1
|
Song Y, Wang J. The first mitochondrial genome of Meroplius fukuharai (Diptera: Sepsidae). Mitochondrial DNA B Resour 2024; 9:692-695. [PMID: 38835642 PMCID: PMC11149572 DOI: 10.1080/23802359.2024.2353232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 05/05/2024] [Indexed: 06/06/2024] Open
Abstract
Meroplius fukuharai is an important sanitary and ecological resource insect. We sequenced and annotated the mitogenome of Meroplius fukuharai which is the first representative of the genus Meroplius with nearly complete mitochondrial data. This mitogenome is 14,803 bp long, which consists of 22 transfer RNA genes, 13 protein-coding genes (PCGs), and two ribosomal RNA genes. All genes have a conservational arrangement with other published species of Sepsidae. Our results also supported the monophyly of Sepsidae, and the genus Meroplius is more closely related to genus Sepsis, Microsepsis, and Archisepsis.
Collapse
Affiliation(s)
- Yingying Song
- College of Life Science and Bioengineering, Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, Shenyang University, Shenyang, China
| | - Jianfeng Wang
- College of Life Science and Bioengineering, Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, Shenyang University, Shenyang, China
| |
Collapse
|
2
|
Khosravi G, Akbarzadeh K, Karimian F, Koosha M, Saeedi S, Oshaghi MA. A survey of Wolbachia infection in brachyceran flies from Iran. PLoS One 2024; 19:e0301274. [PMID: 38776328 PMCID: PMC11111063 DOI: 10.1371/journal.pone.0301274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/13/2024] [Indexed: 05/24/2024] Open
Abstract
Wolbachia is a maternally inherited intracellular bacterium that is considered to be the most plentiful endosymbiont found in arthropods. It reproductively manipulates its host to increase the chances of being transmitted to the insect progeny; and it is currently used as a means of suppressing disease vector populations or controlling vector-borne diseases. Studies of the dissemination and prevalence of Wolbachia among its arthropod hosts are important for its possible use as a biological control agent. The molecular identification of Wolbachia relies on different primers sets due to Wolbachia strain variation. Here, we screened for the presence of Wolbachia in a broad range of Brachycera fly species (Diptera), collected from different regions of Iran, using nine genetic markers (wsp, ftsZ, fbpA, gatB, CoxA, gltA, GroEL dnaA, and 16s rRNA), for detecting, assessing the sensitivity of primers for detection, and phylogeny of this bacterium. The overall incidence of Wolbachia among 22 species from six families was 27.3%. The most commonly positive fly species were Pollenia sp. and Hydrotaea armipes. However, the bacterium was not found in the most medically important flies or in potential human disease vectors, including Musca domestica, Sarcophaga spp., Calliphora vicinia, Lucilia sericata, and Chrysomya albiceps. The primer sets of 16s rRNA with 53.0% and gatB with 52.0% were the most sensitive primers for detecting Wolbachia. Blast search, phylogenetic, and MLST analysis of the different locus sequences of Wolbachia show that all the six distantly related fly species likely belonging to supergroup A. Our study showed some primer sets generated false negatives in many of the samples, emphasizing the importance of using different loci in detecting Wolbachia. The study provides the groundwork for future studies of a Wolbachia-based program for control of flies.
Collapse
Affiliation(s)
- Ghazal Khosravi
- Department of Vector Biology and Control of Diseases, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Kamran Akbarzadeh
- Department of Vector Biology and Control of Diseases, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Fateh Karimian
- Department of Parasitology, Pasteur Institute of Iran, Tehran, Iran
| | - Mona Koosha
- Department of Vector Biology and Control of Diseases, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Shahin Saeedi
- Department of Vector Biology and Control of Diseases, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Ali Oshaghi
- Department of Vector Biology and Control of Diseases, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
3
|
Kapoor S, Yang YT, Hall RN, Gasser RB, Bowles VM, Perry T, Anstead CA. Complete Mitochondrial Genome for Lucilia cuprina dorsalis (Diptera: Calliphoridae) from the Northern Territory, Australia. Genes (Basel) 2024; 15:506. [PMID: 38674440 PMCID: PMC11050061 DOI: 10.3390/genes15040506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/09/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
The Australian sheep blowfly, Lucilia cuprina dorsalis, is a major sheep ectoparasite causing subcutaneous myiasis (flystrike), which can lead to reduced livestock productivity and, in severe instances, death of the affected animals. It is also a primary colonizer of carrion, an efficient pollinator, and used in maggot debridement therapy and forensic investigations. In this study, we report the complete mitochondrial (mt) genome of L. c. dorsalis from the Northern Territory (NT), Australia, where sheep are prohibited animals, unlike the rest of Australia. The mt genome is 15,943 bp in length, comprising 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), and a non-coding control region. The gene order of the current mt genome is consistent with the previously published L. cuprina mt genomes. Nucleotide composition revealed an AT bias, accounting for 77.5% of total mt genome nucleotides. Phylogenetic analyses of 56 species/taxa of dipterans indicated that L. c. dorsalis and L. sericata are the closest among all sibling species of the genus Lucilia, which helps to explain species evolution within the family Luciliinae. This study provides the first complete mt genome sequence for L. c. dorsalis derived from the NT, Australia to facilitate species identification and the examination of the evolutionary history of these blowflies.
Collapse
Affiliation(s)
- Shilpa Kapoor
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia; (Y.T.Y.); (T.P.)
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia; (R.B.G.); (V.M.B.)
| | - Ying Ting Yang
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia; (Y.T.Y.); (T.P.)
| | - Robyn N. Hall
- CSIRO Health & Biosecurity, Acton, ACT 2601, Australia;
- Ausvet Pty Ltd., Fremantle, WA 6160, Australia
| | - Robin B. Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia; (R.B.G.); (V.M.B.)
| | - Vernon M. Bowles
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia; (R.B.G.); (V.M.B.)
| | - Trent Perry
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia; (Y.T.Y.); (T.P.)
| | - Clare A. Anstead
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia; (R.B.G.); (V.M.B.)
| |
Collapse
|
4
|
Scanlan JL, Robin C. Phylogenomics of the Ecdysteroid Kinase-like (EcKL) Gene Family in Insects Highlights Roles in Both Steroid Hormone Metabolism and Detoxification. Genome Biol Evol 2024; 16:evae019. [PMID: 38291829 PMCID: PMC10859841 DOI: 10.1093/gbe/evae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 11/21/2023] [Accepted: 01/23/2024] [Indexed: 02/01/2024] Open
Abstract
The evolutionary dynamics of large gene families can offer important insights into the functions of their individual members. While the ecdysteroid kinase-like (EcKL) gene family has previously been linked to the metabolism of both steroid molting hormones and xenobiotic toxins, the functions of nearly all EcKL genes are unknown, and there is little information on their evolution across all insects. Here, we perform comprehensive phylogenetic analyses on a manually annotated set of EcKL genes from 140 insect genomes, revealing the gene family is comprised of at least 13 subfamilies that differ in retention and stability. Our results show the only two genes known to encode ecdysteroid kinases belong to different subfamilies and therefore ecdysteroid metabolism functions must be spread throughout the EcKL family. We provide comparative phylogenomic evidence that EcKLs are involved in detoxification across insects, with positive associations between family size and dietary chemical complexity, and we also find similar evidence for the cytochrome P450 and glutathione S-transferase gene families. Unexpectedly, we find that the size of the clade containing a known ecdysteroid kinase is positively associated with host plant taxonomic diversity in Lepidoptera, possibly suggesting multiple functional shifts between hormone and xenobiotic metabolism. Our evolutionary analyses provide hypotheses of function and a robust framework for future experimental studies of the EcKL gene family. They also open promising new avenues for exploring the genomic basis of dietary adaptation in insects, including the classically studied coevolution of butterflies with their host plants.
Collapse
Affiliation(s)
- Jack L Scanlan
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Charles Robin
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| |
Collapse
|
5
|
de Paula LCB, Dios RDVP, Gudin FM, de Santis MD, Alvarez-Garcia DM, Antunes Júnior M, Freire BV, Marques FPDL, Lahr DJG, Nihei SS. Phylogenomic analysis of Tachinidae (Diptera: Calyptratae: Oestroidea): a transcriptomic approach to understanding the subfamily relationships. Cladistics 2024; 40:64-81. [PMID: 37837208 DOI: 10.1111/cla.12562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 08/25/2023] [Accepted: 09/13/2023] [Indexed: 10/15/2023] Open
Abstract
Tachinidae is the second most species-rich family of Diptera. It comprises four subfamilies, and all of its members have parasitoid habits. We present the first phylogenomic analysis of Tachinidae using transcriptomic data, based on 30 species. We constructed four datasets: three using translated data at the amino acid level (100% coverage, with 106 single-copy protein-coding genes; 75% coverage, with 1359 genes; and 50% coverage, with 1942 genes). The trees were estimated by analysing four matrices using maximum likelihood and maximum parsimony inferences, and only minor differences were found among them. Overall, our topologies are well resolved, with high node support. Polleniidae is corroborated as a sister group to Tachinidae. Within Tachinidae, our results confirm the hypothesis (Phasiinae + Dexiinae) + (Tachininae + Exoristinae). Phasiinae, Dexiinae and Exoristinae are recovered as monophyletic, and Tachininae as polyphyletic. Once again, the tribe Myiophasiini (Tachininae) composes a fifth lineage, clade sister to all the remaining Tachinidae. The Neotropical tribe Iceliini, formerly in Tachininae, is recovered within Exoristinae, sister to Winthemiini. In general, our results are congruent with recent phylogenetic studies that include tachinids, with the important confirmation of the subfamilial relationships and the existence of a fifth lineage of Tachinidae.
Collapse
Affiliation(s)
- Letícia Chiara Baldassio de Paula
- Department of Genetics, Institute of Biosciences, University of São Paulo, Rua do Matão, n 277, São Paulo, SP, 05508-090, Brazil
- Department of Zoology, Institute of Biosciences, University of São Paulo, Rua do Matão, Travessa 14, n 101, São Paulo, SP, 05508-090, Brazil
| | - Rodrigo de Vilhena Perez Dios
- Department of Zoology, Institute of Biosciences, University of São Paulo, Rua do Matão, Travessa 14, n 101, São Paulo, SP, 05508-090, Brazil
| | - Filipe Macedo Gudin
- Department of Zoology, Institute of Biosciences, University of São Paulo, Rua do Matão, Travessa 14, n 101, São Paulo, SP, 05508-090, Brazil
| | - Marcelo Domingos de Santis
- Department of Zoology, Institute of Biosciences, University of São Paulo, Rua do Matão, Travessa 14, n 101, São Paulo, SP, 05508-090, Brazil
- Zoologisches Forschungsmuseum Alexander Koenig, Leibniz-Institut zur Analyse des Biodiversitatswandels, Adenauerallee 127, D-53113, Bonn, Germany
| | - Deivys Moises Alvarez-Garcia
- Department of Zoology, Institute of Biosciences, University of São Paulo, Rua do Matão, Travessa 14, n 101, São Paulo, SP, 05508-090, Brazil
- Grupo de Investigación en Zoología y Ecología, Universidad de Sucre, Cra 28 # 5 - 267 Barrio Puerta Roja, Sincelejo, Colombia
| | - Manuel Antunes Júnior
- Department of Zoology, Institute of Biosciences, University of São Paulo, Rua do Matão, Travessa 14, n 101, São Paulo, SP, 05508-090, Brazil
| | - Beatriz Vieira Freire
- Department of Zoology, Institute of Biosciences, University of São Paulo, Rua do Matão, Travessa 14, n 101, São Paulo, SP, 05508-090, Brazil
| | - Fernando Portella de Luna Marques
- Department of Zoology, Institute of Biosciences, University of São Paulo, Rua do Matão, Travessa 14, n 101, São Paulo, SP, 05508-090, Brazil
| | - Daniel José Galafasse Lahr
- Department of Zoology, Institute of Biosciences, University of São Paulo, Rua do Matão, Travessa 14, n 101, São Paulo, SP, 05508-090, Brazil
| | - Silvio Shigueo Nihei
- Department of Zoology, Institute of Biosciences, University of São Paulo, Rua do Matão, Travessa 14, n 101, São Paulo, SP, 05508-090, Brazil
| |
Collapse
|
6
|
Ma T, Zhang C, Huang J. Phylogenetic insights based on the first complete mitochondrial genome of Isomyia nebulosa (Diptera: Calliphoridae). Mitochondrial DNA B Resour 2023; 8:1320-1324. [PMID: 38196796 PMCID: PMC10776078 DOI: 10.1080/23802359.2023.2288916] [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: 10/17/2023] [Accepted: 11/24/2023] [Indexed: 01/11/2024] Open
Abstract
To investigate the phylogenetic position of Isomyia Walker, 1860, a genus that suffered from frequent revisions of the taxonomic status following the subfamily Rhiniinae (Diptera, Calliphoridae), we sequenced, assembled, annotated, and analyzed the first complete mitochondrial genome (mitogenome) of Isomyia nebulosa (Townsend, 1917) in this study. This mitogenome is 16,438 bp in length, with a standard set of 13 protein-coding genes (PCGs), 22 tRNAs, two rRNAs, and an A + T riched non-coding region without genetic rearrangement as most dipteran mitogenomes, but long intergenic nucleotides (IGNs) between trnQ and trnM are found. The phylogeny yielded by both Bayesian inference and maximum-likelihood analysis for all mitochondrial PCGs and rRNAs of 23 mitogenomes supports the monophyly of the family Calliphoridae and the subfamilies Calliphorinae, Chrysomyinae, and Luciliinae. In addition, I. nebulosa diverged anterior to the above-mentioned three calliphorid subfamilies with high genetic distances.
Collapse
Affiliation(s)
- Ting Ma
- Police Experimental Training Center, Guangdong Police College, Guangzhou, Baiyun, China
| | - Caihong Zhang
- Department of Entomology, College of Plant Protection, South China Agricultural University, Tianhe, Guangzhou, China
| | - Jia Huang
- Department of Entomology, College of Plant Protection, South China Agricultural University, Tianhe, Guangzhou, China
| |
Collapse
|
7
|
Shao S, Yang L, Hu G, Li L, Wang Y, Tao L. Application of omics techniques in forensic entomology research. Acta Trop 2023; 246:106985. [PMID: 37473953 DOI: 10.1016/j.actatropica.2023.106985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/22/2023]
Abstract
With the advent of the post-genome era, omics technologies have developed rapidly and are widely used, including in genomics, transcriptomics, proteomics, metabolomics, and microbiome research. These omics techniques are often based on comprehensive and systematic analysis of biological samples using high-throughput analysis methods and bioinformatics, to provide new insights into biological phenomena. Currently, omics techniques are gradually being applied to forensic entomology research and are useful in species identification, phylogenetics, screening for developmentally relevant differentially expressed genes, and the interpretation of behavioral characteristics of forensic-related species at the genetic level. These all provide valuable information for estimating the postmortem interval (PMI). This review mainly discusses the available omics techniques, summarizes the application of omics techniques in forensic entomology, and their future in the field.
Collapse
Affiliation(s)
- Shipeng Shao
- Department of Forensic Medicine, Soochow University, Ganjiang East Road, Suzhou, China
| | - Lijun Yang
- Criminal Police Branch, Suzhou Public Security Bureau, Renmin Road, Suzhou, China
| | - Gengwang Hu
- Department of Forensic Medicine, Soochow University, Ganjiang East Road, Suzhou, China
| | - Liangliang Li
- Department of Forensic Medicine, Soochow University, Ganjiang East Road, Suzhou, China
| | - Yu Wang
- Department of Forensic Medicine, Soochow University, Ganjiang East Road, Suzhou, China.
| | - Luyang Tao
- Department of Forensic Medicine, Soochow University, Ganjiang East Road, Suzhou, China
| |
Collapse
|
8
|
Guo S, Chen J, Song N. Phylogenomic analysis of Syrphoidea (Diptera: Syrphidae, Pipunculidae) based on the expanded mitogenomic data. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2023; 114:1-13. [PMID: 36597178 DOI: 10.1002/arch.21998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/23/2022] [Accepted: 12/25/2022] [Indexed: 09/27/2023]
Abstract
The mitochondrial genome has become the most widely used genomic resource in resolving the insect phylogenetic relationships. In this study, we assess the interrelationships among the syrphid and pipunculid members of Syrphoidea using mitochondrial genome sequences of 152 taxa, 9 of which are newly reported and three are assembled from the existing transcriptome data. The Pipunculidae was found to be deeply nested members of Schizophora, which resulted in a nonmonophyletic Syrphoidea. In the monophyletic Syrphidae, unequivocal robust support was found for Microdontinae as the sister group of all other Syrphidae. The subfamily Eristalinae was nonmonophyletic. The Pipizinae was recovered as the sister group to the Syrphinae, albeit with strong support. As a whole, our results are concord with previously established hypotheses on Syrphoidea from the genome scale data. The mitochondrial genomes were successful in producing a robustly supported phylogenetic framework for the Syrphoidea.
Collapse
Affiliation(s)
- Shibao Guo
- Department of Plant Protection, College of Agronomy,Xinyang Agriculture and Forestry University, Xinyang, Henan, China
| | - Junhua Chen
- Department of Plant Protection, College of Agronomy,Xinyang Agriculture and Forestry University, Xinyang, Henan, China
| | - Nan Song
- Department of Entomology, College of Plant Protection, Henan Agricultural University, Zhengzhou, Henan, China
| |
Collapse
|
9
|
Xuan JL, Scheffer SJ, Lewis M, Cassel BK, Liu WX, Wiegmann BM. The phylogeny and divergence times of leaf-mining flies (Diptera: Agromyzidae) from anchored phylogenomics. Mol Phylogenet Evol 2023; 184:107778. [PMID: 37030415 DOI: 10.1016/j.ympev.2023.107778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 02/24/2023] [Accepted: 03/31/2023] [Indexed: 04/10/2023]
Abstract
Leaf-mining flies (Diptera: Agromyzidae) are a diverse clade of phytophagous Diptera known largely for their economic impact as leaf- or stem-miners on vegetable and ornamental plants. Higher-level phylogenetic relationships of Agromyzidae have remained uncertain because of challenges in sampling of both taxa and characters for morphology and PCR-based Sanger-era molecular systematics. Here, we used hundreds of orthologous single-copy nuclear loci obtained from anchored hybrid enrichment (AHE) to reconstruct phylogenetic relationships among the major lineages of leaf-mining flies. The resulting phylogenetic trees are highly congruent and well-supported, except for a few deep nodes, when using different molecular data types and phylogenetic methods. Based on divergence time dating using a relaxed clock and model-based historical biogeography analysis, leaf-mining flies are shown to have diversified in multiple lineages since the early Paleocene, approximately 65 million years ago. Our study not only reveals a revised classification system of leaf-mining flies, but also provides a new phylogenetic framework to understand their macroevolution.
Collapse
Affiliation(s)
- Jing-Li Xuan
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA; Anhui Bio-breeding Engineering Research Center for Water melon and Melon, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, P. R. China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
| | - Sonja J Scheffer
- Systematic Entomology Laboratory, USDA, Beltsville Agricultural Research Station, Beltsville, MD, 20705, USA.
| | - Matt Lewis
- Systematic Entomology Laboratory, USDA, Beltsville Agricultural Research Station, Beltsville, MD, 20705, USA
| | - Brian K Cassel
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
| | - Wan-Xue Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
| | - Brian M Wiegmann
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA.
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Tsz Long Wong D, Norman H, Creedy TJ, Jordaens K, Moran KM, Young A, Mengual X, Skevington JH, Vogler AP. The phylogeny and evolutionary ecology of hoverflies (Diptera: Syrphidae) inferred from mitochondrial genomes. Mol Phylogenet Evol 2023; 184:107759. [PMID: 36921697 DOI: 10.1016/j.ympev.2023.107759] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 03/01/2023] [Accepted: 03/08/2023] [Indexed: 03/16/2023]
Abstract
Hoverflies (Diptera: Syrphidae) are a diverse group of pollinators and a major research focus in ecology, but their phylogenetic relationships remain incompletely known. Using a genome skimming approach we generated mitochondrial genomes for 91 species, capturing a wide taxonomic diversity of the family. To reduce the required amount of input DNA and overall cost of the library construction, sequencing and assembly was conducted on mixtures of specimens, which raises the problem of chimera formation of mitogenomes. We present a novel chimera detection test based on gene tree incongruence, but identified only a single mitogenome of chimeric origin. Together with existing data for a final set of 127 taxa, phylogenetic analysis on nucleotide and amino acid sequences using Maximum Likelihood and Bayesian Inference revealed a basal split of Microdontinae from all other syrphids. The remainder consists of several deep clades assigned to the subfamily Eristalinae in the current classification, including a clade comprising the subfamily Syrphinae (plus Pipizinae). These findings call for a re-definition of subfamilies, but basal nodes had insufficient support to allow such action. Molecular-clock dating placed the origin of the Syrphidae crown group in the mid-Cretaceous while the Eristalinae-Syrphinae clade likely originated near the K/Pg boundary. Transformation of larval life history characters on the tree suggests that Syrphidae initially had sap feeding larvae, which diversified greatly in diet and habitat association during the Eocene and Oligocene, coinciding with the diversification of angiosperms and the evolution of various insect groups used as larval host, prey, or mimicry models. Mitogenomes proved to be a powerful phylogenetic marker for studies of Syrphidae at subfamily and tribe levels, allowing dense taxon sampling that provided insight into the great ecological diversity and rapid evolution of larval life history traits of the hoverflies.
Collapse
Affiliation(s)
- Daniel Tsz Long Wong
- Department of Life Sciences, Imperial College London, Exhibition Road, London, SW7 2BX, U.K; Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, U.K.
| | - Hannah Norman
- Department of Life Sciences, Imperial College London, Exhibition Road, London, SW7 2BX, U.K; Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, U.K.
| | - Thomas J Creedy
- Department of Life Sciences, Imperial College London, Exhibition Road, London, SW7 2BX, U.K; Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, U.K.
| | - Kurt Jordaens
- Department of Biology-Invertebrates Unit, Royal Museum for Central Africa, Joint Experimental Molecular Unit Leuvensesteenweg 13, B-3080 Tervuren, Belgium.
| | - Kevin M Moran
- Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri-Food Canada, K.W. Neatby Building, 960 Carling Avenue, Ottawa, Ontario, ON K1A 0C6, Canada; Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, ON K1S 5B6, Canada.
| | - Andrew Young
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, ON N1G 2W1, Canada.
| | - Ximo Mengual
- Zoologisches Forschungsmuseum Alexander Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Adenauerallee 127, 53113 Bonn, Germany.
| | - Jeffrey H Skevington
- Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri-Food Canada, K.W. Neatby Building, 960 Carling Avenue, Ottawa, Ontario, ON K1A 0C6, Canada; Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, ON K1S 5B6, Canada.
| | - Alfried P Vogler
- Department of Life Sciences, Imperial College London, Exhibition Road, London, SW7 2BX, U.K; Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, U.K.
| |
Collapse
|
12
|
Li H, Yan Y, Li J. Eighteen mitochondrial genomes of Syrphidae (Insecta: Diptera: Brachycera) with a phylogenetic analysis of Muscomorpha. PLoS One 2023; 18:e0278032. [PMID: 36602958 DOI: 10.1371/journal.pone.0278032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 11/08/2022] [Indexed: 01/06/2023] Open
Abstract
In this study, 18 mitochondrial genomes (mitogenomes) of Syrphidae were sequenced. These mitogenomes ranged from 15,648 to 16,405 bp and contained 37 genes that were similar to those from other Syrphidae species. Most protein-coding genes (PCGs) started with a standard ATN codon and ended with TAA/G. All transfer RNAs (tRNAs) could be folded into the cloverleaf secondary structure except tRNA-Ser (AGN), which lacks a dihydrouridine arm. The secondary structures of ribosomal RNAs (rRNAs) were predicted. Six domains (III is absent in arthropods) and 44 helices were included in the 16S rRNA, and three domains and 24 helices were included in the 12S rRNA. We found three conserved fragments in all syrphid mitogenomes. Phylogenetic analyses were performed based on the nucleotide data of 13 PCGs and two rRNAs from 76 Muscomorpha and three outgroup species. In results the paraphyly of Aschiza and Schizophora were supported, the Acalyptratae was also paraphyletic but the relationships of its superfamilies were difficult to determine, the monophyly of Calyptratea was supported with the relationships of Oestroidea and Muscoidea need to be further reconsidered. Within Syrphidae the monophyly of family level was supported, the Syrphinae were clustered into one branch, while the paraphyly of Eristalinae was still well supported.
Collapse
Affiliation(s)
- Hu Li
- Shaanxi Key Laboratory of Bio-Resources, State Key Laboratory of Biological Resources and Ecological Environment of Qinling-Bashan, School of Biological Science & Engineering, Shaanxi University of Technology, Qinling-Bashan Mountains Bioresources Comprehensive Development C.I.C., Hanzhong, Shaanxi, China
| | - Yan Yan
- Shaanxi Key Laboratory of Bio-Resources, State Key Laboratory of Biological Resources and Ecological Environment of Qinling-Bashan, School of Biological Science & Engineering, Shaanxi University of Technology, Qinling-Bashan Mountains Bioresources Comprehensive Development C.I.C., Hanzhong, Shaanxi, China
| | - Juan Li
- Shaanxi Key Laboratory of Bio-Resources, State Key Laboratory of Biological Resources and Ecological Environment of Qinling-Bashan, School of Biological Science & Engineering, Shaanxi University of Technology, Qinling-Bashan Mountains Bioresources Comprehensive Development C.I.C., Hanzhong, Shaanxi, China
| |
Collapse
|
13
|
Shang J, Xu W, Huang X, Zhang D, Yan L, Pape T. Comparative Mitogenomics of Flesh Flies: Implications for Phylogeny. INSECTS 2022; 13:insects13080718. [PMID: 36005343 PMCID: PMC9408989 DOI: 10.3390/insects13080718] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/04/2022] [Accepted: 08/05/2022] [Indexed: 05/13/2023]
Abstract
Flesh flies (Diptera: Sarcophagidae) represent a rapid radiation belonging to the Calyptratae. With more than 3000 known species, they are extraordinarily diverse in terms of their breeding habits and are therefore of particular importance in human and veterinary medicine, forensics, and ecology. To better comprehend the phylogenetic relationships and evolutionary characteristics of the Sarcophagidae, we sequenced the complete mitochondrial genomes of five species of flesh flies and performed mitogenomic comparisons amongst the three subfamilies. The mitochondrial genomes match the hypothetical condition of the insect ancestor in terms of gene content and gene arrangement. The evolutionary rates of the subfamilies of Sarcophagidae differ significantly, with Miltogramminae exhibiting a higher rate than the other two subfamilies. The monophyly of the Sarcophagidae and each subfamily is strongly supported by phylogenetic analysis, with the subfamily-level relationship inferred as (Sarcophaginae, (Miltogramminae, Paramacronychiinae)). This study suggests that phylogenetic analysis based on mitochondrial genomes may not be appropriate for rapidly evolving groups such as Miltogramminae and that the third-codon positions could play a considerable role in reconstructing the phylogeny of Sarcophagidae. The protein-coding genes ND2 and ND6 have the potential to be employed as DNA markers for species identification and delimitation in flesh flies.
Collapse
Affiliation(s)
- Jin Shang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Wentian Xu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Xiaofang Huang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Dong Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
- Correspondence: (D.Z.); (L.Y.)
| | - Liping Yan
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
- Correspondence: (D.Z.); (L.Y.)
| | - Thomas Pape
- Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| |
Collapse
|
14
|
Phylogenetic Analysis of Mitochondrial Genome of Tabanidae (Diptera: Tabanidae) Reveals the Present Status of Tabanidae Classification. INSECTS 2022; 13:insects13080695. [PMID: 36005320 PMCID: PMC9408937 DOI: 10.3390/insects13080695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 12/04/2022]
Abstract
Simple Summary Tabanidae suck the blood of humans and animals, are important biological vectors for the transmission of diseases, and are of considerable economic and medical significance. However, current knowledge about the mitochondrial genome of this family is limited. Therefore, six newly completed mitochondrial genomes of four genera of Tabanidae (Haematopota turkestanica, Chrysops vanderwulpi, Chrysops dissectus, Tabanus chrysurus, Tabanus pleskei, and Hybomitra sp. species) were sequenced and analyzed. The results show that the six newly mitochondrial genomes have quite similar structures and features. Phylogeny was inferred by analyzing the 13 amino acid sequences coded by mitochondrial genes of 22 mitogenomes (all available complete mitochondrial genomes of tabanidae). Bayesian inference, maximum likelihood trees, and maximum parsimony inference analyses all showed consistent results. This study supports the concept of monophyly of all groups, ratifies the current taxonomic classification, and provides useful genetic markers for studying the molecular ecology, systematics, and population genetics of Tabanidae. Abstract Tabanidae suck the blood of humans and animals, are important biological vectors for the transmission of diseases, and are of considerable economic and medical significance. However, current knowledge about the mitochondrial genome of this family is limited. More complete mitochondrial genomes of Tabanidae are essential for the identification and phylogeny. Therefore, this study sequenced and analyzed six complete mitochondrial (mt) genome sequences of four genera of Tabanidae for the first time. The complete mt genomes of the six new sequences are circular molecules ranging from 15,851 to 16,107 base pairs (bp) in size, with AT content ranging from 75.64 to 77.91%. The six complete mitochondrial genomes all consist of 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (RRNA), 22 transfer RNA genes (tRNAs), and a control region, making a total of 37 functional subunits. ATT/ATG was the most common start codon, and the stop codon was TAA of all PCGS. All tRNA except tRNA Ser1 had a typical clover structure. Phylogeny was inferred by analyzing the 13 concatenated amino acid sequences of the 22 mt genomes. Bayesian inference, maximum-likelihood trees, and maximum-parsimony inference analyses all showed consistent results. This study supports the concept of monophyly of all genus, ratifies the current taxonomic classification, and provides effective genetic markers for molecular classification, systematics, and genetic studies of Tabanidae.
Collapse
|
15
|
The Impact of Fast Radiation on the Phylogeny of Bactrocera Fruit Flies as Revealed by Multiple Evolutionary Models and Mutation Rate-Calibrated Clock. INSECTS 2022; 13:insects13070603. [PMID: 35886779 PMCID: PMC9319077 DOI: 10.3390/insects13070603] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/22/2022] [Accepted: 06/28/2022] [Indexed: 11/16/2022]
Abstract
Several true fruit flies (Tephritidae) cause major damage to agriculture worldwide. Among them, species of the genus Bactrocera are extensively studied to understand the traits associated with their invasiveness and ecology. Comparative approaches based on a reliable phylogenetic framework are particularly effective, but several nodes of the Bactrocera phylogeny are still controversial, especially concerning the reciprocal affinities of the two major pests B. dorsalis and B. tryoni. Here, we analyzed a newly assembled genomic-scaled dataset using different models of evolution to infer a phylogenomic backbone of ten representative Bactrocera species and two outgroups. We further provide the first genome-scaled inference of their divergence by calibrating the clock using fossil records and the spontaneous mutation rate. The results reveal a closer relationship of B. dorsalis with B. latifrons than to B. tryoni, contrary to what was previously supported by mitochondrial-based phylogenies. By employing coalescent-aware and heterogeneous evolutionary models, we show that this incongruence likely derives from a hitherto undetected systematic error, exacerbated by incomplete lineage sorting and possibly hybridization. This agrees with our clock analysis, which supports a rapid and recent radiation of the clade to which B. dorsalis, B. latifrons and B. tryoni belong. These results provide a new picture of Bactrocera phylogeny that can serve as the basis for future comparative analyses.
Collapse
|
16
|
Universal Mitochondrial Multi-Locus Sequence Analysis (mtMLSA) to Characterise Populations of Unanticipated Plant Pest Biosecurity Detections. BIOLOGY 2022; 11:biology11050654. [PMID: 35625382 PMCID: PMC9138331 DOI: 10.3390/biology11050654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/11/2022] [Accepted: 04/21/2022] [Indexed: 12/02/2022]
Abstract
Simple Summary Agricultural and environmental sustainability requires effective biosecurity responses that prevent the establishment or spread of exotic insect pests. Understanding where new detections may have come from or if recurrent detections are connected contributes to this. Suitable population genetic markers use relatively rapidly evolving gene regions which render the PCR method species-specific at best. Because resource limitations mean these are pre-emptively developed for the highest risk species, populations of other exotic pests are unable to be characterised at the time. Here we have developed a generic method that is useful across species within the same taxonomic Order, including where there is little or no prior knowledge of their gene sequences. Markers are formed by concomitant sequencing of four gene regions. Sequence concatenation was shown to retrieve higher resolution signatures than standard DNA barcoding. The method is encouragingly universal, as illustrated across species in ten fly and 11 moth superfamilies. Although as-yet untested in a biosecurity situation, this relatively low-tech, off-the-shelf method makes a proactive contribution to the toolbox of quarantine agencies at the time of detection without the need for impromptu species-specific research and development. Abstract Biosecurity responses to post-border exotic pest detections are more effective with knowledge of where the species may have originated from or if recurrent detections are connected. Population genetic markers for this are typically species-specific and not available in advance for any but the highest risk species, leaving other less anticipated species difficult to assess at the time. Here, new degenerate PCR primer sets are designed for within the Lepidoptera and Diptera for the 3′ COI, ND3, ND6, and 3′ plus 5′ 16S gene regions. These are shown to be universal at the ordinal level amongst species of 14 and 15 families across 10 and 11 dipteran and lepidopteran superfamilies, respectively. Sequencing the ND3 amplicons as an example of all the loci confirmed detection of population-level variation. This supported finding multiple population haplotypes from the publicly available sequences. Concatenation of the sequences also confirmed that higher population resolution is achieved than for the individual genes. Although as-yet untested in a biosecurity situation, this method is a relatively simple, off-the-shelf means to characterise populations. This makes a proactive contribution to the toolbox of quarantine agencies at the time of detection without the need for unprepared species-specific research and development.
Collapse
|
17
|
Li H, Li J. Comparative analysis of four complete mitogenomes from hoverfly genus Eristalinus with phylogenetic implications. Sci Rep 2022; 12:4164. [PMID: 35264733 PMCID: PMC8907203 DOI: 10.1038/s41598-022-08172-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 03/03/2022] [Indexed: 11/27/2022] Open
Abstract
The genus Eristalinus is widely distributed globally. Four complete mitochondrial genomes (i.e., mitogenomes) of Eristalinus were sequenced and analyzed in this study: Eristalinus viridis (Coquillett, 1898), E. quinquestriatus (Fabricius, 1781), E. tarsalis (Macquart, 1855), and E. sp. Within these four sequenced mitogenomes, most protein-coding genes (ND2, CO1, COX2, COX3, ND3, ND5, ND4, ND4L, ND6, and Cytb) began with a typical ATN (T/C/G/A) start codon and ended with a stop codon TAA or incomplete T, whereas ND1 began with the start codon TTG. ND3 ended with TAG. The secondary tRNA structure was that of a typical cloverleaf, and only the tRNA-Ser1 lacked a DHU arm. Three and five domains appeared in the 12S and 16S rRNA secondary structures, respectively. The phylogenetic relationships among the four Eristalinus species combined with the published mitogenomes of Syrphidae were reconstructed using the maximum likelihood and Bayesian inference methods, which support the monophyly of the subfamily Syrphinae but do not support that of the subfamily Eristalinae. Of note, Eristalini and Syrphini are monophyletic groups. The mitogenomes of E. viridis, E. quinquestriatus, E. sp., and E. tarsalis are useful for determining the phylogenetic relationships and evolution of Syrphidae.
Collapse
Affiliation(s)
- Hu Li
- Shaanxi Key Laboratory of Bio-Resources, School of Biological Science & Engineering, Shaanxi University of Technology, Hanzhong, 723000, Shaanxi, China.
| | - Juan Li
- Shaanxi Key Laboratory of Bio-Resources, School of Biological Science & Engineering, Shaanxi University of Technology, Hanzhong, 723000, Shaanxi, China
| |
Collapse
|
18
|
Shang Y, Ren L, Zhang X, Li Y, Zhang C, Guo Y. Characterization and Comparative Analysis of Mitochondrial Genomes Among the Calliphoridae (Insecta: Diptera: Oestroidea) and Phylogenetic Implications. Front Genet 2022; 13:799203. [PMID: 35251125 PMCID: PMC8891575 DOI: 10.3389/fgene.2022.799203] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/27/2022] [Indexed: 11/21/2022] Open
Abstract
The Calliphoridae (blowflies) are significant for forensic science, veterinary management, medical science, and economic issues. However, the phylogenetic relationships within this family are poorly understood and controversial, and the status of the Calliphoridae has been a crucial problem for understanding the evolutionary relationships of the Oestroidea these years. In the present study, seven mitochondrial genomes (mitogenomes), including six calliphorid species and one Polleniidae species, were sequenced and annotated. Then a comparative mitochondrial genomic analysis among the Calliphoridae is presented. Additionally, the phylogenetic relationship of the Calliphoridae within the larger context of the other Oestroidea was reconstructed based on the mitogenomic datasets using maximum likelihood (ML) and Bayesian methods (BI). The results suggest that the gene arrangement, codon usage, and base composition are conserved within the calliphorid species. The phylogenetic analysis based on the mitogenomic dataset recovered the Calliphoridae as monophyletic and inferred the following topology within Oestroidea: (Oestridae (Sarcophagidae (Calliphoridae + (Polleniidae + (Mesembrinellidae + Tachinidae))))). Although the number of exemplar species is limited, further studies are required. Within the Calliphoridae, the Chrysomyinae were recovered as sister taxon to Luciliinae + Calliphorinae. Our analyses indicated that mitogenomic data have the potential for illuminating the phylogenetic relationships in the Oestroidea as well as for the classification of the Calliphoridae.
Collapse
Affiliation(s)
| | | | | | | | | | - Yadong Guo
- *Correspondence: Changquan Zhang, ; Yadong Guo,
| |
Collapse
|
19
|
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]
|
20
|
Yan L, Pape T, Meusemann K, Kutty SN, Meier R, Bayless KM, Zhang D. Monophyletic blowflies revealed by phylogenomics. BMC Biol 2021; 19:230. [PMID: 34706743 PMCID: PMC8555136 DOI: 10.1186/s12915-021-01156-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 09/23/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Blowflies are ubiquitous insects, often shiny and metallic, and the larvae of many species provide important ecosystem services (e.g., recycling carrion) and are used in forensics and debridement therapy. Yet, the taxon has repeatedly been recovered to be para- or polyphyletic, and the lack of a well-corroborated phylogeny has prevented a robust classification. RESULTS We here resolve the relationships between the different blowfly subclades by including all recognized subfamilies in a phylogenomic analysis using 2221 single-copy nuclear protein-coding genes of Diptera. Maximum likelihood (ML), maximum parsimony (MP), and coalescent-based phylogeny reconstructions all support the same relationships for the full data set. Based on this backbone phylogeny, blowflies are redefined as the most inclusive monophylum within the superfamily Oestroidea not containing Mesembrinellidae, Mystacinobiidae, Oestridae, Polleniidae, Sarcophagidae, Tachinidae, and Ulurumyiidae. The constituent subfamilies are re-classified as Ameniinae (including the Helicoboscinae, syn. nov.), Bengaliinae, Calliphorinae (including Aphyssurinae, syn. nov., Melanomyinae, syn. nov., and Toxotarsinae, syn. nov.), Chrysomyinae, Luciliinae, Phumosiinae, Rhiniinae stat. rev., and Rhinophorinae stat. rev. Metallic coloration in the adult is shown to be widespread but does not emerge as the most likely ground plan feature. CONCLUSIONS Our study provides the first phylogeny of oestroid calyptrates including all blowfly subfamilies. This allows settling a long-lasting controversy in Diptera by redefining blowflies as a well-supported monophylum, and blowfly classification is adjusted accordingly. The archetypical blowfly trait of carrion-feeding maggots most likely evolved twice, and the metallic color may not belong to the blowfly ground plan.
Collapse
Affiliation(s)
- Liping Yan
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Thomas Pape
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Karen Meusemann
- Evolutionary Biology & Ecology, University of Freiburg, Freiburg, Germany
- Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum für Molekulare Biodiversitätsforschung (ZMB), Bonn, Germany
- Australian National Insect Collection, CSIRO National Research Collections Australia (NRCA), Canberra, Australia
| | - Sujatha Narayanan Kutty
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Berlin, Germany
| | - Keith M Bayless
- Australian National Insect Collection, CSIRO National Research Collections Australia (NRCA), Canberra, Australia
- Department of Entomology, California Academy of Sciences, San Francisco, USA
| | - Dong Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China.
| |
Collapse
|
21
|
Bessa MH, Ré FCD, Moura RDD, Loreto EL, Robe LJ. Comparative mitogenomics of Drosophilidae and the evolution of the Zygothrica genus group (Diptera, Drosophilidae). Genetica 2021; 149:267-281. [PMID: 34609625 DOI: 10.1007/s10709-021-00132-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 09/08/2021] [Indexed: 11/27/2022]
Abstract
The Zygothrica genus group of Drosophilidae encompasses more than 437 species and five genera. Although knowledge regarding its diversity has increased, uncertainties about its monophyly and position within Drosophilidae remain. Genomic approaches have been widely used to address different phylogenetic questions and analyses involving the mitogenome have revealed a cost-efficient tool to these studies. Thus, this work aims to characterize mitogenomes of three species of the Zygothrica genus group (from the Hirtodrosophila, Paraliodrosophila and Zygothrica genera), while comparing them with orthologous sequences from other 23 Drosophilidae species and addressing their phylogenetic position. General content concerning gene order and overlap, nucleotide composition, start and stop codon, codon usage and tRNA structures were compared, and phylogenetic trees were constructed under different datasets. The complete mitogenomes characterized for H. subflavohalterata affinis H002 and P. antennta present the PanCrustacea gene order with 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, 13 protein coding genes and an A+T rich region with two T-stretched elements. Some peculiarities such as the almost complete overlap of genes tRNAH/ND4, tRNAF/ND5 and tRNAS2/ND1 are reported for different Drosophilidae species. Non-canonical secondary structures were encountered for tRNAS1 and tRNAY, revealing patterns that apply at different phylogenetic scales. According to the best depiction of the mitogenomes evolutionary history, the three Neotropical species of the Zygothrica genus group encompass a monophyletic lineage sister to Zaprionus, composing with this genus a clade that is sister to the Drosophila subgenus.
Collapse
Affiliation(s)
- Maiara Hartwig Bessa
- Programa de Pós-Graduação Em Biodiversidade Animal, Universidade Federal de Santa Maria - UFSM, Santa Maria, RS, Brazil
| | - Francine Cenzi de Ré
- Programa de Pós-Graduação Em Biodiversidade Animal, Universidade Federal de Santa Maria - UFSM, Santa Maria, RS, Brazil
| | - Rafael Dias de Moura
- Curso de Ciências Biológicas, Universidade Federal de Santa Maria - UFSM, Santa Maria, RS, Brazil
| | - Elgion Lucio Loreto
- Programa de Pós-Graduação Em Biodiversidade Animal, Universidade Federal de Santa Maria - UFSM, Santa Maria, RS, Brazil
| | - Lizandra Jaqueline Robe
- Programa de Pós-Graduação Em Biodiversidade Animal, Universidade Federal de Santa Maria - UFSM, Santa Maria, RS, Brazil.
| |
Collapse
|
22
|
Yan L, Buenaventura E, Pape T, Narayanan Kutty S, Bayless KM, Zhang D. A phylotranscriptomic framework for flesh fly evolution (Diptera, Calyptratae, Sarcophagidae). Cladistics 2021; 37:540-558. [PMID: 34570937 DOI: 10.1111/cla.12449] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2020] [Indexed: 11/28/2022] Open
Abstract
The Sarcophagidae (flesh flies) comprise a large and widely distributed radiation within the Calyptratae (Diptera). Larval feeding habits are ecologically diverse and include sarcosaprophagy, coprophagy, herbivory, invertebrate and vertebrate predation, and kleptoparasitism. To elucidate the geographic origin and evolution of flesh fly life-history, we inferred a backbone phylogeny based on transcriptomic data from 26 sarcophagid species covering all three subfamilies plus 15 outgroups. The phylogeny was inferred using maximum parsimony and maximum likelihood methods based on a series of supermatrices, one set with overall information content improved by MARE (2290 loci), one set with 100% gene coverage for all included species (587 loci), and the last set including mitochondrial and nuclear genes (589 loci) and additional taxa. In order to obtain a more detailed hypothesis, we utilized the supertree approach to combine results from the present study with previously published hypotheses. This resulted supertree covers 84 of the one hundred currently recognized sarcophagid genera and formed the basis for the ancestral state reconstructions. The monophyletic Sarcophagidae is well-supported as sister to {Mystacinobiidae + Oestridae}, and relationships at the subfamily level are inferred as {Sarcophaginae, (Paramacronychiinae + Miltogramminae)}. The Sarcophagidae and each subfamily originated in the Americas, with Sarcophaginae diversifying mainly in the Neotropics, whereas the major radiation of both Miltogramminae and Paramacronychiinae occurred in the Palaearctic. Sarcosaprophagy is reconstructed as the ancestral larval feeding habit of the family Sarcophagidae and each subfamily. The ancestral sarcophagid larva probably utilized dead invertebrates as food, and the food spectrum expanded together with the diversification of breeding strategies. Particularly, kleptoparasitism in Miltogramminae is derived from sarcosaprophagy and may be seen as having derived from the breeding biology of 'lower' miltogrammines, the larvae of which feed on buried vertebrate carrion.
Collapse
Affiliation(s)
- Liping Yan
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Eliana Buenaventura
- Center for Integrative Biodiversity Discovery, Museum für Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity, Berlin, 10115, Germany
| | - Thomas Pape
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, 2100, Denmark
| | - Sujatha Narayanan Kutty
- Department of Biological Sciences, National University of Singapore, 14 Science Dr 4, Singapore, 117543, Singapore.,Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore, 119227, Singapore
| | - Keith M Bayless
- Australian National Insect Collection, CSIRO National Research Collections Australia (NRCA), Acton, Canberra, ACT, 2601, Australia.,Department of Entomology, California Academy of Sciences, San Francisco, CA, 94118, USA
| | - Dong Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| |
Collapse
|
23
|
Savini G, Scolari F, Ometto L, Rota-Stabelli O, Carraretto D, Gomulski LM, Gasperi G, Abd-Alla AMM, Aksoy S, Attardo GM, Malacrida AR. Viviparity and habitat restrictions may influence the evolution of male reproductive genes in tsetse fly (Glossina) species. BMC Biol 2021; 19:211. [PMID: 34556101 PMCID: PMC8461966 DOI: 10.1186/s12915-021-01148-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 09/06/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Glossina species (tsetse flies), the sole vectors of African trypanosomes, maintained along their long evolutionary history a unique reproductive strategy, adenotrophic viviparity. Viviparity reduces their reproductive rate and, as such, imposes strong selective pressures on males for reproductive success. These species live in sub-Saharan Africa, where the distributions of the main sub-genera Fusca, Morsitans, and Palpalis are restricted to forest, savannah, and riverine habitats, respectively. Here we aim at identifying the evolutionary patterns of the male reproductive genes of six species belonging to these three main sub-genera. We then interpreted the different patterns we found across the species in the light of viviparity and the specific habitat restrictions, which are known to shape reproductive behavior. RESULTS We used a comparative genomic approach to build consensus evolutionary trees that portray the selective pressure acting on the male reproductive genes in these lineages. Such trees reflect the long and divergent demographic history that led to an allopatric distribution of the Fusca, Morsitans, and Palpalis species groups. A dataset of over 1700 male reproductive genes remained conserved over the long evolutionary time scale (estimated at 26.7 million years) across the genomes of the six species. We suggest that this conservation may result from strong functional selective pressure on the male imposed by viviparity. It is noteworthy that more than half of these conserved genes are novel sequences that are unique to the Glossina genus and are candidates for selection in the different lineages. CONCLUSIONS Tsetse flies represent a model to interpret the evolution and differentiation of male reproductive biology under different, but complementary, perspectives. In the light of viviparity, we must take into account that these genes are constrained by a post-fertilization arena for genomic conflicts created by viviparity and absent in ovipositing species. This constraint implies a continuous antagonistic co-evolution between the parental genomes, thus accelerating inter-population post-zygotic isolation and, ultimately, favoring speciation. Ecological restrictions that affect reproductive behavior may further shape such antagonistic co-evolution.
Collapse
Affiliation(s)
- Grazia Savini
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Francesca Scolari
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
- Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza", Pavia, Italy
| | - Lino Ometto
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Omar Rota-Stabelli
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
- Center Agriculture Food Environment (C3A), University of Trento, Trento, Italy
| | - Davide Carraretto
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Ludvik M Gomulski
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Giuliano Gasperi
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Adly M M Abd-Alla
- Insect Pest Control Laboratory, Joint FAO/IAEA Programme of Nuclear Techniques in Food & Agriculture, Vienna, Vienna, Austria.
| | - Serap Aksoy
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Geoffrey M Attardo
- Department of Entomology and Nematology, University of California, Davis, Davis, CA, USA
| | - Anna R Malacrida
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy.
| |
Collapse
|
24
|
Retzinger AC, Retzinger GS. The Acari Hypothesis, II: Interspecies Operability of Pattern Recognition Receptors. Pathogens 2021; 10:pathogens10091220. [PMID: 34578252 PMCID: PMC8468033 DOI: 10.3390/pathogens10091220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 09/14/2021] [Indexed: 11/16/2022] Open
Abstract
Hypersensitivity to galactose-α-1,3-galactose (α-gal) is an informative example of a pathologic IgE-mediated process. By way of their saliva, ticks are able to sensitize humans to tick dietary elements that express α-gal. Mites, which along with ticks constitute the phyletic subclass Acari, feed on proteinaceous foodstuffs that represent most, if not all, human allergens. Given: (1) the gross nature of the pathophysiological reactions of allergy, especially anaphylaxis, (2) the allergenicity of acarian foodstuffs, and (3) the relatedness of ticks and mites, it has been hypothesized that human-acarian interactions are cardinal to the pathogenesis of allergy. In this report, a means by which such interactions contribute to that pathogenesis is proposed.
Collapse
Affiliation(s)
- Andrew C. Retzinger
- Department of Emergency Medicine, Camden Clark Medical Center, West Virginia University, Parkersburg, WV 26101, USA
- Correspondence:
| | - Gregory S. Retzinger
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA;
| |
Collapse
|
25
|
Ullastres A, Merenciano M, González J. Regulatory regions in natural transposable element insertions drive interindividual differences in response to immune challenges in Drosophila. Genome Biol 2021; 22:265. [PMID: 34521452 PMCID: PMC8439047 DOI: 10.1186/s13059-021-02471-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 08/19/2021] [Indexed: 02/08/2023] Open
Abstract
Background Variation in gene expression underlies interindividual variability in relevant traits including immune response. However, the genetic variation responsible for these gene expression changes remains largely unknown. Among the non-coding variants that could be relevant, transposable element insertions are promising candidates as they have been shown to be a rich and diverse source of cis-regulatory elements. Results In this work, we use a population genetics approach to identify transposable element insertions likely to increase the tolerance of Drosophila melanogaster to bacterial infection by affecting the expression of immune-related genes. We identify 12 insertions associated with allele-specific expression changes in immune-related genes. We experimentally validate three of these insertions including one likely to be acting as a silencer, one as an enhancer, and one with a dual role as enhancer and promoter. The direction in the change of gene expression associated with the presence of several of these insertions is consistent with an increased survival to infection. Indeed, for one of the insertions, we show that this is the case by analyzing both natural populations and CRISPR/Cas9 mutants in which the insertion is deleted from its native genomic context. Conclusions We show that transposable elements contribute to gene expression variation in response to infection in D. melanogaster and that this variation is likely to affect their survival capacity. Because the role of transposable elements as regulatory elements is not restricted to Drosophila, transposable elements are likely to play a role in immune response in other organisms as well. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02471-3.
Collapse
Affiliation(s)
- Anna Ullastres
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Miriam Merenciano
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Josefa González
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain.
| |
Collapse
|
26
|
Disruption of the odorant coreceptor Orco impairs foraging and host finding behaviors in the New World screwworm fly. Sci Rep 2021; 11:11379. [PMID: 34059738 PMCID: PMC8167109 DOI: 10.1038/s41598-021-90649-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 05/12/2021] [Indexed: 12/03/2022] Open
Abstract
The evolution of obligate ectoparasitism in blowflies (Diptera: Calliphoridae) has intrigued scientists for over a century, and surprisingly, the genetics underlying this lifestyle remain largely unknown. Blowflies use odors to locate food and oviposition sites; therefore, olfaction might have played a central role in niche specialization within the group. In insects, the coreceptor Orco is a required partner for all odorant receptors (ORs), a major gene family involved in olfactory-evoked behaviors. Hence, we characterized the Orco gene in the New World screwworm, Cochliomyia hominivorax, a blowfly that is an obligate ectoparasite of warm-blooded animals. In contrast, most of the closely related blowflies are scavengers that lay their eggs on dead animals. We show that the screwworm Orco orthologue (ChomOrco) is highly conserved within Diptera, showing signals of strong purifying selection. Expression of ChomOrco is broadly detectable in chemosensory appendages, and is related to morphological, developmental, and behavioral aspects of the screwworm biology. We used CRISPR/Cas9 to disrupt ChomOrco and evaluate the consequences of losing the OR function on screwworm behavior. In two-choice assays, Orco mutants displayed an impaired response to floral-like and animal host-associated odors, suggesting that OR-mediated olfaction is involved in foraging and host-seeking behaviors in C. hominivorax. These results broaden our understanding of the chemoreception basis of niche occupancy by blowflies.
Collapse
|
27
|
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
| |
Collapse
|
28
|
Gomez-Puerta LA, Cribillero NG, Silva W, Ayala P. Cloacal myiasis by Lucilia spp. (Diptera: Calliphoridae) in a rooster (Gallus gallus domesticus) and two Harris's hawks (Parabuteo unicinctus). Parasitol Int 2021; 83:102363. [PMID: 33901677 DOI: 10.1016/j.parint.2021.102363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 04/18/2021] [Accepted: 04/19/2021] [Indexed: 10/21/2022]
Abstract
In this study, cloacal myiasis caused by dipterans of Lucilia genus was found in a rooster (Gallus gallus domesticus) and two Harris's hawks (Parabuteo unicinctus) from Peru. Larval dipteran were collected and preserved in ethanol. Morphological analysis indicated two species: Lucilia sericata in the rooster and in one Harris's hawk, and Lucilia cuprina in the other Harris's hawk. Molecular analysis confirmed the diagnosis by amplification of the nucleotide sequences of the cytochrome c oxidase subunit 1 gene and internal transcribed spacer 2 region. The sequences were compared with sequence references from a public sequence database, which showed a 100% matched identity. This study demonstrated for first time cloacal myiasis by L. sericata in a domestic bird from Peru and in Harris's hawk. Also, for the first time, L. cuprina was found in a bird of prey.
Collapse
Affiliation(s)
- Luis A Gomez-Puerta
- School of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima, Peru.
| | - Nelly G Cribillero
- School of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Walter Silva
- Administración Técnicas Forestal y de Fauna Silvestre (ATFFS), Servicio Nacional Forestal y de Fauna Silvestre (SERFOR), Lima, Peru
| | - Pilar Ayala
- Administración Técnicas Forestal y de Fauna Silvestre (ATFFS), Servicio Nacional Forestal y de Fauna Silvestre (SERFOR), Lima, Peru
| |
Collapse
|
29
|
Stireman JO, Cerretti P, O’hara JE, Moulton JK. Extraordinary diversification of the “bristle flies” (Diptera: Tachinidae) and its underlying causes. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The family Tachinidae (“bristle flies”) is the most diverse and ecologically important group of insect parasitoids outside the parasitic wasps. It is among the most species rich families of flies (Diptera) and has experienced a recent adaptive radiation across the globe. We make use of a molecular phylogeny of the family to examine its rapid radiation and explore the traits of tachinid lineages that may have contributed to variation in their diversification. We apply a range of diversification analyses to assess the consistency and robustness of effects. We find that the Tachinidae are among the most rapidly diversifying families of animals. Six to eight clades of bristle flies, distributed across the phylogeny, exhibit strong evidence of accelerated diversification. Our results suggest that the use of holometabolous insect larvae, and specifically caterpillars (Lepidoptera), as hosts, is associated with increased diversification rates. However, these effects were inconsistent across analyses. We detected little influence of oviposition strategy (egg type) or host feeding habit, and we recovered evidence that unmeasured “hidden” traits may explain greater variance in diversification. We evaluated the strengths and weaknesses of different Maximum Likelihood and Bayesian approaches for analysing diversification and the potential for extrinsic factors, such as geography, to influence patterns of richness and diversification. In general, we conclude that although certain traits may provide opportunities for diversification, whether this is capitalized on may depend on additional traits and/or historical contingency.
Collapse
Affiliation(s)
- John O Stireman
- Department of Biological Sciences, Wright State University, Dayton, OH, USA
| | - Pierfilippo Cerretti
- Dipartimento di Biologia e Biotecnologie ‘Charles Darwin’, ‘Sapienza’ Università di Roma, Piazzale A. Moro 5, Rome, Italy
- Australian National Insect Collection, CSIRO National Facilities and Collections, Black Mountain, Canberra, Australia
| | - James E O’hara
- Canadian National Collection of Insects, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - John K Moulton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| |
Collapse
|
30
|
Yan Y, Hu L. The complete mitochondrial genome of Platycheirus albimanus (Diptera: Syrphidae: Syrphinae) and phylogenetic analysis of the Syrphidae. Mitochondrial DNA B Resour 2021; 6:528-530. [PMID: 33628915 PMCID: PMC7889080 DOI: 10.1080/23802359.2021.1872455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The complete mitochondrial genome of Platycheirus albimanus (Fabricius, 1781) was sequenced. The length of the mitogenome is 16,648 bp and consists of 37 genes including 22 transfer RNA (tRNAs), 13 protein-coding (PCGs) and 2 ribosomal RNA (rRNAs). The 13 PCGs initiate with the start codon ATN, except for COX1 and ATP6 which use TTG. All of the PCGs ended with TAA, apart from ND4 and ND4L terminated by incomplete T––. The ML tree based on complete mitogenomes from 25 species (22 Syrphidae and 3 outgroup taxa) suggests that the tribe Melanostomini is more closely related to the Syrphini. The phylogenetic analysis supports the monophyly of Syrphinae, and the paraphyly of the Eristalinae. This mitogenome information for P. albimanus could facilitate future studies of evolutionarily related insects.
Collapse
Affiliation(s)
- Yan Yan
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shannxi, China
| | - Li Hu
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shannxi, China
| |
Collapse
|
31
|
Ramesh B, Firneno TJ, Demuth JP. Divergence time estimation of genus Tribolium by extensive sampling of highly conserved orthologs. Mol Phylogenet Evol 2021; 159:107084. [PMID: 33540077 DOI: 10.1016/j.ympev.2021.107084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/13/2021] [Accepted: 01/22/2021] [Indexed: 11/15/2022]
Abstract
Tribolium castaneum, the red flour beetle, is among the most well-studied eukaryotic genetic model organisms. Tribolium often serves as a comparative bridge from highly derived Drosophila traits to other organisms. Simultaneously, as a member of the most diverse order of metazoans, Coleoptera, Tribolium informs us about innovations that accompany hyper diversity. However, understanding the tempo and mode of evolutionary innovation requires well-resolved, time-calibrated phylogenies, which are not available for Tribolium. The most recent effort to understand Tribolium phylogenetics used two mitochondrial and three nuclear markers. The study concluded that the genus may be paraphyletic and reported a broad range for divergence time estimates. Here we employ recent advances in Bayesian methods to estimate the relationships and divergence times among Tribolium castaneum, T. brevicornis, T. confusum, T. freemani, and Gnatocerus cornutus using 1368 orthologs conserved across all five species and an independent substitution rate estimate. We find that the most basal split within Tribolium occurred ~86 Mya [95% HPD 85.90-87.04 Mya] and that the most recent split was between T. freemani and T. castaneum at ~14 Mya [95% HPD 13.55-14.00]. Our results are consistent with broader phylogenetic analyses of insects and suggest that Cenozoic climate changes played a role in the Tribolium diversification.
Collapse
Affiliation(s)
- Balan Ramesh
- Department of Biology, The University of Texas at Arlington, TX 76019, USA.
| | - Thomas J Firneno
- Department of Biology, The University of Texas at Arlington, TX 76019, USA
| | - Jeffery P Demuth
- Department of Biology, The University of Texas at Arlington, TX 76019, USA.
| |
Collapse
|
32
|
Andere AA, Pimsler ML, Tarone AM, Picard CJ. The genomes of a monogenic fly: views of primitive sex chromosomes. Sci Rep 2020; 10:15728. [PMID: 32978490 PMCID: PMC7519133 DOI: 10.1038/s41598-020-72880-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/07/2020] [Indexed: 11/10/2022] Open
Abstract
The production of male and female offspring is often determined by the presence of specific sex chromosomes which control sex-specific expression, and sex chromosomes evolve through reduced recombination and specialized gene content. Here we present the genomes of Chrysomya rufifacies, a monogenic blow fly (females produce female or male offspring, exclusively) by separately sequencing and assembling each type of female and the male. The genomes (> 25X coverage) do not appear to have any sex-linked Muller F elements (typical for many Diptera) and exhibit little differentiation between groups supporting the morphological assessments of C. rufifacies homomorphic chromosomes. Males in this species are associated with a unimodal coverage distribution while females exhibit bimodal coverage distributions, suggesting a potential difference in genomic architecture. The presence of the individual-sex draft genomes herein provides new clues regarding the origination and evolution of the diverse sex-determining mechanisms observed within Diptera. Additional genomic analysis of sex chromosomes and sex-determining genes of other blow flies will allow a refined evolutionary understanding of how flies with a typical X/Y heterogametic amphogeny (male and female offspring in similar ratios) sex determination systems evolved into one with a dominant factor that results in single sex progeny in a chromosomally monomorphic system.
Collapse
Affiliation(s)
- Anne A. Andere
- Department of Biology, Indiana University- Purdue University Indianapolis, Indianapolis, IN USA
| | - Meaghan L. Pimsler
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL USA
| | - Aaron M. Tarone
- Department of Entomology, Texas A&M University, College Station, TX USA
| | - Christine J. Picard
- Department of Biology, Indiana University- Purdue University Indianapolis, Indianapolis, IN USA
| |
Collapse
|
33
|
Ren L, Zhang X, Li Y, Shang Y, Chen S, Wang S, Qu Y, Cai J, Guo Y. Comparative analysis of mitochondrial genomes among the subfamily Sarcophaginae (Diptera: Sarcophagidae) and phylogenetic implications. Int J Biol Macromol 2020; 161:214-222. [PMID: 32526299 DOI: 10.1016/j.ijbiomac.2020.06.043] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/25/2020] [Accepted: 06/05/2020] [Indexed: 12/16/2022]
Abstract
The subfamily Sarcophaginae is extremely diverse in morphology, habit and geographical distribution, and usually considered to be of significant ecological, medical, and forensic significance. In the present study, 18 mitochondrial genomes (mitogenomes) of sarcophagid flies were first obtained. The rearrangement and orientation of genes were identical with that of ancestral insects. The degrees of compositional heterogeneity in the datasets were extremely low. Furthermore, 13 protein-coding genes were evolving under purifying selection. The phylogenic relationship of the genus-group taxa Boettcheria + (Sarcophaga + (Peckia + (Ravinia + Oxysarcodexia))) was strongly supported. Four subgenera were recovered as monophyletic (Liopygia, Liosarcophaga, Pierretia, Heteronychia) in addition to Parasarcophaga as polyphyletic. The sister-relationships between S. dux and S. aegyptiaca, S. pingi and S. kawayuensis were recovered, respectively. Moreover, the molecular phylogenetic relationships among the subgenera Helicophagella, Kozlovea, Kramerea, Pandelleisca, Phallocheira, Pseudothyrsocnema, Sinonipponia and Seniorwhitea were rarely put forward prior to this study. This study provides insight into the population genetics, molecular biology, and phylogeny for the subfamily Sarcophaginae, especially for the subgeneric classification of Sarcophaga. However, compared with the enormous species diversity of flesh flies, the available mitogenomes are still limited for recovering the phylogeny of Sarcophaginae.
Collapse
Affiliation(s)
- Lipin Ren
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Xiangyan Zhang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Yi Li
- 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
| | - Shan Chen
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Shiwen Wang
- Department of Forensic Science, School of Basic Medical Sciences, Xinjiang Medical University, Ürümqi, Xinjiang, China
| | - Yihong Qu
- 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.
| |
Collapse
|
34
|
Schenk J, Kleinbölting N, Traunspurger W. Comparison of morphological, DNA barcoding, and metabarcoding characterizations of freshwater nematode communities. Ecol Evol 2020; 10:2885-2899. [PMID: 32211163 PMCID: PMC7083658 DOI: 10.1002/ece3.6104] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 01/12/2020] [Accepted: 01/28/2020] [Indexed: 11/30/2022] Open
Abstract
Biomonitoring approaches and investigations of many ecological questions require assessments of the biodiversity of a given habitat. Small organisms, ranging from protozoans to metazoans, are of great ecological importance and comprise a major share of the planet's biodiversity but they are extremely difficult to identify, due to their minute body sizes and indistinct structures. Thus, most biodiversity studies that include small organisms draw on several methods for species delimitation, ranging from traditional microscopy to molecular techniques. In this study, we compared the efficiency of these methods by analyzing a community of nematodes. Specifically, we evaluated the performances of traditional morphological identification, single-specimen barcoding (Sanger sequencing), and metabarcoding in the identification of 1500 nematodes from sediment samples. The molecular approaches were based on the analysis of the 28S ribosomal large and 18S small subunits (LSU and SSU). The morphological analysis resulted in the determination of 22 nematode species. Barcoding identified a comparable number of operational taxonomic units (OTUs) based on 28S rDNA (n = 20) and fewer OTUs based on 18S rDNA (n = 12). Metabarcoding identified a higher OTU number but fewer amplicon sequence variants (AVSs) (n = 48 OTUs, n = 17 ASVs for 28S rDNA, and n = 31 OTUs, n = 6 ASVs for 18S rDNA). Between the three approaches (morphology, barcoding, and metabarcoding), only three species (13.6%) were shared. This lack of taxonomic resolution hinders reliable community identifications to the species level. Further database curation will ensure the effective use of molecular species identification.
Collapse
Affiliation(s)
- Janina Schenk
- Department of Animal EcologyBielefeld UniversityBielefeldGermany
| | | | | |
Collapse
|
35
|
Crews SC, Esposito LA. Towards a synthesis of the Caribbean biogeography of terrestrial arthropods. BMC Evol Biol 2020; 20:12. [PMID: 31980017 PMCID: PMC6979080 DOI: 10.1186/s12862-019-1576-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 12/30/2019] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The immense geologic and ecological complexity of the Caribbean has created a natural laboratory for interpreting when and how organisms disperse through time and space. However, competing hypotheses compounded with this complexity have resulted in a lack of unifying principles of biogeography for the region. Though new data concerning the timing of geologic events and dispersal events are emerging, powerful new analytical tools now allow for explicit hypothesis testing. Arthropods, with varying dispersal ability and high levels of endemism in the Caribbean, are an important, albeit understudied, biogeographic model system. Herein, we include a comprehensive analysis of every publicly available genetic dataset (at the time of writing) of terrestrial Caribbean arthropod groups using a statistically robust pipeline to explicitly test the current extent of biogeographic hypotheses for the region. RESULTS Our findings indicate several important biogeographic generalizations for the region: the South American continent is the predominant origin of Caribbean arthropod fauna; GAARlandia played a role for some taxa in aiding dispersal from South America to the Greater Antilles; founder event dispersal explains the majority of dispersal events by terrestrial arthropods, and distance between landmasses is important for dispersal; most dispersal events occurred via island hopping; there is evidence of 'reverse' dispersal from islands to the mainland; dispersal across the present-day Isthmus of Panama generally occurred prior to 3 mya; the Greater Antilles harbor more lineage diversity than the Lesser Antilles, and the larger Greater Antilles typically have greater lineage diversity than the smaller islands; basal Caribbean taxa are primarily distributed in the Greater Antilles, the basal-most being from Cuba, and derived taxa are mostly distributed in the Lesser Antilles; Jamaican taxa are usually endemic and monophyletic. CONCLUSIONS Given the diversity and deep history of terrestrial arthropods, incongruence of biogeographic patterns is expected, but focusing on both similarities and differences among divergent taxa with disparate life histories emphasizes the importance of particular qualities responsible for resulting diversification patterns. Furthermore, this study provides an analytical toolkit that can be used to guide researchers interested in answering questions pertaining to Caribbean biogeography using explicit hypothesis testing.
Collapse
Affiliation(s)
- Sarah C Crews
- California Academy of Sciences, Institute for Biodiversity Science and Sustainability, 55 Music Concourse Drive, San Francisco, CA, 94118, USA
| | - Lauren A Esposito
- California Academy of Sciences, Institute for Biodiversity Science and Sustainability, 55 Music Concourse Drive, San Francisco, CA, 94118, USA.
| |
Collapse
|
36
|
Arias-Robledo G, Wall R, Szpila K, Shpeley D, Whitworth T, Stark T, King R, Stevens J. Ecological and geographical speciation in Lucilia bufonivora: The evolution of amphibian obligate parasitism. INTERNATIONAL JOURNAL FOR PARASITOLOGY-PARASITES AND WILDLIFE 2019; 10:218-230. [PMID: 31667085 PMCID: PMC6812060 DOI: 10.1016/j.ijppaw.2019.09.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/17/2019] [Accepted: 09/20/2019] [Indexed: 11/16/2022]
Abstract
Lucilia (Diptera: Calliphoridae) is a genus of blowflies comprised largely of saprophagous and facultative parasites of livestock. Lucilia bufonivora, however, exhibits a unique form of obligate parasitism of amphibians, typically affecting wild hosts. The evolutionary route by which amphibian myiasis arose, however, is not well understood due to the low phylogenetic resolution in existing nuclear DNA phylogenies. Furthermore, the timing of when specificity for amphibian hosts arose in L. bufonivora is also unknown. In addition, this species was recently reported for the first time in North America (Canada) and, to date, no molecular studies have analysed the evolutionary relationships between individuals from Eastern and Western hemispheres. To provide broader insights into the evolution of the amphibian parasitic life history trait and to estimate when the trait first arose, a time-scaled phylogeny was inferred from a concatenated data set comprising mtDNA, nDNA and non-coding rDNA (COX1, per and ITS2 respectively). Specimens from Canada, the UK, Poland, Switzerland, the Netherlands and Germany were analysed, as well as individuals from its sister taxa, the saprophage Lucilia silvarum and a Nearctic species also implicated in amphibian myiasis, Lucilia elongata. Obligate amphibian parasitism appears to have arisen ~4 mya, likely as a result of niche displacement of a saprophagous/facultative parasite ancestor. Consistent paraphyly of L. bufonivora with respect to L. elongata across single-gene phylogenies and high mtDNA genetic distances between Nearctic and Palearctic individuals suggest on-going cryptic speciation facilitated by geographical isolation. These findings suggest that recent reports of L. bufonivora in the Nearctic do not constitute a recent introduction, but instead suggest that it remained unrecorded due to taxonomic confusion and low abundance. This is the first study to confirm the involvement of L. bufonivora in amphibian myiasis in Canada using DNA-based identification methods. Within Lucilia, a small genus of blowflies mostly comprised of carrion-breeding species, obligate parasitism for amphibians evolved around 4 mya. Geographic isolation between Nearctic and Palearctic lineages is facilitating on-going cryptic speciation of Lucilia bufonivora. First positive identification of L. bufonivora from two confirmed cases of amphibian myiasis in North America.
Collapse
Affiliation(s)
- G. Arias-Robledo
- Biosciences, College of Life and Environmental Sciences, University of Exeter, UK
- School of Biological Sciences, University of Bristol, UK
- Corresponding author. College of Life and Environmental Sciences, University of Exeter, Prince of Wales Rd, Exeter, EX4 4PS, UK.
| | - R. Wall
- School of Biological Sciences, University of Bristol, UK
| | - K. Szpila
- Department of Ecology and Biogeography, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Toruń, Poland
| | - D. Shpeley
- E.H. Strickland Entomological Museum, Department of Biological Sciences, University of Alberta, Canada
| | - T. Whitworth
- Department of Entomology, Washington State University, Pullman, USA
| | - T. Stark
- Reptile, Amphibian and Fish Conservation Netherlands (RAVON), Nijmegen, the Netherlands
| | - R.A. King
- Biosciences, College of Life and Environmental Sciences, University of Exeter, UK
| | - J.R. Stevens
- Biosciences, College of Life and Environmental Sciences, University of Exeter, UK
| |
Collapse
|
37
|
Li H, Li J. The complete mitochondrial genome of Helophilus virgatus (Diptera: Syrphidae: Eristalinae) with a phylogenetic analysis of Syrphidae. Mitochondrial DNA B Resour 2019; 4:3106-3107. [PMID: 33365873 PMCID: PMC7706692 DOI: 10.1080/23802359.2019.1667890] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 08/30/2019] [Indexed: 11/07/2022] Open
Abstract
The complete mitochondrial genome (mitogenome) of Helophilus virgatus (Coquilletti, 1898) was sequenced. Its whole mitogenome was 15,742 bp in length, and all 37 genes were in the ancestral gene arrangement. ATN was used as start codon in most of PCGs except for ND1 and COX1, which used TTG. Besides, ATP8, ND3, ND5, and ND6 ended with an incomplete T, the others used TAA as termination codons. A phylogenetic tree based on 13 PCGs from 14 species (11 Syrphidae and 3 outgroup species) shows that Syrphinae and Eristalinae form a sister group, and supports the monophyly of Syrphidae.
Collapse
Affiliation(s)
- Hu Li
- College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
- Shaanxi Key Laboratory of Bio-resources, School of Biological Science & Engineering, Shaanxi University of Technology, Hanzhong,Shaanxi, China
| | - Juan Li
- Shaanxi Key Laboratory of Bio-resources, School of Biological Science & Engineering, Shaanxi University of Technology, Hanzhong,Shaanxi, China
| |
Collapse
|
38
|
Paulo DF, Williamson ME, Arp AP, Li F, Sagel A, Skoda SR, Sanchez-Gallego J, Vasquez M, Quintero G, Pérez de León AA, Belikoff EJ, Azeredo-Espin AML, McMillan WO, Concha C, Scott MJ. Specific Gene Disruption in the Major Livestock Pests Cochliomyia hominivorax and Lucilia cuprina Using CRISPR/Cas9. G3 (BETHESDA, MD.) 2019; 9:3045-3055. [PMID: 31340950 PMCID: PMC6723136 DOI: 10.1534/g3.119.400544] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 07/23/2019] [Indexed: 02/07/2023]
Abstract
Cochliomyia hominivorax and Lucilia cuprina are major pests of livestock. Their larvae infest warm-blooded vertebrates and feed on host's tissues, resulting in severe industry losses. As they are serious pests, considerable effort has been made to develop genomic resources and functional tools aiming to improve their management and control. Here, we report a significant addition to the pool of genome manipulation tools through the establishment of efficient CRISPR/Cas9 protocols for the generation of directed and inheritable modifications in the genome of these flies. Site-directed mutations were introduced in the C hominivorax and L cuprina yellow genes (ChY and LcY) producing lightly pigmented adults. High rates of somatic mosaicism were induced when embryos were injected with Cas9 ribonucleoprotein complexes (RNPs) pre-assembled with guide RNAs (sgRNAs) at high concentrations. Adult flies carrying disrupted yellow alleles lacked normal pigmentation (brown body phenotype) and efficiently transmitted the mutated alleles to the subsequent generation, allowing the rapid creation of homozygous strains for reverse genetics of candidate loci. We next used our established CRISPR protocol to disrupt the C hominivorax transformer gene (Chtra). Surviving females carrying mutations in the Chtra locus developed mosaic phenotypes of transformed ovipositors with characteristics of male genitalia while exhibiting abnormal reproductive tissues. The CRISPR protocol described here is a significant improvement on the existing toolkit of molecular methods in calliphorids. Our results also suggest that Cas9-based systems targeting Chtra and Lctra could be an effective means for controlling natural populations of these important pests.
Collapse
Affiliation(s)
- Daniel F Paulo
- Centre for Molecular Biology and Genetic Engineering, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas
- Laboratory of Ecological and Evolutionary Genomics, Smithsonian Tropical Research Institute, Gamboa, Panama
| | - Megan E Williamson
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh NC
| | - Alex P Arp
- USDA-ARS, Knipling-Bushland U.S. Livestock Insects Research Laboratory and Veterinary Pest Genomics Center, Kerrville TX, and
| | - Fang Li
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh NC
| | - Agustin Sagel
- USDA-ARS, Knipling-Bushland U.S. Livestock Insects Research Laboratory and Veterinary Pest Genomics Center, Screwworm Research Site, Pacora, Panama
| | - Steven R Skoda
- USDA-ARS, Knipling-Bushland U.S. Livestock Insects Research Laboratory and Veterinary Pest Genomics Center, Screwworm Research Site, Pacora, Panama
| | - Joel Sanchez-Gallego
- USDA-ARS, Knipling-Bushland U.S. Livestock Insects Research Laboratory and Veterinary Pest Genomics Center, Screwworm Research Site, Pacora, Panama
| | - Mario Vasquez
- USDA-ARS, Knipling-Bushland U.S. Livestock Insects Research Laboratory and Veterinary Pest Genomics Center, Screwworm Research Site, Pacora, Panama
| | - Gladys Quintero
- USDA-ARS, Knipling-Bushland U.S. Livestock Insects Research Laboratory and Veterinary Pest Genomics Center, Screwworm Research Site, Pacora, Panama
| | - Adalberto A Pérez de León
- USDA-ARS, Knipling-Bushland U.S. Livestock Insects Research Laboratory and Veterinary Pest Genomics Center, Kerrville TX, and
| | - Esther J Belikoff
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh NC
| | - Ana M L Azeredo-Espin
- Centre for Molecular Biology and Genetic Engineering, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas
| | - W Owen McMillan
- Laboratory of Ecological and Evolutionary Genomics, Smithsonian Tropical Research Institute, Gamboa, Panama
| | - Carolina Concha
- Laboratory of Ecological and Evolutionary Genomics, Smithsonian Tropical Research Institute, Gamboa, Panama
| | - Maxwell J Scott
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh NC
| |
Collapse
|
39
|
Pons J, Bover P, Bidegaray-Batista L, Arnedo MA. Arm-less mitochondrial tRNAs conserved for over 30 millions of years in spiders. BMC Genomics 2019; 20:665. [PMID: 31438844 PMCID: PMC6706885 DOI: 10.1186/s12864-019-6026-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 08/12/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND In recent years, Next Generation Sequencing (NGS) has accelerated the generation of full mitogenomes, providing abundant material for studying different aspects of molecular evolution. Some mitogenomes have been observed to harbor atypical sequences with bizarre secondary structures, which origins and significance could only be fully understood in an evolutionary framework. RESULTS Here we report and analyze the mitochondrial sequences and gene arrangements of six closely related spiders in the sister genera Parachtes and Harpactocrates, which belong to the nocturnal, ground dwelling family Dysderidae. Species of both genera have compacted mitogenomes with many overlapping genes and strikingly reduced tRNAs that are among the shortest described within metazoans. Thanks to the conservation of the gene order and the nucleotide identity across close relatives, we were able to predict the secondary structures even on arm-less tRNAs, which would be otherwise unattainable for a single species. They exhibit aberrant secondary structures with the lack of either DHU or TΨC arms and many miss-pairings in the acceptor arm but this degeneracy trend goes even further since at least four tRNAs are arm-less in the six spider species studied. CONCLUSIONS The conservation of at least four arm-less tRNA genes in two sister spider genera for about 30 myr suggest that these genes are still encoding fully functional tRNAs though they may be post-transcriptionally edited to be fully functional as previously described in other species. We suggest that the presence of overlapping and truncated tRNA genes may be related and explains why spider mitogenomes are smaller than those of other invertebrates.
Collapse
Affiliation(s)
- Joan Pons
- Departamento de Biodiversidad y Conservación, Instituto Mediterráneo de Estudios Avanzados (CSIC-UIB), Miquel Marquès, 21, 07190 Esporles, Illes Balears Spain
| | - Pere Bover
- ARAID Foundation – IUCA Grupo-Aragosaurus, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12 -, 50009 Zaragoza, Spain
| | - Leticia Bidegaray-Batista
- Departamento de Biodiversidad y Genética, Instituto de Investigaciones Biológicas Clemente Estable, Avenida Italia 3318, 11600 Montevideo, CP Uruguay
| | - Miquel A. Arnedo
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals & Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Av. Diagonal 643, E-8028 Barcelona, Catalonia Spain
| |
Collapse
|
40
|
Li H. Characterization and Phylogenetic Implications of the Complete Mitochondrial Genome of Syrphidae. Genes (Basel) 2019; 10:E563. [PMID: 31349702 PMCID: PMC6723807 DOI: 10.3390/genes10080563] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/19/2019] [Accepted: 07/24/2019] [Indexed: 11/16/2022] Open
Abstract
In this study, the complete mitochondrial genomes (mitogenomes) of two hoverfly species of Korinchia angustiabdomena (Huo, Ren, and Zheng) and Volucella nigricans Coquillett (Diptera: Syrphidae) were determined and analyzed. The circular mitogenomes were 16,473 bp in K. angustiabdomena (GenBank No. MK870078) and 15,724 bp in V. nigricans (GenBank No. MK870079). Two newly sequenced mitogenomes both contained 37 genes, and the gene order was similar with other syrphine species. All the protein-coding genes (PCGs) were started with the standard ATN codons; and most of PCGs were terminated with a TAA stop codon, while ND1 in K. angustiabdomena ended with a TAG codon, and ND5 terminated with truncated T stop codons in both species. The phylogenetic relationship between K. angustiabdomena and V. nigricans with related lineages was reconstructed using Bayesian inference and Maximum-likelihood analyses. The monophyly of each family considered within Muscomorpha was confirmed by the clades in the phylogenetic tree, and superfamily of the Oestroidea (Calliphoridae, Sarcophagidae, and Oestridae) was unexpectedly found to be a paraphyletic group based on our selected data. This mitogenome information for K. angustiabdomena and V. nigricans could facilitate future studies of evolutionarily related insects.
Collapse
Affiliation(s)
- Hu Li
- Shaanxi Key Laboratory of Bio-Resources, School of Biological Science & Engineering, Shaanxi University of Technology, Hanzhong 723000, China.
- College of Life Sciences, Northwest University, Xi'an 710069, China.
| |
Collapse
|
41
|
Sonet G, De Smet Y, Tang M, Virgilio M, Young AD, Skevington JH, Mengual X, Backeljau T, Liu S, Zhou X, De Meyer M, Jordaens K. First mitochondrial genomes of five hoverfly species of the genus Eristalinus (Diptera: Syrphidae). Genome 2019; 62:677-687. [PMID: 31283887 DOI: 10.1139/gen-2019-0009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The hoverfly genus Eristalinus (Diptera, Syrphidae) contains many widespread pollinators. The majority of the species of Eristalinus occur in the Afrotropics and their molecular systematics still needs to be investigated. This study presents the first complete and annotated mitochondrial genomes for five species of Eristalinus. They were obtained by high-throughput sequencing of total genomic DNA. The total length of the mitogenomes varied between 15 757 and 16 245 base pairs. Gene composition, positions, and orientation were shared across species, and were identical to those observed for other Diptera. Phylogenetic analyses (maximum likelihood and Bayesian inference) based on the 13 protein coding and both rRNA genes suggested that the subgenus Eristalinus was paraphyletic with respect to the subgenus Eristalodes. An analysis of the phylogenetic informativeness of all protein coding and rRNA genes suggested that NADH dehydrogenase subunit 5 (nad5), cytochrome c oxidase subunit 1, nad4, nad2, cytochrome b, and 16S rRNA genes are the most promising mitochondrial molecular markers to result in supported phylogenetic hypotheses of the genus. In addition to the five complete mitogenomes currently available for hoverflies, the five mitogenomes published here will be useful for broader molecular phylogenetic analyses among hoverflies.
Collapse
Affiliation(s)
- Gontran Sonet
- Royal Belgian Institute of Natural Sciences, JEMU and BopCo, Vautierstraat 29, B-1000 Brussels, Belgium
| | - Yannick De Smet
- Royal Museum for Central Africa, JEMU and BopCo, Leuvensesteenweg 13, B-3080 Tervuren, Belgium
| | - Min Tang
- Department of Entomology, China Agricultural University, Beijing 100193, China
| | - Massimiliano Virgilio
- Royal Museum for Central Africa, JEMU and BopCo, Leuvensesteenweg 13, B-3080 Tervuren, Belgium
| | - Andrew Donovan Young
- Plant Pest Diagnostics Center, California Department of Food and Agriculture, 3294 Meadowview Road, Sacramento, CA 95832, USA.,Department of Entomology and Nematology, University of California, Davis, Briggs Hall, Davis, CA 95616-5270, USA
| | - Jeffrey H Skevington
- Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri-Food Canada, K.W. Neatby Building, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada.,Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | - Ximo Mengual
- Zoologisches Forschungsmuseum Alexander Koenig, Leibniz-Institut für Biodiversität der Tiere, Adenauerallee 160, D-53113 Bonn, Germany
| | - Thierry Backeljau
- Royal Belgian Institute of Natural Sciences, JEMU and BopCo, Vautierstraat 29, B-1000 Brussels, Belgium.,University of Antwerp, Evolutionary Ecology Group, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Shanlin Liu
- China National GeneBank, BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Xin Zhou
- Department of Entomology, China Agricultural University, Beijing 100193, China
| | - Marc De Meyer
- Royal Museum for Central Africa, JEMU and BopCo, Leuvensesteenweg 13, B-3080 Tervuren, Belgium
| | - Kurt Jordaens
- Royal Museum for Central Africa, JEMU and BopCo, Leuvensesteenweg 13, B-3080 Tervuren, Belgium.,University of Antwerp, Evolutionary Ecology Group, Universiteitsplein 1, B-2610 Antwerp, Belgium
| |
Collapse
|
42
|
Tang L, Yan L, Gao Y, Zhang D. First report of mitochondrial genome from the subfamily Bengaliinae (Diptera: Calliphoridae). MITOCHONDRIAL DNA PART B 2019. [DOI: 10.1080/23802359.2019.1601037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Liping Tang
- School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Liping Yan
- School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yunyun Gao
- School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Dong Zhang
- School of Nature Conservation, Beijing Forestry University, Beijing, China
| |
Collapse
|
43
|
Kirsip H, Abroi A. Protein Structure-Guided Hidden Markov Models (HMMs) as A Powerful Method in the Detection of Ancestral Endogenous Viral Elements. Viruses 2019; 11:v11040320. [PMID: 30986983 PMCID: PMC6520822 DOI: 10.3390/v11040320] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/23/2019] [Accepted: 03/27/2019] [Indexed: 12/19/2022] Open
Abstract
It has been believed for a long time that the transfer and fixation of genetic material from RNA viruses to eukaryote genomes is very unlikely. However, during the last decade, there have been several cases in which “virus-to-host” gene transfer from various viral families into various eukaryotic phyla have been described. These transfers have been identified by sequence similarity, which may disappear very quickly, especially in the case of RNA viruses. However, compared to sequences, protein structure is known to be more conserved. Applying protein structure-guided protein domain-specific Hidden Markov Models, we detected homologues of the Virgaviridae capsid protein in Schizophora flies. Further data analysis supported “virus-to-host” transfer into Schizophora ancestors as a single transfer event. This transfer was not identifiable by BLAST or by other methods we applied. Our data show that structure-guided Hidden Markov Models should be used to detect ancestral virus-to-host transfers.
Collapse
Affiliation(s)
- Heleri Kirsip
- Department of Bioinformatics, University of Tartu, Tartu, 51010, Riia 23, Estonia.
| | - Aare Abroi
- Institute of Technology, University of Tartu, Tartu, 50411, Nooruse 1, Estonia.
| |
Collapse
|
44
|
Zhang SK, Shu JP, Wang YD, Liu YN, Peng H, Zhang W, Wang HJ. The complete mitochondrial genomes of two sibling species of camellia weevils (Coleoptera: Curculionidae) and patterns of Curculionini speciation. Sci Rep 2019; 9:3412. [PMID: 30833607 PMCID: PMC6399312 DOI: 10.1038/s41598-019-39895-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 02/01/2019] [Indexed: 11/09/2022] Open
Abstract
Complete mitochondrial genomes contain large and diverse datasets for species delineation. To better understand the divergence of the two morphologically indistinguishable weevil species in Curculionini, we first sequenced and compared their complete mitochondrial genomes. The complete mitochondrial genomes of Curculio chinensis and Curculio sp. were 19,713 bp with an A + T content of 76.61% and 19,216 bp with an A + T content of 76.85%, respectively. All 37 of the typical mitochondrial genes were determined in both species. The 13 protein sequences of the two species shared high homology (about 90%) except for ATP8 (73.08%). The differences in secondary structure of ATP8 were the number of possible proteins and nucleic acid binding sites. There were 22 and 15 mismatched base-pairs in the tRNA secondary structures from C. chinensis and Curculio sp., respectively. Maximum Likelihood and Bayesian analyses indicated that Curculio sp. is a novel species closely related to C. chinensis. The divergence time estimation suggests that Cryptorhynchinae and Curculionini lines diverged in the Cenozoic Period, while C. chinensis and Curculio sp. diverged at 6.7079 (95% CI 5-13) Mya. This study demonstrates the utility of using complete mitochondrial gene sets for phylogenetic analysis and enhances our understanding of the genetic basis for the evolution of the Curculionini.
Collapse
Affiliation(s)
- Shou-Ke Zhang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, No. 1, Dongxiaofu Xiangshan Road, Haidian District, Beijing, 100091, P. R. China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, No. 73, Daqiao Road, Fuyang District, Hangzhou, Zhejiang, 311400, P. R. China
| | - Jin-Ping Shu
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, No. 73, Daqiao Road, Fuyang District, Hangzhou, Zhejiang, 311400, P. R. China.
| | - Yang-Dong Wang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, No. 1, Dongxiaofu Xiangshan Road, Haidian District, Beijing, 100091, P. R. China.
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, No. 73, Daqiao Road, Fuyang District, Hangzhou, Zhejiang, 311400, P. R. China.
| | - Ya-Ning Liu
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, No. 73, Daqiao Road, Fuyang District, Hangzhou, Zhejiang, 311400, P. R. China
| | - Han Peng
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, No. 73, Daqiao Road, Fuyang District, Hangzhou, Zhejiang, 311400, P. R. China
| | - Wei Zhang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, No. 73, Daqiao Road, Fuyang District, Hangzhou, Zhejiang, 311400, P. R. China
| | - Hao-Jie Wang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, No. 73, Daqiao Road, Fuyang District, Hangzhou, Zhejiang, 311400, P. R. China
| |
Collapse
|
45
|
Shang Y, Ren L, Chen W, Zha L, Cai J, Dong J, Guo Y. Comparative Mitogenomic Analysis of Forensically Important Sarcophagid Flies (Diptera: Sarcophagidae) and Implications of Species Identification. JOURNAL OF MEDICAL ENTOMOLOGY 2019; 56:392-407. [PMID: 30239827 DOI: 10.1093/jme/tjy162] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Indexed: 06/08/2023]
Abstract
The flesh flies (Diptera: Sarcophagidae) are significant in forensic investigations. The mitochondrial genome (mitogeome) has been widely used as genetic markers for phylogenetic analysis and species identification. To further understand the mitogenome-level features in Sarcophagidae, the complete mitogenome of Sarcophaga formosensis (Kirneret Lopes, 1961) (Diptera: Sarcophagidae) and Sarcophaga misera (Walker, 1849) (Diptera: Sarcophagidae) was firstly sequenced, annotated, and compared with other 13 Sarcophagidae species. The result indicated that the gene arrangement, gene content, base composition, and codon usage were conserved in the ancestral arthropod. Evolutionary rate of the mitogenome fragments revealed that the nonsynonymous and synonymous substitution rates (Ka and Ks) ratio was less than 1.00, indicating these variable sites under strong purifying selection. Almost all transfer RNA genes (tRNAs) have typical clover-leaf structures within these sarcophagid mitogenomes, except tRNA-Ser (AGN) is lack of the dihydrouridine arm. This comparative mitogenomic analysis sheds light on the architecture and evolution of mitogenomes in the Sarcophagidae. Phylogenetic analyses containing the interspecific distances from different regions in these species provided us new insights into the application of these effective genetic markers for species identification of flesh flies.
Collapse
Affiliation(s)
- Yanjie Shang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - 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
| | - Lagabaiyila Zha
- 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
| | - Jianan Dong
- XiangYa school of Medicine, Central South University, Changsha, Hunan, China
| | - Yadong Guo
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| |
Collapse
|
46
|
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
| |
Collapse
|
47
|
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.
Collapse
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.
| |
Collapse
|
48
|
Huang J, Ma T. Comparative analysis of two mitochondrial genomes of flesh flies (Sarcophaga antilope and Sarcophaga dux) with phylogeny and evolutionary timescale for Sarcophagidae. Int J Biol Macromol 2018; 120:1955-1964. [DOI: 10.1016/j.ijbiomac.2018.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/29/2018] [Accepted: 10/01/2018] [Indexed: 11/28/2022]
|
49
|
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]
|
50
|
Dupuis JR, Guerrero FD, Skoda SR, Phillips PL, Welch JB, Schlater JL, Azeredo-Espin AML, Pérez de León AA, Geib SM. Molecular Characterization of the 2016 New World Screwworm (Diptera: Calliphoridae) Outbreak in the Florida Keys. JOURNAL OF MEDICAL ENTOMOLOGY 2018; 55:938-946. [PMID: 29788142 DOI: 10.1093/jme/tjy078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Indexed: 06/08/2023]
Abstract
New World screwworm (NWS), Cochliomyia hominivorax (Coquerel 1858) (Diptera: Calliphoridae), is a myiasis-causing fly that can be a serious threat to the health of livestock, wildlife, and humans. Its progressive eradication from the southern United States, Mexico, and Central America from the 1950s to 2000s is an excellent example of successful pest management using sterile insect technique (SIT). In late 2016, autochthonous NWS were detected in the Florida Keys, representing this species' first invasion in the United States in >30 yr. Rapid use of quarantine and SIT was successful in eliminating the infestation by early 2017; however, the geographic source of this infestation remains unknown. Here, we use amplicon sequencing to generate mitochondrial and nuclear sequence data representing all confirmed cases of NWS from this infestation, and compare these sequences to preexisting data sets sampling the native distribution of NWS. We ask two questions regarding the FL Keys outbreak. First, is this infestation the result of a single invasion from one source, or multiple invasions from different sources? And second, what is the geographic origin of this invasion? We found virtually no sequence variation between specimens collected from the FL Keys outbreak, which is consistent with a single source of introduction. However, we also found very little geographic resolution in any of the data sets, which precludes identification of the source of this outbreak. Our lack of success in answering our second question speaks to the need for finer-scale genetic or genomic assessments of NWS population structure, which would facilitate source determination of potential future outbreaks.
Collapse
Affiliation(s)
- Julian R Dupuis
- U.S. Department of Agriculture-Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, HI
- Department of Plant and Environmental Protection Services, University of Hawaii at Manoa, Honolulu, HI
| | - Felix D Guerrero
- USDA-ARS, Knipling-Bushland U.S. Livestock Insects Research Laboratory and Veterinary Pest Genomics Center, Kerrville, TX
| | - Steven R Skoda
- USDA-ARS, Knipling-Bushland U.S. Livestock Insects Research Laboratory and Veterinary Pest Genomics Center, Kerrville, TX
| | - Pamela L Phillips
- USDA-ARS, Knipling-Bushland U.S. Livestock Insects Research Laboratory and Veterinary Pest Genomics Center, Kerrville, TX
| | - John B Welch
- USDA-APHIS, International Services, Action Programs, College Station, TX
| | - Jack L Schlater
- USDA-APHIS, National Veterinary Services Laboratory, Ames, IA
| | - Ana Maria L Azeredo-Espin
- Centro de Biologia Molecular e Engenharia Genética and Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas Instituto de Biologia, São Paulo, Brazil
| | - Adalberto A Pérez de León
- USDA-ARS, Knipling-Bushland U.S. Livestock Insects Research Laboratory and Veterinary Pest Genomics Center, Kerrville, TX
| | - Scott M Geib
- U.S. Department of Agriculture-Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, HI
| |
Collapse
|