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He R, Wang S, Li Q, Wang Z, Mei Y, Li F. Phylogenomic analysis and molecular identification of true fruit flies. Front Genet 2024; 15:1414074. [PMID: 38974385 PMCID: PMC11224437 DOI: 10.3389/fgene.2024.1414074] [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: 04/08/2024] [Accepted: 05/30/2024] [Indexed: 07/09/2024] Open
Abstract
The family Tephritidae in the order Diptera, known as true fruit flies, are agriculturally important insect pests. However, the phylogenetic relationships of true fruit flies, remain controversial. Moreover, rapid identification of important invasive true fruit flies is essential for plant quarantine but is still challenging. To this end, we sequenced the genome of 16 true fruit fly species at coverage of 47-228×. Together with the previously reported genomes of nine species, we reconstructed phylogenetic trees of the Tephritidae using benchmarking universal single-copy ortholog (BUSCO), ultraconserved element (UCE) and anchored hybrid enrichment (AHE) gene sets, respectively. The resulting trees of 50% taxon-occupancy dataset for each marker type were generally congruent at 88% nodes for both concatenation and coalescent analyses. At the subfamily level, both Dacinae and Trypetinae are monophyletic. At the species level, Bactrocera dorsalis is more closely related to Bactrocera latifrons than Bactrocera tryoni. This is inconsistent with previous conclusions based on mitochondrial genes but consistent with recent studies based on nuclear data. By analyzing these genome data, we screened ten pairs of species-specific primers for molecular identification of ten invasive fruit flies, which PCR validated. In summary, our work provides draft genome data of 16 true fruit fly species, addressing the long-standing taxonomic controversies and providing species-specific primers for molecular identification of invasive fruit flies.
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Affiliation(s)
- Rong He
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Shuping Wang
- Technical Centre for Animal, Plant and Food Inspection and Quarantine, Shanghai Customs, Shanghai, China
| | - Qiang Li
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Zuoqi Wang
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yang Mei
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Fei Li
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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Skojec C, Earl C, Couch CD, Masonick P, Kawahara AY. Phylogeny and divergence time estimation of Io moths and relatives (Lepidoptera: Saturniidae: Automeris). PeerJ 2024; 12:e17365. [PMID: 38827314 PMCID: PMC11144400 DOI: 10.7717/peerj.17365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 04/18/2024] [Indexed: 06/04/2024] Open
Abstract
The saturniid moth genus Automeris includes 145 described species. Their geographic distribution ranges from the eastern half of North America to as far south as Peru. Automeris moths are cryptically colored, with forewings that resemble dead leaves, and conspicuously colored, elaborate eyespots hidden on their hindwings. Despite their charismatic nature, the evolutionary history and relationships within Automeris and between closely related genera, remain poorly understood. In this study, we present the most comprehensive phylogeny of Automeris to date, including 80 of the 145 described species. We also incorporate two morphologically similar hemileucine genera, Pseudautomeris and Leucanella, as well as a morphologically distinct genus, Molippa. We obtained DNA data from both dry-pinned and ethanol-stored museum specimens and conducted Anchored Hybrid Enrichment (AHE) sequencing to assemble a high-quality dataset for phylogenetic analysis. The resulting phylogeny supports Automeris as a paraphyletic genus, with Leucanella and Pseudautomeris nested within, with the most recent common ancestor dating back to 21 mya. This study lays the foundation for future research on various aspects of Automeris biology, including geographical distribution patterns, potential drivers of speciation, and ecological adaptations such as antipredator defense mechanisms.
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Affiliation(s)
- Chelsea Skojec
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, United States of America
- Department of Biology, University of Florida, Gainesville, FL, United States of America
| | - Chandra Earl
- Bishop Museum, Bernice Pauahi, Honolulu, HI, United States of America
| | - Christian D. Couch
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, United States of America
- Department of Biology, University of Florida, Gainesville, FL, United States of America
| | - Paul Masonick
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, United States of America
| | - Akito Y. Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, United States of America
- Department of Biology, University of Florida, Gainesville, FL, United States of America
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Li X, Breinholt JW, Martinez JI, Keegan K, Ellis EA, Homziak NT, Zwick A, Storer CG, McKenna D, Kawahara AY. Large-scale genomic data reveal the phylogeny and evolution of owlet moths (Noctuoidea). Cladistics 2024; 40:21-33. [PMID: 37787424 DOI: 10.1111/cla.12559] [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: 04/21/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 10/04/2023] Open
Abstract
The owlet moths (Noctuoidea; ~43-45K described species) are one of the most ecologically diverse and speciose superfamilies of animals. Moreover, they comprise some of the world's most notorious pests of agriculture and forestry. Despite their contributions to terrestrial biodiversity and impacts on ecosystems and economies, the evolutionary history of Noctuoidea remains unclear because the superfamily lacks a statistically robust phylogenetic and temporal framework. We reconstructed the phylogeny of Noctuoidea using data from 1234 genes (946.4 kb nucleotides) obtained from the genome and transcriptome sequences of 76 species. The relationships among the six families of Noctuoidea were well resolved and consistently recovered based on both concatenation and gene coalescence approaches, supporting the following relationships: Oenosandridae + (Notodontidae + (Erebidae + (Nolidae + (Euteliidae + Noctuidae)))). A Yule tree prior with three unlinked molecular clocks was identified as the preferred BEAST analysis using marginal-likelihood estimations. The crown age of Noctuoidea was estimated at 74.5 Ma, with most families originating before the end of the Paleogene (23 Ma). Our study provides the first statistically robust phylogenetic and temporal framework for Noctuoidea, including all families of owlet moths, based on large-scale genomic data.
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Affiliation(s)
- Xuankun Li
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biological Sciences, University of Memphis, Memphis, TN, 38152, USA
- Center for Biodiversity Research, University of Memphis, Memphis, TN, 38152, USA
| | - Jesse W Breinholt
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Precision Genomics, Intermountain Healthcare, St George, UT, 84790, USA
| | - Jose I Martinez
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Entomology and Nematology Department, University of Florida, Gainesville, FL, 32608, USA
| | - Kevin Keegan
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06268, USA
- Section of Invertebrate Zoology, Carnegie Museum of Natural History, 4400 Forbes Ave, Pittsburgh, PA, 15213-4080, USA
| | - Emily A Ellis
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Nicholas T Homziak
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Andreas Zwick
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT, 2601, Australia
| | - Caroline G Storer
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Duane McKenna
- Department of Biological Sciences, University of Memphis, Memphis, TN, 38152, USA
- Center for Biodiversity Research, University of Memphis, Memphis, TN, 38152, USA
| | - Akito Y Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Entomology and Nematology Department, University of Florida, Gainesville, FL, 32608, USA
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Nunes R, Storer C, Doleck T, Kawahara AY, Pierce NE, Lohman DJ. Predictors of sequence capture in a large-scale anchored phylogenomics project. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.943361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023] Open
Abstract
Next-generation sequencing (NGS) technologies have revolutionized phylogenomics by decreasing the cost and time required to generate sequence data from multiple markers or whole genomes. Further, the fragmented DNA of biological specimens collected decades ago can be sequenced with NGS, reducing the need for collecting fresh specimens. Sequence capture, also known as anchored hybrid enrichment, is a method to produce reduced representation libraries for NGS sequencing. The technique uses single-stranded oligonucleotide probes that hybridize with pre-selected regions of the genome that are sequenced via NGS, culminating in a dataset of numerous orthologous loci from multiple taxa. Phylogenetic analyses using these sequences have the potential to resolve deep and shallow phylogenetic relationships. Identifying the factors that affect sequence capture success could save time, money, and valuable specimens that might be destructively sampled despite low likelihood of sequencing success. We investigated the impacts of specimen age, preservation method, and DNA concentration on sequence capture (number of captured sequences and sequence quality) while accounting for taxonomy and extracted tissue type in a large-scale butterfly phylogenomics project. This project used two probe sets to extract 391 loci or a subset of 13 loci from over 6,000 butterfly specimens. We found that sequence capture is a resilient method capable of amplifying loci in samples of varying age (0–111 years), preservation method (alcohol, papered, pinned), and DNA concentration (0.020 ng/μl - 316 ng/ul). Regression analyses demonstrate that sequence capture is positively correlated with DNA concentration. However, sequence capture and DNA concentration are negatively correlated with sample age and preservation method. Our findings suggest that sequence capture projects should prioritize the use of alcohol-preserved samples younger than 20 years old when available. In the absence of such specimens, dried samples of any age can yield sequence data, albeit with returns that diminish with increasing age.
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Ghanavi HR, Twort V, Hartman TJ, Zahiri R, Wahlberg N. The (non) accuracy of mitochondrial genomes for family‐level phylogenetics in Erebidae (Lepidoptera). ZOOL SCR 2022. [DOI: 10.1111/zsc.12559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hamid Reza Ghanavi
- Systematic Biology Group, Biology Department Lund University Lund Sweden
| | - Victoria Twort
- Systematic Biology Group, Biology Department Lund University Lund Sweden
- Zoology Unit, The Finnish Museum of Natural History Luomus University of Helsinki Helsinki Finland
| | | | - Reza Zahiri
- Center of Natural History University of Hamburg Hamburg Germany
- Ottawa Plant Laboratory, Canadian Food Inspection Agency Entomology Diagnostic Laboratory Ottawa Ontario Canada
| | - Niklas Wahlberg
- Systematic Biology Group, Biology Department Lund University Lund Sweden
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Davis RB, Õunap E, Tammaru T. A supertree of Northern European macromoths. PLoS One 2022; 17:e0264211. [PMID: 35180261 PMCID: PMC8856531 DOI: 10.1371/journal.pone.0264211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 02/05/2022] [Indexed: 11/19/2022] Open
Abstract
Ecological and life-history data on the Northern European macromoth (Lepidoptera: Macroheterocera) fauna is widely available and ideal for use in answering phylogeny-based research questions: for example, in comparative biology. However, phylogenetic information for such studies lags behind. Here, as a synthesis of all currently available phylogenetic information on the group, we produce a supertree of 114 Northern European macromoth genera (in four superfamilies, with Geometroidea considered separately), providing the most complete phylogenetic picture of this fauna available to date. In doing so, we assess those parts of the phylogeny that are well resolved and those that are uncertain. Furthermore, we identify those genera for which phylogenetic information is currently too poor to include in such a supertree, or entirely absent, as targets for future work. As an aid to studies involving these genera, we provide information on their likely positions within the macromoth tree. With phylogenies playing an ever more important role in the field, this supertree should be useful in informing future ecological and evolutionary studies.
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Affiliation(s)
- Robert B. Davis
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Erki Õunap
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Toomas Tammaru
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
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Organization and phylogenetic relationships of the mitochondrial genomes of Speiredonia retorta and other lepidopteran insects. Sci Rep 2021; 11:2957. [PMID: 33536496 PMCID: PMC7859238 DOI: 10.1038/s41598-021-82561-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/21/2021] [Indexed: 11/08/2022] Open
Abstract
In this study, we analyzed the complete mitochondrial genome (mitogenome) of Speiredonia retorta, which is a pest and a member of the Lepidoptera order. In total, the S. retorta mitogenome was found to contain 15,652 base pairs encoding 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, as well as an adenine (A) + thymine (T)-rich region. These findings were consistent with the mitogenome composition of other lepidopterans, as we identified all 13 PCGs beginning at ATN codons. We also found that 11 PCGs terminated with canonical stop codons, whereas cox2 and nad4 exhibited incomplete termination codons. By analyzing the mitogenome of S. retorta using Bayesian inference (BI) and maximum likelihood (ML) models, we were able to further confirm that this species is a member of the Erebidae family.
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Toussaint EFA, Ellis EA, Gott RJ, Warren AD, Dexter KM, Storer C, Lohman DJ, Kawahara AY. Historical biogeography of Heteropterinae skippers via Beringian and post‐Tethyan corridors. ZOOL SCR 2020. [DOI: 10.1111/zsc.12457] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Emmanuel F. A. Toussaint
- Natural History Museum of Geneva Geneva Switzerland
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History University of Florida Gainesville FL USA
| | - Emily A. Ellis
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History University of Florida Gainesville FL USA
| | - Riley J. Gott
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History University of Florida Gainesville FL USA
| | - Andrew D. Warren
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History University of Florida Gainesville FL USA
| | - Kelly M. Dexter
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History University of Florida Gainesville FL USA
| | - Caroline Storer
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History University of Florida Gainesville FL USA
| | - David J. Lohman
- Biology Department City College of New YorkCity University of New York New York NY USA
- Ph.D. Program in Biology, Graduate Center City University of New York New York NY USA
- Entomology Section National Museum of Natural History Manila Philippines
| | - Akito Y. Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History University of Florida Gainesville FL USA
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