1
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Rubio AO, Dye AM, Ifill KE, Summers K. On the wings of dragons: Wing morphometric differences in the sexually dichromatic common whitetail skimmer dragonfly, Plathemis lydia (Odonata: Libellulidae). PLoS One 2024; 19:e0303690. [PMID: 38809838 PMCID: PMC11135787 DOI: 10.1371/journal.pone.0303690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 04/29/2024] [Indexed: 05/31/2024] Open
Abstract
Sexual dimorphism is common throughout the animal kingdom, leading to sex-specific phenotypic differences. The common whitetail skimmer dragonfly, Plathemis lydia (Drury, 1773), is sexually dichromatic, where males of this species display a conspicuous white abdomen and females display a dark brown abdomen. Differences in abdomen conspicuousness between male and female P. lydia are likely attributed to differences in selective pressure where males use their white conspicuous abdomen during male-male territorial chases. We hypothesized that male P. lydia would exhibit wing morphology adaptations to better offset the costs of predation and territoriality and that these adaptations would differ from females. We used field-collected images to quantify differences in body length, wing length, wing area, wing shape, and wing loading between male and female P. lydia. Our results show that male P. lydia have significantly shorter fore and hind wings relative to body size with a higher wing loading when compared to females. We also found that male P. lydia have narrower and pointier fore and hind wings compared to females. These results are consistent with the idea that males are adapted for faster flight, specifically higher acceleration capacity, and higher agility whereas females are adapted for higher maneuverability.
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Affiliation(s)
- Andrew O. Rubio
- Department of Biology, East Carolina University, Greenville, North Carolina, United States of America
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Ashley M. Dye
- Department of Biology, East Carolina University, Greenville, North Carolina, United States of America
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Kyle E. Ifill
- Department of Biology, East Carolina University, Greenville, North Carolina, United States of America
| | - Kyle Summers
- Department of Biology, East Carolina University, Greenville, North Carolina, United States of America
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2
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Drosopoulou E, Syllas A, Goutakoli P, Zisiadis GA, Konstantinou T, Pangea D, Sentis G, van Sauers-Muller A, Wee SL, Augustinos AA, Zacharopoulou A, Bourtzis K. Τhe Complete Mitochondrial Genome of Bactrocera carambolae (Diptera: Tephritidae): Genome Description and Phylogenetic Implications. INSECTS 2019; 10:E429. [PMID: 31795125 PMCID: PMC6955806 DOI: 10.3390/insects10120429] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 11/15/2019] [Accepted: 11/21/2019] [Indexed: 01/09/2023]
Abstract
Bactrocera carambolae is one of the approximately 100 sibling species of the Bactrocera dorsalis complex and considered to be very closely related to B. dorsalis. Due to their high morphological similarity and overlapping distribution, as well as to their economic impact and quarantine status, the development of reliable markers for species delimitation between the two taxa is of great importance. Here we present the complete mitochondrial genome of B. carambolae sourced from its native range in Malaysia and its invaded territory in Suriname. The mitogenome of B. carambolae presents the typical organization of an insect mitochondrion. Comparisons of the analyzed B. carambolae sequences to all available complete mitochondrial sequences of B. dorsalis revealed several species-specific polymorphic sites. Phylogenetic analysis based on Bactrocera mitogenomes supports that B. carambolae is a differentiated taxon though closely related to B. dorsalis. The present complete mitochondrial sequences of B. carambolae could be used, in the frame of Integrative Taxonomy, for species discrimination and resolution of the phylogenetic relationships within this taxonomically challenging complex, which would facilitate the application of species-specific population suppression strategies, such as the sterile insect technique.
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Affiliation(s)
- Elena Drosopoulou
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.S.); (P.G.); (G.-A.Z.); (T.K.); (D.P.); (G.S.)
| | - Alexandros Syllas
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.S.); (P.G.); (G.-A.Z.); (T.K.); (D.P.); (G.S.)
| | - Panagiota Goutakoli
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.S.); (P.G.); (G.-A.Z.); (T.K.); (D.P.); (G.S.)
| | - Georgios-Alkis Zisiadis
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.S.); (P.G.); (G.-A.Z.); (T.K.); (D.P.); (G.S.)
| | - Theodora Konstantinou
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.S.); (P.G.); (G.-A.Z.); (T.K.); (D.P.); (G.S.)
| | - Dimitra Pangea
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.S.); (P.G.); (G.-A.Z.); (T.K.); (D.P.); (G.S.)
| | - George Sentis
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.S.); (P.G.); (G.-A.Z.); (T.K.); (D.P.); (G.S.)
| | - Alies van Sauers-Muller
- Consultant, retired from Ministry of Agriculture, Animal Husbandry and Fisheries, Carambola Fruit Fly Project, Damboentong 282, Tijgerkreek, Saramacca, Suriname;
| | - Suk-Ling Wee
- Center for Insect Systematics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia;
| | - Antonios A. Augustinos
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Seibersdorf, A-1400 Vienna, Austria; (A.A.A.); (K.B.)
| | | | - Kostas Bourtzis
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Seibersdorf, A-1400 Vienna, Austria; (A.A.A.); (K.B.)
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3
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Leblanc L, Hossain MA, Doorenweerd C, Ahmed Khan S, Momen M, San Jose M, Rubinoff D. Six years of fruit fly surveys in Bangladesh: a new species, 33 new country records and discovery of the highly invasive Bactrocera carambolae (Diptera, Tephritidae). Zookeys 2019; 876:87-109. [PMID: 31592216 PMCID: PMC6775173 DOI: 10.3897/zookeys.876.38096] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 08/13/2019] [Indexed: 11/15/2022] Open
Abstract
We engaged in six years of snap-shot surveys for fruit flies in rural environments and ten protected forest areas of Bangladesh, using traps baited with male lures (cue-lure, methyl eugenol, zingerone). Our work has increased the recorded number of species of Tephritidae in the country from seven to 37. We summarize these surveys and report eight new country occurrence records, and a new species (Zeugodacusmadhupuri Leblanc & Doorenweerd, sp. nov.) is described. The highlight among the new records is the discovery, and significant westward range extension, of Bactroceracarambolae Drew & Hancock, a major fruit pest detected in the Chattogram and Sylhet Divisions. We rectify the previously published erroneous record of Bactrocerabogorensis (Hardy), which was based on a misidentification of Zeugodacusdiaphorus (Hendel). We also report the occurrence in Bangladesh of nine other Tephritidae, the rearing of three primary fruit fly parasitoids from Zeugodacus, and records of non-target attraction to fruit fly lures.
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Affiliation(s)
- Luc Leblanc
- University of Idaho, Department of Entomology, Plant Pathology and Nematology (EPPN), 875 Perimeter Drive MS 2329, Moscow, Idaho, USA University of Idaho Moscow United States of America
| | - M Aftab Hossain
- Insect Biotechnology Division, Institute of Food and Radiation Biology, Bangladesh Atomic Energy Commission, Dhaka-1349, Bangladesh Bangladesh Atomic Energy Commission Dhaka Bangladesh
| | - Camiel Doorenweerd
- University of Hawaii at Manoa, Department of Plant and Environmental Protection Sciences, 3050 Maile Way, Gilmore 310, Honolulu, HI 96822, USA University of Hawaii at Manoa Honolulu United States of America
| | - Shakil Ahmed Khan
- Insect Biotechnology Division, Institute of Food and Radiation Biology, Bangladesh Atomic Energy Commission, Dhaka-1349, Bangladesh Bangladesh Atomic Energy Commission Dhaka Bangladesh
| | - Mahfuza Momen
- Insect Biotechnology Division, Institute of Food and Radiation Biology, Bangladesh Atomic Energy Commission, Dhaka-1349, Bangladesh Bangladesh Atomic Energy Commission Dhaka Bangladesh
| | - Michael San Jose
- University of Hawaii at Manoa, Department of Plant and Environmental Protection Sciences, 3050 Maile Way, Gilmore 310, Honolulu, HI 96822, USA University of Hawaii at Manoa Honolulu United States of America
| | - Daniel Rubinoff
- University of Hawaii at Manoa, Department of Plant and Environmental Protection Sciences, 3050 Maile Way, Gilmore 310, Honolulu, HI 96822, USA University of Hawaii at Manoa Honolulu United States of America
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4
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Li D, Waite DW, Gunawardana DN, McCarthy B, Anderson D, Flynn A, George S. DNA barcoding and real-time PCR detection of Bactrocera xanthodes (Tephritidae: Diptera) complex. BULLETIN OF ENTOMOLOGICAL RESEARCH 2019; 109:102-110. [PMID: 29729674 DOI: 10.1017/s0007485318000251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Immature fruit fly stages of the family Tephritidae are commonly intercepted on breadfruit from Pacific countries at the New Zealand border but are unable to be identified to the species level using morphological characters. Subsequent molecular identification showed that they belong to Bactrocera xanthodes, which is part of a species complex that includes Bactrocera paraxanthodes, Bactrocera neoxanthodes and an undescribed species. To establish a more reliable molecular identification system for B. xanthodes, a reference database of DNA barcode sequences for the 5'-fragment of COI gene region was constructed for B. xanthodes from Fiji, Samoa and Tonga. To better understand the species complex, B. neoxanthodes from Vanuatu and B. paraxanthodes from New Caledonia were also barcoded. Using the results of this analysis, real-time TaqMan polymerase chain reaction (PCR) assays for the detection of B. xanthodes complex and for the three individual species of the complex were developed and validated. The assay showed high specificity for the target species, with no cross-reaction observed for closely related organisms. Each of the real-time PCR assays is sensitive, detecting the target sequences at concentrations as low as ten copies µl-1 and can be used as either singleplex or multiplex formats. This real-time PCR assay for B. xanthodes has been successfully applied at the borders in New Zealand, leading to the rapid identification of intercepted Tephritidae eggs and larvae. The developed assays will be useful biosecurity tools for rapid detection of species in the B. xanthodes complex worldwide.
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Affiliation(s)
- D Li
- Plant Health and Environment Laboratory,Ministry for Primary Industries,P.O. Box 2095,Auckland 1140,New Zealand
| | - D W Waite
- Plant Health and Environment Laboratory,Ministry for Primary Industries,P.O. Box 2095,Auckland 1140,New Zealand
| | - D N Gunawardana
- Plant Health and Environment Laboratory,Ministry for Primary Industries,P.O. Box 2095,Auckland 1140,New Zealand
| | - B McCarthy
- Plant Health and Environment Laboratory,Ministry for Primary Industries,PO Box 14018,Christchurch 8544,New Zealand
| | - D Anderson
- Plant Health and Environment Laboratory,Ministry for Primary Industries,PO Box 14018,Christchurch 8544,New Zealand
| | - A Flynn
- Plant Health and Environment Laboratory,Ministry for Primary Industries,P.O. Box 2095,Auckland 1140,New Zealand
| | - S George
- Plant Health and Environment Laboratory,Ministry for Primary Industries,P.O. Box 2095,Auckland 1140,New Zealand
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5
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Catullo RA, Yeap HL, Lee SF, Bragg JG, Cheesman J, De Faveri S, Edwards O, Hee AKW, Popa AD, Schiffer M, Oakeshott JG. A genome-wide approach for uncovering evolutionary relationships of Australian Bactrocera species complexes (Diptera: Tephritidae). INVERTEBR SYST 2019. [DOI: 10.1071/is18065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Australia and Southeast Asia are hotspots of global diversity in the fruit-fly genus Bactrocera. Although a great diversity of species has been long recognised, evolutionary relationships are poorly understood, largely because previous sequencing techniques have provided insufficient historical signal for phylogenetic reconstruction. Poorly understood biogeographic history in Bactrocera has prevented a deeper understanding of migratory patterns in this economically important pest group. Using representatives from Australia and Malaysia, we tested the utility of a genome-reduction approach that generates thousands of single-nucleotide polymorphisms for phylogenetic reconstructions. This approach has high utility for species identification because of the ease of sample addition over time, and the species-level specificity able to be achieved with the markers. These data have provided a strongly supported phylogenetic tree congruent with topologies generated using more intensive sequencing approaches. In addition, our results do not support taxonomic assignments to species complex for a number of species, such as B. endiandrae in the dorsalis complex, yet find a close relationship between B. pallida and the dorsalis species. Our data have further validated non-monophyletic evolution of male response to primary attractants. We also showed at least two diversification events between Australia and Southeast Asia, indicating trans-regional dispersal in important pest species.
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6
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San Jose M, Doorenweerd C, Leblanc L, Barr N, Geib S, Rubinoff D. Tracking the Origins of Fly Invasions; Using Mitochondrial Haplotype Diversity to Identify Potential Source Populations in Two Genetically Intertwined Fruit Fly Species (Bactrocera carambolae and Bactrocera dorsalis [Diptera: Tephritidae]). JOURNAL OF ECONOMIC ENTOMOLOGY 2018; 111:2914-2926. [PMID: 30247661 DOI: 10.1093/jee/toy272] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Indexed: 06/08/2023]
Abstract
Bactrocera carambolae Drew and Hancock and Bactrocera dorsalis (Hendel) (Diptera: Tephritidae) are important pests of many fruits. These flies have been spread across the world through global travel and trade, and new areas are at risk of invasion. Whenever new invasive populations are discovered, quick and accurate identification is needed to mitigate the damage they can cause. Determining invasive pathways can prevent further spread of pests as well as subsequent reinvasions through the same pathway. Molecular markers can be used for both species identification and pathway analysis. We analyzed 1,601 individuals from 19 populations using 765 base pairs of the mitochondrial cytochrome oxidase I (COI) gene to infer the haplotype diversity and population structure within these flies from across their native and invasive ranges. We analyzed these samples by either grouping by species or geographic populations due to the genetic similarity in the mitochondrial genome. We found no genetic structure between B. dorsalis and B. carambolae and our findings suggest recent and most likely ongoing, genetic exchange between these two species in the wild. Hyper-diverse mitochondrial genetic diversity in the native range suggests large population sizes and relatively high mutation rates. Only 52% of the haplotypes found in the trap captures from California are shared with haplotypes from flies found in our global survey, indicating significant genetic diversity in the native range that is missing from our samples. However, these results provide a foundation for the accurate determination of the provenance of invasive populations around the world.
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Affiliation(s)
- Michael San Jose
- University of Hawai'i at Manoa Department of Plant and Environmental Protection Sciences, Gilmore Honolulu, HI
| | - Camiel Doorenweerd
- University of Hawai'i at Manoa Department of Plant and Environmental Protection Sciences, Gilmore Honolulu, HI
| | - Luc Leblanc
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Perimeter Drive MS, Moscow, ID
| | - Norman Barr
- Center for Plant Health Science and Technology, Mission Laboratory, USDA-APHIS, Moore Air Base, North Moorefield Rd., Edinburg, TX
| | - Scott Geib
- Tropical Crop and Commodity Protection Research Unit, Daniel K Inouye U.S. Pacific Basin Agricultural Research Center, USDA Agricultural Research Services, Hilo, HI
| | - Daniel Rubinoff
- University of Hawai'i at Manoa Department of Plant and Environmental Protection Sciences, Gilmore Honolulu, HI
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7
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Nugnes F, Russo E, Viggiani G, Bernardo U. First Record of an Invasive Fruit Fly Belonging to Bactrocera dorsalis Complex (Diptera: Tephritidae) in Europe. INSECTS 2018; 9:E182. [PMID: 30513969 PMCID: PMC6316371 DOI: 10.3390/insects9040182] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 11/27/2018] [Accepted: 11/29/2018] [Indexed: 11/16/2022]
Abstract
Emerging pests are increasingly threatening fruit orchard health across the Mediterranean area. Tephritidae, representing serious threats for Europe, are numerous, and the fruit flies Bactrocera zonata and those belonging to Bactrocera dorsalis complex are among the most alarming species. These species are highly polyphagous and B. zonata has already spread to some Mediterranean countries. Due to these ongoing threats, in the Campania Region (southern Italy), a survey with traps and infested fruits analysis was performed with the aim of detecting the presence of species of Bactrocera dorsalis complex. In two mixed fruit-trees fields, some adults belonging to a species of Bactrocera were captured in traps baited with the highly attractive male lure (methyl eugenol). They were distinguished from similar-looking Bactrocera spp. by morphological and molecular comparative analyses. Considering the existing morphological keys, specimens were tentatively identified as B. dorsalis but molecular characterization with COI split them into two clades. Some specimens were grouped with B. dorsalis similar to B. kandiensis and B. kandiensis and others in a clade including B. dorsalis and B. invadens (syn. B. dorsalis). ITS1 sequences instead confirmed morphological identification. The integrative approach allowed identifying all the specimens collected as belonging to the B. dorsalis complex. This finding represents the first field interception in Europe of a member of one of the most dangerous groups of fruit flies.
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Affiliation(s)
- Francesco Nugnes
- CNR, Institute for Sustainable Plant Protection, 80055 Portici, Italy.
| | - Elia Russo
- CNR, Institute for Sustainable Plant Protection, 80055 Portici, Italy.
| | - Gennaro Viggiani
- Department of Agriculture, University of Naples "Federico II", 80055 Portici, Italy.
| | - Umberto Bernardo
- CNR, Institute for Sustainable Plant Protection, 80055 Portici, Italy.
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8
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Leblanc L, Doorenweerd C, Jose MS, Pham HT, Rubinoff D. Descriptions of four new species of Bactrocera and new country records highlight the high biodiversity of fruit flies in Vietnam (Diptera, Tephritidae, Dacinae). Zookeys 2018:87-115. [PMID: 30505163 PMCID: PMC6255883 DOI: 10.3897/zookeys.797.29138] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/22/2018] [Indexed: 01/01/2023] Open
Abstract
Recent snap-shot surveys for fruit flies in Vietnam in 2015 and 2017 using traps baited with the male Dacinae fruit fly lures methyl eugenol, cue-lure and zingerone, collected 56 species, including 11 new country records and another 11 undescribed species, four of which are described in this paper. This increases the number of described species known to occur in Vietnam from 78 to 93. Species accumulation curves, based on the Chao 2 mean estimate, suggest that we collected 60-85 % of the local fauna at the sites sampled, and that species diversity decreases with increasing latitude. The four new species are named: Bactrocera (Tetradacus) ernesti Leblanc & Doorenweerd sp. n., B. (Asiadacus) connecta Leblanc & Doorenweerd sp. n., B. (Parazeugodacus) clarifemur Leblanc & Doorenweerd sp. n., and B. (Bactrocera) adamantea Leblanc & Doorenweerd sp. n. In addition to morphological data COI DNA sequence data of both the COI-5P and COI-3P mitochondrial DNA gene regions is provided. Three of the four newly described species are morphologically and genetically easily distinguished from all other members of Dacini. Bactroceraclarifemur sp. n. is superficially similar to B.pendleburyi (Perkins) based on morphology, but there are several apomorphic characters to distinguish the two. Both COI and a segment of the nuclear gene Elongation Factor 1 alpha separate the two species as well.
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Affiliation(s)
- Luc Leblanc
- University of Idaho, Department of Entomology, Plant Pathology and Nematology, 875 Perimeter Drive, MS2329, Moscow, Idaho, 83844-2329, USA
| | - Camiel Doorenweerd
- University of Hawaii, Department of Plant and Environmental Protection Services, 3050 Maile Way, Honolulu, Hawaii, 96822-2231, USA
| | - Michael San Jose
- University of Hawaii, Department of Plant and Environmental Protection Services, 3050 Maile Way, Honolulu, Hawaii, 96822-2231, USA
| | - Hong Thai Pham
- Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, Hoang Quoc Viet St, Hanoi, Vietnam
| | - Daniel Rubinoff
- University of Hawaii, Department of Plant and Environmental Protection Services, 3050 Maile Way, Honolulu, Hawaii, 96822-2231, USA
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9
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Rapid identification of Bactrocera zonata (Dip.: Tephritidae) using TaqMan real-time PCR assay. PLoS One 2018; 13:e0205136. [PMID: 30286152 PMCID: PMC6171934 DOI: 10.1371/journal.pone.0205136] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 09/19/2018] [Indexed: 11/29/2022] Open
Abstract
Tephritid fruit flies are ranked as one of the most damaging groups of insect pests. Morphological identification of fruit flies is mainly performed on adults due to the lack of adequate identification keys for immature stages. The peach fruit fly, Bactrocera zonata (Saunders), infests some of the principal commercial fruits and vegetables. It is, therefore important to avert its global dispersal, particularly by accurately identifying this species at ports of entry. In this study, a TaqMan real-time polymerase chain reaction (PCR) was developed for the accurate identification and sensitive detection of the peach fruit fly. A novel set of primers and probe were designed to specifically identify the mitochondrial cytochrome oxidase I (COI) gene. All specimens of peach fruit fly (including various life stages) were detected, and no cross reactivity with other tested tephritids were observed. Since this assay performed equally well with crushed insects and purified DNA, we note added efficiency by eliminating DNA extraction step. Considering the speed, specificity as well as sensitivity of the assay, Taqman real-time PCR can be used as a swift and specific method for pest species at ports of entry.
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10
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Dupuis JR, Bremer FT, Kauwe A, San Jose M, Leblanc L, Rubinoff D, Geib SM. HiMAP: Robust phylogenomics from highly multiplexed amplicon sequencing. Mol Ecol Resour 2018. [PMID: 29633537 DOI: 10.1101/213454] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
High-throughput sequencing has fundamentally changed how molecular phylogenetic data sets are assembled, and phylogenomic data sets commonly contain 50- to 100-fold more loci than those generated using traditional Sanger sequencing-based approaches. Here, we demonstrate a new approach for building phylogenomic data sets using single-tube, highly multiplexed amplicon sequencing, which we name HiMAP (highly multiplexed amplicon-based phylogenomics) and present bioinformatic pipelines for locus selection based on genomic and transcriptomic data resources and postsequencing consensus calling and alignment. This method is inexpensive and amenable to sequencing a large number (hundreds) of taxa simultaneously and requires minimal hands-on time at the bench (<1/2 day), and data analysis can be accomplished without the need for read mapping or assembly. We demonstrate this approach by sequencing 878 amplicons in single reactions for 82 species of tephritid fruit flies across seven genera (384 individuals), including some of the most economically important agricultural insect pests. The resulting filtered data set (>150,000-bp concatenated alignment, ~20% missing character sites across all individuals and amplicons) contained >40,000 phylogenetically informative characters, and although some discordance was observed between analyses, it provided unparalleled resolution of many phylogenetic relationships in this group. Most notably, we found high support for the generic status of Zeugodacus and the sister relationship between Dacus and Zeugodacus. We discuss HiMAP, with regard to its molecular and bioinformatic strengths, and the insight the resulting data set provides into relationships of this diverse insect group.
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Affiliation(s)
- Julian R Dupuis
- U.S. Department of Agriculture-Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, Hawaii
- Department of Plant and Environmental Protection Services, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Forest T Bremer
- U.S. Department of Agriculture-Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, Hawaii
- Department of Plant and Environmental Protection Services, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Angela Kauwe
- U.S. Department of Agriculture-Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, Hawaii
| | - Michael San Jose
- Department of Plant and Environmental Protection Services, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Luc Leblanc
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, Idaho
| | - Daniel Rubinoff
- Department of Plant and Environmental Protection Services, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Scott M Geib
- U.S. Department of Agriculture-Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, Hawaii
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11
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Dupuis JR, Bremer FT, Kauwe A, San Jose M, Leblanc L, Rubinoff D, Geib SM. HiMAP: Robust phylogenomics from highly multiplexed amplicon sequencing. Mol Ecol Resour 2018; 18:1000-1019. [PMID: 29633537 DOI: 10.1111/1755-0998.12783] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 03/07/2018] [Accepted: 03/19/2018] [Indexed: 01/22/2023]
Abstract
High-throughput sequencing has fundamentally changed how molecular phylogenetic data sets are assembled, and phylogenomic data sets commonly contain 50- to 100-fold more loci than those generated using traditional Sanger sequencing-based approaches. Here, we demonstrate a new approach for building phylogenomic data sets using single-tube, highly multiplexed amplicon sequencing, which we name HiMAP (highly multiplexed amplicon-based phylogenomics) and present bioinformatic pipelines for locus selection based on genomic and transcriptomic data resources and postsequencing consensus calling and alignment. This method is inexpensive and amenable to sequencing a large number (hundreds) of taxa simultaneously and requires minimal hands-on time at the bench (<1/2 day), and data analysis can be accomplished without the need for read mapping or assembly. We demonstrate this approach by sequencing 878 amplicons in single reactions for 82 species of tephritid fruit flies across seven genera (384 individuals), including some of the most economically important agricultural insect pests. The resulting filtered data set (>150,000-bp concatenated alignment, ~20% missing character sites across all individuals and amplicons) contained >40,000 phylogenetically informative characters, and although some discordance was observed between analyses, it provided unparalleled resolution of many phylogenetic relationships in this group. Most notably, we found high support for the generic status of Zeugodacus and the sister relationship between Dacus and Zeugodacus. We discuss HiMAP, with regard to its molecular and bioinformatic strengths, and the insight the resulting data set provides into relationships of this diverse insect group.
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Affiliation(s)
- Julian R Dupuis
- U.S. Department of Agriculture-Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, Hawaii
- Department of Plant and Environmental Protection Services, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Forest T Bremer
- U.S. Department of Agriculture-Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, Hawaii
- Department of Plant and Environmental Protection Services, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Angela Kauwe
- U.S. Department of Agriculture-Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, Hawaii
| | - Michael San Jose
- Department of Plant and Environmental Protection Services, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Luc Leblanc
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, Idaho
| | - Daniel Rubinoff
- Department of Plant and Environmental Protection Services, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Scott M Geib
- U.S. Department of Agriculture-Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, Hawaii
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12
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Incongruence between molecules and morphology: A seven-gene phylogeny of Dacini fruit flies paves the way for reclassification (Diptera: Tephritidae). Mol Phylogenet Evol 2018; 121:139-149. [DOI: 10.1016/j.ympev.2017.12.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 12/02/2017] [Accepted: 12/03/2017] [Indexed: 11/23/2022]
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Doorenweerd C, Leblanc L, Norrbom AL, Jose MS, Rubinoff D. A global checklist of the 932 fruit fly species in the tribe Dacini (Diptera, Tephritidae). Zookeys 2018; 730:19-56. [PMID: 29416395 PMCID: PMC5799784 DOI: 10.3897/zookeys.730.21786] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 12/14/2017] [Indexed: 12/31/2022] Open
Abstract
The correct application of the scientific names of species is neither easy nor trivial. Mistakes can lead to the wrong interpretation of research results or, when pest species are involved, inappropriate regulations and limits on trade, and possibly quarantine failures that permit the invasion of new pest species. Names are particularly challenging to manage when groups of organisms encompass a large number of species, when different workers employ different philosophical views, or when species are in a state of taxonomic flux. The fruit fly tribe Dacini is a species-rich taxon within Tephritidae and contains around a fifth of all known species in the family. About 10% of the 932 currently recognized species are pests of commercial fruits and vegetables, precipitating quarantines and trade embargos. Authoritative species lists consist largely of scattered regional treatments and outdated online resources. The checklist presented here is the first global overview of valid species names for the Dacini in almost two decades, and includes new lure records. By publishing this list both in paper and digitally, we aim to provide a resource for those studying fruit flies as well as researchers studying components of their impact on agriculture. The list is largely a consolidation of previous works, but following the results from recent phylogenetic work, we transfer one subgenus and eight species to different genera: members of the Bactrocera subgenus Javadacus Hardy, considered to belong to the Zeugodacus group of subgenera, are transferred to genus Zeugodacus; Bactrocera pseudocucurbitae White, 1999, stat. rev., is transferred back to Bactrocera from Zeugodacus; Zeugodacus arisanicus Shiraki, 1933, stat. rev., is transferred back to Zeugodacus from Bactrocera; and Z. brevipunctatus (David & Hancock, 2017), comb. n.; Z. javanensis (Perkins, 1938), comb. n.; Z. montanus (Hardy, 1983), comb. n.; Z. papuaensis (Malloch, 1939), comb. n.; Z. scutellarius (Bezzi, 1916), comb. n.; Z. semisurstyli (Drew & Romig, 2013), comb. n.; and Z. trilineatus (Hardy, 1955), comb. n. are transferred from Bactrocera to Zeugodacus.
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Affiliation(s)
- Camiel Doorenweerd
- University of Hawaii, Department of Plant and Environmental Protection Services, 3050 Maile Way, Honolulu, Hawaii, 96822-2231, USA
| | - Luc Leblanc
- University of Idaho, Department of Entomology, Plant Pathology and Nematology, 875 Perimeter Drive, MS2329, Moscow, Idaho, 83844-2329, USA
| | - Allen L. Norrbom
- Systematic Entomology Laboratory, ARS, USDA, c/o Smithsonian Institution, P.O. Box 37012, MRC 168, Washington, DC 20013-7012, USA
| | - Michael San Jose
- University of Hawaii, Department of Plant and Environmental Protection Services, 3050 Maile Way, Honolulu, Hawaii, 96822-2231, USA
| | - Daniel Rubinoff
- University of Hawaii, Department of Plant and Environmental Protection Services, 3050 Maile Way, Honolulu, Hawaii, 96822-2231, USA
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Yong HS, Song SL, Lim PE, Eamsobhana P. Complete mitochondrial genome of Zeugodacus tau (Insecta: Tephritidae) and differentiation of Z. tau species complex by mitochondrial cytochrome c oxidase subunit I gene. PLoS One 2017; 12:e0189325. [PMID: 29216281 PMCID: PMC5720772 DOI: 10.1371/journal.pone.0189325] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 11/23/2017] [Indexed: 01/19/2023] Open
Abstract
The tephritid fruit fly Zeugodacus tau (Walker) is a polyphagous fruit pest of economic importance in Asia. Studies based on genetic markers indicate that it forms a species complex. We report here (1) the complete mitogenome of Z. tau from Malaysia and comparison with that of China as well as the mitogenome of other congeners, and (2) the relationship of Z. tau taxa from different geographical regions based on sequences of cytochrome c oxidase subunit I gene. The complete mitogenome of Z. tau had a total length of 15631 bp for the Malaysian specimen (ZT3) and 15835 bp for the China specimen (ZT1), with similar gene order comprising 37 genes (13 protein-coding genes-PCGs, 2 rRNA genes, and 22 tRNA genes) and a non-coding A + T-rich control region (D-loop). Based on 13 PCGs and 15 mt-genes, Z. tau NC_027290 (China) and Z. tau ZT1 (China) formed a sister group in the lineage containing also Z. tau ZT3 (Malaysia). Phylogenetic analysis based on partial sequences of cox1 gene indicates that the taxa from China, Japan, Laos, Malaysia, Bangladesh, India, Sri Lanka, and Z. tau sp. A from Thailand belong to Z. tau sensu stricto. A complete cox1 gene (or 13 PCGs or 15 mt-genes) instead of partial sequence is more appropriate for determining phylogenetic relationship.
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Affiliation(s)
- Hoi-Sen Yong
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Sze-Looi Song
- Institute of Ocean and Earth Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Phaik-Eem Lim
- Institute of Ocean and Earth Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Praphathip Eamsobhana
- Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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Schutze MK, Virgilio M, Norrbom A, Clarke AR. Tephritid Integrative Taxonomy: Where We Are Now, with a Focus on the Resolution of Three Tropical Fruit Fly Species Complexes. ANNUAL REVIEW OF ENTOMOLOGY 2017; 62:147-164. [PMID: 27813666 DOI: 10.1146/annurev-ento-031616-035518] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Accurate species delimitation underpins good taxonomy. Formalization of integrative taxonomy in the past decade has provided a framework for using multidisciplinary data to make species delimitation hypotheses more rigorous. We address the current state of integrative taxonomy by using as a case study an international project targeted at resolving three important tephritid species complexes: Bactrocera dorsalis complex, Anastrepha fraterculus complex, and Ceratitis FAR (C. fasciventris, C. anonae, C. rosa) complex. The integrative taxonomic approach has helped deliver significant advances in resolving these complexes: It has been used to identify some taxa as belonging to the same biological species as well as to confirm hidden cryptic diversity under a single taxonomic name. Nevertheless, the general application of integrative taxonomy has not been without issue, revealing challenges that must be considered when undertaking an integrative taxonomy project. Scrutiny of this international case study provides a unique opportunity to document lessons learned for the benefit of not only tephritid taxonomists, but also the wider taxonomic community.
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Affiliation(s)
- Mark K Schutze
- School of Earth, Environmental, and Biological Sciences, Queensland University of Technology, Brisbane, 4001 Queensland, Australia;
| | - Massimiliano Virgilio
- Department of Biology, Royal Museum for Central Africa, B3080 Tervuren, Belgium
- Joint Experimental Molecular Unit, Royal Museum for Central Africa, B3080 Tervuren, Belgium ;
| | - Allen Norrbom
- Systematic Entomology Laboratory, United States Department of Agriculture, c/o National Museum of Natural History, Washington, DC 20560;
| | - Anthony R Clarke
- School of Earth, Environmental, and Biological Sciences, Queensland University of Technology, Brisbane, 4001 Queensland, Australia;
- Plant Biosecurity Cooperative Research Centre, University of Canberra, Bruce, Australian Capital Territory 2617, Australia;
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Hendrichs J, Vera MT, De Meyer M, Clarke AR. Resolving cryptic species complexes of major tephritid pests. Zookeys 2015; 540:5-39. [PMID: 26798252 PMCID: PMC4714062 DOI: 10.3897/zookeys.540.9656] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 11/06/2015] [Indexed: 11/12/2022] Open
Abstract
An FAO/IAEA Co-ordinated Research Project (CRP) on "Resolution of Cryptic Species Complexes of Tephritid Pests to Overcome Constraints to SIT Application and International Trade" was conducted from 2010 to 2015. As captured in the CRP title, the objective was to undertake targeted research into the systematics and diagnostics of taxonomically challenging fruit fly groups of economic importance. The scientific output was the accurate alignment of biological species with taxonomic names; which led to the applied outcome of assisting FAO and IAEA Member States in overcoming technical constraints to the application of the Sterile Insect Technique (SIT) against pest fruit flies and the facilitation of international agricultural trade. Close to 50 researchers from over 20 countries participated in the CRP, using coordinated, multidisciplinary research to address, within an integrative taxonomic framework, cryptic species complexes of major tephritid pests. The following progress was made for the four complexes selected and studied: Anastrepha fraterculus complex - Eight morphotypes and their geographic and ecological distributions in Latin America were defined. The morphotypes can be considered as distinct biological species on the basis of differences in karyotype, sexual incompatibility, post-mating isolation, cuticular hydrocarbon, pheromone, and molecular analyses. Discriminative taxonomic tools using linear and geometric morphometrics of both adult and larval morphology were developed for this complex. Bactrocera dorsalis complex - Based on genetic, cytogenetic, pheromonal, morphometric, and behavioural data, which showed no or only minor variation between the Asian/African pest fruit flies Bactrocera dorsalis, Bactrocera papayae, Bactrocera philippinensis and Bactrocera invadens, the latter three species were synonymized with Bactrocera dorsalis. Of the five target pest taxa studied, only Bactrocera dorsalis and Bactrocera carambolae remain as scientifically valid names. Molecular and pheromone markers are now available to distinguish Bactrocera dorsalis from Bactrocera carambolae. Ceratitis FAR Complex (Ceratitis fasciventris, Ceratitis anonae, Ceratitis rosa) - Morphology, morphometry, genetic, genomic, pheromone, cuticular hydrocarbon, ecology, behaviour, and developmental physiology data provide evidence for the existence of five different entities within this fruit fly complex from the African region. These are currently recognised as Ceratitis anonae, Ceratitis fasciventris (F1 and F2), Ceratitis rosa and a new species related to Ceratitis rosa (R2). The biological limits within Ceratitis fasciventris (i.e. F1 and F2) are not fully resolved. Microsatellites markers and morphological identification tools for the adult males of the five different FAR entities were developed based on male leg structures. Zeugodacus cucurbitae (formerly Bactrocera (Zeugodacus) cucurbitae) - Genetic variability was studied among melon fly populations throughout its geographic range in Africa and the Asia/Pacific region and found to be limited. Cross-mating studies indicated no incompatibility or sexual isolation. Host preference and genetic studies showed no evidence for the existence of host races. It was concluded that the melon fly does not represent a cryptic species complex, neither with regard to geographic distribution nor to host range. Nevertheless, the higher taxonomic classification under which this species had been placed, by the time the CRP was started, was found to be paraphyletic; as a result the subgenus Zeugodacus was elevated to genus level.
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Affiliation(s)
- Jorge Hendrichs
- Insect Pest Control Section, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Vienna, Austria
| | - M. Teresa Vera
- Cátedra Terapéutica Vegetal, Facultad de Agronomía y Zootecnia (FAZ), Universidad Nacional de Tucumán (UNT), San Miguel de Tucumán; Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Marc De Meyer
- Royal Museum for Central Africa, Invertebrates Unit, Leuvensesteenweg 13, B3080 Tervuren, Belgium
| | - Anthony R. Clarke
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology (QUT), GPO Box 2434, Brisbane, QLD 4001, Australia
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