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Ercan N, Yildirim A, Duzlu O, Ercan F, Yetismis G, Pekmezci GZ, Inci A. Identification and distribution of some medico-veterinary important pathogens in muscid flies in two geographical regions of Türkiye. MEDICAL AND VETERINARY ENTOMOLOGY 2024. [PMID: 38864653 DOI: 10.1111/mve.12734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/31/2024] [Indexed: 06/13/2024]
Abstract
Some dipteran flies play an important role in the transmission of pathogens such as viruses, bacteria, fungi, protozoan and metazoan parasites in humans and other animals. Despite this importance, knowledge of the prevalence and molecular characteristics of some pathogens in flies is limited, and no data are available for Türkiye. In this study, we investigated the possible vector role of muscid fly species for the transmission of Enterocytozoon bieneusi Desportes (Chytridiopsida: Enterocytozoonidae), Encephalitozoon spp., Coxiella burnetii Derrick (Legionellales: Coxiellaceae) and Thelazia spp. using polymerase chain reaction (PCR) and sequence analysis. The flies were trapped in different animal-related places and surroundings from two different geographical regions of Türkiye including Central Anatolia and Middle Black Sea. According to the morphological keys, 850 (85%), 141 (14.1%) and 6 (0.6%) of the total of 1000 fly specimens identified as Musca domestica Linnaeus (Diptera: Muscidae), Stomoxys calcitrans Linnaeus (Diptera: Muscidae) and Musca autumnalis De Geer (Diptera: Muscidae), respectively. The other species including Haematobia irritans Linnaeus (Diptera: Muscidae), Muscina stabulans Fallén (Diptera: Muscidae) and Hydrotaea ignava Harris (Diptera: Muscidae) were each represented by a single specimen. Screening of the pathogens identified E. bieneusi only in M. domestica with a prevalence of 2.4%. Sequence analyses identified three known genotypes, Type IV, BEB6 and BEB8, and one novel genotype named AEUEb of E. bieneusi in M. domestica. Coxiella burnetii was detected in M. domestica and S. calcitrans with prevalences of 2.9% and 2.8%, respectively. The one specimen of H. ignava was also positive for C. burnetii. Encephalitozoon spp. and Thelazia spp. were not found in the examined specimens. Our results contribute to the current knowledge on the vector potential of muscid flies and their possible role in the transmission dynamics of certain pathogens, especially in regions where diseases are prevalent and affect public and animal health.
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Affiliation(s)
- Nuri Ercan
- Faculty of Agriculture, Kirsehir Ahi Evran University, Kirsehir, Turkey
| | - Alparslan Yildirim
- Department of Parasitology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey
| | - Onder Duzlu
- Department of Parasitology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey
| | - Fahriye Ercan
- Department of Plant Protection, Faculty of Agriculture, Kirsehir Ahi Evran University, Kirsehir, Turkey
| | - Gamze Yetismis
- Department of Parasitology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey
| | - Gokmen Zafer Pekmezci
- Preclinical Sciences, Faculty of Veterinary Medicine, Ondokuz Mayis University, Samsun, Turkey
| | - Abdullah Inci
- Department of Parasitology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey
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2
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Durango-Manrique YS, López-Rubio A, Gutiérrez LA, Isaza JP, Gómez GF. Mitochondrial genome comparison and phylogenetic position of Fannia pusio among the Calyptratae flies. Heliyon 2024; 10:e27697. [PMID: 38524611 PMCID: PMC10958369 DOI: 10.1016/j.heliyon.2024.e27697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/07/2024] [Accepted: 03/05/2024] [Indexed: 03/26/2024] Open
Abstract
Fannia pusio, the chicken dung fly species, remains unexplored despite its forensic, sanitary, and veterinary importance in the Nearctic and Neotropical regions. In this study, we obtained the complete mitochondrial genome of Fannia pusio for the first time using next-generation sequencing. We compared it with previously published mitogenomes of the genus from the Palearctic region, and its phylogenetic position was studied based on the concatenated protein-coding genes (PCGs) dataset of Calyptratae flies. The circular mitochondrial genome of F. pusio is 16,176 bp in length, with a high A + T content (78.3%), whose gene synteny, codon usage analysis, and amino acid frequency are similar to previously reported Fannia mitogenomes. All PCGs underwent purifying selection except the nad2 gene. Interspecific K2P distances of PCGs of Fannia yielded an average of 12.4% (8.1%-21.1%). The Fannia genus is monophyletic and closely related to Muscidae based on molecular data. Further taxonomic sampling is required to deep into the phylogenetic relationships of the originally proposed species-groups and subgroups within the genus. These results provide a valuable dataset for studying the mitochondrial genome evolution and a resource for the taxonomy and systematics of Fannia.
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Affiliation(s)
- Yesica S Durango-Manrique
- Grupo de investigación Bioforense, Facultad de Derecho y Ciencias Forenses, Tecnológico de Antioquia, Institución Universitaria, Medellín, Colombia
| | - Andrés López-Rubio
- Grupo de investigación Bioforense, Facultad de Derecho y Ciencias Forenses, Tecnológico de Antioquia, Institución Universitaria, Medellín, Colombia
| | - Lina A Gutiérrez
- Grupo Biología de Sistemas, Escuela de Ciencias de La Salud, Facultad de Medicina, Universidad Pontificia Bolivariana, Medellín, Colombia
| | - Juan P Isaza
- Grupo Biología de Sistemas, Escuela de Ciencias de La Salud, Facultad de Medicina, Universidad Pontificia Bolivariana, Medellín, Colombia
| | - Giovan F Gómez
- Universidad Nacional de Colombia - Sede de La Paz - Dirección Académica, Escuela de Pregrados - Km 9 vía Valledupar - La Paz, La Paz, Colombia
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Li X, Cai X, Ding S, Wang L, Li W, Liu X, Zhang C, Yang D. Phylogeny and Evolutionary Timescale of Muscidae (Diptera: Calyptratae) Inferred from Mitochondrial Genomes. INSECTS 2023; 14:286. [PMID: 36975971 PMCID: PMC10059281 DOI: 10.3390/insects14030286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/10/2023] [Accepted: 03/12/2023] [Indexed: 06/18/2023]
Abstract
House flies (Muscidae) comprise the most species-rich family of the muscoid grade with over 5000 described species worldwide, and they are abundant in various terrestrial and aquatic ecosystems. The high number of species, varied appearances, complex feeding habits, and wide distributions have hindered researchers from understanding their phylogeny and evolutionary history. Here, we newly sequenced fifteen mitochondrial genomes and reconstructed the phylogenetic relationships and divergence time among eight subfamilies of Muscidae (Diptera). The best phylogenetic tree, which was inferred by IQ-Tree, recovered the monophyly for seven out of eight subfamilies (except for Mydaeinae). Based on phylogenetic analyses and morphological characteristics, we prefer the subfamily status of Azeliinae and Reinwardtiinae, and separate Stomoxyinae from Muscinae. Genus Helina Robineau-Desvoidy, 1830 was synonymized with Phaonia Robineau-Desvoidy, 1830. The divergence time estimation indicated Muscidae originated at 51.59 Ma (early Eocene). Most subfamilies had originated around 41 Ma. We provided a mtgenomic viewpoint on the phylogenetic relationships and divergence time estimation of Muscidae.
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Affiliation(s)
- Xin Li
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Xiaodong Cai
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Shuangmei Ding
- The Institute of Scientific and Technical Research on Archives, National Archives Administration of China, Beijing 100050, China
| | - Liang Wang
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Wenliang Li
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China
| | - Xiaoyan Liu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chuntian Zhang
- College of Life Science, Shenyang Normal University, Shenyang 110034, China
| | - Ding Yang
- College of Plant Protection, China Agricultural University, Beijing 100193, China
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Identity of the numerous bloodstains at the murder scene: molecular identification of fly artifacts and fly species by CO1 analysis. Int J Legal Med 2022; 137:835-842. [PMID: 36542144 DOI: 10.1007/s00414-022-02939-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022]
Abstract
Crime scenes may contain insect artifacts as well as samples of human origin. While the presence of insects can be important evidence in forensic medicine and forensic entomology, the insect artifacts sometimes interfere with the interpretation of bloodstain pattern analysis (BPA) which can be critical for accurate crime reconstruction. Fly artifacts are especially complicated to distinguish from true bloodstains. Indeed, we encountered a murder scene with numerous bloodstains inconsistent with the cause of death and had trouble interpreting them. The morphological method has been developed to distinguish them, but this method has to rely on the analyst's experience and opinion. This study aims not only to distinguish fly artifacts from true bloodstains but also to identify fly species by detecting fly DNA in small amounts of bloodstains at the scenes. Melt curve analysis of real-time PCR (qPCR) targeting cytochrome c oxidase subunit 1 (CO1) of mitochondrial DNA (mtDNA) was able to detect fly DNA in bloodstains from a murder scene. The fly DNA was sequenced from the qPCR product, and the fly species were identified by BLAST search. Fluorescence-labeled specific primers for four species of necrophagous flies were designed based on the sequences of the CO1 region, and differences in the length of the amplification products were used to identify fly species from trace amounts of fly DNA in the artifacts.
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Gao Y, Ge Y, Yan L, Vikhrev NE, Wang Q, Butterworth NJ, Zhang D. Phylogenetic Analyses Support the Monophyly of the Genus Lispe Latreille (Diptera: Muscidae) with Insights into Intrageneric Relationships. INSECTS 2022; 13:1015. [PMID: 36354839 PMCID: PMC9697789 DOI: 10.3390/insects13111015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/17/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
Lispe Latreille (Diptera: Muscidae) are a widespread group of predatory flies that inhabit semi-aquatic environments. Previous studies on this genus have mainly focused on morphological classification, so molecular data are entirely lacking, and there has been no attempt at a phylogenetic placement of the genus or the resolution of intragenic relationships. To address the phylogenetic placement of Lispe and to fill its gap in the Tree of Life Web Project, 58 Lispe spp. (covering 11 out of 13 acknowledged Lispe species groups) were selected to reconstruct a phylogeny using Maximum likelihood (ML) estimates, Maximum Parsimony (MP) analyses, and Bayesian inference (BI) based on two mitochondrial protein-coding genes (cytochrome c oxidase subunit I (COXI) and cytochrome b gene (CYTB)) and one nuclear gene (a fragment of the carbamoyl phosphate synthetase region of the CAD gene). The phylogenetic analyses indicated that the monophyletic Lispe is the sister group of the monophyletic Limnophora, together forming the tribe Limnophorini under the subfamily Coenosiinae. Three generic categories are proven obsolete: Chaetolispa Malloch, Lispacoenosia Snyder, and Xenolispa Malloch. Within the genus, the validity of 11 species groups is clarified by both molecular and morphological data. This study provides a sound basis for continuing intergeneric and intrageneric research into this fascinating and widespread genus.
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Affiliation(s)
- Yunyun Gao
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Yingqiang Ge
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Liping Yan
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Nikita E. Vikhrev
- Zoological Museum of Moscow University, Bolshaya Nikitskaya 6, Moscow 125009, Russia
| | - Qike Wang
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | | | - Dong Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
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Ovtshinnikova OG, Sorokina VS. Musculature of the male abdominal segments and terminalia of
Zaphne barbiventris
(Zetterstedt, 1845) and
Delia fabricii
(Holmgren, 1872) (Diptera: Anthomyiidae). ACTA ZOOL-STOCKHOLM 2022. [DOI: 10.1111/azo.12445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
| | - Vera S. Sorokina
- Institute of Systematics and Ecology of Animals Siberian Branch of the Russian Academy of Sciences Novosibirsk Russia
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The Phylogenetic Relationships of the Fanniidae within the Muscoid Grade (Diptera: Calyptrata) Based on the Musculature of the Male Terminalia. INSECTS 2022; 13:insects13020210. [PMID: 35206783 PMCID: PMC8877065 DOI: 10.3390/insects13020210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 02/04/2023]
Abstract
Simple Summary The Fanniidae is a small dipteran family in the muscoid grade of the Calyptrata. To resolve controversial issues of phylogeny, in addition to molecular analyses, the study of the muscles of the pregenital and genital segments of males can significantly help because they are considered to provide important information relating to the phylogenetic branching of the Cyclorrhapha. Here, the authors report on the structure of the sclerites and the muscles of terminal segments of three species of the Fanniidae. These structures are compared with other members of the muscoid grade, as well as the Oestroidea and Hippoboscoidea. In comparison with the majority of the Calyptrata, there is a significant reduction of the sclerites and muscles of the pregenital segments of the male genitalia of the Fanniidae. The presence of the lateral bacilliform sclerites, as well as the presence and position of the epandrial muscles of the Fanniidae as in primitive Muscidae and also in Tachina and Calliphora, is best interpreted as a plesiomorphic state, while the reductions are considered as derived relative to the ground plan of the Calyptrata. Abstract The abdominal and pregenital segments and the genitalia were studied in males of Fannia subpellucens (Zetterstedt, 1845), Fannia canicularis (Linnaeus, 1761) and Fannia incisurata (Zetterstedt, 1838). In comparison with the remaining members of the muscoid grade, in addition to the symmetry of the pregenital segments, significant reductions of the sclerites and musculature of the male terminalia have been observed in Fanniidae. The muscular structure of pregenital segments confirms that the fused pregenital ring is syntergosternite VI + VII + VIII. Symmetry and fusion, as well as the lower number of the sclerites and muscles of the pregenital segments and male genitalia of the Fanniidae, can be considered apomorphic character states. The presence of the lateral bacilliform sclerite, as well as the presence and position of the epandrial muscles M 26, three pairs of muscles M 19 and paired muscles M 18, can be considered as a plesiomorphic character state of the Fanniidae. The structure of the sclerites and muscles of the male abdominal segments and terminalia place the Fanniidae at the base of the muscoid grade and Oestroidea, as has been confirmed by recent molecular studies.
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8
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OUP accepted manuscript. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlab125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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9
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Gomes LRP, Souza DDS, de Carvalho CJB. First insights into the evolution of neotropical anthomyiid flies (Diptera: Anthomyiidae). SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1914765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Lucas Roberto Pereira Gomes
- Laboratório de Biodiversidade e Biogeografia de Diptera, Departamento de Zoologia, Universidade Federal do Paraná, C.P. 19020, Curitiba, 81531-980, PR, Brazil
| | - Diego de Santana Souza
- Departamento de Entomologia, Museu Nacional, Universidade Federal do Rio de Janeiro, Horto Botânico, Parque Quinta da Boa Vista, São Cristóvão, Rio de Janeiro, 20940-040, RJ, Brazil
| | - Claudio José Barros de Carvalho
- Laboratório de Biodiversidade e Biogeografia de Diptera, Departamento de Zoologia, Universidade Federal do Paraná, C.P. 19020, Curitiba, 81531-980, PR, Brazil
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10
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Changbunjong T, Ruangsittichai J, Duvallet G, Pont AC. Molecular Identification and Geometric Morphometric Analysis of Haematobosca aberrans (Diptera: Muscidae). INSECTS 2020; 11:E451. [PMID: 32708722 PMCID: PMC7412132 DOI: 10.3390/insects11070451] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/08/2020] [Accepted: 07/13/2020] [Indexed: 11/17/2022]
Abstract
The genus Haematobosca Bezzi, 1907 (Diptera: Muscidae) contains haematophagous flies of veterinary importance. A new fly species of this genus was recognised from northern Thailand based on morphological characters and described as Haematobosca aberrans Pont, Duvallet & Changbunjong, 2020. In the present study, the mitochondrial cytochrome c oxidase I (COI) gene was used to confirm the morphological identification of H. aberrans. In addition, landmark-based geometric morphometrics was used to determine sexual dimorphism. The molecular analysis was conducted with 10 COI sequences. The results showed that all sequences were 100% identical. The sequence was not highly similar to reference sequences from GenBank and did not match any identified species from Barcode of Life Data Systems (BOLD). Phylogenetic analysis clearly differentiated this species from other species within the subfamily Stomoxyinae. For geometric morphometric analysis, a total of 16 wing pictures were analysed using the landmark-based approach. The results showed significant differences in wing shape between males and females, with a cross-validated classification score of 100%. The allometric analysis showed that wing shape has no correlation with size. Therefore, the COI gene is effective in species identification of H. aberrans, and geometric morphometrics is also effective in determining sexual dimorphism.
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Affiliation(s)
- Tanasak Changbunjong
- Department of Pre-clinic and Applied Animal Science, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals (MoZWE), Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Jiraporn Ruangsittichai
- Department of Medical Entomology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
| | - Gerard Duvallet
- UMR5175 CEFE, Centre d’Ecologie Fonctionnelle et Evolutive, Université Paul-Valéry, 34090 Montpellier, France;
| | - Adrian C. Pont
- Oxford University Museum of Natural History, Parks Road, Oxford OX1 3PW, UK;
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Pérez S, Fogaça JM, Wolff M, De Carvalho CJB. Morphological phylogeny of Reinwardtia Brauer & Bergenstamm (Diptera, Muscidae), with the description of a new species from the Neotropical region. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1776782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Sandra Pérez
- Grupo de Entomología, Universidad de Antioquia, Apartado aéreo 1226, Medellín, Colombia
| | - João Manuel Fogaça
- Laboratório de Biodiversidade e Biogeografia de Diptera, Departamento de Zoologia, Universidade Federal do Paraná, C.P. 19020, 81531–980, Curitiba, PR, Brazil
| | - Marta Wolff
- Grupo de Entomología, Universidad de Antioquia, Apartado aéreo 1226, Medellín, Colombia
| | - Claudio José Barros De Carvalho
- Laboratório de Biodiversidade e Biogeografia de Diptera, Departamento de Zoologia, Universidade Federal do Paraná, C.P. 19020, 81531–980, Curitiba, PR, Brazil
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12
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Fuentes-López A, Ruiz C, Galián J, Romera E. Molecular identification of forensically important fly species in Spain using COI barcodes. Sci Justice 2019; 60:293-302. [PMID: 32381246 DOI: 10.1016/j.scijus.2019.12.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 10/10/2019] [Accepted: 12/08/2019] [Indexed: 12/25/2022]
Abstract
Species identification with DNA barcodes has been proven to be effective on different organisms and, particularly, has become a routinely used and quite accurate tool in forensic entomology to study necrophagous Diptera species. In this study, we analysed 215 specimens belonging to 42 species of 17 genera, from 9 different Diptera families. Flies were collected in 39 Spanish localities of the Iberian Peninsula sampled across three years in the four seasons. Intraspecific variation ranged from 0 to 2.46% whereas interspecific variation fluctuated from 3.07 to 14.59%, measuring 651 pb of the cytochrome oxidase subunit one (COI) gene. Neighbour-Joining analysis was carried out to investigate the molecular identification capabilities of the barcoding region, recovering almost all species as distinct monophyletic groups. The species groupings were generally consistent with morphological and molecular identifications. This work, which is the first with this intensive and extensive sampling in this area, shows that the COI barcode is an appropriate marker for unambiguous identification of forensically important Diptera in Spain.
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Affiliation(s)
- Alberto Fuentes-López
- Departamento de Zoología y Antropología Física, Campus Mare Nostrum, Universidad de Murcia, Campus de Espinardo, 30100 Murcia, Spain.
| | - Carlos Ruiz
- Departamento de Zoología y Antropología Física, Campus Mare Nostrum, Universidad de Murcia, Campus de Espinardo, 30100 Murcia, Spain; Departamento de Biología Animal, Edafología y Geología, Universidad de La Laguna, 38200 La Laguna, Tenerife, Canary Islands, Spain.
| | - José Galián
- Departamento de Zoología y Antropología Física, Campus Mare Nostrum, Universidad de Murcia, Campus de Espinardo, 30100 Murcia, Spain.
| | - Elena Romera
- Departamento de Zoología y Antropología Física, Campus Mare Nostrum, Universidad de Murcia, Campus de Espinardo, 30100 Murcia, Spain.
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Narayanan Kutty S, Meusemann K, Bayless KM, Marinho MAT, Pont AC, Zhou X, Misof B, Wiegmann BM, Yeates D, Cerretti P, Meier R, Pape T. Phylogenomic analysis of Calyptratae: resolving the phylogenetic relationships within a major radiation of Diptera. Cladistics 2019; 35:605-622. [DOI: 10.1111/cla.12375] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2019] [Indexed: 12/21/2022] Open
Affiliation(s)
- Sujatha Narayanan Kutty
- Department of Biological Sciences National University of Singapore 14 Science Dr 4 Singapore 117543 Singapore
| | - Karen Meusemann
- Biology I, Evolutionary Biology & Ecology University of Freiburg Hauptstraße 1 Freiburg (Brsg.) Germany
- Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum für Molekulare Biodiversitätsforschung (ZMB) Bonn Germany
- Australian National Insect Collection CSIRO National Research Collections Australia (NRCA) Acton, ACT Canberra Australia
| | - Keith M. Bayless
- Department of Entomology California Academy of Sciences San Francisco CA USA
- Department of Entomology North Carolina State University Raleigh NC 27695 USA
| | - Marco A. T. Marinho
- Departamento de Ecologia, Zoologia e Genética Instituto de Biologia Universidade Federal de Pelotas Pelotas RS Brazil
| | - Adrian C. Pont
- Oxford University Museum of Natural History Parks Road Oxford OX1 3PW UK
| | - Xin Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health China Agricultural University Beijing 100193 China
- Department of Entomology China Agricultural University Beijing 100193 China
| | - Bernhard Misof
- Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum für Molekulare Biodiversitätsforschung (ZMB) Bonn Germany
| | - Brian M. Wiegmann
- Department of Entomology North Carolina State University Raleigh NC 27695 USA
| | - David Yeates
- Australian National Insect Collection CSIRO National Research Collections Australia (NRCA) Acton, ACT Canberra Australia
| | - Pierfilippo Cerretti
- Dipartimento di Biologia e Biotecnologie ‘Charles Darwin’ Sapienza Università di Roma Rome Italy
| | - Rudolf Meier
- Department of Biological Sciences National University of Singapore 14 Science Dr 4 Singapore 117543 Singapore
| | - Thomas Pape
- Natural History Museum of Denmark University of Copenhagen Universitetsparken 15 Copenhagen DK–2100 Denmark
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Savage J, Borkent A, Brodo F, Cumming JM, Gregory Curler, Currie DC, deWaard JR, Gibson JF, Hauser M, Laplante L, Lonsdale O, Marshall SA, O’Hara JE, Sinclair BJ, Skevington JH. Diptera of Canada. Zookeys 2019; 819:397-450. [PMID: 30713456 PMCID: PMC6355757 DOI: 10.3897/zookeys.819.27625] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 09/27/2018] [Indexed: 01/26/2023] Open
Abstract
The Canadian Diptera fauna is updated. Numbers of species currently known from Canada, total Barcode Index Numbers (BINs), and estimated numbers of undescribed or unrecorded species are provided for each family. An overview of recent changes in the systematics and Canadian faunistics of major groups is provided as well as some general information on biology and life history. A total of 116 families and 9620 described species of Canadian Diptera are reported, representing more than a 36% increase in species numbers since the last comparable assessment by JF McAlpine et al. (1979). Almost 30,000 BINs have so far been obtained from flies in Canada. Estimates of additional number of species remaining to be documented in the country range from 5200 to 20,400.
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Affiliation(s)
- Jade Savage
- Bishop’s University, Sherbrooke, Quebec, CanadaBishop's UniversitySherbrookeCanada
| | - Art Borkent
- Royal British Columbia Museum, Victoria, British Columbia, CanadaCanadian Museum of NatureOttawaCanada
| | - Fenja Brodo
- Canadian Museum of Nature, Ottawa, Ontario, CanadaCanadian Food Inspection AgencyOttawaCanada
| | - Jeffrey M. Cumming
- Agriculture and Agri-Food Canada, Canadian National Collection of Insects, Arachnids and Nematodes, Ottawa, Ontario, CanadaRoyal British Columbia MuseumSalmon ArmCanada
| | - Gregory Curler
- Mississippi Entomological Museum, Mississippi State University, Starksville, Mississippi, USAAgriculture and Agri-Food CanadaOttawaCanada
| | - Douglas C. Currie
- Royal Ontario Museum, Toronto, Ontario, CanadaMississippi State UniversityStarksvilleUnited States of America
| | - Jeremy R. deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, CanadaRoyal Ontario MuseumTorontoCanada
| | - Joel F. Gibson
- Royal British Columbia Museum, Victoria, British Columbia, CanadaCanadian Museum of NatureOttawaCanada
| | - Martin Hauser
- California Department of Food and Agriculture, Sacramento, California, USAUniversity of GuelphGuelphCanada
| | - Louis Laplante
- Unaffiliated, Montreal, Quebec, CanadaRoyal British Columbia MuseumVictoriaCanada
| | - Owen Lonsdale
- Agriculture and Agri-Food Canada, Canadian National Collection of Insects, Arachnids and Nematodes, Ottawa, Ontario, CanadaRoyal British Columbia MuseumSalmon ArmCanada
| | - Stephen A. Marshall
- University of Guelph, Guelph, Ontario, CanadaCalifornia Department of Food and AgricultureSacramentoUnited States of America
| | - James E. O’Hara
- Agriculture and Agri-Food Canada, Canadian National Collection of Insects, Arachnids and Nematodes, Ottawa, Ontario, CanadaRoyal British Columbia MuseumSalmon ArmCanada
| | - Bradley J. Sinclair
- Canadian Food Inspection Agency, Ottawa, Ontario, CanadaUnaffiliatedMontrealCanada
| | - Jeffrey H. Skevington
- Agriculture and Agri-Food Canada, Canadian National Collection of Insects, Arachnids and Nematodes, Ottawa, Ontario, CanadaRoyal British Columbia MuseumSalmon ArmCanada
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Ren L, Shang Y, Yang L, Shen X, Chen W, Wang Y, Cai J, Guo Y. Comparative analysis of mitochondrial genomes among four species of muscid flies (Diptera: Muscidae) and its phylogenetic implications. Int J Biol Macromol 2019; 127:357-364. [PMID: 30658142 DOI: 10.1016/j.ijbiomac.2019.01.063] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 01/14/2019] [Accepted: 01/14/2019] [Indexed: 10/27/2022]
Abstract
Muscidae, commonly known as house flies and their close relatives, is one of the dipteran insects of recognized medical, veterinary, and ecological importance. Mitochondrial genomes (Mitogenomes) have been widely used for exploring phylogenetic analysis and taxonomic diagnosis due to the difficulty in distinguishing them morphologically. In this study, our complete mitogenomes of muscid flies were sequenced and aligned, which ranged from 15,117 bp (Synthesiomyia nudiseta) to 16,089 bp (Musca sorbens) in length, and contained a typical circular molecule comprising 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs) and a non-coding control region. The order and orientation of genes were identical with that from the ancestral insects. The phylogenetic analysis based on the mitochondrial genes indicated that the subfamily relationships within Muscidae were reconstructed as (Mydaeinae (Muscinae (Reinwardtiinae + Azeliinae))). Similar tree topologies were recovered from both Maximum Likelihood (ML) and Bayesian Inference (BI) analysis. Furthermore, we compared the phylogenetic analyses that were constructed using internal transcribed spacer 2 (ITS2), elongation factor-1α (EF-1α), 13 PCGs and 13 PCGs + ITS2 + EF-1α, respectively. Combined analysis of nuclear gene partitions improved support and resolution for resulting topologies but the positions of branches were obviously inconsistent due to limited species. More mitogenomes should be sequenced representing various taxonomic levels, especially close related species, which will enhance our understanding of phylogenetic relationships among muscids.
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Affiliation(s)
- Lipin Ren
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Yanjie Shang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Li Yang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Xiao Shen
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Wei Chen
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Yong Wang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Jifeng Cai
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Yadong Guo
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China.
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16
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A new species of the genus Morellia Robineau-Desvoidy (Diptera: Muscidae) from Yunnan, China, with analysis of available DNA barcoding sequences. Biologia (Bratisl) 2018. [DOI: 10.2478/s11756-018-0134-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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17
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Strong host specialization in fungus genus Strongwellsea (Entomophthorales). J Invertebr Pathol 2018; 157:112-116. [DOI: 10.1016/j.jip.2018.08.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 08/10/2018] [Accepted: 08/11/2018] [Indexed: 12/16/2022]
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18
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Ren L, Chen W, Shang Y, Meng F, Zha L, Wang Y, Guo Y. The Application of COI Gene for Species Identification of Forensically Important Muscid Flies (Diptera: Muscidae). JOURNAL OF MEDICAL ENTOMOLOGY 2018; 55:1150-1159. [PMID: 29788324 DOI: 10.1093/jme/tjy076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Indexed: 06/08/2023]
Abstract
Muscid Flies (Diptera: Muscidae) are of great forensic importance due to their wide distribution, ubiquitous and synanthropic nature. They are frequently neglected as they tend to arrive at the corpses later than the flesh flies and blow flies. Moreover, the lack of species-level identification also hinders investigation of medicolegal purposes. To overcome the difficulty of morphological identification, molecular method has gained relevance. Cytochrome c oxidase subunit I (COI) gene has been widely utilized. Nonetheless, to achieve correct identification of an unknown sample, it is important to survey certain muscid taxa from its geographic distribution range. Accordingly, the aim of this study is to contribute more geographically specific. We sequenced the COI gene of 51 muscid specimens of 12 species, and added all correct sequences available in GenBank to yield a total data set of 125 COI sequences from 33 muscid species to evaluate the COI gene as a molecular diagnostic tool. The interspecific distances were extremely high (4.7-19.8%) in either the standard barcoding fragment (658 bp) or the long COI sequence (1,019-1,535 bp), demonstrating that these two genetic markers were nearly identical in the species identification. However, the intraspecific distances of the long COI sequences were significantly higher than the barcoding region for the conspecific species that geographical locations vary greatly. Therefore, genetic diversity presented in this study provides a reference for species identification of muscid flies. Nevertheless, further investigation and data from more muscid species are required to enhance the efficacy of species-level identification using COI gene as a genetic marker.
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Affiliation(s)
- Lipin Ren
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Wei Chen
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Yanjie Shang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Fanming Meng
- Department of Histology and Embryology, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Lagabaiyila Zha
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Yong Wang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Yadong Guo
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
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Cerretti P, Stireman JO, Pape T, O’Hara JE, Marinho MAT, Rognes K, Grimaldi DA. First fossil of an oestroid fly (Diptera: Calyptratae: Oestroidea) and the dating of oestroid divergences. PLoS One 2017; 12:e0182101. [PMID: 28832610 PMCID: PMC5568141 DOI: 10.1371/journal.pone.0182101] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 07/12/2017] [Indexed: 01/30/2023] Open
Abstract
Calyptrate flies include about 22,000 extant species currently classified into Hippoboscoidea (tsetse, louse, and bat flies), the muscoid grade (house flies and relatives) and the Oestroidea (blow flies, bot flies, flesh flies, and relatives). Calyptrates are abundant in nearly all terrestrial ecosystems, often playing key roles as decomposers, parasites, parasitoids, vectors of pathogens, and pollinators. For oestroids, the most diverse group within calyptrates, definitive fossils have been lacking. The first unambiguous fossil of Oestroidea is described based on a specimen discovered in amber from the Dominican Republic. The specimen was identified through digital dissection by CT scans, which provided morphological data for a cladistic analysis of its phylogenetic position among extant oestroids. The few known calyptrate fossils were used as calibration points for a molecular phylogeny (16S, 28S, CAD) to estimate the timing of major diversification events among the Oestroidea. Results indicate that: (a) the fossil belongs to the family Mesembrinellidae, and it is identified and described as Mesembrinella caenozoica sp. nov.; (b) the mesembrinellids form a sister clade to the Australian endemic Ulurumyia macalpinei (Ulurumyiidae) (McAlpine's fly), which in turn is sister to all remaining oestroids; (c) the most recent common ancestor of extant Calyptratae lived just before the K-Pg boundary (ca. 70 mya); and (d) the radiation of oestroids began in the Eocene (ca. 50 mya), with the origin of the family Mesembrinellidae dated at ca. 40 mya. These results provide new insight into the timing and rate of oestroid diversification and highlight the rapid radiation of some of the most diverse and ecologically important families of flies. ZooBank accession number-urn:lsid:zoobank.org:pub:0DC5170B-1D16-407A-889E-56EED3FE3627.
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Affiliation(s)
- Pierfilippo Cerretti
- Dipartimento di Biologia e Biotecnologie ‘Charles Darwin’, Sapienza Università di Roma, Rome, Italy
| | - John O. Stireman
- Department of Biological Sciences, Wright State University, Dayton, OH, United States of America
| | - Thomas Pape
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - James E. O’Hara
- Canadian National Collection of Insects, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Marco A. T. Marinho
- Laboratório de Morfologia e Evolução de Diptera, Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras, Universidade de São Paulo, São Paulo, SP, Brazil
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Knut Rognes
- University of Stavanger, Faculty of Arts and Education, Department of Early Childhood Education, Stavanger, Norway
| | - David A. Grimaldi
- Division of Invertebrate Zoology, American Museum of Natural History, New York, United States of America
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20
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Mashaly A, Alajmi R, Mustafa AEZ, Rady A, Alkhedir H. Species Abundance and Identification of Forensically Important Flies of Saudi Arabia by DNA Barcoding. JOURNAL OF MEDICAL ENTOMOLOGY 2017; 54:837-843. [PMID: 28399228 DOI: 10.1093/jme/tjx049] [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: 10/31/2016] [Indexed: 06/07/2023]
Abstract
Because they may demonstrate characteristics of the environment where a body has been laying prior to the discovery, flies are insects of forensic interest. We investigated the fly abundance and the effect of location in Kingdom of Saudi Arabia on fly species diversity that attack decomposing human and animal remains. Using baited traps deployed in each location, we collected 3,697 flies of seven species belonging to three families. Chrysomya albiceps Wiedmann represented 60.86% of the collected flies, whereas Musca domestica L. represented 25.8%; the other species made up < 6% each. To facilitate species identification by DNA barcoding, we sequenced a 710-bp "Folmer region" of cytochrome oxidase subunit 1 (COI) gene for 22 samples from collection sites distributed through entire Saudi Arabia. The COI sequences from Musca albina Wiedmann, Musca lucidula Loew, Musca calleva Walker, Musca sorbens Wiedmann, and Physiphora alceae Preyssler were obtained for the first time. This primary study indicates that even when Folmer primers were widely used in DNA barcoding, the Folmer's region is not adequate when discriminating between Musca species, and sequencing the whole COI or other genes is required for forensic purpose.
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Affiliation(s)
- Ashraf Mashaly
- Department of Zoology, College of Sciences, King Saud University, PO. Box: 2455, Riyadh 11451, Kingdom of Saudi Arabia
- Department of Zoology, Faculty of Science, Minia University, 61519 El Minia, Egypt
| | - Reem Alajmi
- Department of Zoology, College of Sciences, King Saud University, PO. Box: 2455, Riyadh 11451, Kingdom of Saudi Arabia
| | - Abd El-Zaher Mustafa
- Botany and Microbiology Department, College of Sciences, King Saud University, PO. Box: 2455, Riyadh 11451, Kingdom of Saudi Arabia
- Botany Department, Faculty of Science, Tanta University, Tanta, Egypt
| | - Ahmed Rady
- Department of Zoology, College of Sciences, King Saud University, PO. Box: 2455, Riyadh 11451, Kingdom of Saudi Arabia
| | - Hussein Alkhedir
- Agricultural Entomology, Georg-August-University Göttingen, Grisebachstrasse 6, 37077 Göttingen, Germany
- Molecular Phytopathology and Mycotoxin Research, Georg-August-University Göttingen, Grisebachstrasse 6, 37077 Göttingen, Germany
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21
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Muscidae (Diptera) of forensic importance-an identification key to third instar larvae of the western Palaearctic region and a catalogue of the muscid carrion community. Int J Legal Med 2016; 131:855-866. [PMID: 27924407 PMCID: PMC5388714 DOI: 10.1007/s00414-016-1495-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 11/08/2016] [Indexed: 11/17/2022]
Abstract
The Muscidae is one of the main dipteran families recognized as important for medico-legal purposes. Although an association of adult flies with decomposing human and animal bodies is documented for about 200 taxa worldwide, cadavers and carrion represents a breeding habitat for considerably fewer species. Species that do colonize dead human bodies can do so under diverse environmental conditions and, under certain circumstances, Muscidae may be the only colonizers of a body. Because of difficulties in identification, many studies have identified immature and/or adult muscids only to the genus or family level. This lack of detailed species-level identifications hinders detailed investigation of their medico-legal usefulness in carrion succession-oriented experiments. Identification to species level of third instars of Muscidae of forensic importance and the utility of larval morphological characters for taxonomic purposes were subjected to an in-depth revision. A combination of characters allowing for the discrimination of third instar muscids from other forensically important dipterans is proposed. An identification key for third instar larvae, which covers the full set of cadaver-colonising species of Muscidae from the western Palaearctic (Europe, North Africa, Middle East), is provided. This key will facilitate more detailed and species-specific knowledge of the occurrence of Muscidae in forensic entomology experiments and real cases. The carrion-visiting Muscidae worldwide are catalogued, and those species breeding in animal carrion and dead human bodies are briefly discussed with regard to their forensic importance.
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22
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Ge Y, Gao Y, Yan L, Liu X, Zhang D. Review of theLispe tentaculata-group (Diptera: Muscidae) in China, with one new synonym. ZOOSYSTEMA 2016. [DOI: 10.5252/z2016n3a4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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23
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Yusseff-Vanegas S, Agnarsson I. Molecular phylogeny of the forensically important genus Cochliomyia (Diptera: Calliphoridae). Zookeys 2016:107-20. [PMID: 27563274 PMCID: PMC4984421 DOI: 10.3897/zookeys.609.8638] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 07/25/2016] [Indexed: 11/12/2022] Open
Abstract
Cochliomyia Townsend includes several abundant and one of the most broadly distributed, blow flies in the Americas, and is of significant economic and forensic importance. For decades, Cochliomyia hominivorax (Coquerel) and Cochliomyia macellaria (Fabricius) have received attention as livestock parasites and primary indicator species in forensic entomology. However, Cochliomyia minima Shannon and Cochliomyia aldrichi Del Ponte have only been subject to basic taxonomy and faunistic studies. Here we present the first complete phylogeny of Cochliomyia including numerous specimens per species, collected from 13 localities in the Caribbean. Four genes, the mitochondrial COI and the nuclear EF-1α, 28S rRNA, and ITS2, were analyzed. While we found some differences among gene trees, a concatenated gene matrix recovered a robustly supported monophyletic Cochliomyia with Compsomyiops Townsend as its sister group and recovered the monophyly of Cochliomyia hominivorax, Cochliomyia macellaria and Cochliomyia minima. Our results support a close relationship between Cochliomyia minima and Cochliomyia aldrichi. However, we found Cochliomyia aldrichi containing Cochliomyia minima, indicating recent speciation, or issues with the taxonomy of the group. We provide basic information on habitat preference, distribution and feeding habits of Cochliomyia minima and Cochliomyia aldrichi that will be useful for future forensic studies in the Caribbean.
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Affiliation(s)
- Sohath Yusseff-Vanegas
- Department of Biology, University of Vermont, 109 Carrigan Drive, Burlington, VT 05405, USA
| | - Ingi Agnarsson
- Department of Biology, University of Vermont, 109 Carrigan Drive, Burlington, VT 05405, USA
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24
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Zajac BK, Sontigun N, Wannasan A, Verhoff MA, Sukontason K, Amendt J, Zehner R. Application of DNA barcoding for identifying forensically relevant Diptera from northern Thailand. Parasitol Res 2016; 115:2307-20. [PMID: 26965427 DOI: 10.1007/s00436-016-4977-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 03/01/2016] [Indexed: 01/31/2023]
Abstract
In recent decades, forensic entomology has become a useful tool in criminal investigations all over the world. Species-specific identification of flies plays an important role in this field and is obligatory for accurate calculation of the post-mortem interval. However, not all important colonizers of a corpse can be identified by common morphological keys. Due to similar morphology and the lack of keys for some taxa, especially for immature stages, DNA barcoding has become more popular during the last recent years. This development is particularly important for countries like Thailand, in which forensic entomology is a newly developing research area and which faces several challenges such as a high biodiversity of fly species. The most commonly used barcoding region in forensic entomology, the mitochondrial cytochrome oxidase subunit 1 (coI) gene, as well as a 1000-bp-long region of the 28S nuclear rRNA gene, was used to analyze and establish the molecular barcodes of 13 different species of flies of forensic relevance in northern Thailand.
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Affiliation(s)
- Barbara Karolina Zajac
- Institute of Legal Medicine, Forensic Biology/Entomology, Kennedyallee 104, 60596, Frankfurt am Main, Germany.
| | - Narin Sontigun
- Department of Parasitology, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Anchalee Wannasan
- Department of Parasitology, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Marcel A Verhoff
- Institute of Legal Medicine, Forensic Biology/Entomology, Kennedyallee 104, 60596, Frankfurt am Main, Germany
| | - Kabkaew Sukontason
- Department of Parasitology, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Jens Amendt
- Institute of Legal Medicine, Forensic Biology/Entomology, Kennedyallee 104, 60596, Frankfurt am Main, Germany
| | - Richard Zehner
- Institute of Legal Medicine, Forensic Biology/Entomology, Kennedyallee 104, 60596, Frankfurt am Main, Germany
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25
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Zhang D, Yan L, Zhang M, Chu H, Cao J, Li K, Hu D, Pape T. Phylogenetic inference of calyptrates, with the first mitogenomes for Gasterophilinae (Diptera: Oestridae) and Paramacronychiinae (Diptera: Sarcophagidae). Int J Biol Sci 2016; 12:489-504. [PMID: 27019632 PMCID: PMC4807417 DOI: 10.7150/ijbs.12148] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 12/22/2015] [Indexed: 11/05/2022] Open
Abstract
The complete mitogenome of the horse stomach bot fly Gasterophilus pecorum (Fabricius) and a near-complete mitogenome of Wohlfahrt's wound myiasis fly Wohlfahrtia magnifica (Schiner) were sequenced. The mitogenomes contain the typical 37 mitogenes found in metazoans, organized in the same order and orientation as in other cyclorrhaphan Diptera. Phylogenetic analyses of mitogenomes from 38 calyptrate taxa with and without two non-calyptrate outgroups were performed using Bayesian Inference and Maximum Likelihood. Three sub-analyses were performed on the concatenated data: (1) not partitioned; (2) partitioned by gene; (3) 3rd codon positions of protein-coding genes omitted. We estimated the contribution of each of the mitochondrial genes for phylogenetic analysis, as well as the effect of some popular methodologies on calyptrate phylogeny reconstruction. In the favoured trees, the Oestroidea are nested within the muscoid grade. Relationships at the family level within Oestroidea are (remaining Calliphoridae (Sarcophagidae (Oestridae, Pollenia + Tachinidae))). Our mito-phylogenetic reconstruction of the Calyptratae presents the most extensive taxon coverage so far, and the risk of long-branch attraction is reduced by an appropriate selection of outgroups. We find that in the Calyptratae the ND2, ND5, ND1, COIII, and COI genes are more phylogenetically informative compared with other mitochondrial protein-coding genes. Our study provides evidence that data partitioning and the inclusion of conserved tRNA genes have little influence on calyptrate phylogeny reconstruction, and that the 3rd codon positions of protein-coding genes are not saturated and therefore should be included.
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Affiliation(s)
- Dong Zhang
- 1. School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Liping Yan
- 1. School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Ming Zhang
- 1. School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Hongjun Chu
- 3. Wildlife Conservation Office of Altay Prefecture, Altay, Xinjiang, China
| | - Jie Cao
- 4. Xinjiang Research Centre for Breeding Przewalski's Horse, Ürümqi, Xinjiang, China
| | - Kai Li
- 1. School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Defu Hu
- 1. School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Thomas Pape
- 2. Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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26
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Zhang NX, Yu G, Li TJ, He QY, Zhou Y, Si FL, Ren S, Chen B. The Complete Mitochondrial Genome of Delia antiqua and Its Implications in Dipteran Phylogenetics. PLoS One 2015; 10:e0139736. [PMID: 26427045 PMCID: PMC4591329 DOI: 10.1371/journal.pone.0139736] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Accepted: 09/15/2015] [Indexed: 11/28/2022] Open
Abstract
Delia antiqua is a major underground agricultural pest widely distributed in Asia, Europe and North America. In this study, we sequenced and annotated the complete mitochondrial genome of this species, which is the first report of complete mitochondrial genome in the family Anthomyiidae. This genome is a double-stranded circular molecule with a length of 16,141 bp and an A+T content of 78.5%. It contains 37 genes (13 protein-coding genes, 22 tRNAs and 2 rRNAs) and a non-coding A+T rich region or control region. The mitochondrial genome of Delia antiqua presents a clear bias in nucleotide composition with a positive AT-skew and a negative GC-skew. All of the 13 protein-coding genes use ATN as an initiation codon except for the COI gene that starts with ATCA. Most protein-coding genes have complete termination codons but COII and ND5 that have the incomplete termination codon T. This bias is reflected in both codon usage and amino acid composition. The protein-coding genes in the D. antiqua mitochondrial genome prefer to use the codon UUA (Leu). All of the tRNAs have the typical clover-leaf structure, except for tRNASer(AGN) that does not contain the dihydrouridine (DHU) arm like in many other insects. There are 7 mismatches with U-U in the tRNAs. The location and structure of the two rRNAs are conservative and stable when compared with other insects. The control region between 12S rRNA and tRNAIle has the highest A+T content of 93.7% in the D. antiqua mitochondrial genome. The control region includes three kinds of special regions, two highly conserved poly-T stretches, a (TA)n stretch and several G(A)nT structures considered important elements related to replication and transcription. The nucleotide sequences of 13 protein-coding genes are used to construct the phylogenetics of 26 representative Dipteran species. Both maximum likelihood and Bayesian inference analyses suggest a closer relationship of D. antiqua in Anthomyiidae with Calliphoridae, Calliphoridae is a paraphyly, and both Oestroidea and Muscoidea are polyphyletic.
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Affiliation(s)
- Nai-Xin Zhang
- Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing, 401331, China
| | - Guo Yu
- Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing, 401331, China
| | - Ting-Jing Li
- Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing, 401331, China
| | - Qi-Yi He
- Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing, 401331, China
| | - Yong Zhou
- Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing, 401331, China
| | - Feng-Ling Si
- Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing, 401331, China
| | - Shuang Ren
- Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing, 401331, China
| | - Bin Chen
- Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing, 401331, China
- * E-mail:
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27
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Ding S, Li X, Wang N, Cameron SL, Mao M, Wang Y, Xi Y, Yang D. The Phylogeny and Evolutionary Timescale of Muscoidea (Diptera: Brachycera: Calyptratae) Inferred from Mitochondrial Genomes. PLoS One 2015; 10:e0134170. [PMID: 26225760 PMCID: PMC4520480 DOI: 10.1371/journal.pone.0134170] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 07/06/2015] [Indexed: 11/19/2022] Open
Abstract
Muscoidea is a significant dipteran clade that includes house flies (Family Muscidae), latrine flies (F. Fannidae), dung flies (F. Scathophagidae) and root maggot flies (F. Anthomyiidae). It is comprised of approximately 7000 described species. The monophyly of the Muscoidea and the precise relationships of muscoids to the closest superfamily the Oestroidea (blow flies, flesh flies etc) are both unresolved. Until now mitochondrial (mt) genomes were available for only two of the four muscoid families precluding a thorough test of phylogenetic relationships using this data source. Here we present the first two mt genomes for the families Fanniidae (Euryomma sp.) (family Fanniidae) and Anthomyiidae (Delia platura (Meigen, 1826)). We also conducted phylogenetic analyses containing of these newly sequenced mt genomes plus 15 other species representative of dipteran diversity to address the internal relationship of Muscoidea and its systematic position. Both maximum-likelihood and Bayesian analyses suggested that Muscoidea was not a monophyletic group with the relationship: (Fanniidae + Muscidae) + ((Anthomyiidae + Scathophagidae) + (Calliphoridae + Sarcophagidae)), supported by the majority of analysed datasets. This also infers that Oestroidea was paraphyletic in the majority of analyses. Divergence time estimation suggested that the earliest split within the Calyptratae, separating (Tachinidae + Oestridae) from the remaining families, occurred in the Early Eocene. The main divergence within the paraphyletic muscoidea grade was between Fanniidae + Muscidae and the lineage ((Anthomyiidae + Scathophagidae) + (Calliphoridae + Sarcophagidae)) which occurred in the Late Eocene.
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Affiliation(s)
- Shuangmei Ding
- Department of Entomology, China Agricultural University, Beijing, China
| | - Xuankun Li
- Department of Entomology, China Agricultural University, Beijing, China
| | - Ning Wang
- Department of Entomology, China Agricultural University, Beijing, China
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Stephen L. Cameron
- Earth, Environmental and Biological Sciences School, Science & Engineering Faculty, Queensland University of Technology, Brisbane, Australia
| | - Meng Mao
- Centre for Medical Bioscience, School of Biological Sciences, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Yuyu Wang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Yuqiang Xi
- Department of Entomology, China Agricultural University, Beijing, China
| | - Ding Yang
- Department of Entomology, China Agricultural University, Beijing, China
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Say goodbye to tribes in the new house fly classification: A new molecular phylogenetic analysis and an updated biogeographical narrative for the Muscidae (Diptera). Mol Phylogenet Evol 2015; 89:1-12. [PMID: 25869937 DOI: 10.1016/j.ympev.2015.04.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 04/02/2015] [Accepted: 04/07/2015] [Indexed: 02/03/2023]
Abstract
House flies are one of the best known groups of flies and comprise about 5000 species worldwide. Despite over a century of intensive taxonomic research on these flies, classification of the Muscidae is still poorly resolved. Here we brought together the most diverse molecular dataset ever examined for the Muscidae, with 142 species in 67 genera representing all tribes and all biogeographic regions. Four protein coding genes were analyzed: mitochondrial CO1 and nuclear AATS, CAD (region 4) and EF1-α. Maximum likelihood and Bayesian approaches were used to analyze five different partitioning schemes for the alignment. We also used Bayes factors to test monophyly of the traditionally accepted tribes and subfamilies. Most subfamilial taxa were not recovered in our analyses, and accordingly monophyly was rejected by Bayes factor tests. Our analysis consistently found three main clades of Muscidae and so we propose a new classification with only three subfamilies without tribes. Additionally, we provide the first timeframe for the diversification of all major lineages of house flies and examine contemporary biogeographic hypotheses in light of this timeframe. We conclude that the muscid radiation began in the Paleocene to Eocene and is congruent with the final stages of the breakup of Gondwana, which resulted in the complete separation of Antarctica, Australia, and South America. With this newly proposed classification and better understanding of the timing of evolutionary events, we provide new perspectives for integrating morphological and ecological evolutionary understanding of house flies, their taxonomy, phylogeny, and biogeography.
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Rapid discrimination of maggots utilising ATR-FTIR spectroscopy. Forensic Sci Int 2015; 249:189-96. [PMID: 25703014 DOI: 10.1016/j.forsciint.2015.01.036] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 12/01/2014] [Accepted: 01/28/2015] [Indexed: 11/20/2022]
Abstract
Entomological evidence is used in forensic investigations to indicate time since death. The species and age of maggots or flies that are present at the scene can be used when estimating how much time has passed since death. Current methods that are used to identify species and developmental stage of larvae and fly samples are highly subjective, costly and often time consuming processes and require the expertise of an entomologist or species identification via DNA analysis. The use of vibrational spectroscopy, as an alternative identification method, would allow for a quicker, cheaper and less subjective technique and would allow entomological evidence to be used more commonly in the forensic process. This proof of principle study shows the potential for using attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR) as a rapid tool for differentiating between various species of larvae, such as those commonly found at crime scenes. The proposed regime would provide a rapid and valuable tool resulting in reduced time for both species identification and life cycle determination, particularly in forensic situations.
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Seabra SG, Brás PG, Martins J, Martins R, Wyatt N, Shirazi J, Rebelo MT, Franco JC, Mateus C, Figueiredo E, Paulo OS. Phylogeographical patterns inCoenosia attenuata(Diptera: Muscidae): a widespread predator of insect species associated with greenhouse crops. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12419] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sofia G. Seabra
- Centre for Ecology, Evolution and Environmental Changes; Departamento de Biologia Animal; Faculdade de Ciências; Universidade de Lisboa; 1749-016 Lisboa Portugal
| | - Patrícia G. Brás
- Centre for Ecology, Evolution and Environmental Changes; Departamento de Biologia Animal; Faculdade de Ciências; Universidade de Lisboa; 1749-016 Lisboa Portugal
| | - Joana Martins
- Centro de Engenharia dos Biossistemas; Instituto Superior de Agronomia; Universidade de Lisboa; Tapada da Ajuda 1349-017 Lisboa Portugal
| | - Renata Martins
- Centre for Ecology, Evolution and Environmental Changes; Departamento de Biologia Animal; Faculdade de Ciências; Universidade de Lisboa; 1749-016 Lisboa Portugal
| | - Nigel Wyatt
- Natural History Museum; Cromwell Road London SW7 5BD UK
| | - Jalal Shirazi
- Biocontrol Research Department; Iranian Research Institute of Plant Protection (IRIPP); PO Box 1454 Tehran 19395 Iran
| | - Maria Teresa Rebelo
- Centro de Estudos do Ambiente e do Mar (CESAM); Departamento de Biologia Animal; Faculdade de Ciências; Universidade de Lisboa; 1749-016 Lisboa Portugal
| | - José Carlos Franco
- Centro de Estudos Florestais; Instituto Superior de Agronomia; Universidade de Lisboa; Tapada da Ajuda 1349-017 Lisboa Portugal
| | - Célia Mateus
- Instituto Nacional de Investigação Agrária e Veterinária; Av. República Quinta do Marquês 2784-505 Oeiras Portugal
| | - Elisabete Figueiredo
- Centro de Engenharia dos Biossistemas; Instituto Superior de Agronomia; Universidade de Lisboa; Tapada da Ajuda 1349-017 Lisboa Portugal
| | - Octávio S. Paulo
- Centre for Ecology, Evolution and Environmental Changes; Departamento de Biologia Animal; Faculdade de Ciências; Universidade de Lisboa; 1749-016 Lisboa Portugal
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Kutty SN, Pont AC, Meier R, Pape T. Complete tribal sampling reveals basal split in Muscidae (Diptera), confirms saprophagy as ancestral feeding mode, and reveals an evolutionary correlation between instar numbers and carnivory. Mol Phylogenet Evol 2014; 78:349-64. [DOI: 10.1016/j.ympev.2014.05.027] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 05/09/2014] [Accepted: 05/21/2014] [Indexed: 12/16/2022]
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Li X, Wang Y, Su S, Yang D. The complete mitochondrial genomes of Musca domestica and Scathophaga stercoraria (Diptera: Muscoidea: Muscidae and Scathophagidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1435-6. [PMID: 25163032 DOI: 10.3109/19401736.2014.953080] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genomes of Musca domestica (Muscidae) and Scathophaga stercoraria (Scathophagidae) are circular molecules of 16,108 bp and 16,223 bp in length, respectively. The first complete mitochondrial genome of Scathophagidae is reported here. Both genomes contain all 37 genes, including 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a large control region, with conserved arrangement pattern reported in all cyclorrhaphan flies. All PCGs start with standard ATN codons except for the CO1 which starts with TCG in both species. All PCGs terminate with the common stop codons TAA or TAG, except for the CO2 and ND5 in both species and ND4 in S. stercoraria which end with a single T.
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Affiliation(s)
- Xuankun Li
- a Department of Entomology , China Agricultural University , Beijing , P.R. China
| | - Yuyu Wang
- a Department of Entomology , China Agricultural University , Beijing , P.R. China
| | - Shuai Su
- a Department of Entomology , China Agricultural University , Beijing , P.R. China
| | - Ding Yang
- a Department of Entomology , China Agricultural University , Beijing , P.R. China
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Molecular identification of necrophagous muscidae and sarcophagidae fly species collected in Korea by mitochondrial cytochrome C oxidase subunit I nucleotide sequences. ScientificWorldJournal 2014; 2014:275085. [PMID: 24982938 PMCID: PMC4058124 DOI: 10.1155/2014/275085] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 04/29/2014] [Accepted: 04/29/2014] [Indexed: 11/25/2022] Open
Abstract
Identification of insect species is an important task in forensic entomology. For more convenient species identification, the nucleotide sequences of cytochrome c oxidase subunit I (COI) gene have been widely utilized. We analyzed full-length COI nucleotide sequences of 10 Muscidae and 6 Sarcophagidae fly species collected in Korea. After DNA extraction from collected flies, PCR amplification and automatic sequencing of the whole COI sequence were performed. Obtained sequences were analyzed for a phylogenetic tree and a distance matrix. Our data showed very low intraspecific sequence distances and species-level monophylies. However, sequence comparison with previously reported sequences revealed a few inconsistencies or paraphylies requiring further investigation. To the best of our knowledge, this study is the first report of COI nucleotide sequences from Hydrotaea occulta, Muscina angustifrons, Muscina pascuorum, Ophyra leucostoma, Sarcophaga haemorrhoidalis, Sarcophaga harpax, and Phaonia aureola.
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Sonet G, Jordaens K, Braet Y, Bourguignon L, Dupont E, Backeljau T, De Meyer M, Desmyter S. Utility of GenBank and the Barcode of Life Data Systems (BOLD) for the identification of forensically important Diptera from Belgium and France. Zookeys 2013:307-28. [PMID: 24453564 PMCID: PMC3890684 DOI: 10.3897/zookeys.365.6027] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 11/13/2013] [Indexed: 11/12/2022] Open
Abstract
Fly larvae living on dead corpses can be used to estimate post-mortem intervals. The identification of these flies is decisive in forensic casework and can be facilitated by using DNA barcodes provided that a representative and comprehensive reference library of DNA barcodes is available. We constructed a local (Belgium and France) reference library of 85 sequences of the COI DNA barcode fragment (mitochondrial cytochrome c oxidase subunit I gene), from 16 fly species of forensic interest (Calliphoridae, Muscidae, Fanniidae). This library was then used to evaluate the ability of two public libraries (GenBank and the Barcode of Life Data Systems – BOLD) to identify specimens from Belgian and French forensic cases. The public libraries indeed allow a correct identification of most specimens. Yet, some of the identifications remain ambiguous and some forensically important fly species are not, or insufficiently, represented in the reference libraries. Several search options offered by GenBank and BOLD can be used to further improve the identifications obtained from both libraries using DNA barcodes.
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Affiliation(s)
- Gontran Sonet
- Royal Belgian Institute of Natural Sciences, OD Taxonomy and Phylogeny (JEMU), Vautierstraat 29, 1000 Brussels, Belgium
| | - Kurt Jordaens
- Royal Museum for Central Africa, Department of Biology (JEMU), Leuvensesteenweg 13, 3080 Tervuren, Belgium ; University of Antwerp, Evolutionary Ecology Group, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Yves Braet
- National Institute of Criminalistics and Criminology, Vilvoordsesteenweg 100, 1120 Brussels, Belgium
| | - Luc Bourguignon
- National Institute of Criminalistics and Criminology, Vilvoordsesteenweg 100, 1120 Brussels, Belgium
| | - Eréna Dupont
- National Institute of Criminalistics and Criminology, Vilvoordsesteenweg 100, 1120 Brussels, Belgium
| | - Thierry Backeljau
- Royal Belgian Institute of Natural Sciences, OD Taxonomy and Phylogeny (JEMU), Vautierstraat 29, 1000 Brussels, Belgium ; University of Antwerp, Evolutionary Ecology Group, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Marc De Meyer
- Royal Museum for Central Africa, Department of Biology (JEMU), Leuvensesteenweg 13, 3080 Tervuren, Belgium
| | - Stijn Desmyter
- National Institute of Criminalistics and Criminology, Vilvoordsesteenweg 100, 1120 Brussels, Belgium
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Singh B, Wells JD. Molecular systematics of the Calliphoridae (Diptera: Oestroidea): evidence from one mitochondrial and three nuclear genes. JOURNAL OF MEDICAL ENTOMOLOGY 2013; 50:15-23. [PMID: 23427647 DOI: 10.1603/me11288] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Approximately 8% of calyptrate species diversity comes from the Calliphoridae, which includes flies of medical, veterinary, and forensic importance. The status of family Calliphoridae has for years been the central systematic problem of the superfamily Oestroidea, and phylogenetic relationships between the key groups of the Calliphoridae are unresolved and controversial. We reconstructed phylogenies of the Calliphoridae within the larger context of the other Oestroidea based on 5,189 bp of combined data from one mitochondrial (cytochrome oxidase subunit one) and three nuclear (carbamoylphosphate synthetase, elongation factor one alpha, and 28S ribosomal RNA) genes using maximum parsimony, maximum likelihood, and Bayesian methods. Trees obtained from the different phylogenetic methods were almost identical. Calliphoridae is polyphyletic, with the phylogenetic position of Mesembrinellinae still uncertain but clearly outside the lineage that includes other Calliphoridae and some noncalliphorids, and Polleniinae is the sister group of the family Tachinidae. Strong support for a sister group relationship between Rhiniinae and traditional calliphorid subfamilies conflicts with a recent proposal to give Rhiniinae family status. All calliphorid subfamilies (except Calliphorinae) for which we had more than one species were monophyletic. Melanomyinae was nested within Calliphorinae. Toxotarsinae was more closely related to Calliphorinae rather than, as indicated by morphology, to Chrysomyinae. Efforts to resolve the relationships of the Oestroid families were largely inconclusive, although the monophyly of the superfamily was strongly supported.
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Affiliation(s)
- Baneshwar Singh
- Department of Entomology, Texas A&M University, 2475 TAMU, College Station, TX 77843, USA.
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36
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Marinho M, Junqueira A, Paulo D, Esposito M, Villet M, Azeredo-Espin A. Molecular phylogenetics of Oestroidea (Diptera: Calyptratae) with emphasis on Calliphoridae: Insights into the inter-familial relationships and additional evidence for paraphyly among blowflies. Mol Phylogenet Evol 2012; 65:840-54. [DOI: 10.1016/j.ympev.2012.08.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 08/08/2012] [Accepted: 08/10/2012] [Indexed: 10/28/2022]
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Renaud AK, Savage J, Adamowicz SJ. DNA barcoding of Northern Nearctic Muscidae (Diptera) reveals high correspondence between morphological and molecular species limits. BMC Ecol 2012; 12:24. [PMID: 23173946 PMCID: PMC3537539 DOI: 10.1186/1472-6785-12-24] [Citation(s) in RCA: 55] [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: 06/25/2012] [Accepted: 10/16/2012] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Various methods have been proposed to assign unknown specimens to known species using their DNA barcodes, while others have focused on using genetic divergence thresholds to estimate "species" diversity for a taxon, without a well-developed taxonomy and/or an extensive reference library of DNA barcodes. The major goals of the present work were to: a) conduct the largest species-level barcoding study of the Muscidae to date and characterize the range of genetic divergence values in the northern Nearctic fauna; b) evaluate the correspondence between morphospecies and barcode groupings defined using both clustering-based and threshold-based approaches; and c) use the reference library produced to address taxonomic issues. RESULTS Our data set included 1114 individuals and their COI sequences (951 from Churchill, Manitoba), representing 160 morphologically-determined species from 25 genera, covering 89% of the known fauna of Churchill and 23% of the Nearctic fauna. Following an iterative process through which all specimens belonging to taxa with anomalous divergence values and/or monophyly issues were re-examined, identity was modified for 9 taxa, including the reinstatement of Phaonia luteva (Walker) stat. nov. as a species distinct from Phaonia errans (Meigen). In the post-reassessment data set, no distinct gap was found between maximum pairwise intraspecific distances (range 0.00-3.01%) and minimum interspecific distances (range: 0.77-11.33%). Nevertheless, using a clustering-based approach, all individuals within 98% of species grouped with their conspecifics with high (>95%) bootstrap support; in contrast, a maximum species discrimination rate of 90% was obtained at the optimal threshold of 1.2%. DNA barcoding enabled the determination of females from 5 ambiguous species pairs and confirmed that 16 morphospecies were genetically distinct from named taxa. There were morphological differences among all distinct genetic clusters; thus, no cases of cryptic species were detected. CONCLUSIONS Our findings reveal the great utility of building a well-populated, species-level reference barcode database against which to compare unknowns. When such a library is unavailable, it is still possible to obtain a fairly accurate (within ~10%) rapid assessment of species richness based upon a barcode divergence threshold alone, but this approach is most accurate when the threshold is tuned to a particular taxon.
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Affiliation(s)
- Anaïs K Renaud
- Department of Entomology, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
- Department of Biological Sciences, Bishop’s University, Sherbrooke, Québec J1M 1Z7, Canada
| | - Jade Savage
- Department of Biological Sciences, Bishop’s University, Sherbrooke, Québec J1M 1Z7, Canada
| | - Sarah J Adamowicz
- Biodiversity Institute of Ontario & Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
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Sonet G, Jordaens K, Braet Y, Desmyter S. Why is the molecular identification of the forensically important blowfly species Lucilia caesar and L. illustris (family Calliphoridae) so problematic? Forensic Sci Int 2012; 223:153-9. [PMID: 22964163 DOI: 10.1016/j.forsciint.2012.08.020] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 08/18/2012] [Indexed: 11/18/2022]
Abstract
Species of the fly genus Lucilia are commonly used in forensic investigations to estimate the postmortem interval (PMI). Two close-related species Lucilia caesar and L. illustris are difficult to identify. Previous studies showed that the mitochondrial cytochrome c oxidase subunit I (COI) marker could be used to identify many Lucilia species. However, mixed results were obtained for L. caesar and L. illustris due to some European specimens showing identical haplotypes. Here, we investigated 58 new European male specimens of L. illustris and L. caesar whose morphological identifications were checked and for which COI fragments were sequenced. In addition, two other mitochondrial (cytochrome c oxidase subunit II and 16S) and two nuclear (internal transcribed spacer 2 and 28S ribosomal RNA) markers were obtained for a subset of these samples. For each marker, genetic divergence within each species was in the same range as between species, confirming the close relationship between both species. Moreover, for each of the gene fragments, both species shared at least one haplotype/genotype. Hence, none of the molecular markers tested could be used, alone or in combination, to discriminate between L. illustris and L. caesar.
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Affiliation(s)
- Gontran Sonet
- Joint Experimental Molecular Unit, Royal Museum for Central Africa, Leuvensesteenweg 13, 3080 Tervuren, Belgium.
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Grzywacz A, Pape T, Szpila K. Larval morphology of the lesser housefly, Fannia canicularis. MEDICAL AND VETERINARY ENTOMOLOGY 2012; 26:70-82. [PMID: 21707683 DOI: 10.1111/j.1365-2915.2011.00968.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The morphology of all larval instars of Fannia canicularis (Linnaeus) (Diptera: Fanniidae) is documented using a combination of light and scanning electron microscopy. The following structures are documented for all instars: antennal complex; maxillary palpus; facial mask; cephaloskeleton; ventral organ; anterior spiracle; Keilin's organ; posterior spiracle; fleshy processes, and anal pad. Structures reported for the first time for all instars include: two pairs of lateral prominences on the prothoracic segment; additional ventrolateral prominences on the second thoracic segment, and a papilla at the base of the posterior spiracle. Other structures reported for the first time are anterior spiracles in the first instar and a serrated tip on the mouthhook in the second instar. A trichoid sensillum on the posterior spiracular plate, representing a sensory organ otherwise unknown in the Calyptratae, is described in the second and third instars. Results are discussed and compared with existing knowledge on dipteran larval morphology.
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Affiliation(s)
- A Grzywacz
- Department of Animal Ecology, Institute of Ecology and Environmental Protection, Nicolaus Copernicus University, Gagarina 9, Toruń, Poland.
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40
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The molecular systematics of blowflies and screwworm flies (Diptera: Calliphoridae) using 28S rRNA, COX1 and EF-1α: insights into the evolution of dipteran parasitism. Parasitology 2011; 138:1760-77. [PMID: 21867590 DOI: 10.1017/s0031182011001089] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The Calliphoridae include some of the most economically significant myiasis-causing flies in the world - blowflies and screwworm flies - with many being notorious for their parasitism of livestock. However, despite more than 50 years of research, key taxonomic relationships within the family remain unresolved. This study utilizes nucleotide sequence data from the protein-coding genes COX1 (mitochondrial) and EF1α (nuclear), and the 28S rRNA (nuclear) gene, from 57 blowfly taxa to improve resolution of key evolutionary relationships within the family Calliphoridae. Bayesian phylogenetic inference was carried out for each single-gene data set, demonstrating significant topological difference between the three gene trees. Nevertheless, all gene trees supported a Calliphorinae-Luciliinae subfamily sister-lineage, with respect to Chrysomyinae. In addition, this study also elucidates the taxonomic and evolutionary status of several less well-studied groups, including the genus Bengalia (either within Calliphoridae or as a separate sister-family), genus Onesia (as a sister-genera to, or sub-genera within, Calliphora), genus Dyscritomyia and Lucilia bufonivora, a specialised parasite of frogs and toads. The occurrence of cross-species hybridisation within Calliphoridae is also further explored, focusing on the two economically significant species Lucilia cuprina and Lucilia sericata. In summary, this study represents the most comprehensive molecular phylogenetic analysis of family Calliphoridae undertaken to date.
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41
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Molecular characterization and expression pattern of an odorant receptor from the myiasis-causing blowfly, Lucilia sericata (Diptera: Calliphoridae). Parasitol Res 2011; 110:843-51. [DOI: 10.1007/s00436-011-2563-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Accepted: 07/13/2011] [Indexed: 10/18/2022]
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Vaidya G, Lohman DJ, Meier R. SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information. Cladistics 2011; 27:171-180. [DOI: 10.1111/j.1096-0031.2010.00329.x] [Citation(s) in RCA: 1356] [Impact Index Per Article: 104.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Germann C, Wimmer C, Bernasconi MV. Molecular data sheds light on the classification of long-legged flies (Diptera:Dolichopodidae). INVERTEBR SYST 2011. [DOI: 10.1071/is11029] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Dolichopodidae (long-legged flies) is the world’s fourth largest dipteran family, but a phylogeny based on a broad global taxon sample is still lacking. We present here a first molecular phylogenetic hypothesis for Dolichopodidae, based on 157 dolichopodid species in 68 genera and 15 subfamilies from the Old and New World, and seven empidoid species (Empididae, Hybotidae) as outgroups. Both relatively fast-evolving mitochondrial markers (COI, 12S, 16S) and a more conserved nuclear marker (18S) were used, the latter being widely employed to study the phylogeny at higher taxonomic levels. We present strong evidence for Microphorinae as sister group to Dolichopodidae sensu stricto, and for the monophyletic Parathalassiinae as part of Dolichopodidae sensu stricto. Monophyly of Achalcinae, Dolichopodinae, and Sciapodinae is supported and Stolidosomatinae are placed within Sympycninae. Diaphorinae, Medeterinae, Neurigoninae, Rhaphiinae, and Sympycninae are paraphyletic, and Hydrophorinae and Peloropeodinae polyphyletic. Our broad taxon sample allows us to gain new insights into the complex systematics of Dolichopodidae. Our results highlight several problems with the traditional classification, which have considerable consequences for the systematic status of some taxa. The poor resolution observed in deep divergences supports previous hypotheses suggesting a rapid early radiation of Dolichopodidae.
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Ohshima I, Tanikawa-Dodo Y, Saigusa T, Nishiyama T, Kitani M, Hasebe M, Mohri H. Phylogeny, biogeography, and host–plant association in the subfamily Apaturinae (Insecta: Lepidoptera: Nymphalidae) inferred from eight nuclear and seven mitochondrial genes. Mol Phylogenet Evol 2010; 57:1026-36. [DOI: 10.1016/j.ympev.2010.09.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2009] [Revised: 09/20/2010] [Accepted: 09/21/2010] [Indexed: 10/19/2022]
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Placement of Conopidae (Diptera) within Schizophora based on mtDNA and nrDNA gene regions. Mol Phylogenet Evol 2010; 56:91-103. [PMID: 20362064 DOI: 10.1016/j.ympev.2010.03.026] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Revised: 03/10/2010] [Accepted: 03/25/2010] [Indexed: 11/23/2022]
Abstract
The first attempt to phylogenetically place Conopidae using molecular characters, as well as the largest molecular analysis of relationships within Schizophora (Diptera) to date, is presented. Twenty-eight taxa from 11 acalyptrate families and seven acalyptrate superfamilies are represented. Nearly 12,800 bp of sequence data from 10 genes representing both mitochondrial (cytochrome oxidase I (COI), cytochrome b (cytB), and 12S) and nuclear genes (28S, the carbamoyl phosphate synthetase region of CAD (CAD), elongation factor-1alpha (EF-1alpha), white, alanyl-tRNA synthetase (AATS), triose phosphate isomerase (TPI), and phosphogluconate dehydrogenase (PGD)) are analysed. Parsimony and Bayesian analyses strongly support the monophyly of both Conopidae and Schizophora. While in the parsimony analysis, Conopidae are placed as sister to the remaining Schizophora, the Bayesian analysis recovers a Conopidae+Lauxaniidae clade. The value of nuclear, mitochondrial, ribosomal, and protein-coding gene sequence data for answering phylogenetic questions at different levels of divergence is evaluated.
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Winkler IS, Rung A, Scheffer SJ. Hennig's orphans revisited: testing morphological hypotheses in the "Opomyzoidea" (Diptera: Schizophora). Mol Phylogenet Evol 2009; 54:746-62. [PMID: 20040375 DOI: 10.1016/j.ympev.2009.12.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Revised: 12/15/2009] [Accepted: 12/21/2009] [Indexed: 10/20/2022]
Abstract
The acalyptrate fly superfamily Opomyzoidea, as currently recognized, is a poorly-known group of 14 families. The composition of this group and relationships among included families have been controversial. Furthermore, the delimitation of two opomyzoid families, Aulacigastridae and Periscelididae, has been unstable with respect to placement of the genera Stenomicra, Cyamops, and Planinasus. To test the monophyly of Opomyzoidea, previously proposed relationships between families, and the position of the three problematic genera, we sequenced over 3300bp of nucleotide sequence data from the 28S ribosomal DNA and CAD (rudimentary) genes from 29 taxa representing all opomyzoid families, as well as 13 outgroup taxa. Relationships recovered differed between analyses, and only branches supporting well-established monophyletic families were recovered with high support, with a few exceptions. Opomyzoidea and its included subgroup, Asteioinea, were found to be non-monophyletic. Stenomicra, Cyamops, and Planinasus group consistently with Aulacigastridae, contrary to recent classifications. Xenasteiidae and Australimyzidae, two small, monogeneric families placed in separate superfamilies, were strongly supported as sister groups.
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Affiliation(s)
- Isaac S Winkler
- Department of Entomology, North Carolina State University, Raleigh, Campus Box 7613, Raleigh, NC 27695, USA.
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