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Zhang Y, Liu S, De Meyer M, Liao Z, Zhao Y, Virgilio M, Feng S, Qin Y, Singh S, Wee SL, Jiang F, Guo S, Li H, Deschepper P, Vanbergen S, Delatte H, van Sauers-Muller A, Syamsudin TS, Kawi AP, Kasina M, Badji K, Said F, Liu L, Zhao Z, Li Z. Genomes of the cosmopolitan fruit pest Bactrocera dorsalis (Diptera: Tephritidae) reveal its global invasion history and thermal adaptation. J Adv Res 2023; 53:61-74. [PMID: 36574947 PMCID: PMC10658297 DOI: 10.1016/j.jare.2022.12.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 11/29/2022] [Accepted: 12/19/2022] [Indexed: 12/26/2022] Open
Abstract
INTRODUCTION The oriental fruit fly Bactrocera dorsalis is one of the most destructive agricultural pests worldwide, with highly debated species delimitation, origin, and global spread routes. OBJECTIVES Our study intended to (i) resolve the taxonomic uncertainties between B. dorsalis and B. carambolae, (ii) reveal the population structure and global invasion routes of B. dorsalis across Asia, Africa, and Oceania, and (iii) identify genomic regions that are responsible for the thermal adaptation of B. dorsalis. METHODS Based on a high-quality chromosome-level reference genome assembly, we explored the population relationship using a genome-scale single nucleotide polymorphism dataset generated from the resequencing data of 487 B. dorsalis genomes and 25 B. carambolae genomes. Genome-wide association studies and silencing using RNA interference were used to identify and verify the candidate genes associated with extreme thermal stress. RESULTS We showed that B. dorsalis originates from the Southern India region with three independent invasion and spread routes worldwide: (i) from Northern India to Northern Southeast Asia, then to Southern Southeast Asia; (ii) from Northern India to Northern Southeast Asian, then to China and Hawaii; and (iii) from Southern India toward the African mainland, then to Madagascar, which is mainly facilitated by human activities including trade and immigration. Twenty-seven genes were identified by a genome-wide association study to be associated with 11 temperature bioclimatic variables. The Cyp6a9 gene may enhance the thermal adaptation of B. dorsalis and thus boost its invasion, which tended to be upregulated at a hardening temperature of 38 °C. Functional verification using RNA interference silencing against Cyp6a9, led to the specific decrease in Cyp6a9 expression, reducing the survival rate of dsRNA-feeding larvae exposed to extreme thermal stress of 45 °C after heat hardening treatments in B. dorsalis. CONCLUSION This study provides insights into the evolutionary history and genetic basis of temperature adaptation in B. dorsalis.
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Affiliation(s)
- Yue Zhang
- College of Plant Protection, China Agricultural University, Beijing 100193, China; Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Shanlin Liu
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Marc De Meyer
- Royal Museum for Central Africa, Invertebrates Section and JEMU, Tervuren B3080, Belgium
| | - Zuxing Liao
- College of Plant Protection, China Agricultural University, Beijing 100193, China; Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Yan Zhao
- College of Plant Protection, China Agricultural University, Beijing 100193, China; Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Massimiliano Virgilio
- Royal Museum for Central Africa, Invertebrates Section and JEMU, Tervuren B3080, Belgium
| | - Shiqian Feng
- College of Plant Protection, China Agricultural University, Beijing 100193, China; Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Yujia Qin
- College of Plant Protection, China Agricultural University, Beijing 100193, China; Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Sandeep Singh
- Department of Fruit Science, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Suk Ling Wee
- Centre for Insect Systematics, Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor Darul Ehsan, Malaysia
| | - Fan Jiang
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Shaokun Guo
- College of Plant Protection, China Agricultural University, Beijing 100193, China; Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Hu Li
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Pablo Deschepper
- Royal Museum for Central Africa, Invertebrates Section and JEMU, Tervuren B3080, Belgium
| | - Sam Vanbergen
- Royal Museum for Central Africa, Invertebrates Section and JEMU, Tervuren B3080, Belgium
| | | | | | - Tati Suryati Syamsudin
- School of Life Science and Technology, Bandung Institute of Technology, Bandung 40132, Indonesia
| | | | - Muo Kasina
- Apiculture Research Institute, P.O. Box 32-40302, Marigat, Kenya
| | - Kemo Badji
- Crop Protection Directorate, Dakar, Senegal
| | - Fazal Said
- Department of Agriculture, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Mardan, Pakistan
| | - Lijun Liu
- College of Plant Protection, China Agricultural University, Beijing 100193, China; Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Zihua Zhao
- College of Plant Protection, China Agricultural University, Beijing 100193, China; Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Zhihong Li
- College of Plant Protection, China Agricultural University, Beijing 100193, China; Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, Beijing 100193, China.
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Aguirre-Ramirez E, Velasco-Cuervo S, Toro-Perea N. Genomic Traces of the Fruit Fly Anastrepha obliqua Associated with Its Polyphagous Nature. INSECTS 2021; 12:1116. [PMID: 34940204 PMCID: PMC8704581 DOI: 10.3390/insects12121116] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/24/2021] [Accepted: 11/27/2021] [Indexed: 12/23/2022]
Abstract
Anastrepha obliqua (Macquart) (Diptera: Tephritidae) is an important pest in the neotropical region. It is considered a polyphagous insect, meaning it infests plants of different taxonomic families and readily colonizes new host plants. The change to new hosts can lead to diversification and the formation of host races. Previous studies investigating the effect of host plants on population structure and selection in Anastrepha obliqua have focused on the use of data from the mitochondrial DNA sequence and microsatellite markers of nuclear DNA, and there are no analyses at the genomic level. To better understand this issue, we used a pooled restriction site-associated DNA sequencing (pooled RAD-seq) approach to assess genomic differentiation and population structure across sympatric populations of Anastrepha obliqua that infest three host plants-Spondias purpurea (red mombin), Mangifera indica (mango) of the family Anacardiaceae and Averrhoa carambola (carambola) of the family Oxalidaceae-in sympatric populations of the species Anastrepha obliqua of Inter-Andean Valley of the Cauca River in southwestern Colombia. Our results show genomic differentiation of populations from carambola compared to mango and red mombin populations, but the genetic structure was mainly established by geography rather than by the host plant. On the other hand, we identified 54 SNPs in 23 sequences significantly associated with the use of the host plant. Of these 23 sequences, we identified 17 candidate genes and nine protein families, of which four protein families are involved in the nutrition of these flies. Future studies should investigate the adaptive processes undergone by phytophagous insects in the Neotropics, using fruit flies as a model and state-of-the-art molecular tools.
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Affiliation(s)
- Elkin Aguirre-Ramirez
- Grupo de Estudios Ecogenéticos y Biología Molecular, Departamento de Biología, Universidad del Valle, Cali 760032, Colombia; (S.V.-C.); (N.T.-P.)
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Morrow JL, Riegler M. Genome analyses of four Wolbachia strains and associated mitochondria of Rhagoletis cerasi expose cumulative modularity of cytoplasmic incompatibility factors and cytoplasmic hitchhiking across host populations. BMC Genomics 2021; 22:616. [PMID: 34388986 PMCID: PMC8361831 DOI: 10.1186/s12864-021-07906-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/20/2021] [Indexed: 11/16/2022] Open
Abstract
Background The endosymbiont Wolbachia can manipulate arthropod reproduction and invade host populations by inducing cytoplasmic incompatibility (CI). Some host species are coinfected with multiple Wolbachia strains which may have sequentially invaded host populations by expressing different types of modular CI factor (cif) genes. The tephritid fruit fly Rhagoletis cerasi is a model for CI and Wolbachia population dynamics. It is associated with at least four Wolbachia strains in various combinations, with demonstrated (wCer2, wCer4), predicted (wCer1) or unknown (wCer5) CI phenotypes. Results We sequenced and assembled the draft genomes of the Wolbachia strains wCer1, wCer4 and wCer5, and compared these with the previously sequenced genome of wCer2 which currently invades R. cerasi populations. We found complete cif gene pairs in all strains: four pairs in wCer2 (three Type I; one Type V), two pairs in wCer1 (both Type I) and wCer4 (one Type I; one Type V), and one pair in wCer5 (Type IV). Wolbachia genome variant analyses across geographically and genetically distant host populations revealed the largest diversity of single nucleotide polymorphisms (SNPs) in wCer5, followed by wCer1 and then wCer2, indicative of their different lengths of host associations. Furthermore, mitogenome analyses of the Wolbachia genome-sequenced individuals in combination with SNP data from six European countries revealed polymorphic mitogenome sites that displayed reduced diversity in individuals infected with wCer2 compared to those without. Conclusions Coinfections with Wolbachia are common in arthropods and affect options for Wolbachia-based management strategies of pest and vector species already infected by Wolbachia. Our analyses of Wolbachia genomes of a host naturally coinfected by several strains unravelled signatures of the evolutionary dynamics in both Wolbachia and host mitochondrial genomes as a consequence of repeated invasions. Invasion of already infected populations by new Wolbachia strains requires new sets of functionally different cif genes and thereby may select for a cumulative modularity of cif gene diversity in invading strains. Furthermore, we demonstrated at the mitogenomic scale that repeated CI-driven Wolbachia invasions of hosts result in reduced mitochondrial diversity and hitchhiking effects. Already resident Wolbachia strains may experience similar cytoplasmic hitchhiking effects caused by the invading Wolbachia strain. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07906-6.
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Affiliation(s)
- Jennifer L Morrow
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Markus Riegler
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia.
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Ruiz-Montoya L, Vallejo RV, Haymer D, Liedo P. Genetic and Ecological Relationships of Anastrepha ludens (Diptera: Tephritidae) Populations in Southern Mexico. INSECTS 2020; 11:E815. [PMID: 33227892 PMCID: PMC7699260 DOI: 10.3390/insects11110815] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 11/02/2020] [Accepted: 11/08/2020] [Indexed: 01/16/2023]
Abstract
Knowledge of the influence of evolutionary factors that promote either the differentiation or cohesion of pest insect populations is critical for the improvement of control strategies. Here, we explore the extent to which genetic differentiation occurs between populations of the Mexican fruit fly, Anastrepha ludens, in association with four plant hosts (Citrus sinensis, C. paradisi, Mangifera indica and Casimiroa edulis) in the Soconusco region of Chiapas (Mexico). Using variants from six enzymatic loci, we obtained measures of genetic diversity for three sample arrangements: (1) by sex per locality, (2) by locality and (3) by host. The extent of genetic differentiation in populations was assessed using the Analyses of Molecular Variance (AMOVA) method for each array of samples, and moderate to high levels of genetic variation were observed between the sexes, as well as among localities and host plants. A Bayesian approach was then used to assess any population structure underlying the genetic data we obtained, but this analysis showed no significant structuring due to locality or host plant. We also considered whether the observed genotypic frequencies in male and females matched those expected under a hypothesis of random mating. Here we found significant deviations from expected genotypic frequencies, suggesting that sexual selection is acting on these populations. Overall, our results indicate that sexual selection, along with the presence of some heterogeneity in environments provided by both geographical factors and availability of host plants, has influenced the evolution of pest populations in this region of Mexico. Implications for area-wide pest management strategies are discussed.
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Affiliation(s)
- Lorena Ruiz-Montoya
- Departamento de Conservación de la Biodiversidad, El Colegio de la Frontera sur (ECOSUR), Carretera Panamericana y Periférico Sur s/n, San Cristóbal de las Casas, Chiapas 29290, Mexico;
| | - Rodrigo Verónica Vallejo
- Departamento de Conservación de la Biodiversidad, El Colegio de la Frontera sur (ECOSUR), Carretera Panamericana y Periférico Sur s/n, San Cristóbal de las Casas, Chiapas 29290, Mexico;
| | - David Haymer
- Department of Cell and Molecular Biology, 1960 East-West Rd, Biomed T511, University of Hawaii, Honolulu, HI 96822, USA;
| | - Pablo Liedo
- Departamento de Agricultura, Sociedad y Ambiente, El Colegio e la Frontera Sur (ECOSUR), Carretera Antiguo Aeropuerto km 2.5, Tapachula, Chiapas 30700, Mexico;
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Bakovic V, Schebeck M, Stauffer C, Schuler H. Wolbachia-Mitochondrial DNA Associations in Transitional Populations of Rhagoletis cerasi. INSECTS 2020; 11:E675. [PMID: 33027888 PMCID: PMC7650823 DOI: 10.3390/insects11100675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/25/2020] [Accepted: 10/03/2020] [Indexed: 12/13/2022]
Abstract
The endosymbiont Wolbachia can manipulate arthropod host reproduction by inducing cytoplasmic incompatibility (CI), which results in embryonic mortality when infected males mate with uninfected females. A CI-driven invasion of Wolbachia can result in a selective sweep of associated mitochondrial haplotype. The co-inheritance of Wolbachia and host mitochondrial DNA can therefore provide significant information on the dynamics of an ongoing Wolbachia invasion. Therefore, transition zones (i.e., regions where a Wolbachia strain is currently spreading from infected to uninfected populations) represent an ideal area to investigate the relationship between Wolbachia and host mitochondrial haplotype. Here, we studied Wolbachia-mitochondrial haplotype associations in the European cherry fruit fly, Rhagoletis cerasi, in two transition zones in the Czech Republic and Hungary, where the CI-inducing strain wCer2 is currently spreading. The wCer2-infection status of 881 individuals was compared with the two known R. cerasi mitochondrial haplotypes, HT1 and HT2. In accordance with previous studies, wCer2-uninfected individuals were associated with HT1, and wCer2-infected individuals were mainly associated with HT2. We found misassociations only within the transition zones, where HT2 flies were wCer2-uninfected, suggesting the occurrence of imperfect maternal transmission. We did not find any HT1 flies that were wCer2-infected, suggesting that Wolbachia was not acquired horizontally. Our study provides new insights into the dynamics of the early phase of a Wolbachia invasion.
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Affiliation(s)
- Vid Bakovic
- Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences Vienna, BOKU, Peter-Jordan-Strasse 82/I, A-1190 Vienna, Austria; (M.S.); (C.S.)
| | - Martin Schebeck
- Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences Vienna, BOKU, Peter-Jordan-Strasse 82/I, A-1190 Vienna, Austria; (M.S.); (C.S.)
| | - Christian Stauffer
- Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences Vienna, BOKU, Peter-Jordan-Strasse 82/I, A-1190 Vienna, Austria; (M.S.); (C.S.)
| | - Hannes Schuler
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Universitätsplatz 5, I-39100 Bozen-Bolzano, Italy;
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Poveda-Martínez D, Aguirre MB, Logarzo G, Hight SD, Triapitsyn S, Diaz-Sotero H, Diniz Vitorino M, Hasson E. Species complex diversification by host plant use in an herbivorous insect: The source of Puerto Rican cactus mealybug pest and implications for biological control. Ecol Evol 2020; 10:10463-10480. [PMID: 33072273 PMCID: PMC7548167 DOI: 10.1002/ece3.6702] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 01/06/2023] Open
Abstract
Cryptic taxa have often been observed in the form of host‐associated species that diverged as the result of adaptation to alternate host plants. Untangling cryptic diversity in species complexes that encompass invasive species is a mandatory task for pest management. Moreover, investigating the evolutionary history of a species complex may help to understand the drivers of their diversification. The mealybug Hypogeococcus pungens was believed to be a polyphagous species from South America and has been reported as a pest devastating native cacti in Puerto Rico, also threatening cactus diversity in the Caribbean and North America. There is neither certainty about the identity of the pest nor the source population from South America. Recent studies pointed to substantial genetic differentiation among local populations, suggesting that H. pungens is a species complex. In this study, we used a combination of genome‐wide SNPs and mtDNA variation to investigate species diversity within H. pungens sensu lato to establish host plant ranges of each one of the putative members of the complex, to evaluate whether the pattern of host plant association drove diversification in the species complex, and to determine the source population of the Puerto Rican cactus pest. Our results suggested that H. pungens comprises at least five different species, each one strongly associated with specific host plants. We also established that the Puerto Rican cactus pest derives from southeastern Brazilian mealybugs. This is an important achievement because it will help to design reliable strategies for biological control using natural enemies of the pest from its native range.
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Affiliation(s)
- Daniel Poveda-Martínez
- Fundación para el Estudio de Especies Invasivas (FuEDEI) Hurlingham Argentina.,Instituto de Ecología Genética y Evolución de Buenos Aires (IEGEBA) Departamento de Ecología Genética y Evolución Universidad de Buenos Aires Buenos Aires Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Ciudad Autónoma de Buenos Aires Argentina.,Grupo de investigación en Evolución, Ecología y Conservación (EECO) Universidad del Quindío Armenia Colombia
| | - María Belén Aguirre
- Fundación para el Estudio de Especies Invasivas (FuEDEI) Hurlingham Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Ciudad Autónoma de Buenos Aires Argentina
| | - Guillermo Logarzo
- Fundación para el Estudio de Especies Invasivas (FuEDEI) Hurlingham Argentina
| | | | | | - Hilda Diaz-Sotero
- Caribbean Advisor to the APHIS Administrator USDA San Juan Puerto Rico
| | - Marcelo Diniz Vitorino
- Departamento de Engenharia Florestal Programa de Pós-graduação em Engenharia Florestal - PPGEF Lab. de Monitoramento e Proteção Florestal - LAMPF Universidade Regional de Blumenau - FURB Blumenau Brazil
| | - Esteban Hasson
- Instituto de Ecología Genética y Evolución de Buenos Aires (IEGEBA) Departamento de Ecología Genética y Evolución Universidad de Buenos Aires Buenos Aires Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Ciudad Autónoma de Buenos Aires Argentina
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Bakovic V, Schuler H, Schebeck M, Feder JL, Stauffer C, Ragland GJ. Host plant-related genomic differentiation in the European cherry fruit fly, Rhagoletis cerasi. Mol Ecol 2019; 28:4648-4666. [PMID: 31495015 PMCID: PMC6899720 DOI: 10.1111/mec.15239] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 08/29/2019] [Accepted: 08/30/2019] [Indexed: 12/13/2022]
Abstract
Elucidating the mechanisms and conditions facilitating the formation of biodiversity are central topics in evolutionary biology. A growing number of studies imply that divergent ecological selection may often play a critical role in speciation by counteracting the homogenising effects of gene flow. Several examples involve phytophagous insects, where divergent selection pressures associated with host plant shifts may generate reproductive isolation, promoting speciation. Here, we use ddRADseq to assess the population structure and to test for host‐related genomic differentiation in the European cherry fruit fly, Rhagoletis cerasi (L., 1758) (Diptera: Tephritidae). This tephritid is distributed throughout Europe and western Asia, and has adapted to two different genera of host plants, Prunus spp. (cherries) and Lonicera spp. (honeysuckle). Our data imply that geographic distance and geomorphic barriers serve as the primary factors shaping genetic population structure across the species range. Locally, however, flies genetically cluster according to host plant, with consistent allele frequency differences displayed by a subset of loci between Prunus and Lonicera flies across four sites surveyed in Germany and Norway. These 17 loci display significantly higher FST values between host plants than others. They also showed high levels of linkage disequilibrium within and between Prunus and Lonicera flies, supporting host‐related selection and reduced gene flow. Our findings support the existence of sympatric host races in R. cerasi embedded within broader patterns of geographic variation in the fly, similar to the related apple maggot, Rhagoletis pomonella, in North America.
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Affiliation(s)
- Vid Bakovic
- Department of Forest and Soil Sciences, BOKU, University of Natural Resources and Life Sciences Vienna, Vienna, Austria.,Department of Biology, IFM, University of Linköping, Linköping, Sweden
| | - Hannes Schuler
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Bolzano, Italy
| | - Martin Schebeck
- Department of Forest and Soil Sciences, BOKU, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Christian Stauffer
- Department of Forest and Soil Sciences, BOKU, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Gregory J Ragland
- Department of Integrative Biology, University of Colorado-Denver, Denver, CO, USA
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