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Kołodziejczyk J, Fijarczyk A, Porth I, Robakowski P, Vella N, Vella A, Kloch A, Biedrzycka A. Genomic investigations of successful invasions: the picture emerging from recent studies. Biol Rev Camb Philos Soc 2025. [PMID: 39956989 DOI: 10.1111/brv.70005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 01/30/2025] [Accepted: 01/31/2025] [Indexed: 02/18/2025]
Abstract
Invasion biology aims to identify traits and mechanisms that contribute to successful invasions, while also providing general insights into the mechanisms underlying population expansion and adaptation to rapid climate and habitat changes. Certain phenotypic attributes have been linked to successful invasions, and the role of genetics has been critical in understanding adaptation of invasive species. Nevertheless, a comprehensive summary evaluating the most common evolutionary mechanisms associated with successful invasions across species and environments is still lacking. Here we present a systematic review of studies since 2015 that have applied genomic tools to investigate mechanisms of successful invasions across different organisms. We examine demographic patterns such as changes in genomic diversity at the population level, the presence of genetic bottlenecks and gene flow in the invasive range. We review mechanisms of adaptation such as selection from standing genetic variation and de novo mutations, hybridisation and introgression, all of which can have an impact on invasion success. This comprehensive review of recent articles on the genomic diversity of invasive species led to the creation of a searchable database to provide researchers with an accessible resource. Analysis of this database allowed quantitative assessment of demographic and adaptive mechanisms acting in invasive species. A predominant role of admixture in increasing levels of genetic diversity enabling molecular adaptation in novel habitats is the most important finding of our study. The "genetic paradox" of invasive species was not validated in genomic data across species and ecosystems. Even though the presence of genetic drift and bottlenecks is commonly reported upon invasion, a large reduction in genomic diversity is rarely observed. Any decrease in genetic diversity is often relatively mild and almost always restored via gene flow between different invasive populations. The fact that loci under selection are frequently detected suggests that adaptation to novel habitats on a molecular level is not hindered. The above findings are confirmed herein for the first time in a semi-quantitative manner by molecular data. We also point to gaps and potential improvements in the design of studies of mechanisms driving rapid molecular adaptation in invasive populations. These include the scarcity of comprehensive studies that include sampling from multiple native and invasive populations, identification of invasion sources, longitudinal population sampling, and the integration of fitness measures into genomic analyses. We also note that the potential of whole genome studies is often not exploited fully in predicting invasive potential. Comparative genomic studies identifying genome features promoting invasions are underrepresented despite their potential for use as a tool in invasive species control.
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Affiliation(s)
- Joanna Kołodziejczyk
- Institute of Nature Conservation, Polish Academy of Sciences, Mickiewicza 33, Kraków, 31-120, Poland
| | - Anna Fijarczyk
- Natural Resources Canada, Laurentian Forestry Centre, 1055 Rue du Peps, Québec City, Quebec, G1V 4C7, Canada
- Department of Biology, Laval University, 1045 Avenue de la Médecine, Québec City, Quebec, G1V 0A6, Canada
- Institute of Integrative Biology and Systems, Laval University, 1030 Avenue de La Médecine, Québec City, Quebec, G1V 0A6, Canada
| | - Ilga Porth
- Institute of Integrative Biology and Systems, Laval University, 1030 Avenue de La Médecine, Québec City, Quebec, G1V 0A6, Canada
- Department of Wood and Forest Sciences, Laval University, 1030 Avenue de La Médecine, Québec City, Quebec, G1V 0A6, Canada
- Centre for Forest Research, Laval University, 2405 Rue de La Terrasse, Québec City, Quebec, G1V 0A6, Canada
| | - Piotr Robakowski
- Faculty of Forestry and Wood Technology, Poznań University of Life Sciences, 71E Wojska Polskiego Street, Poznań, PL 60-625, Poland
| | - Noel Vella
- Conservation Biology Research Group, Department of Biology, University of Malta, Msida, MSD2080, Malta
| | - Adriana Vella
- Conservation Biology Research Group, Department of Biology, University of Malta, Msida, MSD2080, Malta
| | - Agnieszka Kloch
- Faculty of Biology, University of Warsaw, Miecznikowa 1, Warsaw, 02-089, Poland
| | - Aleksandra Biedrzycka
- Institute of Nature Conservation, Polish Academy of Sciences, Mickiewicza 33, Kraków, 31-120, Poland
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Erickson PA, Bangerter A, Gunter A, Polizos NT, Bergland AO. Limited population structure but signals of recent selection in introduced African Fig Fly (Zaprionus indianus) in North America. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.20.614190. [PMID: 39386550 PMCID: PMC11463544 DOI: 10.1101/2024.09.20.614190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Invasive species have devastating consequences for human health, food security, and the environment. Many invasive species adapt to new ecological niches following invasion, but little is known about the early steps of adaptation. Here we examine population genomics of a recently introduced drosophilid in North America, the African Fig Fly, Zaprionus indianus. This species is likely intolerant of subfreezing temperatures and recolonizes temperate environments yearly. We generated a new chromosome-level genome assembly for Z. indianus. Using resequencing of over 200 North American individuals collected over four years in temperate Virginia, plus a single collection from subtropical Florida, we tested for signatures of recolonization, population structure, and adaptation within invasive populations. We show founding populations are sometimes small and contain close genetic relatives, yet temporal population structure and differentiation of populations is mostly absent across recurrent recolonization events. Although we find limited signals of genome-wide spatial or temporal population structure, we identify haplotypes on the X chromosome that are repeatedly differentiated between Virginia and Florida populations. These haplotypes show signatures of natural selection and are not found in African populations. We also find evidence for several large structural polymorphisms segregating within North America populations and show X chromosome evolution in invasive populations is strikingly different from the autosomes. These results show that despite limited population structure, populations may rapidly evolve genetic differences early in an invasion. Further uncovering how these genomic regions influence invasive potential and success in new environments will advance our understanding of how organisms evolve in changing environments.
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Horníková M, Lanier HC, Marková S, Escalante MA, Searle JB, Kotlík P. Genetic admixture drives climate adaptation in the bank vole. Commun Biol 2024; 7:863. [PMID: 39009753 PMCID: PMC11251159 DOI: 10.1038/s42003-024-06549-z] [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: 07/20/2023] [Accepted: 07/03/2024] [Indexed: 07/17/2024] Open
Abstract
Genetic admixture introduces new variants at relatively high frequencies, potentially aiding rapid responses to environmental changes. Here, we evaluate its role in adaptive variation related to climatic conditions in bank voles (Clethrionomys glareolus) in Britain, using whole-genome data. Our results reveal loci showing excess ancestry from one of the two postglacial colonist populations inconsistent with overall admixture patterns. Notably, loci associated with climate adaptation exhibit disproportionate amounts of excess ancestry, highlighting the impact of admixture between colonist populations on local adaptation. The results suggest strong and localized selection on climate-adaptive loci, as indicated by steep clines and/or shifted cline centres, during population replacement. A subset, including a haemoglobin gene, is associated with oxidative stress responses, underscoring a role of oxidative stress in local adaptation. Our study highlights the important contribution of admixture during secondary contact between populations from distinct climatic refugia enriching adaptive diversity. Understanding these dynamics is crucial for predicting future adaptive capacity to anthropogenic climate change.
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Affiliation(s)
- Michaela Horníková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Hayley C Lanier
- Department of Biology, Program in Ecology & Evolutionary Biology, University of Oklahoma, Norman, OK, USA
- Sam Noble Museum, University of Oklahoma, Norman, OK, USA
| | - Silvia Marková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Marco A Escalante
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Petr Kotlík
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic.
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Yang R, Yu X, Nie P, Cao R, Feng J, Hu X. Climatic niche and range shifts of grey squirrels (Sciurus carolinensis Gmelin) in Europe: An invasive pest displacing native squirrels. PEST MANAGEMENT SCIENCE 2023; 79:3731-3739. [PMID: 37194192 DOI: 10.1002/ps.7554] [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: 01/30/2023] [Revised: 05/08/2023] [Accepted: 05/16/2023] [Indexed: 05/18/2023]
Abstract
BACKGROUND As an invasive pest from North America, grey squirrels (GSs; Sciurus carolinensis Gmelin) are displacing native squirrels in Europe. However, the climatic niche and range dynamics of GSs in Europe remain largely unknown. Through niche and range dynamic models, we investigated climatic niche and range shifts between introduced GSs in Europe and native GSs in North America. RESULTS GSs in North America can survive in more variable climatic conditions and have much wider climatic niche breadth than do GSs in Europe. Based on climate, the potential range of GSs in Europe included primarily Britain, Ireland, and Italy, whereas the potential range of GSs in North America included vast regions of western and southern Europe. If GSs in Europe could occupy the same climatic niche space and potential range as GSs in North America, they would occupy an area ca. 2.45 times the size of their current range. The unfilling ranges of GSs in Europe relative to those of GSs in North America were primarily in France, Italy, Spain, Croatia, and Portugal. CONCLUSION Our observations implied that GSs in Europe have significant invasion potential, and that range projections based on their occurrence records in Europe may underestimate their invasion risk. Given that small niche shifts between GSs in Europe and in North America could lead to large range shifts, niche shifts could be a sensitive indicator in invasion risk assessment. The identified unfilling ranges of the GS in Europe should be prioritized in combating GS invasions in the future. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Rujing Yang
- College of Agriculture and Biological Science, Dali University, Dali, China
- Research Center for Agroecology in Erhai Lake Watershed of Dali University, Dali, China
- Cangshan Forest Ecosystem Observation and Research Station of Yunnan Province, Dali University, Dali, China
| | - Xiaoli Yu
- College of Agriculture and Biological Science, Dali University, Dali, China
- Research Center for Agroecology in Erhai Lake Watershed of Dali University, Dali, China
- Cangshan Forest Ecosystem Observation and Research Station of Yunnan Province, Dali University, Dali, China
| | - Peixiao Nie
- College of Agriculture and Biological Science, Dali University, Dali, China
- Research Center for Agroecology in Erhai Lake Watershed of Dali University, Dali, China
- Cangshan Forest Ecosystem Observation and Research Station of Yunnan Province, Dali University, Dali, China
| | - Runyao Cao
- College of Agriculture and Biological Science, Dali University, Dali, China
- Research Center for Agroecology in Erhai Lake Watershed of Dali University, Dali, China
- Cangshan Forest Ecosystem Observation and Research Station of Yunnan Province, Dali University, Dali, China
| | - Jianmeng Feng
- College of Agriculture and Biological Science, Dali University, Dali, China
- Research Center for Agroecology in Erhai Lake Watershed of Dali University, Dali, China
- Cangshan Forest Ecosystem Observation and Research Station of Yunnan Province, Dali University, Dali, China
| | - Xiaokang Hu
- College of Agriculture and Biological Science, Dali University, Dali, China
- Research Center for Agroecology in Erhai Lake Watershed of Dali University, Dali, China
- Cangshan Forest Ecosystem Observation and Research Station of Yunnan Province, Dali University, Dali, China
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Lake TA, Briscoe Runquist RD, Flagel LE, Moeller DA. Chronosequence of invasion reveals minimal losses of population genomic diversity, niche expansion, and trait divergence in the polyploid, leafy spurge. Evol Appl 2023; 16:1680-1696. [PMID: 38020872 PMCID: PMC10660801 DOI: 10.1111/eva.13593] [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: 04/03/2023] [Revised: 07/05/2023] [Accepted: 08/25/2023] [Indexed: 12/01/2023] Open
Abstract
Rapid evolution may play an important role in the range expansion of invasive species and modify forecasts of invasion, which are the backbone of land management strategies. However, losses of genetic variation associated with colonization bottlenecks may constrain trait and niche divergence at leading range edges, thereby impacting management decisions that anticipate future range expansion. The spatial and temporal scales over which adaptation contributes to invasion dynamics remain unresolved. We leveraged detailed records of the ~130-year invasion history of the invasive polyploid plant, leafy spurge (Euphorbia virgata), across ~500 km in Minnesota, U.S.A. We examined the consequences of range expansion for population genomic diversity, niche breadth, and the evolution of germination behavior. Using genotyping-by-sequencing, we found some population structure in the range core, where introduction occurred, but panmixia among all other populations. Range expansion was accompanied by only modest losses in sequence diversity, with small, isolated populations at the leading edge harboring similar levels of diversity to those in the range core. The climatic niche expanded during most of the range expansion, and the niche of the range core was largely non-overlapping with the invasion front. Ecological niche models indicated that mean temperature of the warmest quarter was the strongest determinant of habitat suitability and that populations at the leading edge had the lowest habitat suitability. Guided by these findings, we tested for rapid evolution in germination behavior over the time course of range expansion using a common garden experiment and temperature manipulations. Germination behavior diverged from the early to late phases of the invasion, with populations from later phases having higher dormancy at lower temperatures. Our results suggest that trait evolution may have contributed to niche expansion during invasion and that distribution models, which inform future management planning, may underestimate invasion potential without accounting for evolution.
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Affiliation(s)
- Thomas A. Lake
- Department of Plant and Microbial BiologyUniversity of MinnesotaSt. PaulMinnesotaUSA
| | | | - Lex E. Flagel
- Department of Plant and Microbial BiologyUniversity of MinnesotaSt. PaulMinnesotaUSA
- GencoveLong Island CityNew YorkUSA
| | - David A. Moeller
- Department of Plant and Microbial BiologyUniversity of MinnesotaSt. PaulMinnesotaUSA
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Nie P, Yang R, Cao R, Hu X, Feng J. Niche and Range Shifts of the Fall Webworm ( Hyphantria cunea Dury) in Europe Imply Its Huge Invasion Potential in the Future. INSECTS 2023; 14:316. [PMID: 37103131 PMCID: PMC10141053 DOI: 10.3390/insects14040316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/24/2023] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
The fall webworm (Hyphantria cunea Dury) has a strong impact on agricultural systems in Europe. However, its invasive potential, which was inherited from its native niche in North America, remains unknown. Here, we investigated the climatic niche and range shifts of the fall webworm in Europe and compared them with those in native North America, then assessed the worms' invasive potential in Europe. Compared with the fall webworm in Europe, those in North America survived in more diverse climatic conditions, which was closely associated with their broader niche and larger potential ranges in Europe. If the fall webworm in Europe could exploit the native niche inherited from those in North America to adapt to climatic conditions in Europe, their potential ranges in Europe could be 5.5-fold those based on the niche as introduced in Europe. The potentially unfilled ranges of the fall webworm in Europe were mainly detected in vast regions of Europe, excluding Norway, Sweden, Finland, North Russia, Hungary, Croatia, Romania, and Ukraine, suggesting that, without strict control, these vast regions might be preferably invaded by the fall webworm in Europe in the future. Therefore, strict control against its invasion is needed. Given that small niche shifts in this invasive insect could result in large range shifts, the niche shifts represent a more sensitive indicator of invasion risk than range shifts.
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Affiliation(s)
- Peixiao Nie
- Division of Plant Ecology, College of Agriculture and Biological Science, Dali University, Dali 671003, China
- Research Center for Agroecology in Erhai Lake Watershed, Division of Plant Ecology, Dali University, Dali 671003, China
- Cangshan Forest Ecosystem Observation and Research Station of Yunnan Province, Division of Plant Ecology, Dali University, Dali 671003, China
| | - Rujing Yang
- Division of Plant Ecology, College of Agriculture and Biological Science, Dali University, Dali 671003, China
| | - Runyao Cao
- Research Center for Agroecology in Erhai Lake Watershed, Division of Plant Ecology, Dali University, Dali 671003, China
| | - Xiaokang Hu
- Division of Plant Ecology, College of Agriculture and Biological Science, Dali University, Dali 671003, China
- Research Center for Agroecology in Erhai Lake Watershed, Division of Plant Ecology, Dali University, Dali 671003, China
- Cangshan Forest Ecosystem Observation and Research Station of Yunnan Province, Division of Plant Ecology, Dali University, Dali 671003, China
| | - Jianmeng Feng
- Division of Plant Ecology, College of Agriculture and Biological Science, Dali University, Dali 671003, China
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Poveda-Martínez D, Salinas NA, Aguirre MB, Sánchez-Restrepo AF, Hight S, Díaz-Soltero H, Logarzo G, Hasson E. Genomic and ecological evidence shed light on the recent demographic history of two related invasive insects. Sci Rep 2022; 12:19629. [PMID: 36385480 PMCID: PMC9669014 DOI: 10.1038/s41598-022-21548-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/28/2022] [Indexed: 11/17/2022] Open
Abstract
Hypogeococcus pungens is a species complex native to southern South America that is composed of at least five putative species, each one specialized in the use of different host plants. Two of these undescribed species were registered as invasive in Central and North America: Hyp-C is a cactophagous mealybug that became an important pest that threatens endemic cactus species in Puerto Rico, and Hyp-AP feeds on Amaranthaceae and Portulacaceae hosts, but does not produce severe damage to the host plants. We quantified genomic variation and investigated the demographic history of both invasive species by means of coalescent-based simulations using high throughput sequencing data. We also evaluated the incidence of host plant infestation produced by both species and used an ecological niche modeling approach to assess potential distribution under current and future climatic scenarios. Our genetic survey evinced the footprints of strong effective population size reduction and signals of genetic differentiation among populations within each species. Incidence of plant attacks varied between species and among populations within species, with some host plant species preferred over others. Ecological niche modeling suggested that under future climatic scenarios both species would expand their distribution ranges in Puerto Rico. These results provide valuable information for the design of efficient management and control strategies of the Puerto Rican cactus pest and shed light on the evolutionary pathways of biological invasions.
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Affiliation(s)
- Daniel Poveda-Martínez
- Fundación Para El Estudio de Especies Invasivas (FuEDEI), Hurlingham, Argentina.
- Facultad de Ciencias Exactas Y Naturales, Instituto de Ecología Genética Y Evolución de Buenos Aires (IEGEBA), Universidad de Buenos Aires, Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Nicolas A Salinas
- Fundación Para El Estudio de Especies Invasivas (FuEDEI), Hurlingham, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - María Belén Aguirre
- Fundación Para El Estudio de Especies Invasivas (FuEDEI), Hurlingham, Argentina.
| | - Andrés F Sánchez-Restrepo
- Fundación Para El Estudio de Especies Invasivas (FuEDEI), Hurlingham, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Stephen Hight
- Insect Behavior and Biocontrol Research Unit (IBBRU), USDA-ARS, Tallahassee, FL, USA
| | | | - Guillermo Logarzo
- Fundación Para El Estudio de Especies Invasivas (FuEDEI), Hurlingham, Argentina
| | - Esteban Hasson
- Facultad de Ciencias Exactas Y Naturales, Instituto de Ecología Genética Y Evolución de Buenos Aires (IEGEBA), Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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Zhang L, Dietrich CH, Xu Y, Yang Z, Chen M, Pham TH, Le CCV, Qiao L, Matsumura M, Qin D. Unraveling the hierarchical genetic structure of tea green leafhopper, Matsumurasca onukii, in East Asia based on SSRs and SNPs. Ecol Evol 2022; 12:e9377. [PMID: 36203634 PMCID: PMC9526121 DOI: 10.1002/ece3.9377] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 08/30/2022] [Accepted: 09/12/2022] [Indexed: 12/02/2022] Open
Abstract
Matsumurasca onukii (Matsuda, R. (1952). Oyo-Kontyu Tokyo, 8(1): 19-21), one of the dominant pests in major tea production areas in Asia, currently is known to occur in Japan, Vietnam, and China, and severely threatens tea production, quality, and international trade. To elucidate the population genetic structure of this species, 1633 single nucleotide polymorphisms (SNPs) and 18 microsatellite markers (SSRs) were used to genotype samples from 27 sites representing 18 geographical populations distributed throughout the known range of the species in East Asia. Analyses of both SNPs and SSRs showed that M. onukii populations in Yunnan exhibit high-genetic differentiation and structure compared with the other populations. The Kagoshima (JJ) and Shizuoka (JS) populations from Japan were separated from populations from China by SNPs, but clustered with populations from Jinhua (JH), Yingde (YD), Guilin (GL), Fuzhou (FZ), Hainan (HQ), Leshan (CT), Chongqing (CY), and Zunyi (ZY) tea plantations in China and the Vietnamese Vinh Phuc (VN) population based on the SSR data. In contrast, CT, CY, ZY, and Shaanxi (SX) populations clustered together based on SNPs, but were separated by SSRs. Both marker datasets identified significant geographic differentiation among the 18 populations. Various environmental and anthropogenic factors, including geographical barriers to migration, human transport of hosts (Camellia sinesis [L.] O. Kuntze) and adaptation of M. onukii to various local climatic zones possibly account for the rapid spread of this pest in Asia. The results demonstrate that SNPs from high-throughput genotyping data can be used to reveal subtle genetic substructure at broad scales in r-strategist insects.
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Affiliation(s)
- Li Zhang
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, Entomological MuseumNorthwest A&F UniversityYanglingShaanxiChina
- Institute of Jiangxi Oil‐Tea Camellia, Jiujiang UniversityJiujiangJiangxiChina
| | - Christopher H. Dietrich
- Illinois Natural History SurveyPrairie Research Institute, University of IllinoisChampaignIllinoisUSA
| | - Ye Xu
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, Entomological MuseumNorthwest A&F UniversityYanglingShaanxiChina
- College of Agriculture, Jiangxi Agricultural UniversityNanchangJiangxiChina
| | - Zhaofu Yang
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, Entomological MuseumNorthwest A&F UniversityYanglingShaanxiChina
| | - Maohua Chen
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, Entomological MuseumNorthwest A&F UniversityYanglingShaanxiChina
| | - Thai H. Pham
- Mientrung Institute for Scientific Research, Vietnam National Museum of Nature, VASTHueVietnam
- Graduate School of Science and Technology, Vietnam Academy of Science and TechnologyHanoiVietnam
| | - Cuong C. V. Le
- Mientrung Institute for Scientific Research, Vietnam National Museum of Nature, VASTHueVietnam
| | - Li Qiao
- College of Agronomy, Xinyang Agricultural and Forestry UniversityXinyangHenanChina
| | - Masaya Matsumura
- Institute for Plant Protection, National Agriculture and Food Research OrganizationTsukubaIbarakiJapan
| | - Daozheng Qin
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, Entomological MuseumNorthwest A&F UniversityYanglingShaanxiChina
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Microsatellite Variation in the Most Devastating Beetle Pests (Coleoptera: Curculionidae) of Agricultural and Forest Crops. Int J Mol Sci 2022; 23:ijms23179847. [PMID: 36077247 PMCID: PMC9456221 DOI: 10.3390/ijms23179847] [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: 07/25/2022] [Revised: 08/19/2022] [Accepted: 08/24/2022] [Indexed: 12/03/2022] Open
Abstract
Weevils, classified in the family Curculionidae (true weevils), constitute a group of phytophagous insects of which many species are considered significant pests of crops. Within this family, the red palm weevil (RPW), Rhynchophorus ferrugineus, has an integral role in destroying crops and has invaded all countries of the Middle East and many in North Africa, Southern Europe, Southeast Asia, Oceania, and the Caribbean Islands. Simple sequence repeats (SSRs), also termed microsatellites, have become the DNA marker technology most applied to study population structure, evolution, and genetic diversity. Although these markers have been widely examined in many mammalian and plant species, and draft genome assemblies are available for many species of true weevils, very little is yet known about SSRs in weevil genomes. Here we carried out a comparative analysis examining and comparing the relative abundance, relative density, and GC content of SSRs in previously sequenced draft genomes of nine true weevils, with an emphasis on R. ferrugineus. We also used Illumina paired-end sequencing to generate draft sequence for adult female RPW and characterized it in terms of perfect SSRs with 1–6 bp nucleotide motifs. Among weevil genomes, mono- to trinucleotide SSRs were the most frequent, and mono-, di-, and hexanucleotide SSRs exhibited the highest GC content. In these draft genomes, SSR number and genome size were significantly correlated. This work will aid our understanding of the genome architecture and evolution of Curculionidae weevils and facilitate exploring SSR molecular marker development in these species.
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Waqas MS, Shi Z, Yi TC, Xiao R, Shoaib AA, Elabasy AS, Jin DC. Biology, ecology, and management of cotton mealybug Phenacoccus solenopsis Tinsley (Hemiptera: Pseudococcidae). PEST MANAGEMENT SCIENCE 2021; 77:5321-5333. [PMID: 34312983 DOI: 10.1002/ps.6565] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 07/15/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
The cotton mealybug Phenacoccus solenopsis Tinsley (Hemiptera: Pseudococcidae), is a highly invasive and harmful pest. It causes considerable loss of cotton crops in China, India and Pakistan. Little is known about its bionomics since it was first recorded in Pakistan and India in 2005. Rapid spread of this pest worldwide has accelerated research on its biology, ecology and management. The P. solenopsis has a short life cycle, and optimal temperatures lead to an increase in the number of generations per year, which is a serious threat to cotton crop production. Cotton mealybug is native to the USA, although it has now spread to >43 countries. Insecticidal control is the primary and dominant practice for this pest, and its resistance to commonly used insecticides is increasing. Biocontrol agents have strong potential for the management of nymphal instar stages. We read >250 articles related to our review title and finally reviewed recent advances in the understanding of P. solenopsis biology, ecology and control approaches, aiming to highlight integrated and biological management practices of this pest. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Muhammad S Waqas
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, and Scientific Observing and Experimental Station of Crop Pest in Guiyang, Institute of Entomology, Ministry of Agricultural and Rural Affairs, Guizhou University, Guiyang, China
| | - Zuhua Shi
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Tian-Ci Yi
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, and Scientific Observing and Experimental Station of Crop Pest in Guiyang, Institute of Entomology, Ministry of Agricultural and Rural Affairs, Guizhou University, Guiyang, China
| | - Rong Xiao
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, and Scientific Observing and Experimental Station of Crop Pest in Guiyang, Institute of Entomology, Ministry of Agricultural and Rural Affairs, Guizhou University, Guiyang, China
| | - Ali Az Shoaib
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
- Department of Pesticides, Plant Protection Research Institute, Agriculture Research Center, Cairo, Egypt
| | - Asem Ss Elabasy
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
- Department of Pesticides, Plant Protection Research Institute, Agriculture Research Center, Cairo, Egypt
| | - Dao-Chao Jin
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, and Scientific Observing and Experimental Station of Crop Pest in Guiyang, Institute of Entomology, Ministry of Agricultural and Rural Affairs, Guizhou University, Guiyang, China
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11
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Cao LJ, Li BY, Chen JC, Zhu JY, Hoffmann AA, Wei SJ. Local climate adaptation and gene flow in the native range of two co-occurring fruit moths with contrasting invasiveness. Mol Ecol 2021; 30:4204-4219. [PMID: 34278603 DOI: 10.1111/mec.16055] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 05/23/2021] [Accepted: 06/29/2021] [Indexed: 12/24/2022]
Abstract
Invasive species pose increasing threats to global biodiversity and ecosystems. While previous studies have characterized successful invaders based on ecological traits, characteristics related to evolutionary processes have rarely been investigated. Here we compared gene flow and local adaptation using demographic analyses and outlier tests in two co-occurring moth pests across their common native range of China, one of which (the peach fruit moth, Carposina sasakii) has maintained its native distribution, while the other (the oriental fruit moth, Grapholita molesta) has expanded its range globally during the past century. We found that both species showed a pattern of genetic differentiation and an evolutionary history consistent with a common southwestern origin and northward expansion in their native range. However, for the noninvasive species, genetic differentiation was closely aligned with the environment, and there was a relatively low level of gene flow, whereas in the invasive species, genetic differentiation was associated with geography. Genome scans indicated stronger patterns of climate-associated loci in the noninvasive species. While strong local adaptation and reduced gene flow across its native range may have decreased the invasiveness of C. sasakii, this requires further validation with additional comparisons of invasive and noninvasive species across their native range.
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Affiliation(s)
- Li-Jun Cao
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Bing-Yan Li
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.,Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Jin-Cui Chen
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jia-Ying Zhu
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Ary A Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Shu-Jun Wei
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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12
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Comeault AA, Kautt AF, Matute DR. Genomic signatures of admixture and selection are shared among populations of Zaprionus indianus across the western hemisphere. Mol Ecol 2021; 30:6193-6210. [PMID: 34233050 PMCID: PMC9290797 DOI: 10.1111/mec.16066] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 06/27/2021] [Accepted: 07/01/2021] [Indexed: 11/28/2022]
Abstract
Introduced species have become an increasingly common component of biological communities around the world. A central goal in invasion biology is therefore to identify the demographic and evolutionary factors that underlie successful introductions. Here we use whole genome sequences, collected from populations in the native and introduced range of the African fig fly, Zaprionus indianus, to quantify genetic relationships among them, identify potential sources of the introductions, and test for selection at different spatial scales. We find that geographically widespread populations in the western hemisphere are genetically more similar to each other than to lineages sampled across Africa, and that these populations share a mixture of alleles derived from differentiated African lineages. Using patterns of allele‐sharing and demographic modelling we show that Z. indinaus have undergone a single expansion across the western hemisphere with admixture between African lineages predating this expansion. We also find support for selection that is shared across populations in the western hemisphere, and in some cases, with a subset of African populations. This suggests either that parallel selection has acted across a large part of Z. indianus's introduced range; or, more parsimoniously, that Z. indianus has experienced selection early on during (or prior‐to) its expansion into the western hemisphere. We suggest that the range expansion of Z. indianus has been facilitated by admixture and selection, and that management of this invasion could focus on minimizing future admixture by controlling the movement of individuals within this region rather than between the western and eastern hemisphere.
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Affiliation(s)
- Aaron A Comeault
- Molecular Ecology and Evolution Group, School of Natural Sciences, Bangor University, Bangor, UK
| | - Andreas F Kautt
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Daniel R Matute
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
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13
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Vilardi JC, Freilij D, Ferreyra LI, Gómez-Cendra P. Ecological phylogeography and coalescent models suggest a linear population expansion of Anastrepha fraterculus (Diptera: Tephritidae) in southern South America. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
This work is a first approach to an integrated view of the genetics, ecology and dispersion patterns of Anastrepha fraterculus in southern South America. We studied the association of genetic variation with geographical patterns and environmental variables to provide insight into the crucial factors that drive the structure and dynamics of fly populations. Data from a 417 bp mitochondrial COII gene fragment from seven Argentinian populations and one South Brazilian population (from five ecoregions grouped in three biomes) were used to identify population clusters using a model-based Bayesian phylogeographical and ecological clustering approach. The sequences were also analysed under a coalescent model to evaluate historical demographic changes. We identified 19 different haplotypes and two clusters differing in all the environmental covariables. The assumption of neutral evolution and constant population size was rejected, and the population growth parameters suggested a linear population expansion starting 2500 years before present. The most likely ancestral location is Posadas, from where A. fraterculus would have expanded southwards and westwards in Argentina. This result is consistent with Holocene changes and anthropic factors related to the expansion of the Tupí–Guaraní culture, 3000–1500 years before present.
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Affiliation(s)
- Juan César Vilardi
- Genética de Poblaciones Aplicada (GPA), Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Ecología, Genética y Evolución (IEGEBA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Damián Freilij
- Genética de Poblaciones Aplicada (GPA), Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Laura Inés Ferreyra
- Genética de Poblaciones Aplicada (GPA), Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Paula Gómez-Cendra
- Genética de Poblaciones Aplicada (GPA), Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Ecología, Genética y Evolución (IEGEBA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
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14
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Rapid, strong population genetic differentiation, genomic signatures of climatic adaptation in an invasive mealybug. DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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15
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Song X, Yang T, Yan X, Zheng F, Xu X, Zhou C. Comparison of microsatellite distribution patterns in twenty-nine beetle genomes. Gene 2020; 757:144919. [PMID: 32603771 DOI: 10.1016/j.gene.2020.144919] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 06/15/2020] [Accepted: 06/20/2020] [Indexed: 01/20/2023]
Abstract
Simple sequence repeats (SSRs) represent an important source of genetic variation that provides a basis for adaptation to different environments in organisms. In this study, we examined the distribution patterns of SSRs in twenty-nine beetle genomes and carried out Gene Ontology (GO) analysis of CDSs embedded with perfect SSRs (P-SSRs). The results demonstrated that imperfect SSRs (I-SSRs) represented the most abundant SSR category in beetle genomes and in different genomic regions (CDS, exon, and intron regions). The numbers of P-SSRs, I-SSRs, compound SSRs, and variable number tandem repeats were positively correlated with beetle genome size, whereas neither the frequency nor the density of the SSRs was correlated with genome size. Moreover, our results demonstrated that common genomic features of P-SSRs within the same suborder or family of Coleoptera were rare. Mono-, di-, tri-, or tetranucleotide SSRs were the most abundant P-SSR categories in beetle genomes. The preferred predominant repeat motif among the mononucleotide P-SSRs was (A)n, but the most frequent repeat motifs for other length classes varied differentially among these genomes. Furthermore, the P-SSR type with the highest GC content differed in the beetle genomes and in different genomic regions. CV (coefficient of variability) analysis demonstrated that the repeat copy numbers of P-SSRs presented relatively higher variation in introns than in CDSs and exons. The GO terms of CDSs containing P-SSRs for molecular functions were mainly enriched in "binding" and "transcription". Our findings will be useful for studying the functional roles of microsatellite heterogeneity in beetle adaptation.
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Affiliation(s)
- Xuhao Song
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, Sichuan Province, China.
| | - Tingbang Yang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, Sichuan Province, China
| | - Xianghui Yan
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, Sichuan Province, China
| | - Fake Zheng
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, Sichuan Province, China
| | - Xiaoqin Xu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, Sichuan Province, China
| | - Caiquan Zhou
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, Sichuan Province, China.
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