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Wang S, Li Y, Jiang K, Zhou J, Chen J, Liang J, Ndoni A, Xue H, Ye Z, Bu W. Identifying a potentially invasive population in the native range of a species: The enlightenment from the phylogeography of the yellow spotted stink bug, Erthesina fullo (Hemiptera: Pentatomidae). Mol Phylogenet Evol 2024; 195:108056. [PMID: 38493987 DOI: 10.1016/j.ympev.2024.108056] [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: 11/28/2023] [Revised: 02/15/2024] [Accepted: 03/09/2024] [Indexed: 03/19/2024]
Abstract
The yellow spotted stink bug (YSSB), Erthesina fullo (Thunberg, 1783) is an important Asian pest that has recently successfully invaded Europe and an excellent material for research on the initial stage of biological invasion. Here, we reported the native evolutionary history, recent invasion history, and potential invasion threats of YSSB for the first time based on population genetic methods [using double digest restriction-site associated DNA (ddRAD) data and mitochondrial COI and CYTB] and ecological niche modelling. The results showed that four lineages (east, west, southwest, and Hainan Island) were established in the native range with a strong east-west differentiation phylogeographical structure, and the violent climate fluctuation might cause population divergence during the Middle and Upper Pleistocene. In addition, land bridges and monsoon promote dispersal and directional genetic exchanging between island populations and neighboring continental populations. The east lineage (EA) was identified as the source of invasion in Albania. EA had the widest geographical distribution among all other lineages, with a star-like haplotype network with the main haplotype as the core. It also had a rapid population expansion history, indicating that the source lineage might have stronger diffusion ability and adaptability. Our findings provided a significant biological basis for fine tracking of invasive source at the lineage or population level and promote early invasion warning of potential invasive species on a much subtler lineage level.
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Affiliation(s)
- Shujing Wang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Yanfei Li
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Kun Jiang
- School of Ecology and Environment, Anhui Normal University, Wuhu 241002, PR China
| | - Jiayue Zhou
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Juhong Chen
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Jingyu Liang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | | | - Huaijun Xue
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, PR China.
| | - Zhen Ye
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, PR China.
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, PR China.
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Dai JX, Cao LJ, Chen JC, Yang F, Shen XJ, Ma LJ, Hoffmann AA, Chen M, Wei SJ. Testing for adaptive changes linked to range expansion following a single introduction of the fall webworm. Mol Ecol 2024; 33:e17038. [PMID: 37277936 DOI: 10.1111/mec.17038] [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: 12/30/2022] [Accepted: 05/24/2023] [Indexed: 06/07/2023]
Abstract
Adaptive evolution following colonization can affect the impact of invasive species. The fall webworm (FWW) invaded China 40 years ago through a single introduction event involving a severe bottleneck and subsequently diverged into two genetic groups. The well-recorded invasion history of FWW, coupled with a clear pattern of genetic divergence, provides an opportunity to investigate whether there is any sign of adaptive evolution following the invasion. Based on genome-wide SNPs, we identified genetically separated western and eastern groups of FWW and correlated spatial variation in SNPs with geographical and climatic factors. Geographical factors explained a similar proportion of the genetic variation across all populations compared with climatic factors. However, when the two population groups were analysed separately, environmental factors explained more variation than geographical factors. SNP outliers in populations of the western group had relatively stronger response to precipitation than temperature-related variables. Functional annotation of SNP outliers identified genes associated with insect cuticle protein potentially related to desiccation adaptation in the western group and genes associated with lipase biosynthesis potentially related to temperature adaptation in the eastern group. Our study suggests that invasive species may maintain the evolutionary potential to adapt to heterogeneous environments despite a single invasion event. The molecular data suggest that quantitative trait comparisons across environments would be worthwhile.
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Affiliation(s)
- Jin-Xu Dai
- Beijing Key Laboratory for Forest Pests Control, Beijing Forestry University, Beijing, China
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Li-Jun Cao
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jin-Cui Chen
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Fangyuan Yang
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xiu-Jing Shen
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Li-Jun Ma
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ary Anthony Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Min Chen
- Beijing Key Laboratory for Forest Pests Control, Beijing Forestry University, Beijing, China
| | - Shu-Jun Wei
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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Cao Z, Bakumenko O, Vlasenko V, Li W, Cao J. Molecular characterization and functional analysis of the ecdysone receptor isoform (EcR) from the oriental fruit moth Grapholita molesta (Lepidoptera: Tortricidae). ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2024; 115:e22110. [PMID: 38605666 DOI: 10.1002/arch.22110] [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: 11/14/2023] [Revised: 03/20/2024] [Accepted: 04/02/2024] [Indexed: 04/13/2024]
Abstract
20-Hydroxyecdysone (20E) plays a vital role in a series of biological processes, via the nuclear receptors, EcR/USP by activating the ecdysone regulatory cascade. To clarify the role of EcR during the development of Grapholita molesta, the complementary DNA of ecdysone receptor isoform B1 (GmEcR-B1) was obtained from the transcriptome of G. molesta and verified by PCR. Alignment analysis revealed that the deduced protein sequence of GmEcR-B1 was highly homologous to EcR proteins identified in other lepidopteran species, especially the EcR-B1 isoform in Spodoptera litura. Quantitative real-time PCR showed that GmEcRs was expressed at all test developmental stages, and the expression level of GmEcRs was relatively higher during the period of the 3rd day of fifth instar larvae to 2nd of pupa than those in other stages. Moreover, the messenger RNA of GmEcRs was much more strongly expressed in the Malpighian tubule and epidermis than those in other tissues, which suggests that this gene may function in a tissue-specific manner during larval development. Silencing of GmEcRs could significantly downregulate the transcriptional level of ecdysone-inducible genes and result in increased mortality during metamorphosis and prolonged prepupal duration. Taken together, the present results indicate that GmEcRs may directly or indirectly affect the development of G. molesta.
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Affiliation(s)
- Zhishan Cao
- Department of Plant Protection, International Joint Laboratory of Taxonomy and Systematic Evolution of Insecta, Henan Institute of Science and Technology, Xinxiang, Henan, China
- Department of Plant Protection, Sumy National Agrarian University, Sumy, Ukraine
| | - Olha Bakumenko
- Department of Plant Protection, Sumy National Agrarian University, Sumy, Ukraine
| | - Volodymyr Vlasenko
- Department of Plant Protection, Sumy National Agrarian University, Sumy, Ukraine
| | - Weihai Li
- Department of Plant Protection, International Joint Laboratory of Taxonomy and Systematic Evolution of Insecta, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Jinjun Cao
- Department of Plant Protection, International Joint Laboratory of Taxonomy and Systematic Evolution of Insecta, Henan Institute of Science and Technology, Xinxiang, Henan, China
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Ma LJ, Cao LJ, Chen JC, Tang MQ, Song W, Yang FY, Shen XJ, Ren YJ, Yang Q, Li H, Hoffmann AA, Wei SJ. Rapid and Repeated Climate Adaptation Involving Chromosome Inversions following Invasion of an Insect. Mol Biol Evol 2024; 41:msae044. [PMID: 38401527 PMCID: PMC10924284 DOI: 10.1093/molbev/msae044] [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: 10/25/2023] [Revised: 01/23/2024] [Accepted: 02/20/2024] [Indexed: 02/26/2024] Open
Abstract
Following invasion, insects can become adapted to conditions experienced in their invasive range, but there are few studies on the speed of adaptation and its genomic basis. Here, we examine a small insect pest, Thrips palmi, following its contemporary range expansion across a sharp climate gradient from the subtropics to temperate areas. We first found a geographically associated population genetic structure and inferred a stepping-stone dispersal pattern in this pest from the open fields of southern China to greenhouse environments of northern regions, with limited gene flow after colonization. In common garden experiments, both the field and greenhouse groups exhibited clinal patterns in thermal tolerance as measured by critical thermal maximum (CTmax) closely linked with latitude and temperature variables. A selection experiment reinforced the evolutionary potential of CTmax with an estimated h2 of 6.8% for the trait. We identified 3 inversions in the genome that were closely associated with CTmax, accounting for 49.9%, 19.6%, and 8.6% of the variance in CTmax among populations. Other genomic variations in CTmax outside the inversion region were specific to certain populations but functionally conserved. These findings highlight rapid adaptation to CTmax in both open field and greenhouse populations and reiterate the importance of inversions behaving as large-effect alleles in climate adaptation.
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Affiliation(s)
- Li-Jun Ma
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Li-Jun Cao
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Jin-Cui Chen
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Meng-Qing Tang
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Wei Song
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Fang-Yuan Yang
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Xiu-Jing Shen
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Ya-Jing Ren
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Qiong Yang
- Bio21 Institute, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Ary Anthony Hoffmann
- Bio21 Institute, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Shu-Jun Wei
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
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Parvizi E, Vaughan AL, Dhami MK, McGaughran A. Genomic signals of local adaptation across climatically heterogenous habitats in an invasive tropical fruit fly (Bactrocera tryoni). Heredity (Edinb) 2024; 132:18-29. [PMID: 37903919 PMCID: PMC10798995 DOI: 10.1038/s41437-023-00657-y] [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: 02/14/2023] [Revised: 09/21/2023] [Accepted: 10/17/2023] [Indexed: 11/01/2023] Open
Abstract
Local adaptation plays a key role in the successful establishment of pest populations in new environments by enabling them to tolerate novel biotic and abiotic conditions experienced outside their native range. However, the genomic underpinnings of such adaptive responses remain unclear, especially for agriculturally important pests. We investigated population genomic signatures in the tropical/subtropical Queensland fruit fly, Bactrocera tryoni, which has an expanded range encompassing temperate and arid zones in Australia, and tropical zones in the Pacific Islands. Using reduced representation sequencing data from 28 populations, we detected allele frequency shifts associated with the native/invasive status of populations and identified environmental factors that have likely driven population differentiation. We also determined that precipitation, temperature, and geographic variables explain allelic shifts across the distribution range of B. tryoni. We found spatial heterogeneity in signatures of local adaptation across various climatic conditions in invaded areas. Specifically, disjunct invasive populations in the tropical Pacific Islands and arid zones of Australia were characterised by multiple significantly differentiated single nucleotide polymorphisms (SNPs), some of which were associated with genes with well-understood function in environmental stress (e.g., heat and desiccation) response. However, invasive populations in southeast Australian temperate zones showed higher gene flow with the native range and lacked a strong local adaptive signal. These results suggest that population connectivity with the native range has differentially affected local adaptive patterns in different invasive populations. Overall, our findings provide insights into the evolutionary underpinnings of invasion success of an important horticultural pest in climatically distinct environments.
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Affiliation(s)
- Elahe Parvizi
- Te Aka Mātuatua/School of Science, University of Waikato, Hamilton, New Zealand
| | - Amy L Vaughan
- Biocontrol and Molecular Ecology, Manaaki Whenua Landcare Research, Lincoln, New Zealand
| | - Manpreet K Dhami
- Biocontrol and Molecular Ecology, Manaaki Whenua Landcare Research, Lincoln, New Zealand
| | - Angela McGaughran
- Te Aka Mātuatua/School of Science, University of Waikato, Hamilton, New Zealand.
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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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Warson J, Baguette M, Stevens VM, Honnay O, De Kort H. The impact of habitat loss on molecular signatures of coevolution between an iconic butterfly (Alcon blue) and its host plant (Marsh gentian). J Hered 2023; 114:22-34. [PMID: 36749638 DOI: 10.1093/jhered/esac059] [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: 03/23/2022] [Accepted: 10/19/2022] [Indexed: 11/30/2022] Open
Abstract
Habitat loss is threatening natural communities worldwide. Small and isolated populations suffer from inbreeding and genetic drift, which jeopardize their long-term survival and adaptive capacities. However, the consequences of habitat loss for reciprocal coevolutionary interactions remain poorly studied. In this study, we investigated the effects of decreasing habitat patch size and connectivity associated with habitat loss on molecular signatures of coevolution in the Alcon blue butterfly (Phengaris alcon) and its most limited host, the marsh gentian (Gentiana pneumonanthe). Because reciprocal coevolution is characterized by negative frequency-dependent selection as a particular type of balancing selection, we investigated how signatures of balancing selection vary along a gradient of patch size and connectivity, using single nucleotide polymorphisms (SNPs). We found that signatures of coevolution were unaffected by patch characteristics in the host plants. On the other hand, more pronounced signatures of coevolution were observed in both spatially isolated and in large Alcon populations, together with pronounced spatial variation in SNPs that are putatively involved in coevolution. These findings suggest that habitat loss can facilitate coevolution in large butterfly populations through limiting swamping of locally beneficial alleles by maladaptive ones. We also found that allelic richness (Ar) of the coevolutionary SNPs is decoupled from neutral Ar in the butterfly, indicating that habitat loss has different effects on coevolutionary as compared with neutral processes. We conclude that this specialized coevolutionary system requires particular conservation interventions aiming at generating a spatial mosaic of both connected and of isolated habitat to maintain coevolutionary dynamics.
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Affiliation(s)
- Jonas Warson
- Plant Conservation and Population Biology, Department of Biology, University of Leuven, Heverlee, Belgium
- Leuven Plant Institute, Heverlee, Belgium
| | - Michel Baguette
- Centre National de la Recherche Scientifique, SETE Station d'Ecologie Théorique et Expérimentale, UMR 5321, Moulis, France
- Institut Systématique, Evolution, Biodiversité (ISYEB), UMR 7205 Museum National d'HistoireNaturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Virginie M Stevens
- Centre National de la Recherche Scientifique, SETE Station d'Ecologie Théorique et Expérimentale, UMR 5321, Moulis, France
| | - Olivier Honnay
- Plant Conservation and Population Biology, Department of Biology, University of Leuven, Heverlee, Belgium
- Leuven Plant Institute, Heverlee, Belgium
| | - Hanne De Kort
- Plant Conservation and Population Biology, Department of Biology, University of Leuven, Heverlee, Belgium
- Leuven Plant Institute, Heverlee, Belgium
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Zhao Y, Hu J, Wu J, Li Z. ChIP-seq profiling of H3K4me3 and H3K27me3 in an invasive insect, Bactrocera dorsalis. Front Genet 2023; 14:1108104. [PMID: 36911387 PMCID: PMC9996634 DOI: 10.3389/fgene.2023.1108104] [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: 11/25/2022] [Accepted: 02/10/2023] [Indexed: 02/25/2023] Open
Abstract
Introduction: While it has been suggested that histone modifications can facilitate animal responses to rapidly changing environments, few studies have profiled whole-genome histone modification patterns in invasive species, leaving the regulatory landscape of histone modifications in invasive species unclear. Methods: Here, we screen genome-wide patterns of two important histone modifications, trimethylated Histone H3 Lysine 4 (H3K4me3) and trimethylated Histone H3 Lysine 27 (H3K27me3), in adult thorax muscles of a notorious invasive pest, the Oriental fruit fly Bactrocera dorsalis (Hendel) (Diptera: Tephritidae), using Chromatin Immunoprecipitation with high-throughput sequencing (ChIP-seq). Results: We identified promoters featured by the occupancy of H3K4me3, H3K27me3 or bivalent histone modifications that were respectively annotated with unique genes key to muscle development and structure maintenance. In addition, we found H3K27me3 occupied the entire body of genes, where the average enrichment was almost constant. Transcriptomic analysis indicated that H3K4me3 is associated with active gene transcription, and H3K27me3 is mostly associated with transcriptional repression. Importantly, we identified genes and putative motifs modified by distinct histone modification patterns that may possibly regulate flight activity. Discussion: These findings provide the first evidence of histone modification signature in B. dorsalis, and will be useful for future studies of epigenetic signature in other invasive insect species.
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Affiliation(s)
- Yan Zhao
- Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, College of Plant Protection, China Agricultural University, Beijing, China
| | - Juntao Hu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Jiajiao Wu
- Technology Center of Guangzhou Customs, Guangzhou, China
| | - Zhihong Li
- Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, College of Plant Protection, China Agricultural University, Beijing, China
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Li J, Shi L, Vasseur L, Zhao Q, Chen J, You M, You S. Genetic analyses reveal regional structure and demographic expansion of the predominant tea pest Empoasca onukii (Hemiptera: Cicadellidae) in China. PEST MANAGEMENT SCIENCE 2022; 78:2838-2850. [PMID: 35393736 DOI: 10.1002/ps.6908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 03/30/2022] [Accepted: 04/07/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND The tea green leafhopper, Empoasca onukii Matsuda, is the most destructive insect pest of tea plantations in East Asia. Despite its economic importance and previous studies on this species, it remains unclear as to how this small-sized pest can have such wide range. RESULTS By sequencing three mitochondrial genes and 17 microsatellite loci, we revealed the regional structure and demographic expansion of 59 E. onukii populations in China. Bayesian analysis of population genetic structure (BAPS) on microsatellites identified four genetic groups with spatial discontinuities, while analysis on mitochondrial genes inferred five nested and differentiated clusters. Both the Mantel test and the generalized linear model indicated a significant pattern of isolation by geographic distance in E. onukii populations. Based on the approximate Bayesian computation approach, E. onukii was found to have originated from southwestern China and expanded northward and eastward. While MIGRATE-N and Bayesian stochastic search variable selection (BSSVS) procedure in BEAST confirmed the possible eastward and northward dispersal from Yunnan, they also detected more gene flow from the derived populations in central and southeastern China. CONCLUSION Our results suggest that the current distribution and structure of E. onukii is complicatedly influenced by human activities of cultivation, wide dissemination of tea in ancient China as well as recent transportation of tea seedlings for establishing new tea plantations. Insights into genetic differentiation and demographic expansion patterns from this study provide an important basis for the development of area-wide management of the E. onukii populations. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Jinyu Li
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Tea Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Longqing Shi
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Rice, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Liette Vasseur
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Department of Biological Sciences, Brock University, St. Catharines, Canada
| | - Qian Zhao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Biological Sciences, Brock University, St. Catharines, Canada
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
| | - Jie Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Biological Sciences, Brock University, St. Catharines, Canada
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
| | - Minsheng You
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Biological Sciences, Brock University, St. Catharines, Canada
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
| | - Shijun You
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Biological Sciences, Brock University, St. Catharines, Canada
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
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Li F, Liu X, Zhu J, Li J, Gao K, Zhao C. The Role of Genetic Factors in the Differential Invasion Success of Two Spartina Species in China. FRONTIERS IN PLANT SCIENCE 2022; 13:909429. [PMID: 35712568 PMCID: PMC9196123 DOI: 10.3389/fpls.2022.909429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/02/2022] [Indexed: 06/15/2023]
Abstract
Biological invasions have become one of the greatest threats to global biodiversity and ecosystem conservation. Most previous studies have revealed how successful invasive species adapt to new environments and climate change through phenotypic and genetic evolution. Some researchers suggested that understanding unsuccessful or less successful biological invasions might be important for understanding the relationships between invasion adaptability and climate factors. We compared the sexual reproduction ability, genetic diversity, and gene × environment interaction in two intentionally introduced alien species in China (Spartina anglica and Spartina alterniflora) based on restriction site-associated DNA (RAD) sequencing. After more than 50 years, the distribution of S. alterniflora has rapidly expanded, while S. anglica has experienced extreme dieback. A total of 212,939 single nucleotide polymorphisms (SNPs) for the two Spartina species were used for analysis. The multilocus genotype (MLG) analysis revealed that clonal reproduction was the prevalent mode of reproduction in both species, indicating that a change in the mode of reproduction was not the key factor enabling successful invasion by Spartina. All genetic diversity indicators (He, Ho, π) in S. alterniflora populations were at least two times higher than those in S. anglica populations, respectively (p < 0.001). Furthermore, the population genetic structure and stronger patterns of climate-associated loci provided support for rapid adaptive evolution in the populations of S. alterniflora in China. Altogether, our results highlight the importance of genetic diversity and local adaptation, which were driven by multiple source populations, in increasing the invasiveness of S. alterniflora.
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Cao LJ, Song W, Chen JC, Fan XL, Hoffmann AA, Wei SJ. Population genomic signatures of the oriental fruit moth related to the Pleistocene climates. Commun Biol 2022; 5:142. [PMID: 35177826 PMCID: PMC8854661 DOI: 10.1038/s42003-022-03097-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 01/31/2022] [Indexed: 12/31/2022] Open
Abstract
The Quaternary climatic oscillations are expected to have had strong impacts on the evolution of species. Although legacies of the Quaternary climates on population processes have been widely identified in diverse groups of species, adaptive genetic changes shaped during the Quaternary have been harder to decipher. Here, we assembled a chromosome-level genome of the oriental fruit moth and compared genomic variation among refugial and colonized populations of this species that diverged in the Pleistocene. High genomic diversity was maintained in refugial populations. Demographic analysis showed that the effective population size of refugial populations declined during the penultimate glacial maximum (PGM) but remained stable during the last glacial maximum (LGM), indicating a strong impact of the PGM rather than the LGM on this pest species. Genome scans identified one chromosomal inversion and a mutation of the circadian gene Clk on the neo-Z chromosome potentially related to the endemicity of a refugial population. In the colonized populations, genes in pathways of energy metabolism and wing development showed signatures of selection. These different genomic signatures of refugial and colonized populations point to multiple impacts of Quaternary climates on adaptation in an extant species.
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Affiliation(s)
- Li-Jun Cao
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguanghuayuan Middle Road, Haidian District, Beijing, 100097, China
| | - Wei Song
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguanghuayuan Middle Road, Haidian District, Beijing, 100097, China
- Beijing Key Laboratory for Forest Pests Control, Beijing Forestry University, Beijing, 100083, China
| | - Jin-Cui Chen
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguanghuayuan Middle Road, Haidian District, Beijing, 100097, China
| | - Xu-Lei Fan
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguanghuayuan Middle Road, Haidian District, Beijing, 100097, China
| | - Ary Anthony Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
| | - Shu-Jun Wei
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguanghuayuan Middle Road, Haidian District, Beijing, 100097, China.
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Liu X, Wei S, Du Z, He J, Zhang X, Li H, Zhang R, Cai W. Population Genetic Structure of the Invasive Spotted Alfalfa Aphid Therioaphis trifolii (Hemiptera: Aphididae) in China Inferred From Complete Mitochondrial Genomes. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.759496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Biological invasions represent a natural rapid evolutionary process in which invasive species may present a major threat to biodiversity and ecosystem integrity. Analyzing the genetic structure and demographic history of invaded populations is critical for the effective management of invasive species. The spotted alfalfa aphid (SAA) Therioaphis trifolii is indigenous in the Mediterranean region of Europe and Africa and has invaded China, causing severe damages to the alfalfa industry. However, little is known about its genetic structure and invasion history. In this study, we obtained 167 complete mitochondrial genome sequences from 23 SAA populations across China based on high-throughput sequencing and performed population genetic and phylogenomic analyses. High haplotype diversity and low nucleotide diversity were found in SAA populations in China with distinct genetic structures, i.e., all populations diverged into three phylogenetic lineages. Demographic history analyses showed a recent expansion of the SAA population, consistent with the recent invasion history. Our study indicated that SAA may have invaded through multiple introduction events during commercial trades of alfalfa, although this needs further validation by nuclear markers.
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