in the Heteroptera. In the evolution of this group, the number of follicles and ovarioles both increased and decreased, but the trend towards a decrease clearly prevailed.
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Affiliation(s)
- Snejana Grozeva
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Tsar Osvoboditel 1, Sofia, BulgariaInstitute of Biodiversity and Ecosystem Research, Bulgarian Academy of SciencesSofiaBulgaria
| | - Desislava Stoianova
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Tsar Osvoboditel 1, Sofia, BulgariaInstitute of Biodiversity and Ecosystem Research, Bulgarian Academy of SciencesSofiaBulgaria
| | - Fedor Konstantinov
- St. Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg 199034, RussiaSt. Petersburg State UniversitySt. PetersburgRussia,Zoological Institute, Russian Academy of Sciences, Universitetskaya emb. 1, St. Petersburg 199034, RussiaZoological Institute, Russian Academy of SciencesSt. PetersburgRussia
| | - Nikolay Simov
- National Museum of Natural History, Bulgarian Academy of Sciences, Tsar Osvoboditel 1, Sofia, BulgariaNational Museum of Natural History, Bulgarian Academy of SciencesSofiaBulgaria
| | - Valentina G. Kuznetsova
- Zoological Institute, Russian Academy of Sciences, Universitetskaya emb. 1, St. Petersburg 199034, RussiaZoological Institute, Russian Academy of SciencesSt. PetersburgRussia
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Govindharaj GPP, Babu SB, Choudhary JS, Asad M, Chidambaranathan P, Gadratagi BG, Rath PC, Naaz N, Jaremko M, Qureshi KA, Kumar U. Genome Organization and Comparative Evolutionary Mitochondriomics of Brown Planthopper, Nilaparvata lugens Biotype 4 Using Next Generation Sequencing (NGS). Life (Basel) 2022; 12:life12091289. [PMID: 36143326 PMCID: PMC9506247 DOI: 10.3390/life12091289] [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] [Received: 07/17/2022] [Revised: 08/13/2022] [Accepted: 08/15/2022] [Indexed: 11/27/2022] Open
Abstract
Nilaparvata lugens is the main rice pest in India. Until now, the Indian N. lugens mitochondrial genome has not been sequenced, which is a very important basis for population genetics and phylogenetic evolution studies. An attempt was made to sequence two examples of the whole mitochondrial genome of N. lugens biotype 4 from the Indian population for the first time. The mitogenomes of N. lugens are 16,072 and 16,081 bp long with 77.50% and 77.45% A + T contents, respectively, for both of the samples. The mitochondrial genome of N. lugens contains 37 genes, including 13 protein-coding genes (PCGs) (cox1-3, atp6, atp8, nad1-6, nad4l, and cob), 22 transfer RNA genes, and two ribosomal RNA (rrnS and rrnL) subunits genes, which are typical of metazoan mitogenomes. However, both samples of N. lugens mitogenome in the present study retained one extra copy of the trnC gene. Additionally, we also found 93 bp lengths for the atp8 gene in both of the samples, which were 60–70 bp less than that of the other sequenced mitogenomes of hemipteran insects. The phylogenetic analysis of the 19 delphacids mitogenome dataset yielded two identical topologies when rooted with Ugyops sp. in one clade, and the remaining species formed another clade with P. maidis and M. muiri being sisters to the remaining species. Further, the genus Nilaparvata formed a separate subclade with the other genera (Sogatella, Laodelphax, Changeondelphax, and Unkanodes) of Delphacidae. Additionally, the relationship among the biotypes of N. lugens was recovered as the present study samples (biotype-4) were separated from the three biotypes reported earlier. The present study provides the reference mitogenome for N. lugens biotype 4 that may be utilized for biotype differentiation and molecular-aspect-based future studies of N. lugens.
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Affiliation(s)
- Guru-Pirasanna-Pandi Govindharaj
- Division of Crop Protection, ICAR-National Rice Research Institute, Cuttack 753006, India
- Correspondence: (G.-P.-P.G.); (J.S.C.); (U.K.)
| | - Soumya Bharti Babu
- Division of Crop Protection, ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Jaipal Singh Choudhary
- ICAR-Research Complex for Eastern Region, Farming System Research Centre for Hill and Plateau Region, Ranchi 834010, India
- Correspondence: (G.-P.-P.G.); (J.S.C.); (U.K.)
| | - Muhammad Asad
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | | | - Basana-Gowda Gadratagi
- Division of Crop Protection, ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Prakash Chandra Rath
- Division of Crop Protection, ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Naiyar Naaz
- ICAR-Research Complex for Eastern Region, Farming System Research Centre for Hill and Plateau Region, Ranchi 834010, India
| | - Mariusz Jaremko
- Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Kamal Ahmad Qureshi
- Department of Pharmaceutics, Unaizah College of Pharmacy, Qassim University, Unaizah 51911, Saudi Arabia
| | - Uttam Kumar
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (G.-P.-P.G.); (J.S.C.); (U.K.)
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Morphology of the Antennal Sensilla of Notonectoidea and Comparison of Evolutionary Changes in Sensilla Types and Distribution in Infraorder Nepomorpha (Insecta: Heteroptera). INSECTS 2021; 12:insects12121121. [PMID: 34940209 PMCID: PMC8703933 DOI: 10.3390/insects12121121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/09/2021] [Accepted: 12/11/2021] [Indexed: 11/28/2022]
Abstract
Simple Summary Antennal sensilla are important sensory organs for insects. According to their morphological structures, they respond to different chemical or mechanical stimuli. The antennae of the studied families of water insects (Notonectidae, Pleidae and Helotrephidae) are short and concealed under the head, leaving a small amount of space for the existence of sensory structures. Nevertheless, six main types of sensilla have been discovered on the surfaces of these antennae. The morphological types described in this study were further compared with other studies on the antennal sensilla of water bugs (Nepomorpha) in order to compare their evolutionary changes within the group. Abstract This article introduces the results of a study of three families of Nepomorpha and is the last part of a series of studies that sums up our work on the morphologies of the antennal sensory structures in this taxon. The morphologies and distribution of the sensilla in the families Notonectidae, Pleidae and Helotrephidae were studied under a scanning electron microscope. Six main types (sensilla trichodea, chaetica, campaniformia, basiconica, ampullacea and coeloconica) and ten subtypes (five subtypes of sensilla trichodea and five subtypes of sensilla basiconica) were described. The results were compared with other studies on the antennal sensilla of Nepomorpha in order to assess evolutionary changes within the infraorder. With the use of cladistics analysis, the monophyly of the families Nepidae, Micronectidae, Corixidae and Gelastocoridae was supported. On the other hand, the occurrence of some clades forming superfamilies was weakly supported by bootstrap analysis. These results, supported by presence of the numerous autapomorphies, suggest that antennal sensilla evolved within inner groups.
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Dallai R, Fanciulli PP, Mercati D, Lupetti P. Coevolution between female seminal receptacle and sperm morphology in the semiaquatic measurer bug Hydrometra stagnorum L. (Heteroptera, Hydrometridae). ARTHROPOD STRUCTURE & DEVELOPMENT 2021; 60:101001. [PMID: 33120187 DOI: 10.1016/j.asd.2020.101001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/01/2020] [Accepted: 10/07/2020] [Indexed: 06/11/2023]
Abstract
The coevolution between sperm length and size of the female sperm-storage organs is described for the first time within Heteroptera. The long sperm of the measurer bug Hydrometra stagnorum is characterized by the unusually long acrosome with its anterior region helically arranged, and by a very short nucleus. The sperm flagellum has a 9 + 9+2 conventional axoneme and crystallized mitochondrial derivatives. The female spermatheca consists of an extraordinarily long spermathecal duct ending with an apical spermathecal bulb into which flows also the secretions of a relatively short spermathecal gland. Both spermathecal duct and gland have a thin epithelium lined by a cuticle, beneath which a complex of secretory and duct forming cells are present. The secretions of these two structures flow into the apical spermathecal bulb. A thick layer of muscle fibers surrounds the epithelium. These results confirm the opinion that the dimensions of the female reproductive sperm-storage organs are able to drive the sperm morphology.
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Affiliation(s)
- Romano Dallai
- Department of Life Sciences, University of Siena, Siena, Italy.
| | | | - David Mercati
- Department of Life Sciences, University of Siena, Siena, Italy.
| | - Pietro Lupetti
- Department of Life Sciences, University of Siena, Siena, Italy.
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Taylor GS, Martoni F. Case of mistaken identity: resolving the taxonomy between Trioza eugeniae Froggatt and T. adventicia Tuthill (Psylloidea: Triozidae). BULLETIN OF ENTOMOLOGICAL RESEARCH 2020; 110:340-351. [PMID: 31865924 DOI: 10.1017/s0007485319000695] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The 'Eugenia psyllid' or 'Lilly pilly psyllid', widely recognized in Australia and in the USA as Trioza eugeniae Froggatt (Hemiptera: Triozidae), is not T. eugeniae, but rather T. adventicia Tuthill. In this study we assessed morphological comparisons of materials from throughout the native and introduced ranges and re-examined original descriptions of both taxa, together with Froggatt's type specimens of T. eugeniae. Furthermore, through DNA barcoding analyses, we confirmed the validity of both T. adventicia and T. eugeniae as separate species. We re-described both species to include additional characters not previously included and designated a lectotype for T. eugeniae. T. eugeniae has smaller fore wings that are slightly more elongate. These lack infuscation around veins R and R1, vein Rs is relatively longer, meeting the costa closer to the wing apex; with certain veins bearing long, fine divergent setae, a character not previously described. It has consistently three inner and one outer metatibial spurs. The male parameres appear narrowly pyriform with a weak dorsolateral lobe and weakly sclerotized apices. T. adventicia has larger fore wings that are slightly more ovate with dark infuscation around veins R and R1; vein Rs is relatively shorter, meeting the costa further from the wing apex, with veins lacking long, fine divergent setae. The usual configuration of two inner and one outer metatibial spurs, previously used to separate the two species, appears inconsistent. The male parameres appear a little more broadly pyriform with slightly more sclerotized apices. T. eugeniae refers to a distinct species which has a restricted distribution only in its native range in southern subcoastal New South Wales, Australia. T. adventicia refers to a separate species, with a natural distribution in eastern subcoastal Australia, but has been introduced widely in southern Australia, to New Zealand and the USA. This study elucidates a long history of misidentification of T. eugeniae in the nursery industry and in almost 30 years of literature on its biological control in the USA. Regardless, the biological control program, unknowingly, targeted the correct species of psyllid, T. adventicia, in its foreign exploration and importation of the appropriate parasitoid as a biocontrol agent in the USA. Despite being firmly entrenched in both the nursery trade and scientific literature, the name T. eugeniae is misapplied. While the acceptance of the valid name, T. adventicia, might be regarded as both problematic and protracted, this is the correct taxonomical attribution.
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Affiliation(s)
- Gary S Taylor
- Department of Genetics & Evolution, Australian Centre for Evolutionary Biology & Biodiversity, School of Biological Sciences, The University of Adelaide, North Terrace, SA5005, Australia
| | - Francesco Martoni
- Agriculture Victoria Research, AgriBio Centre, Bundoora, VIC3083, Australia
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de Souza-Firmino TS, Alevi KCC, Itoyama MM. Chromosomal divergence and evolutionary inferences in Pentatomomorpha infraorder (Hemiptera, Heteroptera) based on the chromosomal location of ribosomal genes. PLoS One 2020; 15:e0228631. [PMID: 32017800 PMCID: PMC6999898 DOI: 10.1371/journal.pone.0228631] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 01/21/2020] [Indexed: 11/23/2022] Open
Abstract
With the objective of assisting in the understanding of the chromosome evolution of Pentatomomorpha and in the quest to understand how the genome organizes/reorganizes for the chromosomal position of the 45S rDNA in this infraorder, we analyzed 15 species (it has being 12 never studied before by FISH) of Pentatomomorpha with the probe of 18S rDNA. The mapping of the 45S gene in the Coreidae family demonstrated that the species presented markings on the autosomes, with the exception of Acanthocephala parensis and Leptoglossus gonagra that showed markers on m-chromosomes. Most species of the Pentatomidae family showed marking in the autosomes, except for two species that had 45S rDNA on X sex chromosome (Odmalea sp. and Graphosoma lineatum) and two that showed marking on the X and Y sex chromosomes. Species of the Pyrrhocoridae family showed 18S rDNA markers in autosomes, X chromosome as well as in Neo X. The Largidae and Scutelleridae families were represented by only one species that showed marking on the X sex chromosome and on a pair of autosomes, respectively. Based on this, we characterized the arrangement of 45S DNAr in the chromosomes of 12 new species of Heteroptera and discussed the main evolutionary events related to the genomic reorganization of these species during the events of chromosome and karyotype evolution in Pentatomomorpha infraorder.
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Affiliation(s)
- Tatiani Seni de Souza-Firmino
- Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Câmpus de São José do Rio Preto, São José do Rio Preto, SP, Brazil
| | - Kaio Cesar Chaboli Alevi
- Departamento de Ciências Biológicas, Faculdade de Ciências Farmacêuticas de Araraquara, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Câmpus de Araraquara, Araraquara, SP, Brazil
| | - Mary Massumi Itoyama
- Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Câmpus de São José do Rio Preto, São José do Rio Preto, SP, Brazil
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The comparative morphology of adult pregenital abdominal ventrites and trichobothria in Pyrrhocoroidea (Hemiptera: Heteroptera: Pentatomomorpha). ZOOL ANZ 2020. [DOI: 10.1016/j.jcz.2019.11.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Song N, Zhang H, Zhao T. Insights into the phylogeny of Hemiptera from increased mitogenomic taxon sampling. Mol Phylogenet Evol 2019; 137:236-249. [PMID: 31121308 DOI: 10.1016/j.ympev.2019.05.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 05/15/2019] [Accepted: 05/16/2019] [Indexed: 10/26/2022]
Abstract
Although reconstruction of the phylogeny of Hemiptera has progressed tremendously over the past two decades, some higher-level relationships remain poorly resolved. Here, we investigated the Hemiptera higher-level relationships using full mitochondrial genome data from 357 ingroup species, representing the most comprehensive sampling yet undertaken for reconstructing the phylogeny of this group. In this study, 92 mitochondrial genomes were newly determined. Various data treatment methods and substitution models were applied to tree reconstructions. Effects of compositional heterogeneity, rate heterogeneity, model adequacy and taxon sampling on support values and topological stability were explored. Phylogenetic analyses (1) confirmed the monophyly of Hemiptera under site-heterogeneous model, (2) placed Sternorrhyncha as sister to all other Hemiptera, (3) recovered Coccoidea as the sister taxon of Aphidoidea, followed successively by Aleyrodoidea and Psylloidea, and (4) indicated that the grouping of Coleorrhyncha and Fulgoromorpha was the result of long-branch attraction effect.
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Affiliation(s)
- Nan Song
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China.
| | - Hao Zhang
- Henan Vocational and Technological College of Communication, Zhengzhou 450015, China
| | - Te Zhao
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China.
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Franielczyk-Pietyra B, Depa Ł, Wegierek P. Morphological and histological study of the forewing of Orthezia urticae (Linnaeus, 1758) (Hemiptera, Sternorrhyncha). Zookeys 2018:101-114. [PMID: 29674906 PMCID: PMC5904441 DOI: 10.3897/zookeys.747.23950] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 03/02/2018] [Indexed: 11/12/2022] Open
Abstract
Wings of Orthezia urticae males were studied. Both ventral and dorsal surfaces of wings were examined under light and scanning electron microscopes. The structure regarded as vein cubitus anterior turned out to be a reinforcement element only. Two elements known as radius sector and media are almost transparent depressions in the wing membrane. Veins at the margin of the fold of the wing anal lobe were not confirmed. Studies indicated a row of sensilla cupola at the beginning of the subcostal ridge. Cross sections of the wing membrane showed a two-layered membrane. The presence of two veins was confirmed in a common stem - subcostal and radius. The change of common stem shape was described. Neither tracheae nor nerves were observed. This is the second paper on cross-sections of wing within Sternorrhyncha.
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Affiliation(s)
- Barbara Franielczyk-Pietyra
- Department of Zoology, Faculty of Biology and Environmental Protection, University of Silesia, Bankowa 9, 40-007 Katowice, Poland
| | - Łukasz Depa
- Department of Zoology, Faculty of Biology and Environmental Protection, University of Silesia, Bankowa 9, 40-007 Katowice, Poland
| | - Piotr Wegierek
- Department of Zoology, Faculty of Biology and Environmental Protection, University of Silesia, Bankowa 9, 40-007 Katowice, Poland
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Is there a relationship between the morphology of the forewing axillary sclerites and the way the wing folds in aphids (Aphidomorpha, Sternorrhyncha, Hemiptera)? ZOOMORPHOLOGY 2018; 137:105-117. [PMID: 29568155 PMCID: PMC5847081 DOI: 10.1007/s00435-017-0390-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 11/17/2017] [Accepted: 11/20/2017] [Indexed: 11/11/2022]
Abstract
The present study describes the relationship between the morphology of the forewing axillary sclerites and the way the wings fold among 24 aphid genera as compared to a representative of coccids. Architecture of the forewing base was imaged with scanning electron and optical (fluorescence) microscopy. Significant differences in morphology of axillary sclerites between aphid species were observed, despite their belonging to one infraorder. Detailed description of 41 features of axillary sclerites was made. There was no difference between axillaries of viviparous (Aphididae) and oviparous (Adelges sp., Phylloxera sp.) species. No clear relationship between morphology of the axillary sclerites and the wing folding could be confirmed. Instead, the thorax structure determines the way the wing folds in aphids. Phylogenetic analysis based on our results cannot be conducted at this stage of study. To show how three-dimensional the structures are and how difficult to describe, a short animation of Aphis fabae (Aphididae) wing base was added. This is a preliminary study about morphology of axillary sclerites among aphids.
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15
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Song N, Lin A, Zhao X. Insight into higher-level phylogeny of Neuropterida: Evidence from secondary structures of mitochondrial rRNA genes and mitogenomic data. PLoS One 2018; 13:e0191826. [PMID: 29381758 PMCID: PMC5790268 DOI: 10.1371/journal.pone.0191826] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 01/11/2018] [Indexed: 01/21/2023] Open
Abstract
It is well known that the rRNA structure information is important to assist phylogenetic analysis through identifying homologous positions to improve alignment accuracy. In addition, the secondary structure of some conserved motifs is highly stable among distantly related taxa, which can provide potentially informative characters for estimating phylogeny. In this paper, we applied the high-throughput pooled sequencing approach to the determination of neuropteran mitogenomes. Four complete mitogenome sequences were obtained: Micromus angulatus (Hemerobiidae), Chrysoperla nipponensis (Chrysopidae), Rapisma sp. (Ithonidae), and Thaumatosmylus sp. (Osmylidae). This allowed us to sample more complete mitochondrial RNA gene sequences. Secondary structure diagrams for the complete mitochondrial small and large ribosomal subunit RNA genes of eleven neuropterid species were predicted. Comparative analysis of the secondary structures indicated a closer relationship of Megaloptera and Neuroptera. This result was congruent with the resulting phylogeny inferred from sequence alignments of all 37 mitochondrial genes, namely the hypothesis of (Raphidioptera + (Megaloptera + Neuroptera)).
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Affiliation(s)
- Nan Song
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Aili Lin
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Xincheng Zhao
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
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16
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Weirauch C, Schuh RT, Cassis G, Wheeler WC. Revisiting habitat and lifestyle transitions in Heteroptera (Insecta: Hemiptera): insights from a combined morphological and molecular phylogeny. Cladistics 2018; 35:67-105. [DOI: 10.1111/cla.12233] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2017] [Indexed: 11/28/2022] Open
Affiliation(s)
- Christiane Weirauch
- Department of Entomology University of California Riverside 900 University Avenue Riverside CA 92521 USA
| | - Randall T. Schuh
- Division of Invertebrate Zoology American Museum of Natural History New York NY 10024‐5192 USA
| | - Gerasimos Cassis
- Evolution & Ecology Research Center School of Biological, Earth, and Environmental Sciences University of New South Wales Sydney NSW 2052 Australia
| | - Ward C. Wheeler
- Division of Invertebrate Zoology American Museum of Natural History New York NY 10024‐5192 USA
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17
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Wang YH, Wu HY, Rédei D, Xie Q, Chen Y, Chen PP, Dong ZE, Dang K, Damgaard J, Štys P, Wu YZ, Luo JY, Sun XY, Hartung V, Kuechler SM, Liu Y, Liu HX, Bu WJ. When did the ancestor of true bugs become stinky? Disentangling the phylogenomics of Hemiptera-Heteroptera. Cladistics 2017; 35:42-66. [DOI: 10.1111/cla.12232] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2017] [Indexed: 01/27/2023] Open
Affiliation(s)
- Yan-Hui Wang
- Department of Ecology and Evolution; College of Life Sciences; Sun Yat-sen University; 135 Xingangxi Road Guangzhou 510275 Guangdong China
- State Key Laboratory of Biocontrol; Sun Yat-sen University; 135 Xingangxi Road Guangzhou 510275 Guangdong China
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Hao-Yang Wu
- Department of Ecology and Evolution; College of Life Sciences; Sun Yat-sen University; 135 Xingangxi Road Guangzhou 510275 Guangdong China
- State Key Laboratory of Biocontrol; Sun Yat-sen University; 135 Xingangxi Road Guangzhou 510275 Guangdong China
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Dávid Rédei
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Qiang Xie
- Department of Ecology and Evolution; College of Life Sciences; Sun Yat-sen University; 135 Xingangxi Road Guangzhou 510275 Guangdong China
- State Key Laboratory of Biocontrol; Sun Yat-sen University; 135 Xingangxi Road Guangzhou 510275 Guangdong China
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Yan Chen
- Chinese Academy of Inspection and Quarantine; No. A3, Gaobeidian Bei Lu Chaoyang District Beijing 100123 China
| | - Ping-Ping Chen
- Netherlands Centre of Biodiversity Naturalis; 2300 RA Leiden Netherlands
| | - Zhuo-Er Dong
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Kai Dang
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Jakob Damgaard
- Natural History Museum of Denmark; Universitetsparken 15 2100 Copenhagen Ø Denmark
| | - Pavel Štys
- Department of Zoology; Faculty of Science; Charles University in Prague; Viničná 7 CZ-128 44 Praha 2 Czech Republic
| | - Yan-Zhuo Wu
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Jiu-Yang Luo
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Xiao-Ya Sun
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Viktor Hartung
- Staatliches Museum für Naturkunde Karslruhe; Erbprinzenstrasse 13 76133 Karlsruhe Germany
- Museum für Naturkunde - Leibniz-Institute for Research on Evolution and Biodiversity; Invalidenstrasse 43 10115 Berlin Germany
| | - Stefan M. Kuechler
- Department of Animal Ecology II; University of Bayreuth; Universitaetsstrasse 30 95440 Bayreuth Germany
| | - Yang Liu
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Hua-Xi Liu
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Wen-Jun Bu
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
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18
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Wu YZ, Rédei D, Eger J, Wang YH, Wu HY, Carapezza A, Kment P, Cai B, Sun XY, Guo PL, Luo JY, Xie Q. Phylogeny and the colourful history of jewel bugs (Insecta: Hemiptera: Scutelleridae). Cladistics 2017; 34:502-516. [DOI: 10.1111/cla.12224] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2017] [Indexed: 11/30/2022] Open
Affiliation(s)
- Yan-Zhuo Wu
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road, Nankai District Tianjin 300071 China
| | - Dávid Rédei
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road, Nankai District Tianjin 300071 China
| | - Joseph Eger
- Dow AgroSciences; LLC; 2606 S. Dundee Street Tampa FL 32629 USA
| | - Yan-Hui Wang
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road, Nankai District Tianjin 300071 China
- Department of Ecology and Evolution; College of Life Sciences; Sun Yat-sen University; No. 135 Xingangxi Road Guangzhou 510275 Guangdong China
- State Key Laboratory of Biocontrol; Sun Yat-sen University; 135 Xingangxi Road Guangzhou 510275 Guangdong China
| | - Hao-Yang Wu
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road, Nankai District Tianjin 300071 China
- Department of Ecology and Evolution; College of Life Sciences; Sun Yat-sen University; No. 135 Xingangxi Road Guangzhou 510275 Guangdong China
- State Key Laboratory of Biocontrol; Sun Yat-sen University; 135 Xingangxi Road Guangzhou 510275 Guangdong China
| | - Attilio Carapezza
- University of Palermo; Via Sandro Botticelli, 15 I-90144 Palermo Italy
| | - Petr Kment
- Department of Entomology; National Museum; Cirkusová 1740 CZ-193 00 Praha 9 Czech Republic
| | - Bo Cai
- Hainan Entry-Exit Inspection and Quarantine Bureau; 9 West Haixiu Road Haikou Hainan 570311 China
| | - Xiao-Ya Sun
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road, Nankai District Tianjin 300071 China
| | - Peng-Lei Guo
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road, Nankai District Tianjin 300071 China
| | - Jiu-Yang Luo
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road, Nankai District Tianjin 300071 China
| | - Qiang Xie
- Department of Ecology and Evolution; College of Life Sciences; Sun Yat-sen University; No. 135 Xingangxi Road Guangzhou 510275 Guangdong China
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19
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Lin A, Zhao X, Li X, Song N. The complete mitochondrial genome of Corythucha marmorata (Hemiptera: Tingidae). Mitochondrial DNA B Resour 2017; 2:897-899. [PMID: 33474027 PMCID: PMC7799590 DOI: 10.1080/23802359.2017.1407712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
The complete mitochondrial genome (mitogenome) of Corythucha marmorata has been sequenced and annotated. The entire mitogenome is a typical circle double-stranded DNA molecule of 15,635b p and consisted of 37 genes and a control region in the typical invertebrate mitochondrial gene arrangement. Phylogenetic analysis recovered the momophyly of Gerromorpha, Enicocephalomorpha and Cimicomorpha.
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Affiliation(s)
- Aili Lin
- College of Plant Protection, Henan Agricultural University, Zhengzhou, People's Republic of China
| | - Xincheng Zhao
- College of Plant Protection, Henan Agricultural University, Zhengzhou, People's Republic of China
| | - Xinxin Li
- College of Plant Protection, Henan Agricultural University, Zhengzhou, People's Republic of China
| | - Nan Song
- College of Plant Protection, Henan Agricultural University, Zhengzhou, People's Republic of China
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Davranoglou LR, Baňař P, Schlepütz CM, Mortimer B, Taylor GK. The pregenital abdomen of Enicocephalomorpha and morphological evidence for different modes of communication at the dawn of heteropteran evolution. ARTHROPOD STRUCTURE & DEVELOPMENT 2017; 46:843-868. [PMID: 28864300 DOI: 10.1016/j.asd.2017.08.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 07/14/2017] [Accepted: 08/27/2017] [Indexed: 06/07/2023]
Abstract
The internal and external anatomy of the posterior metathoracic region, pregenital abdomen, and associated nervous system of the heteropteran infraorder Enicocephalomorpha are thoroughly described, using an array of state-of-the art techniques. Based on morphology, it is hypothesised which modes of communication these insects use. This study is based primarily on an undescribed species of Cocles Bergroth, 1905 (Enicocephalidae) and another undescribed species of Lomagostus Villiers, 1958 (Aenictopecheidae), but additional representatives of the infraorder are also examined. Our results are compared with the literature on other Heteroptera. The metathoracic scent gland system of Enicocephalomorpha uses the same muscles as that of more derived Heteroptera, although the efferent system is different. The presence of a tergal plate and well-developed longitudinal musculature in the families Enicocephalidae and Aenictopecheidae, as well as a sexually dimorphic set of sclerites and membranes that allow an as yet undetermined type of motion, may indicate the presence of vibrational signaling in the infraorder, although experimental confirmation is required. Our findings raise new research questions regarding heteropteran functional morphology and communication.
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Affiliation(s)
| | - Petr Baňař
- Department of Entomology, Moravian Museum, Hviezdoslavova 29a, Brno CZ-627 00, Czech Republic
| | | | - Beth Mortimer
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK; School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Graham K Taylor
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
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21
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Liu Y, Song F, Jiang P, Wilson JJ, Cai W, Li H. Compositional heterogeneity in true bug mitochondrial phylogenomics. Mol Phylogenet Evol 2017; 118:135-144. [PMID: 28986237 DOI: 10.1016/j.ympev.2017.09.025] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 08/28/2017] [Accepted: 09/30/2017] [Indexed: 01/05/2023]
Abstract
Mitochondrial phylogenomics is often controversial, in particular for inferring deep relationships. The recent rapid increase of mitochondrial genome data provides opportunities for better phylogenetic estimates and assessment of potential biases resulting from heterogeneity in nucleotide composition and mutation rates. Here, we gathered 76 mitochondrial genome sequences for Heteroptera representing all seven infraorders, including 17 newly sequenced mitochondrial genomes. We found strong heterogeneity in base composition and contrasting evolutionary rates among heteropteran mitochondrial genomes, which affected analyses with various datasets and partitioning schemes under site-homogeneous models and produced false groupings of unrelated taxa exhibiting similar base composition and accelerated evolutionary rates. Bayesian analyses using a site-heterogeneous mixture CAT+GTR model showed high congruence of topologies with the currently accepted phylogeny of Heteroptera. The results confirm the monophyly of the six infraorders within Heteroptera, except for Cimicomorpha which was recovered as two paraphyletic clades. The monophyly of Terheteroptera (Cimicomorpha and Pentatomomorpha) and Panheteroptera (Nepomorpha, Leptopodomorpha and Terheteroptera) was recovered demonstrating a significant improvement over previous studies using mitochondrial genome data. Our study shows the power of the site-heterogeneous mixture models for resolving phylogenetic relationships with Heteroptera and provides one more case showing that model adequacy is critical for accurate tree reconstruction in mitochondrial phylogenomics.
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Affiliation(s)
- Yingqi Liu
- Key Laboratory of Pest Monitoring and Green Management, Ministry of Agriculture, Department of Entomology, China Agricultural University, Beijing 100193, China
| | - Fan Song
- Key Laboratory of Pest Monitoring and Green Management, Ministry of Agriculture, Department of Entomology, China Agricultural University, Beijing 100193, China
| | - Pei Jiang
- National Agro-Technical Extension and Service Centre, Ministry of Agriculture, Beijing 100125, China
| | - John-James Wilson
- International College Beijing, China Agricultural University, Beijing 100083, China
| | - Wanzhi Cai
- Key Laboratory of Pest Monitoring and Green Management, Ministry of Agriculture, Department of Entomology, China Agricultural University, Beijing 100193, China
| | - Hu Li
- Key Laboratory of Pest Monitoring and Green Management, Ministry of Agriculture, Department of Entomology, China Agricultural University, Beijing 100193, China.
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22
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Ospina-Rozo B, Forero-Shelton M, Molina J. Structure and postembryonic development of the intersegmental nodules in the non-muscular joints of the antennae in Rhodnius prolixus. ARTHROPOD STRUCTURE & DEVELOPMENT 2017; 46:287-296. [PMID: 27998742 DOI: 10.1016/j.asd.2016.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 12/12/2016] [Indexed: 06/06/2023]
Abstract
The antennae of Insecta consist of two basal segments and the distal annulated flagellum lacking intrinsic muscles. Non-muscular joints are important to preserve the flexibility and structure of the long heteropteran antennae which bear an intersegmental nodule on each non-muscular joint. Little is known about their properties or function. Here we characterize the structure and postembryonic development of the non-muscular joints of Rhodnius prolixus antennae. Using Scanning Electron Microscopy, we tracked the changes in shape and size of both intersegmental nodules during the course of the hemimetabolous insect life cycle. Using Atomic Force Microscopy, we established a qualitative correlation between the topography of the surface and the rigidity of the joint between pedicel and flagellum. Our results confirmed the presence of two sub-articulations on each non-muscular joint. Also, the two intersegmental nodules have different origins: the one between the two flagellar segments (intraflagelloid) is a sclerite already present from the early nymph, while the nodule between pedicel and flagellum (prebasiflagellite) originates by gradual separation of the proximal end of the basiflagellum during postembryonic development. Various changes occur in the non-muscular joints and segments of the antenna during the life cycle of R. prolixus.
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Affiliation(s)
- Bibiana Ospina-Rozo
- CIMPAT Laboratory, Biological Sciences Department, Universidad de los Andes Cra 1 No 18 A - 12, Bogotá, Colombia.
| | - Manu Forero-Shelton
- Biophysics Group, Physics Department, Universidad de los Andes Cra 1 No 18 A - 12, Bogotá, Colombia.
| | - Jorge Molina
- CIMPAT Laboratory, Biological Sciences Department, Universidad de los Andes Cra 1 No 18 A - 12, Bogotá, 111711, Colombia.
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23
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Ling C, Hamada T, Gao J, Zhao G, Sun D, Shi W. MrBayes tgMC 3++: A High Performance and Resource-Efficient GPU-Oriented Phylogenetic Analysis Method. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2016; 13:845-854. [PMID: 26529779 DOI: 10.1109/tcbb.2015.2495202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
MrBayes is a widespread phylogenetic inference tool harnessing empirical evolutionary models and Bayesian statistics. However, the computational cost on the likelihood estimation is very expensive, resulting in undesirably long execution time. Although a number of multi-threaded optimizations have been proposed to speed up MrBayes, there are bottlenecks that severely limit the GPU thread-level parallelism of likelihood estimations. This study proposes a high performance and resource-efficient method for GPU-oriented parallelization of likelihood estimations. Instead of having to rely on empirical programming, the proposed novel decomposition storage model implements high performance data transfers implicitly. In terms of performance improvement, a speedup factor of up to 178 can be achieved on the analysis of simulated datasets by four Tesla K40 cards. In comparison to the other publicly available GPU-oriented MrBayes, the tgMC3++ method (proposed herein) outperforms the tgMC3 (v1.0), nMC3 (v2.1.1) and oMC3 (v1.00) methods by speedup factors of up to 1.6, 1.9 and 2.9, respectively. Moreover, tgMC3++ supports more evolutionary models and gamma categories, which previous GPU-oriented methods fail to take into analysis.
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Wu YZ, Yu SS, Wang YH, Wu HY, Li XR, Men XY, Zhang YW, Rédei D, Xie Q, Bu WJ. The evolutionary position of Lestoniidae revealed by molecular autapomorphies in the secondary structure of rRNA besides phylogenetic reconstruction (Insecta: Hemiptera: Heteroptera). Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12385] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yan-Zhuo Wu
- Institute of Entomology; College of Life Sciences; Nankai University; Tianjin 300071 China
| | - Sha-Sha Yu
- Institute of Entomology; College of Life Sciences; Nankai University; Tianjin 300071 China
| | - Yan-Hui Wang
- Institute of Entomology; College of Life Sciences; Nankai University; Tianjin 300071 China
| | - Hao-Yang Wu
- Institute of Entomology; College of Life Sciences; Nankai University; Tianjin 300071 China
| | - Xiu-Rong Li
- Institute of Entomology; College of Life Sciences; Nankai University; Tianjin 300071 China
| | - Xin-Yu Men
- Institute of Entomology; College of Life Sciences; Nankai University; Tianjin 300071 China
| | - Yi-Wei Zhang
- Institute of Entomology; College of Life Sciences; Nankai University; Tianjin 300071 China
| | - Dávid Rédei
- Institute of Entomology; College of Life Sciences; Nankai University; Tianjin 300071 China
| | - Qiang Xie
- Institute of Entomology; College of Life Sciences; Nankai University; Tianjin 300071 China
| | - Wen-Jun Bu
- Institute of Entomology; College of Life Sciences; Nankai University; Tianjin 300071 China
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Wang Y, Cui Y, Rédei D, Baňař P, Xie Q, Štys P, Damgaard J, Chen P, Yi W, Wang Y, Dang K, Li C, Bu W. Phylogenetic divergences of the true bugs (Insecta: Hemiptera: Heteroptera), with emphasis on the aquatic lineages: the last piece of the aquatic insect jigsaw originated in the Late Permian/Early Triassic. Cladistics 2015; 32:390-405. [DOI: 10.1111/cla.12137] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2015] [Indexed: 11/26/2022] Open
Affiliation(s)
- Yan‐hui Wang
- Institute of Entomology College of Life Sciences Nankai University 94 Weijin Road, Nankai District Tianjin 300071 China
| | - Ying Cui
- Tianjin State Key Laboratory of Modern Chinese Medicine Tianjin University of Traditional Chinese Medicine Tianjin 300193 China
| | - Dávid Rédei
- Institute of Entomology College of Life Sciences Nankai University 94 Weijin Road, Nankai District Tianjin 300071 China
| | - Petr Baňař
- Department of Entomology Moravian Museum Hviezdoslavova 29 CZ‐627 00 Czech Republic
| | - Qiang Xie
- Institute of Entomology College of Life Sciences Nankai University 94 Weijin Road, Nankai District Tianjin 300071 China
| | - Pavel Štys
- Faculty of Science Department of Zoology Charles University in Prague Viničná 7 CZ‐128 44 Praha 2 Czech Republic
| | - Jakob Damgaard
- Natural History Museum of Denmark Universitetsparken 15 2100 Copenhagen Ø Denmark
| | - Ping‐ping Chen
- Netherlands Centre of Biodiversity Naturalis 2300 RA Leiden Netherlands
| | - Wen‐bo Yi
- Institute of Entomology College of Life Sciences Nankai University 94 Weijin Road, Nankai District Tianjin 300071 China
| | - Ying Wang
- Institute of Entomology College of Life Sciences Nankai University 94 Weijin Road, Nankai District Tianjin 300071 China
| | - Kai Dang
- Institute of Entomology College of Life Sciences Nankai University 94 Weijin Road, Nankai District Tianjin 300071 China
| | - Chuan‐ren Li
- College of Agriculture Yangtze University Jingzhou Hubei 434025 China
| | - Wen‐jun Bu
- Institute of Entomology College of Life Sciences Nankai University 94 Weijin Road, Nankai District Tianjin 300071 China
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Sequencing of the mitochondrial genome of the avocado lace bug Pseudacysta perseae (Heteroptera, Tingidae) using a genome skimming approach. C R Biol 2015; 338:149-60. [PMID: 25636225 DOI: 10.1016/j.crvi.2014.12.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 12/09/2014] [Accepted: 12/10/2014] [Indexed: 11/23/2022]
Abstract
Lace bugs (Tingidae) are a family of phytophagous heteropterans, some of which are important agricultural and forestry pests. They currently comprise around 2500 species distributed worldwide, for which only one mitochondrial genome has been described so far. We sequenced the complete mitochondrial genome and the nuclear ribosomal gene segment of the avocado lace bug Pseudacysta perseae using a genome skimming approach on an Illumina Hiseq 2000 platform. Fifty-four additional heteropteran mitogenomes, including the one of the sycamore lace bug Corythucha ciliata, were retrieved to allow for comparisons and phylogenetic analyses. P. perseae mitochondrial genome was determined to be 15,850 bp long, and presented the typical organisation of insect mitogenomes. The phylogenetic analysis placed P. perseae as a sister to C. ciliata but did not confirm the monophyly of Miroidae including Tingidae. Our results contradicted widely accepted phylogenetic hypothesis, which highlights the limits of analyses based on mitochondrial data only. Shotgun sequencing approaches should provide substantial improvements in harmonizing mitochondrial and nuclear databases.
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Shotgun assembly of the assassin bug Brontostoma colossus mitochondrial genome (Heteroptera, Reduviidae). Gene 2014; 552:184-94. [PMID: 25240790 DOI: 10.1016/j.gene.2014.09.033] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 08/27/2014] [Accepted: 09/15/2014] [Indexed: 12/26/2022]
Abstract
The complete mitochondrial genome of the assassin bug Brontostoma colossus (Distant, 1902) (Heteroptera: Reduviidae) has been sequenced using a genome-skimming approach on an Illumina Hiseq 2000 platform. Fifty-four additional heteropteran mitogenomes, including five assassin bug species, were retrieved to allow for comparisons and phylogenetic analyses. The mitochondrial genome of B. colossus was determined to be 16,625 bp long, and consists of 13 protein-coding genes (PCGs), 23 transfer-RNA genes (tRNAs), two ribosomal-RNA genes (rRNAs), and one control region. The nucleotide composition is biased toward adenine and thymine (A+T=73.4%). Overall, architecture, nucleotide composition and genome asymmetry are similar among all available assassin bug mitogenomes. All PCGs have usual start-codons (Met and Ile). Three T and two TA incomplete termination codons were identified adjacent to tRNAs, which was consistent with the punctuation model for primary transcripts processing followed by 3' polyadenylation of mature mRNA. All tRNAs exhibit the classic clover-leaf secondary structure except for tRNASer(AGN) in which the DHU arm forms a simple loop. Two notable features are present in the B. colossus mitogenome: (i) a 131 bp duplicated unit including the complete tRNAArg gene, resulting in 23 potentially functional tRNAs in total, and (ii) a 857 bp duplicated region comprising 277 bp of the srRNA gene and 580 bp of the control region. A phylogenetic analysis based on 55 true bug mitogenomes confirmed that B. colossus belongs to Reduviidae, but contradicted a widely accepted hypothesis. This highlights the limits of phylogenetic analyses based on mitochondrial data only.
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Brożek J. Phylogenetic signals from Nepomorpha (Insecta: Hemiptera: Heteroptera) mouthparts: stylets bundle, sense organs, and labial segments. ScientificWorldJournal 2014; 2014:237854. [PMID: 24883360 PMCID: PMC4030475 DOI: 10.1155/2014/237854] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 12/12/2013] [Indexed: 11/25/2022] Open
Abstract
The present study is a cladistic analysis of morphological characters focusing on the file of the mandible, the apices of the maxillae, the rupturing device on the maxillae, the internal structures of the mouthparts, and the external morphology of the labial segments as well as the distribution of labial sensilla in true water bugs (Hemiptera: Heteroptera, infraorder Nepomorpha). The study is based on data referring to sixty-two species representing all nepomorphan families (Heteroptera), together with one outgroup species representing the infraorders Gerromorpha (Mesoveliidae). The morphological data matrix consists of forty-eight characters. The present hypothesis supports the monophyly of the Nepomorpha and the monophyly of all families. The new modification in the systematic classification has been proposed: ((Nepidae + Belostomatidae), (Diaprepocoridae + Corixidae + Micronectidae), (Ochteridae + Gelastocoridae), Aphelocheiridae, Potamocoridae, Naucoridae, Notonectidae, and (Pleidae + Helotrephidae)).
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Affiliation(s)
- Jolanta Brożek
- Department of Zoology, Faculty of Biology and Environmental Protection, University of Silesia, Bankowa Street 9, 40-007 Katowice, Poland
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29
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Yang W, Yu W, Du Y. The complete mitochondrial genome of the sycamore lace bug Corythucha ciliata (Hemiptera: Tingidae). Gene 2013; 532:27-40. [DOI: 10.1016/j.gene.2013.08.087] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Revised: 08/16/2013] [Accepted: 08/29/2013] [Indexed: 11/16/2022]
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30
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Simon S, Hadrys H. A comparative analysis of complete mitochondrial genomes among Hexapoda. Mol Phylogenet Evol 2013; 69:393-403. [DOI: 10.1016/j.ympev.2013.03.033] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 02/13/2013] [Accepted: 03/05/2013] [Indexed: 10/27/2022]
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31
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Yu S, Wang Y, Rédei D, Xie Q, Bu W. Secondary structure models of 18S and 28S rRNAs of the true bugs based on complete rDNA sequences of Eurydema maracandica Oshanin, 1871 (Heteroptera, Pentatomidae). Zookeys 2013; 319:363-77. [PMID: 24039531 PMCID: PMC3764533 DOI: 10.3897/zookeys.319.4178] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2012] [Accepted: 01/07/2013] [Indexed: 11/16/2022] Open
Abstract
The sequences of 18S and 28S rDNAs have been used as molecular markers to resolve phylogenetic relationships of Heteroptera for two decades. The complete sequences of 18S rDNAs have been used in many studies, while in most studies only partial sequences of 28S rDNAs have been used due to technical difficulties of amplifying the complete lengths. In this study, we amplified the complete 18S and 28S rDNA sequences of Eurydema maracandica Oshanin, 1871, and reconstructed the secondary structure models of the corresponding rRNAs. In addition, and more importantly, all of the length variable regions of 18S rRNA were compared among 37 families of Heteroptera based on 140 sequences, and the D3 region of 28S rRNA was compared among 51 families based on 84 sequences. It was found that 8 length variable regions could potentially serve as molecular synapomorphies for some monophyletic groups. Therefore discoveries of more molecular synapomorphies for specific clades can be anticipated from amplification of complete 18S and 28S rDNAs of more representatives of Heteroptera.
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Affiliation(s)
- Shasha Yu
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Yanhui Wang
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Dávid Rédei
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Qiang Xie
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
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32
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Friedemann K, Spangenberg R, Yoshizawa K, Beutel RG. Evolution of attachment structures in the highly diverse Acercaria (Hexapoda). Cladistics 2013; 30:170-201. [DOI: 10.1111/cla.12030] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2013] [Indexed: 11/26/2022] Open
Affiliation(s)
- Katrin Friedemann
- Entomology Group; Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum; FSU Jena 07743 Germany
- Max Planck Institute for Chemical Ecology; 07745 Jena Germany
| | - Rico Spangenberg
- Entomology Group; Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum; FSU Jena 07743 Germany
- Max Planck Institute for Chemical Ecology; 07745 Jena Germany
| | - Kazunori Yoshizawa
- Laboratory of Systematic Entomology; Graduate School of Agriculture; Hokkaido University; Sapporo 060-8589 Japan
| | - Rolf G. Beutel
- Entomology Group; Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum; FSU Jena 07743 Germany
- Max Planck Institute for Chemical Ecology; 07745 Jena Germany
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33
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Ling C, Hamada T, Bai J, Li X, Chesters D, Zheng W, Shi W. MrBayes tgMC³: a tight GPU implementation of MrBayes. PLoS One 2013; 8:e60667. [PMID: 23593277 PMCID: PMC3621901 DOI: 10.1371/journal.pone.0060667] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 03/01/2013] [Indexed: 11/18/2022] Open
Abstract
MrBayes is model-based phylogenetic inference tool using Bayesian statistics. However, model-based assessment of phylogenetic trees adds to the computational burden of tree-searching, and so poses significant computational challenges. Graphics Processing Units (GPUs) have been proposed as high performance, low cost acceleration platforms and several parallelized versions of the Metropolis Coupled Markov Chain Mote Carlo (MC3) algorithm in MrBayes have been presented that can run on GPUs. However, some bottlenecks decrease the efficiency of these implementations. To address these bottlenecks, we propose a tight GPU MC3 (tgMC3) algorithm. tgMC3 implements a different architecture from the one-to-one acceleration architecture employed in previously proposed methods. It merges multiply discrete GPU kernels according to the data dependency and hence decreases the number of kernels launched and the complexity of data transfer. We implemented tgMC3 and made performance comparisons with an earlier proposed algorithm, nMC3, and also with MrBayes MC3 under serial and multiply concurrent CPU processes. All of the methods were benchmarked on the same computing node from DEGIMA. Experiments indicate that the tgMC3 method outstrips nMC3 (v1.0) with speedup factors from 2.1 to 2.7×. In addition, tgMC3 outperforms the serial MrBayes MC3 by a factor of 6 to 30× when using a single GTX480 card, whereas a speedup factor of around 51× can be achieved by using two GTX 480 cards on relatively long sequences. Moreover, tgMC3 was compared with MrBayes accelerated by BEAGLE, and achieved speedup factors from 3.7 to 5.7×. The reported performance improvement of tgMC3 is significant and appears to scale well with increasing dataset sizes. In addition, the strategy proposed in tgMC3 could benefit the acceleration of other Bayesian-based phylogenetic analysis methods using GPUs.
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Affiliation(s)
- Cheng Ling
- Guangzhou Institute of Advanced Technology, Chinese Academy of Science, Guangzhou, China
- * E-mail: (CL); (WS)
| | - Tsuyoshi Hamada
- Department of Computer and Information Science, Nagasaki University, Nagasaki, Japan
| | - Jianing Bai
- Guangzhou Institute of Advanced Technology, Chinese Academy of Science, Guangzhou, China
| | - Xianbin Li
- Guangzhou Institute of Advanced Technology, Chinese Academy of Science, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Douglas Chesters
- Guangzhou Institute of Advanced Technology, Chinese Academy of Science, Guangzhou, China
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Weimin Zheng
- Guangzhou Institute of Advanced Technology, Chinese Academy of Science, Guangzhou, China
| | - Weifeng Shi
- School of Basic Medical Sciences, Taishan Medical College, Taian, Shandong, China
- * E-mail: (CL); (WS)
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34
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Abstract
MrBayes, using Metropolis-coupled Markov chain Monte Carlo (MCMCMC or (MC)3), is a popular program for Bayesian inference. As a leading method of using DNA data to infer phylogeny, the (MC)3 Bayesian algorithm and its improved and parallel versions are now not fast enough for biologists to analyze massive real-world DNA data. Recently, graphics processor unit (GPU) has shown its power as a coprocessor (or rather, an accelerator) in many fields. This article describes an efficient implementation a(MC)3 (aMCMCMC) for MrBayes (MC)3 on compute unified device architecture. By dynamically adjusting the task granularity to adapt to input data size and hardware configuration, it makes full use of GPU cores with different data sets. An adaptive method is also developed to split and combine DNA sequences to make full use of a large number of GPU cards. Furthermore, a new “node-by-node” task scheduling strategy is developed to improve concurrency, and several optimizing methods are used to reduce extra overhead. Experimental results show that a(MC)3 achieves up to 63× speedup over serial MrBayes on a single machine with one GPU card, and up to 170× speedup with four GPU cards, and up to 478× speedup with a 32-node GPU cluster. a(MC)3 is dramatically faster than all the previous (MC)3 algorithms and scales well to large GPU clusters.
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Affiliation(s)
- Jie Bao
- College of Information Technical Science, Nankai University, Tianjin, China
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35
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Wang Y, Engel MS, Rafael JA, Dang K, Wu H, Wang Y, Xie Q, Bu W. A unique box in 28S rRNA is shared by the enigmatic insect order Zoraptera and Dictyoptera. PLoS One 2013; 8:e53679. [PMID: 23301099 PMCID: PMC3536744 DOI: 10.1371/journal.pone.0053679] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 12/03/2012] [Indexed: 01/30/2023] Open
Abstract
The position of the Zoraptera remains one of the most challenging and uncertain concerns in ordinal-level phylogenies of the insects. Zoraptera have been viewed as having a close relationship with five different groups of Polyneoptera, or as being allied to the Paraneoptera or even Holometabola. Although rDNAs have been widely used in phylogenetic studies of insects, the application of the complete 28S rDNA are still scattered in only a few orders. In this study, a secondary structure model of the complete 28S rRNAs of insects was reconstructed based on all orders of Insecta. It was found that one length-variable region, D3-4, is particularly distinctive. The length and/or sequence of D3-4 is conservative within each order of Polyneoptera, but it can be divided into two types between the different orders of the supercohort, of which the enigmatic order Zoraptera and Dictyoptera share one type, while the remaining orders of Polyneoptera share the other. Additionally, independent evidence from phylogenetic results support the clade (Zoraptera+Dictyoptera) as well. Thus, the similarity of D3-4 between Zoraptera and Dictyoptera can serve as potentially valuable autapomorphy or synapomorphy in phylogeny reconstruction. The clades of (Plecoptera+Dermaptera) and ((Grylloblattodea+Mantophasmatodea)+(Embiodea+Phasmatodea)) were also recovered in the phylogenetic study. In addition, considering the other studies based on rDNAs, this study reached the highest congruence with previous phylogenetic studies of Holometabola based on nuclear protein coding genes or morphology characters. Future comparative studies of secondary structures across deep divergences and additional taxa are likely to reveal conserved patterns, structures and motifs that can provide support for major phylogenetic lineages.
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Affiliation(s)
- Yanhui Wang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Michael S. Engel
- Division of Entomology (Paleoentomology), Natural History Museum, London, England
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Jose A. Rafael
- Instituto Nacional de Pesquisas da Amazônia, INPA, Manaus, Amazonas, Brazil
| | - Kai Dang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Haoyang Wu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Ying Wang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Qiang Xie
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
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36
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Kuznetsova VG, Grozeva SM, Anokhin BA. The first finding of (TTAGG)n telomeric repeat in chromosomes of true bugs (Heteroptera, Belostomatidae). COMPARATIVE CYTOGENETICS 2012; 6:341-6. [PMID: 24260674 PMCID: PMC3834568 DOI: 10.3897/compcytogen.v6i4.4058] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 10/02/2012] [Indexed: 05/24/2023]
Abstract
Using the fluorescence in situ hybridization (FISH), the presence of (TTAGG)n telomeric sequence was detected in the chromosomes of Lethocerus patruelis (Stål, 1854) belonging to the family Belostomatidae (Heteroptera: Nepomorpha). This sequence was exclusively present at the ends of chromosomes in this species. This is the first evidence of the insect-type TTAGG telomeric repeats in Heteroptera.
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Affiliation(s)
- Valentina G Kuznetsova
- Zoological Institute, Russian Academy of Sciences, Universitetskaya nab. 1, St. Petersburg 199034, Russia
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37
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Li M, Tian Y, Zhao Y, Bu W. Higher level phylogeny and the first divergence time estimation of Heteroptera (Insecta: Hemiptera) based on multiple genes. PLoS One 2012; 7:e32152. [PMID: 22384163 PMCID: PMC3288068 DOI: 10.1371/journal.pone.0032152] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 01/19/2012] [Indexed: 11/22/2022] Open
Abstract
Heteroptera, or true bugs, are the largest, morphologically diverse and economically important group of insects with incomplete metamorphosis. However, the phylogenetic relationships within Heteroptera are still in dispute and most of the previous studies were based on morphological characters or with single gene (partial or whole 18S rDNA). Besides, so far, divergence time estimates for Heteroptera totally rely on the fossil record, while no studies have been performed on molecular divergence rates. Here, for the first time, we used maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) with multiple genes (18S rDNA, 28S rDNA, 16S rDNA and COI) to estimate phylogenetic relationships among the infraorders, and meanwhile, the Penalized Likelihood (r8s) and Bayesian (BEAST) molecular dating methods were employed to estimate divergence time of higher taxa of this suborder. Major results of the present study included: Nepomorpha was placed as the most basal clade in all six trees (MP trees, ML trees and Bayesian trees of nuclear gene data and four-gene combined data, respectively) with full support values. The sister-group relationship of Cimicomorpha and Pentatomomorpha was also strongly supported. Nepomorpha originated in early Triassic and the other six infraorders originated in a very short period of time in middle Triassic. Cimicomorpha and Pentatomomorpha underwent a radiation at family level in Cretaceous, paralleling the proliferation of the flowering plants. Our results indicated that the higher-group radiations within hemimetabolous Heteroptera were simultaneously with those of holometabolous Coleoptera and Diptera which took place in the Triassic. While the aquatic habitat was colonized by Nepomorpha already in the Triassic, the Gerromorpha independently adapted to the semi-aquatic habitat in the Early Jurassic.
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Affiliation(s)
- Min Li
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Ying Tian
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
- Patent Examination Cooperation Center, State Interllectual Property Office of the Peoples' Republic of China, Beijing, China
| | - Ying Zhao
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
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38
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Li H, Liu H, Shi A, Štys P, Zhou X, Cai W. The complete mitochondrial genome and novel gene arrangement of the unique-headed bug Stenopirates sp. (Hemiptera: Enicocephalidae). PLoS One 2012; 7:e29419. [PMID: 22235294 PMCID: PMC3250431 DOI: 10.1371/journal.pone.0029419] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 11/28/2011] [Indexed: 11/26/2022] Open
Abstract
Many of true bugs are important insect pests to cultivated crops and some are important vectors of human diseases, but few cladistic analyses have addressed relationships among the seven infraorders of Heteroptera. The Enicocephalomorpha and Nepomorpha are consider the basal groups of Heteroptera, but the basal-most lineage remains unresolved. Here we report the mitochondrial genome of the unique-headed bug Stenopirates sp., the first mitochondrial genome sequenced from Enicocephalomorpha. The Stenopirates sp. mitochondrial genome is a typical circular DNA molecule of 15, 384 bp in length, and contains 37 genes and a large non-coding fragment. The gene order differs substantially from other known insect mitochondrial genomes, with rearrangements of both tRNA genes and protein-coding genes. The overall AT content (82.5%) of Stenopirates sp. is the highest among all the known heteropteran mitochondrial genomes. The strand bias is consistent with other true bugs with negative GC-skew and positive AT-skew for the J-strand. The heteropteran mitochondrial atp8 exhibits the highest evolutionary rate, whereas cox1 appears to have the lowest rate. Furthermore, a negative correlation was observed between the variation of nucleotide substitutions and the GC content of each protein-coding gene. A microsatellite was identified in the putative control region. Finally, phylogenetic reconstruction suggests that Enicocephalomorpha is the sister group to all the remaining Heteroptera.
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Affiliation(s)
- Hu Li
- Department of Entomology, China Agricultural University, Beijing, China
| | - Hui Liu
- Entomological Laboratory, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Aimin Shi
- Department of Entomology, China Agricultural University, Beijing, China
| | - Pavel Štys
- Department of Zoology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky, Lexington, Kentucky, United States of America
| | - Wanzhi Cai
- Department of Entomology, China Agricultural University, Beijing, China
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Li H, Gao J, Liu H, Liu H, Liang A, Zhou X, Cai W. The architecture and complete sequence of mitochondrial genome of an assassin bug Agriosphodrus dohrni (Hemiptera: Reduviidae). Int J Biol Sci 2011; 7:792-804. [PMID: 21750648 PMCID: PMC3133887 DOI: 10.7150/ijbs.7.792] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Accepted: 06/18/2011] [Indexed: 11/05/2022] Open
Abstract
The 16, 470 bp nucleotide sequence of the mitochondrial genome (mitogenome) of an assassin bug from the reduviid subfamily Harpactorinae, Agriosphodrus dohrni, has been revealed. The entire genome encodes for two ribosomal RNA genes (rrnL and rrnS), 22 transfer RNA (tRNA) genes, 13 protein-coding genes, and a control region. The nucleotide composition is biased toward adenine and thymine (A+T = 72.2%). Comparative analysis with two other reduviid species Triatoma dimidiata and Valentia hoffmanni, exhibited highly conserved genome architectures including genome contents, gene order, nucleotide composition, codon usage, amino acid composition, as well as genome asymmetry. All protein-coding genes use standard mitochondrial initiation codons (methionine and isoleucine), except that nad1 starts with GTG. All tRNAs have the classic clover-leaf structure, except that the dihydrouridine (DHU) arm of tRNA(Ser(AGN)) forms a simple loop. Secondary structure comparisons of the two mitochondrial ribosomal subunits among sequenced assassin bugs show that the sequence and structure of rrnL is more conservative than that of rrnS. The presence of structural elements in the control region is also discussed, with emphasis on their implications in the regulation of replication and/or transcription of the reduviid mitogenome. The phylogenetic analyses indicated that within Reduviidae, Harpactorinae is a sister group to the Salyavatinae + Triatominae clade.
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Affiliation(s)
- Hu Li
- 1. Department of Entomology, China Agricultural University, Beijing 100193, China
| | - Jianyu Gao
- 1. Department of Entomology, China Agricultural University, Beijing 100193, China
| | - Haiyu Liu
- 1. Department of Entomology, China Agricultural University, Beijing 100193, China
| | - Hui Liu
- 1. Department of Entomology, China Agricultural University, Beijing 100193, China
| | - Aiping Liang
- 2. Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuguo Zhou
- 3. Department of Entomology, University of Kentucky, Lexington, KY 40546-0091, USA
| | - Wanzhi Cai
- 1. Department of Entomology, China Agricultural University, Beijing 100193, China
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40
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Affiliation(s)
- Jianfu Zhou
- Nankai-Baidu Joint Laboratory, College of Information Technical Science, Nankai University, Tianjin, China
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41
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Xie Q, Lin J, Qin Y, Zhou J, Bu W. Structural diversity of eukaryotic 18S rRNA and its impact on alignment and phylogenetic reconstruction. Protein Cell 2011; 2:161-70. [PMID: 21400046 DOI: 10.1007/s13238-011-1017-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Accepted: 01/30/2011] [Indexed: 10/18/2022] Open
Abstract
Ribosomal RNAs are important because they catalyze the synthesis of peptides and proteins. Comparative studies of the secondary structure of 18S rRNA have revealed the basic locations of its many length-conserved and length-variable regions. In recent years, many more sequences of 18S rDNA with unusual lengths have been documented in GenBank. These data make it possible to recognize the diversity of the secondary and tertiary structures of 18S rRNAs and to identify the length-conserved parts of 18S rDNAs. The longest 18S rDNA sequences of almost every known eukaryotic phylum were included in this study. We illustrated the bioinformatics-based structure to show that, the regions that are more length-variable, regions that are less length-variable, the splicing sites for introns, and the sites of A-minor interactions are mostly distributed in different parts of the 18S rRNA. Additionally, this study revealed that some length-variable regions or insertion positions could be quite close to the functional part of the 18S rRNA of Foraminifera organisms. The tertiary structure as well as the secondary structure of 18S rRNA can be more diverse than what was previously supposed. Besides revealing how this interesting gene evolves, it can help to remove ambiguity from the alignment of eukaryotic 18S rDNAs and to improve the performance of 18S rDNA in phylogenetic reconstruction. Six nucleotides shared by Archaea and Eukaryota but rarely by Bacteria are also reported here for the first time, which might further support the supposed origin of eukaryote from archaeans.
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Affiliation(s)
- Qiang Xie
- Department of Zoology and Developmental Biology, College of Life Sciences, Nankai University, Tianjin 300071, China.
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42
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Weirauch C, Schuh RT. Systematics and evolution of Heteroptera: 25 years of progress. ANNUAL REVIEW OF ENTOMOLOGY 2011; 56:487-510. [PMID: 20822450 DOI: 10.1146/annurev-ento-120709-144833] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Heteroptera, or true bugs, are part of the most successful radiation of nonholometabolous insects. Twenty-five years after the first review on the influence of cladistics on systematic research in Heteroptera, we summarize progress, problems, and future directions in the field. The few hypotheses on infraordinal relationships conflict on crucial points. Understanding relationships within Gerromorpha, Nepomorpha, Leptopodomorpha, Cimicomorpha, and Pentatomomorpha is improving, but progress within Enicocephalomorpha and Dipsocoromorpha is lagging behind. Nonetheless, the classifications of several superfamily-level taxa within the Pentatomomorpha, such as Aradoidea, Coreoidea, and Pyrrhocoroidea, are still unaffected by cladistic studies. Progress in comparative morphology is slow and drastically impedes our understanding of the evolution of major clades. Molecular systematics has dramatically contributed to accelerating the generation and testing of hypotheses. Given the fascinating natural history of true bugs and their status as model organisms for evolutionary studies, integration of cladistic analyses in a broader biogeographic and evolutionary context deserves increased attention.
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Affiliation(s)
- Christiane Weirauch
- Department of Entomology, University of California, Riverside, California, USA.
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43
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Perkins EM, Donnellan SC, Bertozzi T, Whittington ID. Closing the mitochondrial circle on paraphyly of the Monogenea (Platyhelminthes) infers evolution in the diet of parasitic flatworms. Int J Parasitol 2010; 40:1237-45. [DOI: 10.1016/j.ijpara.2010.02.017] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Revised: 02/16/2010] [Accepted: 02/16/2010] [Indexed: 11/30/2022]
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44
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Jurassic Progonocimicidae (Hemiptera) from China and phylogenetic evolution of Coleorrhyncha. ACTA ACUST UNITED AC 2009. [DOI: 10.1007/s11430-009-0160-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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45
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Hua J, Li M, Dong P, Cui Y, Xie Q, Bu W. Phylogenetic analysis of the true water bugs (Insecta: Hemiptera: Heteroptera: Nepomorpha): evidence from mitochondrial genomes. BMC Evol Biol 2009; 9:134. [PMID: 19523246 PMCID: PMC2711072 DOI: 10.1186/1471-2148-9-134] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2009] [Accepted: 06/15/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The true water bugs are grouped in infraorder Nepomorpha (Insecta: Hemiptera: Heteroptera) and are of great economic importance. The phylogenetic relationships within Nepomorpha and the taxonomic hierarchies of Pleoidea and Aphelocheiroidea are uncertain. Most of the previous studies were based on morphological characters without algorithmic assessment. In the latest study, the molecular markers employed in phylogenetic analyses were partial sequences of 16S rDNA and 18S rDNA with a total length about 1 kb. Up to now, no mitochondrial genome of the true water bugs has been sequenced, which is one of the largest data sets that could be compared across animal taxa. In this study we analyzed the unresolved problems in Nepomorpha using evidence from mitochondrial genomes. RESULTS Nine mitochondrial genomes of Nepomorpha and five of other hemipterans were sequenced. These mitochondrial genomes contain the commonly found 37 genes without gene rearrangements. Based on the nucleotide sequences of mt-genomes, Pleoidea is not a member of the Nepomorpha and Aphelocheiroidea should be grouped back into Naucoroidea. Phylogenetic relationships among the superfamilies of Nepomorpha were resolved robustly. CONCLUSION The mt-genome is an effective data source for resolving intraordinal phylogenetic problems at the superfamily level within Heteroptera. The mitochondrial genomes of the true water bugs are typical insect mt-genomes. Based on the nucleotide sequences of the mt-genomes, we propose the Pleoidea to be a separate heteropteran infraorder. The infraorder Nepomorpha consists of five superfamilies with the relationships (Corixoidea + ((Naucoroidea + Notonectoidea) + (Ochteroidea + Nepoidea))).
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Affiliation(s)
- Jimeng Hua
- Department of Zoology and Developmental Biology, Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, PR China.
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Light JE, Reed DL. Multigene analysis of phylogenetic relationships and divergence times of primate sucking lice (Phthiraptera: Anoplura). Mol Phylogenet Evol 2008; 50:376-90. [PMID: 19027083 DOI: 10.1016/j.ympev.2008.10.023] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2008] [Revised: 10/28/2008] [Accepted: 10/29/2008] [Indexed: 10/21/2022]
Abstract
Cospeciation between hosts and parasites offers a unique opportunity to use information from parasites to infer events in host evolutionary history. Although lice (Insecta: Phthiraptera) are known to cospeciate with their hosts and have frequently served as important markers to infer host evolutionary history, most molecular studies are based on only one or two markers. Resulting phylogenies may, therefore, represent gene histories (rather than species histories), and analyses of multiple molecular markers are needed to increase confidence in the results of phylogenetic analyses. Herein, we phylogenetically examine nine molecular markers in primate sucking lice (Phthiraptera: Anoplura) and we use these markers to estimate divergence times among louse lineages. Individual and combined analyses of these nine markers are, for the most part, congruent, supporting relationships hypothesized in previous studies. Only one marker, the nuclear protein-coding gene Histone 3, has a significantly different tree topology compared to the other markers. The disparate evolutionary history of this marker, however, has no significant effect on topology or nodal support in the combined phylogenetic analyses. Therefore, phylogenetic results from the combined data set likely represent a solid hypothesis of species relationships. Additionally, we find that simultaneous use of multiple markers and calibration points provides the most reliable estimates of louse divergence times, in agreement with previous studies estimating divergences among species. Estimates of phylogenies and divergence times also allow us to verify the results of [Reed, D.L., Light, J.E., Allen, J.M., Kirchman, J.J., 2007. Pair of lice lost or parasites regained: the evolutionary history of anthropoid primate lice. BMC Biol. 5, 7.]; there was probable contact between gorilla and archaic hominids roughly 3 Ma resulting in a host switch of Pthirus lice from gorillas to archaic hominids. Thus, these results provide further evidence that data from cospeciating organisms can yield important information about the evolutionary history of their hosts.
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Affiliation(s)
- Jessica E Light
- Florida Museum of Natural History, University of Florida, Dickinson Hall, P.O. Box 117800, Gainesville, FL 32611-7800, USA.
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