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Gamba D, Vahsen ML, Maxwell TM, Pirtel N, Romero S, Ee JJV, Penn A, Das A, Ben-Zeev R, Baughman O, Blaney CS, Bodkins R, Budha-Magar S, Copeland SM, Davis-Foust SL, Diamond A, Donnelly RC, Dunwiddie PW, Ensing DJ, Everest TA, Hoitink H, Holdrege MC, Hufbauer RA, Juzėnas S, Kalwij JM, Kashirina E, Kim S, Klisz M, Klyueva A, Langeveld M, Lutfy S, Martin D, Merkord CL, Morgan JW, Nagy DU, Ott JP, Puchalka R, Pyle LA, Rasran L, Rector BG, Rosche C, Sadykova M, Shriver RK, Stanislavschi A, Starzomski BM, Stone RL, Turner KG, Urza AK, VanWallendael A, Wegenschimmel CA, Zweck J, Brown CS, Leger EA, Blumenthal DM, Germino MJ, Porensky LM, Hooten MB, Adler PB, Lasky JR. Local adaptation to climate facilitates a global invasion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.12.612725. [PMID: 39345363 PMCID: PMC11429938 DOI: 10.1101/2024.09.12.612725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Local adaptation may facilitate range expansion during invasions, but the mechanisms promoting destructive invasions remain unclear. Cheatgrass (Bromus tectorum), native to Eurasia and Africa, has invaded globally, with particularly severe impacts in western North America. We sequenced 307 genotypes and conducted controlled experiments. We found that diverse lineages invaded North America, where long-distance gene flow is common. Ancestry and phenotypic clines in the native range predicted those in the invaded range, indicating pre-adapted genotypes colonized different regions. Common gardens showed directional selection on flowering time that reversed between warm and cold sites, potentially maintaining clines. In the Great Basin, genomic predictions of strong local adaptation identified sites where cheatgrass is most dominant. Preventing new introductions that may fuel adaptation is critical for managing ongoing invasions.
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Affiliation(s)
- Diana Gamba
- Department of Biology, Pennsylvania State University; University Park, PA, USA
| | - Megan L. Vahsen
- Department of Wildland Resources and the Ecology Center, Utah State University; Logan, UT, USA
| | - Toby M. Maxwell
- Department of Biological Sciences, Boise State University; Boise, ID, USA
| | - Nikki Pirtel
- Department of Wildland Resources and the Ecology Center, Utah State University; Logan, UT, USA
| | - Seth Romero
- US Department of Agriculture, Agricultural Research Service, Rangeland Resources and Systems Research Unit; Fort Collins, CO, USA
| | - Justin J. Van Ee
- Department of Agricultural Biology, Colorado State University; Fort Collins, CO, USA
| | - Amanda Penn
- Department of Biology, Pennsylvania State University; University Park, PA, USA
| | - Aayudh Das
- Department of Biology, Pennsylvania State University; University Park, PA, USA
| | - Rotem Ben-Zeev
- Department of Biology, Pennsylvania State University; University Park, PA, USA
| | | | - C. Sean Blaney
- Atlantic Canada Conservation Data Centre; Sackville, NB, Canada
| | | | | | - Stella M. Copeland
- US Department of Agriculture, Agricultural Research Service, Eastern Oregon Agricultural Research Center; Burns, OR, USA
| | | | - Alvin Diamond
- Department of Biological and Environmental Sciences, Troy University; Troy, Alabama, USA
| | - Ryan C. Donnelly
- Division of Biology, Kansas State University; Manhattan, KS, USA
| | | | - David J. Ensing
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada; Summerland, BC, Canada
| | | | | | - Martin C. Holdrege
- Northern Arizona University, Center for Adaptable Western Landscapes; Flagstaff, AZ, USA
| | - Ruth A. Hufbauer
- Department of Agricultural Biology, Colorado State University; Fort Collins, CO, USA
| | - Sigitas Juzėnas
- Department of Botany and Genetics, Institute of Biosciences, Life Sciences Center, Vilnius University; Vilnius, Lithuania
| | - Jesse M. Kalwij
- Institute of Geography and Geoecology, Karlsruhe Institute of Technology; Karlsruhe, Germany
| | | | - Sangtae Kim
- Department of Biology, Sungshin Women’s University; Seoul, Republic of Korea
| | - Marcin Klisz
- Department of Silviculture and Genetics of Forest Trees, Forest Research Institute; Raszyn, Poland
| | - Alina Klyueva
- Bryansk State University named after Academician I. G. Petrovsky; Bryansk, Russia
| | | | - Samuel Lutfy
- Caesar Kleberg Wildlife Research Institute, Texas A&M University - Kingsville; Kingsville, TX, USA
| | | | | | - John W. Morgan
- Department of Environment and Genetics, La Trobe University; Bundoora, Victoria, Australia
| | - Dávid U. Nagy
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg; Halle, Saale, Germany
| | - Jacqueline P. Ott
- USDA Forest Service, Rocky Mountain Research Station, Rapid City, SD, USA
| | - Radoslaw Puchalka
- Department of Ecology and Biogeography, Nicolaus Copernicus University; Torun, Poland
| | | | - Leonid Rasran
- University of Natural Resources and Life Sciences, Vienna; Vienna, Austria
| | - Brian G. Rector
- US Department of Agriculture, Agricultural Research Service, Invasive Species and Pollinator Health Research Unit; Albany, CA, USA
| | - Christoph Rosche
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg; Halle, Saale, Germany
| | | | - Robert K. Shriver
- Department of Natural Resources and Environmental Science, University of Nevada; Reno, NV, USA
| | - Alexandr Stanislavschi
- Department of Organic, Biochemical, and Food Engineering, Gheorghe Asachi Technical University of Iasi; Iasi, Romania
| | - Brian M. Starzomski
- School of Environmental Studies, University of Victoria; Victoria, BC, Canada
| | - Rachel L. Stone
- Department of Biology, Case Western Reserve University; Cleveland, OH, USA
| | - Kathryn G. Turner
- Department of Biological Sciences, Idaho State University; Pocatello, ID, USA
| | | | - Acer VanWallendael
- Department of Horticultural Science, North Carolina State University; Raleigh, NC, USA
| | | | - Justin Zweck
- Department of Ecosystem Science and Management, Pennsylvania State University; University Park, PA, USA
| | - Cynthia S. Brown
- Department of Agricultural Biology, Colorado State University; Fort Collins, CO, USA
| | | | - Dana M. Blumenthal
- US Department of Agriculture, Agricultural Research Service, Rangeland Resources and Systems Research Unit; Fort Collins, CO, USA
| | - Matthew J. Germino
- US Geological Survey, Forest and Rangeland Ecosystem Science Center; Boise, Idaho, USA
| | - Lauren M. Porensky
- US Department of Agriculture, Agricultural Research Service, Rangeland Resources and Systems Research Unit; Fort Collins, CO, USA
| | - Mevin B. Hooten
- Department of Statistics and Data Sciences, The University of Texas at Austin; Austin, TX, USA
| | - Peter B. Adler
- Department of Wildland Resources and the Ecology Center, Utah State University; Logan, UT, USA
| | - Jesse R. Lasky
- Department of Biology, Pennsylvania State University; University Park, PA, USA
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Kalsing A, Velini ED, Merotto A, Carbonari CA. The population genomics of Conyza spp. in soybean macroregions suggest the spread of herbicide resistance through intraspecific and interspecific gene flow. Sci Rep 2024; 14:19536. [PMID: 39174662 PMCID: PMC11341714 DOI: 10.1038/s41598-024-70153-8] [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: 01/10/2024] [Accepted: 08/13/2024] [Indexed: 08/24/2024] Open
Abstract
Herbicide-resistant Conyza spp. are a threat to many crops. These widespread weeds are closely related species and often cooccur. To characterize the origins of their resistance and the mechanisms underlying their spread, we assessed the genomic variation in glyphosate-resistant Conyza spp. in Brazil. Twenty populations were sampled from soybean fields across four macroregions (MRSs). A genotyping-by-sequencing study resulted in 2,998 single-nucleotide polymorphisms (SNPs) obtained for C. bonariensis (L.) and the closely related C. sumatrensis (Retz) E. Walker. Higher genomic diversity (π) and heterozygosity (HO/HE) and lower inbreeding coefficient (FIS) values were detected in populations of Conyza spp. from MRS 1 (southern) than in those from other MRSs. Strong genomic structure clustered individuals into three groups (FST = 0.22; p value = 0.000) associated with the MRSs. Thus, resistance to glyphosate originated from independent selection in different MRSs across Brazil. Our dataset supports the occurrence of intraspecific gene flow in Brazil and identified individuals of C. bonariensis that did not group within species. These findings suggest that allelic introgressions within and among species have impacted the evolution and spread of resistance to glyphosate in Conyza spp. We discuss how to mitigate new resistance cases, particularly for the released stacked traits herbicide tolerance in soybeans.
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Affiliation(s)
- Augusto Kalsing
- Crop Health Research and Development, Corteva Agriscience™, Mogi Mirim, SP, Brazil. Postgraduate Group of Crop Protection, School of Agriculture Sciences, São Paulo State University-UNESP, Botucatu, SP, Brazil.
| | - Edivaldo D Velini
- Crop Protection Department, School of Agriculture Sciences, São Paulo State University-UNESP, Botucatu, SP, Brazil
| | - Aldo Merotto
- Crop Science Department, School of Agriculture, Federal University of Rio Grande do Sul-UFRGS, Porto Alegre, RS, Brazil
| | - Caio A Carbonari
- Crop Protection Department, School of Agriculture Sciences, São Paulo State University-UNESP, Botucatu, SP, Brazil
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3
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Snead AA, Tatarenkov A, Taylor DS, Marson K, Earley RL. Centrality to the metapopulation is more important for population genetic diversity than habitat area or fragmentation. Biol Lett 2024; 20:20240158. [PMID: 39044630 PMCID: PMC11267237 DOI: 10.1098/rsbl.2024.0158] [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: 03/24/2024] [Revised: 05/13/2024] [Accepted: 06/18/2024] [Indexed: 07/25/2024] Open
Abstract
Drift and gene flow affect genetic diversity. Given that the strength of genetic drift increases as population size decreases, management activities have focused on increasing population size through preserving habitats to preserve genetic diversity. Few studies have empirically evaluated the impacts of drift and gene flow on genetic diversity. Kryptolebias marmoratus, henceforth 'rivulus', is a small killifish restricted to fragmented New World mangrove forests with gene flow primarily associated with ocean currents. Rivulus form distinct populations across patches, making them a well-suited system to test the extent to which habitat area, fragmentation and connectivity are associated with genetic diversity. Using over 1000 individuals genotyped at 32 microsatellite loci, high-resolution landcover data and oceanographic simulations with graph theory, we demonstrate that centrality (connectivity) to the metapopulation is more strongly associated with genetic diversity than habitat area or fragmentation. By comparing models with and without centrality standardized by the source population's genetic diversity, our results suggest that metapopulation centrality is critical to genetic diversity regardless of the diversity of adjacent populations. While we find evidence that habitat area and fragmentation are related to genetic diversity, centrality is always a significant predictor with a larger effect than any measure of habitat configuration.
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Affiliation(s)
- Anthony A. Snead
- Department of Biological Sciences, University of Alabama, 300 Hackberry Lane, Tuscaloosa, AL35487, USA
- Department of Biology, New York University, New York, NY10003, USA
| | - Andrey Tatarenkov
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA92697, USA
| | - D. Scott Taylor
- The Environmentally Endangered Lands (EEL) Program, Brevard County, Melbourne, FL32904, USA
| | - Kristine Marson
- Department of Biological Sciences, University of Alabama, 300 Hackberry Lane, Tuscaloosa, AL35487, USA
| | - Ryan L. Earley
- Department of Biological Sciences, University of Alabama, 300 Hackberry Lane, Tuscaloosa, AL35487, USA
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4
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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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5
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Munné-Bosch S. Achieving the impossible: prevention and eradication of invasive plants in Mediterranean-type ecosystems. TRENDS IN PLANT SCIENCE 2024; 29:437-446. [PMID: 38040553 DOI: 10.1016/j.tplants.2023.11.007] [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: 05/24/2023] [Revised: 10/30/2023] [Accepted: 11/07/2023] [Indexed: 12/03/2023]
Abstract
An in-depth analysis of the mechanistic processes underlying the evolution and ecophysiology of typical invasive plants such as Carpobrotus spp., Acacia spp., Agave spp., and Opuntia spp. in Mediterranean-type ecosystems shows very sophisticated, complex, and efficient strategies for invasion success, particularly in fragmented habitats. Propagule pressure at both geographical and temporal scales and the establishment of long-term seed banks are determinant for invasion success. A two-sword strategy based on long-term prevention and eradication is proposed for the management of Mediterranean-type ecosystems. Eradication of invasive plants in Mediterranean-type ecosystems appears to be extremely difficult nowadays and, at least for some invaders like Carpobrotus spp., long-term approaches that ultimately culminate in the elimination of seed banks is the only path for success.
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Affiliation(s)
- Sergi Munné-Bosch
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Faculty of Biology, Av. Diagonal 643, 08028 Barcelona, Spain; Institute of Research in Biodiversity (IRBio), University of Barcelona, Faculty of Biology, Av. Diagonal 643, 08028 Barcelona, Spain.
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6
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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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7
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Padilla Perez DJ. Geographic and seasonal variation of the for gene reveal signatures of local adaptation in Drosophila melanogaster. J Evol Biol 2024; 37:201-211. [PMID: 38301664 DOI: 10.1093/jeb/voad018] [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: 07/03/2023] [Revised: 11/18/2023] [Accepted: 12/16/2023] [Indexed: 02/03/2024]
Abstract
In the early 1980s, the observation that Drosophila melanogaster larvae differed in their foraging behaviour laid the foundation for the work that would later lead to the discovery of the foraging gene (for) and its associated foraging phenotypes, rover and sitter. Since then, the molecular characterization of the for gene and our understanding of the mechanisms that maintain its phenotypic variants in the laboratory have progressed enormously. However, the significance and dynamics of such variation are yet to be investigated in nature. With the advent of next-generation sequencing, it is now possible to identify loci underlying the adaptation of populations in response to environmental variation. Here, I present the results of a genotype-environment association analysis that quantifies variation at the for gene among samples of D. melanogaster structured across space and time. These samples consist of published genomes of adult flies collected worldwide, and at least twice per site of collection (during spring and fall). Both an analysis of genetic differentiation based on Fst values and an analysis of population structure revealed an east-west gradient in allele frequency. This gradient may be the result of spatially varying selection driven by the seasonality of precipitation. These results support the hypothesis that different patterns of gene flow as expected under models of isolation by distance and potentially isolation by environment are driving genetic differentiation among populations. Overall, this study is essential for understanding the mechanisms underlying the evolution of foraging behaviour in D. melanogaster.
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8
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Michielini JP, Yi X, Brown LM, Gao SM, Orians C, Crone EE. Novel host plant use by a specialist insect depends on geographic variation in both the host and herbivore species. Oecologia 2024; 204:95-105. [PMID: 38123786 PMCID: PMC10830605 DOI: 10.1007/s00442-023-05490-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: 04/14/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023]
Abstract
Understanding the circumstances under which insect herbivores will adopt a novel host plant is a longstanding question in basic and applied ecology. While geographic variation in host use can arise through differences in both herbivore preference and plant characteristics, there is a tendency to attribute geographic variation in host use to regional differences in herbivore preference alone. This is especially true for herbivores specialized to one or a few plant species. We compared how geographic variation in herbivore preference and host plant origin shape regional differences in host plant use by the specialized herbivore, Euphydryas phaeton. In parts of its range, E. phaeton uses only a native host, Chelone glabra, while in others, it also uses an introduced host, Plantago lanceolata. We offered female butterflies from each region the non-native host plant sourced from both regions and compared their oviposition behavior. The non-native host was almost universally rejected by butterflies in the region where only the native plant is used. In the region where butterflies use both hosts, females accepted non-native plants from their natal region twice as often as non-native plants from the other region where they are not used. Acceptance differed substantially among individual butterflies within regions but not among plants within regions. Thus, both individual preference and regional differences in both the insect and non-native host contributed to the geographic variation in different ways. These results highlight that, in addition to herbivore preference, regional differences in perceived plant suitability may be an important driver of diet breadth.
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Affiliation(s)
- James P Michielini
- Department of Biology, Tufts University, Medford, MA, 02155, USA.
- Department of Evolution and Ecology, University of California, Davis, CA, 95616, USA.
| | - Xianfeng Yi
- College of Life Science, Qufu Normal University, Qufu, China
| | - Leone M Brown
- Department of Biology, Tufts University, Medford, MA, 02155, USA
- Biology Department, James Madison University, Harrisonburg, VA, 22807, USA
| | - Shan Ming Gao
- Biology Department, Pomona College, Claremont, CA, 91711, USA
| | - Colin Orians
- Department of Biology, Tufts University, Medford, MA, 02155, USA
| | - Elizabeth E Crone
- Department of Biology, Tufts University, Medford, MA, 02155, USA
- Department of Evolution and Ecology, University of California, Davis, CA, 95616, USA
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9
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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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10
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Brian JI, Catford JA. A mechanistic framework of enemy release. Ecol Lett 2023; 26:2147-2166. [PMID: 37921034 DOI: 10.1111/ele.14329] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 10/03/2023] [Indexed: 11/04/2023]
Abstract
The enemy release hypothesis (ERH) is the best-known hypothesis explaining high performance (e.g. rapid population growth) of exotic species. However, the current framing of the ERH does not explicitly link evidence of enemy release with exotic performance. This leads to uncertainty regarding the role of enemy release in biological invasions. Here, we demonstrate that the effect of enemy release on exotic performance is the product of three factors: enemy impact, enemy diversity, and host adaptation. These factors are modulated by seven contexts: time since introduction, resource availability, phylogenetic relatedness of exotic and native species, host-enemy asynchronicity, number of introduction events, type of enemy, and strength of growth-defence trade-offs. ERH-focused studies frequently test different factors under different contexts. This can lead to inconsistent findings, which typifies current evidence for the ERH. For example, over 80% of meta-analyses fail to consider ecological contexts which can alter study findings; we demonstrate this by re-analysing a recent ERH synthesis. Structuring the ERH around factors and contexts promotes generalisable predictions about when and where exotic species may benefit from enemy release, empowering effective management. Our mechanistic factor-context framework clearly lays out the evidence required to support the ERH, unifies many enemy-related invasion hypotheses, and enhances predictive capacity.
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Affiliation(s)
- Joshua I Brian
- Department of Geography, King's College London, London, UK
| | - Jane A Catford
- Department of Geography, King's College London, London, UK
- Fenner School of Environment & Society, The Australian National University, Canberra, Australia
- School of Agriculture, Food and Ecosystem Sciences, The University of Melbourne, Parkville, Australia
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11
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Hofmeister NR, Stuart KC, Warren WC, Werner SJ, Bateson M, Ball GF, Buchanan KL, Burt DW, Cardilini APA, Cassey P, De Meyer T, George J, Meddle SL, Rowland HM, Sherman CDH, Sherwin WB, Vanden Berghe W, Rollins LA, Clayton DF. Concurrent invasions of European starlings in Australia and North America reveal population-specific differentiation in shared genomic regions. Mol Ecol 2023. [PMID: 37933429 DOI: 10.1111/mec.17195] [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: 11/04/2022] [Revised: 09/22/2023] [Accepted: 10/23/2023] [Indexed: 11/08/2023]
Abstract
A species' success during the invasion of new areas hinges on an interplay between the demographic processes common to invasions and the specific ecological context of the novel environment. Evolutionary genetic studies of invasive species can investigate how genetic bottlenecks and ecological conditions shape genetic variation in invasions, and our study pairs two invasive populations that are hypothesized to be from the same source population to compare how each population evolved during and after introduction. Invasive European starlings (Sturnus vulgaris) established populations in both Australia and North America in the 19th century. Here, we compare whole-genome sequences among native and independently introduced European starling populations to determine how demographic processes interact with rapid evolution to generate similar genetic patterns in these recent and replicated invasions. Demographic models indicate that both invasive populations experienced genetic bottlenecks as expected based on invasion history, and we find that specific genomic regions have differentiated even on this short evolutionary timescale. Despite genetic bottlenecks, we suggest that genetic drift alone cannot explain differentiation in at least two of these regions. The demographic boom intrinsic to many invasions as well as potential inversions may have led to high population-specific differentiation, although the patterns of genetic variation are also consistent with the hypothesis that this infamous and highly mobile invader adapted to novel selection (e.g., extrinsic factors). We use targeted sampling of replicated invasions to identify and evaluate support for multiple, interacting evolutionary mechanisms that lead to differentiation during the invasion process.
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Affiliation(s)
- Natalie R Hofmeister
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Ithaca, New York, USA
| | - Katarina C Stuart
- School of Biological, Earth and Environmental Sciences, Evolution & Ecology Research Centre, UNSW Sydney, Sydney, New South Wales, Australia
| | - Wesley C Warren
- Department of Animal Sciences and Surgery, Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri, USA
| | - Scott J Werner
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, Colorado, USA
| | - Melissa Bateson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Gregory F Ball
- Department of Psychology, University of Maryland, College Park, Maryland, USA
| | | | - David W Burt
- Office of the Deputy Vice-Chancellor (Research and Innovation), The University of Queensland, Brisbane, Queensland, Australia
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - Adam P A Cardilini
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, Victoria, Australia
| | - Phillip Cassey
- Invasion Science & Wildlife Ecology Lab, University of Adelaide, Adelaide, South Australia, Australia
| | - Tim De Meyer
- Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Julia George
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Simone L Meddle
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - Hannah M Rowland
- Max Planck Institute for Chemical Ecology, Jena, Germany
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Craig D H Sherman
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - William B Sherwin
- School of Biological, Earth and Environmental Sciences, Evolution & Ecology Research Centre, UNSW Sydney, Sydney, New South Wales, Australia
| | - Wim Vanden Berghe
- Department of Biomedical Sciences, University Antwerp, Antwerp, Belgium
| | - Lee Ann Rollins
- School of Biological, Earth and Environmental Sciences, Evolution & Ecology Research Centre, UNSW Sydney, Sydney, New South Wales, Australia
| | - David F Clayton
- Department of Genetics & Biochemistry, Clemson University, Clemson, South Carolina, USA
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12
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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: 14] [Impact Index Per Article: 14.0] [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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13
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Tesfay YB, Blaschke A, Ashley N, Portillo L, Scalisi A, Adli B, Kreyling J. Increased Plasticity in Invasive Populations of a Globally Invasive Cactus. PLANTS (BASEL, SWITZERLAND) 2023; 12:3287. [PMID: 37765451 PMCID: PMC10536680 DOI: 10.3390/plants12183287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/09/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023]
Abstract
Biological invasions pose global threats to biodiversity and ecosystem functions. Invasive species often display a high degree of phenotypic plasticity, enabling them to adapt to new environments. This study examines plasticity to water stress in native and invasive Opuntia ficus-indica populations, a prevalent invader in arid and semi-arid ecosystems. Through controlled greenhouse experiments, we evaluated three native and nine invasive populations. While all plants survived the dry treatment, natives exhibited lower plasticity to high water availability with only a 36% aboveground biomass increase compared to the invasives with a greater increase of 94%. In terms of belowground biomass, there was no significant response to increased water availability for native populations, but plants from the invasive populations showed a 75% increase from the dry to the wet treatment. Enhanced phenotypic plasticity observed in invasive populations of O. ficus-indica is likely a significant driver of their success and invasiveness across different regions, particularly with a clear environmental preference towards less arid conditions. Climate change is expected to amplify the invasion success due to the expansion of arid areas and desertification. Opuntia ficus-indica adapts to diverse environments, survives dry spells, and grows rapidly in times of high-water supply, making it a candidate for increased invasion potential with climate change.
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Affiliation(s)
- Yohannes B. Tesfay
- Institute of Botany and Landscape Ecology, University of Greifswald, 17489 Greifswald, Germany
| | - Annika Blaschke
- Institute of Botany and Landscape Ecology, University of Greifswald, 17489 Greifswald, Germany
| | - Nathan Ashley
- Odum School of Ecology, University of Georgia, Athens, GA 30602, USA
| | - Liberato Portillo
- Department of Botany and Zoology, University of Guadalajara, Guadalajara 44100, Mexico
| | - Alessio Scalisi
- Department of Energy, Environment and Climate Action, Agriculture, Agriculture Victoria Research, Tatura, VIC 3616, Australia
| | - Benziane Adli
- Department of Biology, Faculty of Nature and Life Sciences, University of Djelfa, Djelfa 17000, Algeria
| | - Juergen Kreyling
- Institute of Botany and Landscape Ecology, University of Greifswald, 17489 Greifswald, Germany
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14
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Sato DX, Matsuda Y, Usio N, Funayama R, Nakayama K, Makino T. Genomic adaptive potential to cold environments in the invasive red swamp crayfish. iScience 2023; 26:107267. [PMID: 37520695 PMCID: PMC10371857 DOI: 10.1016/j.isci.2023.107267] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/31/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023] Open
Abstract
Biological invasion refers to the introduction, spread, and establishment of non-native species in a novel habitat. The ways in which invasive species successfully colonize new and different environments remain a fundamental topic of research in ecology and evolutionary biology. Here, we investigated the genomic and transcriptomic characteristics of the red swamp crayfish (Procambarus clarkii), a widespread invader in freshwater environments. Targeting a recently colonized population in Sapporo, Japan that appears to have acquired a high degree of cold tolerance, RNA-seq analysis revealed differentially expressed genes in response to cold exposure, and those involved in protease inhibitors and cuticle development were considered top candidates. We also found remarkable duplications for these gene families during evolution and their concerted expression patterns, suggesting functional amplification against low temperatures. Our study thus provides clues to the unique genetic characteristics of P. clarkii, possibly related to cold adaptation.
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Affiliation(s)
- Daiki X. Sato
- Institute for Advanced Academic Research, Chiba University, Chiba 263-8522, Japan
- Graduate School of Science, Chiba University, Chiba 263-8522, Japan
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Yuki Matsuda
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Nisikawa Usio
- Institute of Nature and Environmental Technology, Kanazawa University, Kanazawa 920-1192, Japan
| | - Ryo Funayama
- Department of Cell Proliferation, United Center for Advanced Research and Translational Medicine, Graduate School of Medicine, Tohoku University, Aoba-ku, Sendai 980-8575, Japan
| | - Keiko Nakayama
- Department of Cell Proliferation, United Center for Advanced Research and Translational Medicine, Graduate School of Medicine, Tohoku University, Aoba-ku, Sendai 980-8575, Japan
| | - Takashi Makino
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
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15
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Korpelainen H, Pietiläinen M. What Makes a Good Plant Invader? Life (Basel) 2023; 13:1596. [PMID: 37511971 PMCID: PMC10381298 DOI: 10.3390/life13071596] [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: 05/26/2023] [Revised: 07/16/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
We explored traits that promote plant invasions. External factors affecting invasion success consist of various abiotic and biotic constraints. How well plants perform under those depends on multiple characteristics, such as life history traits, genetic variation patterns, competitive and dispersal abilities, phenotypic plasticity, resistance, tolerance, and possibly allelopathic interactions. Since the introduction of invasive species is often connected with humans, their geographical distribution and differentiation may not reflect adaptation. However, a lack of adaptation may be compensated for by repeated introductions via mixing genotypes from multiple populations or through novel mutations. As a case study, we used data from the Global Invasive Species Database of IUCN and attempted to reveal factors contributing to invasiveness. The most prevalent features are that the dispersal is strongly human assisted, many species are used as ornamentals, disturbed habitats are favored, and most species are perennial. Distribution features show that the worst invasive species typically have a narrower native distribution, but both groups, i.e., most serious invasive and other listed invasive species, have commonly developed a multicontinental distribution. The change in the multicontinental distribution from 6% to 63% in most serious invasive species reflects their effectiveness in global dispersal and establishment. High proportions of invasive species in both groups have mixed reproduction systems, i.e., they have the ability to propagate both sexually and asexually (57% and 50%, respectively). This provides flexibility for spreading and establishment. A lower proportion of the worst invasive species was mainly/only sexual (23%, often hermaphrodites) when compared to other invasive plants (40%). In the case of sexual reproduction, hermaphroditism combined with self-compatibility may enhance invasiveness, since selfing allows fertilization and recombination even under low population densities. Overall, the ability for asexual propagation and, in the case of sexuality, hermaphroditism, is an asset in the invasion process.
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Affiliation(s)
- Helena Korpelainen
- Department of Agricultural Sciences, Viikki Plant Science Centre, P.O. Box 27, FI-00014 University of Helsinki, Finland
| | - Maria Pietiläinen
- Department of Agricultural Sciences, Viikki Plant Science Centre, P.O. Box 27, FI-00014 University of Helsinki, Finland
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16
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Sias C, Subramanian N, Hodnett G, Rooney W, Bagavathiannan M. Rate of crop-weed hybridization in Sorghum bicolor × Sorghum halepense is influenced by genetic background, pollen load, and the environment. Evol Appl 2023; 16:781-796. [PMID: 37124087 PMCID: PMC10130556 DOI: 10.1111/eva.13536] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 12/22/2022] [Accepted: 02/02/2023] [Indexed: 03/29/2023] Open
Abstract
The potential for gene flow between cultivated species and their weedy relatives poses agronomic and environmental concerns, particularly when there are opportunities for the transfer of adaptive or agronomic traits such as herbicide resistance into the weedy forms. Grain sorghum (Sorghum bicolor) is an important crop capable of interspecific hybridization with its weedy relative johnsongrass (Sorghum halepense). Previous findings have shown that triploid progenies resulting from S. bicolor × S. halepense crosses typically collapse with only a few developing into mature seeds, whereas tetraploids often fully develop. The objective of this experiment was to determine the impact of S. bicolor genotype and pollen competition on the frequency of hybridization between S. bicolor and S. halepense. A total of 12 different cytoplasmic male sterile S. bicolor genotypes were compared with their respective male fertile lines across 2 years, to assess the frequency of hybridization and seed set when S. halepense served as the pollinator parent. Results indicate significant differences in the frequency of interspecific hybridization among the S. bicolor genotypes, and pollen fertility in S. bicolor reduced the rate of this interspecific hybridization by up to two orders of magnitude. Further, hybridization rates greatly varied across the two study environments. Results are helpful for developing appropriate gene flow mitigation strategies and indicate that gene flow could be reduced by the selection of appropriate seed parents for sorghum hybrids.
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Affiliation(s)
- Cynthia Sias
- Department of Soil and Crop SciencesTexas A&M UniversityCollege StationTexasUSA
| | - Nithya Subramanian
- Department of Soil and Crop SciencesTexas A&M UniversityCollege StationTexasUSA
| | - George Hodnett
- Department of Soil and Crop SciencesTexas A&M UniversityCollege StationTexasUSA
| | - William Rooney
- Department of Soil and Crop SciencesTexas A&M UniversityCollege StationTexasUSA
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17
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Chung MY, Merilä J, Li J, Mao K, López-Pujol J, Tsumura Y, Chung MG. Neutral and adaptive genetic diversity in plants: An overview. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1116814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
Genetic diversity is a prerequisite for evolutionary change in all kinds of organisms. It is generally acknowledged that populations lacking genetic variation are unable to evolve in response to new environmental conditions (e.g., climate change) and thus may face an increased risk of extinction. Although the importance of incorporating genetic diversity into the design of conservation measures is now well understood, less attention has been paid to the distinction between neutral (NGV) and adaptive (AGV) genetic variation. In this review, we first focus on the utility of NGV by examining the ways to quantify it, reviewing applications of NGV to infer ecological and evolutionary processes, and by exploring its utility in designing conservation measures for plant populations and species. Against this background, we then summarize the ways to identify and estimate AGV and discuss its potential use in plant conservation. After comparing NGV and AGV and considering their pros and cons in a conservation context, we conclude that there is an urgent need for a better understanding of AGV and its role in climate change adaptation. To date, however, there are only a few AGV studies on non-model plant species aimed at deciphering the genetic and genomic basis of complex trait variation. Therefore, conservation researchers and practitioners should keep utilizing NGV to develop relevant strategies for rare and endangered plant species until more estimates of AGV are available.
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18
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Temporal decline of genetic differentiation among populations of western flower thrips across an invaded range. Biol Invasions 2023. [DOI: 10.1007/s10530-023-03024-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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19
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History cooling events contributed to the endangered status of Pseudotsuga brevifolia endemic to limestone habitats. Glob Ecol Conserv 2023. [DOI: 10.1016/j.gecco.2023.e02414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
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20
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Mairal M, García-Verdugo C, Le Roux JJ, Chau JH, van Vuuren BJ, Hui C, Münzbergová Z, Chown SL, Shaw JD. Multiple introductions, polyploidy and mixed reproductive strategies are linked to genetic diversity and structure in the most widespread invasive plant across Southern Ocean archipelagos. Mol Ecol 2023; 32:756-771. [PMID: 36478264 DOI: 10.1111/mec.16809] [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: 07/08/2022] [Revised: 11/30/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Biological invasions in remote areas that experience low human activity provide unique opportunities to elucidate processes responsible for invasion success. Here we study the most widespread invasive plant species across the isolated islands of the Southern Ocean, the annual bluegrass, Poa annua. To analyse geographical variation in genome size, genetic diversity and reproductive strategies, we sampled all major sub-Antarctic archipelagos in this region and generated microsatellite data for 470 individual plants representing 31 populations. We also estimated genome sizes for a subset of individuals using flow cytometry. Occasional events of island colonization are expected to result in high genetic structure among islands, overall low genetic diversity and increased self-fertilization, but we show that this is not the case for P. annua. Microsatellite data indicated low population genetic structure and lack of isolation by distance among the sub-Antarctic archipelagos we sampled, but high population structure within each archipelago. We identified high levels of genetic diversity, low clonality and low selfing rates in sub-Antarctic P. annua populations (contrary to rates typical of continental populations). In turn, estimates of selfing declined in populations as genetic diversity increased. Additionally, we found that most P. annua individuals are probably tetraploid and that only slight variation exists in genome size across the Southern Ocean. Our findings suggest multiple independent introductions of P. annua into the sub-Antarctic, which promoted the establishment of genetically diverse populations. Despite multiple introductions, the adoption of convergent reproductive strategies (outcrossing) happened independently in each major archipelago. The combination of polyploidy and a mixed reproductive strategy probably benefited P. annua in the Southern Ocean by increasing genetic diversity and its ability to cope with the novel environmental conditions.
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Affiliation(s)
- Mario Mairal
- Departamento de Biodiversidad, Ecología y Evolución, Universidad Complutense de Madrid, Madrid, Spain.,Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa
| | - Carlos García-Verdugo
- Departamento de Botánica, Facultad de Ciencias, Universidad de Granada, Granada, Spain.,Departamento de Biología, Universitat de les Illes Balears - Institut Mediterrani d'Estudis Avançats (CSIC-UIB), Mallorca, Spain
| | - Johannes J Le Roux
- Departamento de Biodiversidad, Ecología y Evolución, Universidad Complutense de Madrid, Madrid, Spain.,School of Natural Sciences, Macquarie University, New South Wales, Sydney, Australia
| | - John H Chau
- Department of Zoology, Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park, South Africa
| | - Bettine Jansen van Vuuren
- Department of Zoology, Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park, South Africa
| | - Cang Hui
- Department of Mathematical Sciences, Centre for Invasion Biology, Stellenbosch University, Stellenbosch, South Africa.,Biodiversity Informatics Unit, African Institute for Mathematical Sciences, Cape Town, South Africa
| | - Zuzana Münzbergová
- Faculty of Science, Department of Botany, Charles University, Prague, Czech Republic.,Institute of Botany, Czech Academy of Science, Průhonice, Czech Republic
| | - Steven L Chown
- Securing Antarctica's Environmental Future, School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Justine D Shaw
- Securing Antarctica's Environmental Future, School of Biology and Environmental Sciences, Queensland University of Technology, Brisbane, Queensland, Australia.,Australian Antarctic Division, Tasmania, Kingston, Australia
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21
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Huang P, Hameed R, Abbas M, Balooch S, Alharthi B, Du Y, Abbas A, Younas A, Du D. Integrated omic techniques and their genomic features for invasive weeds. Funct Integr Genomics 2023; 23:44. [PMID: 36680630 DOI: 10.1007/s10142-023-00971-y] [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: 12/08/2022] [Revised: 01/01/2023] [Accepted: 01/11/2023] [Indexed: 01/22/2023]
Abstract
Many emerging invasive weeds display rapid adaptation against different stressful environments compared to their natives. Rapid adaptation and dispersal habits helped invasive populations have strong diversity within the population compared to their natives. Advances in molecular marker techniques may lead to an in-depth understanding of the genetic diversity of invasive weeds. The use of molecular techniques is rapidly growing, and their implications in invasive weed studies are considered powerful tools for genome purposes. Here, we review different approach used multi-omics by invasive weed studies to understand the functional structural and genomic changes in these species under different environmental fluctuations, particularly, to check the accessibility of advance-sequencing techniques used by researchers in genome sequence projects. In this review-based study, we also examine the importance and efficiency of different molecular techniques in identifying and characterizing different genes, associated markers, proteins, metabolites, and key metabolic pathways in invasive and native weeds. Use of these techniques could help weed scientists to further reduce the knowledge gaps in understanding invasive weeds traits. Although these techniques can provide robust insights about the molecular functioning, employing a single omics platform can rarely elucidate the gene-level regulation and the associated real-time expression of weedy traits due to the complex and overlapping nature of biological interactions. We conclude that different multi-omic techniques will provide long-term benefits in launching new genome projects to enhance the understanding of invasive weeds' invasion process.
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Affiliation(s)
- Ping Huang
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Rashida Hameed
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Manzer Abbas
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, 644000, Sichuan Province, People's Republic of China
| | - Sidra Balooch
- Institute of Botany, Bahauddin Zakariya University, Multan, Punjab, Pakistan
| | - Badr Alharthi
- Department of Biology, University College of Al Khurmah, Taif University, PO. Box 11099, Taif, 21944, Saudi Arabia
| | - Yizhou Du
- Faculty of Engineering, School of Computer Science, University of Sydney, Sydney, New South Wales, Australia
| | - Adeel Abbas
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China.
| | - Afifa Younas
- Department of Botany, Lahore College for Women University, Lahore, Pakistan
| | - Daolin Du
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China.
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22
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Parvizi E, Dhami MK, Yan J, McGaughran A. Population genomic insights into invasion success in a polyphagous agricultural pest, Halyomorpha halys. Mol Ecol 2023; 32:138-151. [PMID: 36261398 PMCID: PMC10099481 DOI: 10.1111/mec.16740] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 10/13/2022] [Accepted: 10/17/2022] [Indexed: 01/07/2023]
Abstract
Invasive species are increasingly threatening ecosystems and agriculture by rapidly expanding their range and adapting to environmental and human-imposed selective pressures. The genomic mechanisms that underlie such rapid changes remain unclear, especially for agriculturally important pests. Here, we used genome-wide polymorphisms derived from native, invasive, and intercepted samples and populations of the brown marmorated stink bug (BMSB), Halyomorpha halys, to gain insights into population genomics processes that have promoted the successful global invasion of this polyphagous pest. Our analysis demonstrated that BMSB exhibits spatial structure but admixture rates are high among introduced populations, resulting in similar levels of genomic diversity across native and introduced populations. These spatial genomic patterns suggest a complex invasion scenario, potentially with multiple bridgehead events, posing a challenge for accurately assigning BMSB incursions to their source using reduced-representation genomic data. By associating allele frequencies with the invasion status of BMSB populations, we found significantly differentiated single nucleotide polymorphisms (SNPs) located in close proximity to genes for insecticide resistance and olfaction. Comparing variations in allele frequencies among populations for outlier SNPs suggests that BMSB invasion success has probably evolved from standing genetic variation. In addition to being a major nuisance of households, BMSB has caused significant economic losses to agriculture in recent years and continues to expand its range. Despite no record of BMSB insecticide resistance to date, our results show high capacity for potential evolution of such traits, highlighting the need for future sustainable and targeted management strategies.
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Affiliation(s)
- Elahe Parvizi
- Te Aka Mātuatua/School of Science, University of Waikato, Hamilton, New Zealand
| | - Manpreet K Dhami
- Biocontrol and Molecular Ecology, Manaaki Whenua Landcare Research, Lincoln, New Zealand
| | - Juncong Yan
- Plant Health and Environment Laboratory, Ministry for Primary Industries, Auckland, New Zealand
| | - Angela McGaughran
- Te Aka Mātuatua/School of Science, University of Waikato, Hamilton, New Zealand
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23
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Jiang YY, Zhang YY, Zhou XY, Hong XY, Chen L. Population genetics reveal multiple independent invasions of Spodoptera frugiperda (Lepidoptera: Noctuidae) in China. BULLETIN OF ENTOMOLOGICAL RESEARCH 2022; 112:796-806. [PMID: 35477502 DOI: 10.1017/s0007485322000190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The fall armyworm (Spodoptera frugiperda), a destructive pest that originated in South and North America, spread to China in early 2019. Controlling this invasive pest requires an understanding of its population structure and migration patterns, yet the invasion genetics of Chinese S. frugiperda is not clear. Here, using the mitochondrial cytochrome oxidase subunit I (COI) gene, triose phosphate isomerase (Tpi) gene and eight microsatellite loci, we investigated genetic structure and genetic diversity of 16 S. frugiperda populations in China. The Tpi locus identified most S. frugiperda populations as the corn-strains, and a few were heterozygous strains. The microsatellite loci revealed that the genetic diversity of this pest in China was lower than that in South America. Furthermore, we found moderate differentiation among the populations, distinct genetic structures between adjacent populations and abundant genetic resources in the S. frugiperda populations from China sampled across 2 years. The survival rate of S. frugiperda was significantly higher when it was fed on corn leaves than on rice leaves, and the larval stage mortality rate was the highest under both treatments. Our results showed that S. frugiperda probably invaded China via multiple independent introductions and careful pesticide control, continuous monitoring and further studies will be needed to minimize its potential future outbreak.
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Affiliation(s)
- Yun-Yuan Jiang
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yi-Yin Zhang
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Xin-Yu Zhou
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Xiao-Yue Hong
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Lei Chen
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
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24
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Lee SR, Son DC. Genetic diversity pattern reveals the primary determinant of burcucumber ( Sicyos angulatus L.) invasion in Korea. FRONTIERS IN PLANT SCIENCE 2022; 13:997521. [PMID: 36457533 PMCID: PMC9706109 DOI: 10.3389/fpls.2022.997521] [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: 07/19/2022] [Accepted: 10/24/2022] [Indexed: 06/17/2023]
Abstract
Biological invasion is a complex process associated with propagule pressure, dispersal ability, environmental constraints, and human interventions, which leave genetic signatures. The population genetics of an invasive species thus provides invaluable insights into the patterns of invasion. Burcucumber, one of the most detrimental weeds for soybean production in US, has recently colonized Korea and rapidly spread posing a great threat to the natural ecosystem. We aim to infer the determinants of the rapid burcucumber invasion by examining the genetic diversity, demography, and spread pattern with advanced genomic tools. We employed 2,696 genome-wide single-nucleotide polymorphisms to assess the level of diversity and the spatial pattern associated with the landscape factors and to infer the demographic changes of 24 populations (364 genotypes) across four major river basins with the east coastal streams in South Korea. Through the approximate Bayesian computation, we inferred the likely invasion scenario of burcucumber in Korea. The landscape genetics approach adopting the circuit theory and MaxEnt model was applied to determine the landscape contributors. Our data suggested that most populations have experienced population bottlenecks, which led to lowered within-population genetic diversity and inflated population divergences. Burcucumber colonization in Korea has strongly been affected by demographic bottlenecks and multiple introductions, whereas environmental factors were not the primary determinant of the invasion. Our work highlighted the significance of preventing secondary introductions, particularly for aggressive weedy plants such as the burcucumber.
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Affiliation(s)
- Soo-Rang Lee
- Department of Biology Education, College of Education, Chosun University, Gwangju, South Korea
| | - Dong Chan Son
- Division of Forest Biodiversity and Herbarium, Korea National Arboretum, Pocheon, South Korea
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25
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Sandvik H, Olsen SL, Töpper JP, Hilmo O. Pathways of introduction of alien species in Norway: analyses of an exhaustive dataset to prioritise management efforts. J Appl Ecol 2022. [DOI: 10.1111/1365-2664.14287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hanno Sandvik
- Norwegian Institute for Nature Research (NINA) Trondheim Norway
| | - Siri L. Olsen
- Norwegian Institute for Nature Research (NINA) Oslo Norway
- Norwegian University of Life Sciences (NMBU) Ås Norway
| | | | - Olga Hilmo
- Norwegian Biodiversity Information Centre Trondheim Norway
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26
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Jousson A, Christe C, Stauffer F, Marazzi B, Aberlenc F, Maspoli G, Naciri Y. Panmixia and active colonisation of the invasive palm Trachycarpus fortunei (Arecaceae) in Southern Switzerland and Northern Italy as inferred by microsatellites and SNP markers. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02874-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
AbstractTrachycarpus fortunei (Arecaceae: Coryphoideae) is an Asian palm that was introduced during the nineteenth century in southern Switzerland and northern Italy as an ornamental plant. In the recent decades, the palm has become an aggressive invasive species in the region. Before this study, the genetic structure and diversity of the naturalised populations were unknown. We aimed at understanding the dynamics of invasion and at comparing the results obtained with two types of markers. This genetic approach aimed at tracing back as far as possible the source of invasive populations comparing historical information found in literature and invasive genetic patterns. The genetic diversity was analysed using eight microsatellites (five were developed for that purpose) and 31′000 SNPs identified through GBS analyses. Genetic analyses were carried out for 200 naturalised individuals sampled from 21 populations in the Canton Ticino (Switzerland) and the provinces of Lombardy and Piedmont (Italy). The observed general panmixia indicates that the expansion of T. fortunei is active in its naturalised areas. The genetic pattern found for both SNPs and microsatellites appears to be related to the colonisation process, with a lack of geographic structure and bottleneck signatures occurring at the colonisation front, distantly from historical sites. This study gives a better understanding of the expansion of T. fortunei and adds new insights to its ecology.
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27
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Byrne D, Scheben A, Scott JK, Webber BL, Batchelor KL, Severn-Ellis AA, Gooden B, Bell KL. Genomics reveals the history of a complex plant invasion and improves the management of a biological invasion from the South African-Australian biotic exchange. Ecol Evol 2022; 12:e9179. [PMID: 36016815 PMCID: PMC9396708 DOI: 10.1002/ece3.9179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 07/12/2022] [Indexed: 11/10/2022] Open
Abstract
Many plants exchanged in the global redistribution of species in the last 200 years, particularly between South Africa and Australia, have become threatening invasive species in their introduced range. Refining our understanding of the genetic diversity and population structure of native and alien populations, introduction pathways, propagule pressure, naturalization, and initial spread, can transform the effectiveness of management and prevention of further introductions. We used 20,221 single nucleotide polymorphisms to reconstruct the invasion of a coastal shrub, Chrysanthemoides monilifera ssp. rotundata (bitou bush) from South Africa, into eastern Australia (EAU), and Western Australia (WAU). We determined genetic diversity and population structure across the native and introduced ranges and compared hypothesized invasion scenarios using Bayesian modeling. We detected considerable genetic structure in the native range, as well as differentiation between populations in the native and introduced range. Phylogenetic analysis showed the introduced samples to be most closely related to the southern-most native populations, although Bayesian analysis inferred introduction from a ghost population. We detected strong genetic bottlenecks during the founding of both the EAU and WAU populations. It is likely that the WAU population was introduced from EAU, possibly involving an unsampled ghost population. The number of private alleles and polymorphic SNPs successively decreased from South Africa to EAU to WAU, although heterozygosity remained high. That bitou bush remains an invasion threat in EAU, despite reduced genetic diversity, provides a cautionary biosecurity message regarding the risk of introduction of potentially invasive species via shipping routes.
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Affiliation(s)
- Dennis Byrne
- CSIRO Health & Biosecurity Floreat Western Australia Australia
- School of Biological Sciences University of Western Australia Crawley Western Australia Australia
| | - Armin Scheben
- School of Biological Sciences University of Western Australia Crawley Western Australia Australia
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory Cold Spring, Harbor New York USA
| | - John K Scott
- CSIRO Health & Biosecurity Floreat Western Australia Australia
- School of Biological Sciences University of Western Australia Crawley Western Australia Australia
| | - Bruce L Webber
- CSIRO Health & Biosecurity Floreat Western Australia Australia
- School of Biological Sciences University of Western Australia Crawley Western Australia Australia
- Western Australian Biodiversity Science Institute Perth Western Australia Australia
| | | | - Anita A Severn-Ellis
- School of Biological Sciences University of Western Australia Crawley Western Australia Australia
| | - Ben Gooden
- CSIRO Health and Biosecurity Canberra Australian Capital Territory Australia
- Centre for Sustainable Ecosystem Solutions School of Earth, Atmospheric and Life Sciences, University of Wollongong Wollongong New South Wales Australia
| | - Karen L Bell
- CSIRO Health & Biosecurity Floreat Western Australia Australia
- School of Biological Sciences University of Western Australia Crawley Western Australia Australia
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28
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Iwanycki Ahlstrand N, Gopalakrishnan S, Vieira FG, Bieker VC, Meudt HM, Dunbar-Co S, Rothfels CJ, Martinez-Swatson KA, Maldonado C, Hassemer G, Shipunov A, Bowers MD, Gardner E, Xu M, Ghorbani A, Amano M, Grace OM, Pringle JS, Bishop M, Manzanilla V, Cotrim H, Blaney S, Zubov D, Choi HK, Yesil Y, Bennett B, Vimolmangkang S, El-Seedi HR, Staub PO, Li Z, Boldbaatar D, Hislop M, Caddy LJ, Muasya AM, Saslis-Lagoudakis CH, Gilbert MTP, Zerega NJC, Rønsted N. Travel Tales of a Worldwide Weed: Genomic Signatures of Plantago major L. Reveal Distinct Genotypic Groups With Links to Colonial Trade Routes. FRONTIERS IN PLANT SCIENCE 2022; 13:838166. [PMID: 35755675 PMCID: PMC9218338 DOI: 10.3389/fpls.2022.838166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
Retracing pathways of historical species introductions is fundamental to understanding the factors involved in the successful colonization and spread, centuries after a species' establishment in an introduced range. Numerous plants have been introduced to regions outside their native ranges both intentionally and accidentally by European voyagers and early colonists making transoceanic journeys; however, records are scarce to document this. We use genotyping-by-sequencing and genotype-likelihood methods on the selfing, global weed, Plantago major, collected from 50 populations worldwide to investigate how patterns of genomic diversity are distributed among populations of this global weed. Although genomic differentiation among populations is found to be low, we identify six unique genotype groups showing very little sign of admixture and low degree of outcrossing among them. We show that genotype groups are latitudinally restricted, and that more than one successful genotype colonized and spread into the introduced ranges. With the exception of New Zealand, only one genotype group is present in the Southern Hemisphere. Three of the most prevalent genotypes present in the native Eurasian range gave rise to introduced populations in the Americas, Africa, Australia, and New Zealand, which could lend support to the hypothesis that P. major was unknowlingly dispersed by early European colonists. Dispersal of multiple successful genotypes is a likely reason for success. Genomic signatures and phylogeographic methods can provide new perspectives on the drivers behind the historic introductions and the successful colonization of introduced species, contributing to our understanding of the role of genomic variation for successful establishment of introduced taxa.
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Affiliation(s)
| | - Shyam Gopalakrishnan
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Filipe G. Vieira
- Center for Genomic Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Vanessa C. Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Heidi M. Meudt
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| | | | - Carl J. Rothfels
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States
| | | | - Carla Maldonado
- Herbario Nacional de Bolivia, Universidad Mayor de San Andres, La Paz, Bolivia
| | | | - Alexey Shipunov
- Department of Biology, Minot University, Minot, ND, United States
| | - M. Deane Bowers
- Ecology and Evolutionary Biology, University of Colorado at Boulder, Boulder, CO, United States
| | - Elliot Gardner
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Chicago, IL, United States
- Plant Biology and Conservation, Northwestern University, Evanston, IL, United States
| | - Maonian Xu
- Faculty of Pharmaceutical Sciences, University of Iceland, Reykjavik, Iceland
| | - Abdolbaset Ghorbani
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Makoto Amano
- Natural History Museum and Institute, Chiba, Japan
| | - Olwen M. Grace
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | | - Madonna Bishop
- Memorial University Botanical Garden, St. John’s, NL, Canada
| | | | - Helena Cotrim
- Centre for Ecology, Evolution and Environmental Changes, University of Lisbon, Lisbon, Portugal
| | - Sean Blaney
- Atlantic Canada Conservation Data Centre, Sackville, NB, Canada
| | | | - Hong-Keun Choi
- Department of Life Sciences, Ajou University, Suweon, South Korea
| | - Yeter Yesil
- Department of Pharmaceutical Botany, Istanbul University, Istanbul, Turkey
| | - Bruce Bennett
- Yukon Conservation Data Centre, Yukon Territory, YT, Canada
| | - Sornkanok Vimolmangkang
- Department of Pharmacognosy and Pharmaceutical Botany, Chulalongkorn University, Bangkok, Thailand
| | - Hesham R. El-Seedi
- Pharmacognosy Group, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - Peter O. Staub
- Department of Biomedical Science, University of Cagliari, Cagliari, Italy
| | - Zhu Li
- Chinese Academy of Sciences, Beijing, China
| | - Delgerbat Boldbaatar
- Department of Liver Center, National University of Mongolia, Ulaanbaatar, Mongolia
| | | | - Laura J. Caddy
- Botanical Garden, The University of British Columbia, Vancouver, BC, Canada
| | - A. Muthama Muasya
- Department of Biological Sciences, University of Cape Town, Cape Town, South Africa
| | | | | | - Nyree J. C. Zerega
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Chicago, IL, United States
- Plant Biology and Conservation, Northwestern University, Evanston, IL, United States
| | - Nina Rønsted
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- National Tropical Botanic Garden, Kaua‘i, HI, United States
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29
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Genetic diversity and structure of an endangered medicinal plant species (Pilocarpus microphyllus) in eastern Amazon: implications for conservation. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01454-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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30
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Ke L, Yan WY, Zhang LZ, Zeng ZJ, Evans JD, Huang Q. Honey Bee Habitat Sharing Enhances Gene Flow of the Parasite Nosema ceranae. MICROBIAL ECOLOGY 2022; 83:1105-1111. [PMID: 34342699 DOI: 10.1007/s00248-021-01827-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
Host-parasite co-evolution is a process of reciprocal, adaptive genetic change. In natural conditions, parasites can shift to other host species, given both host and parasite genotypes allow this. Even though host-parasite co-evolution has been extensively studied both theoretically and empirically, few studies have focused on parasite gene flow between native and novel hosts. Nosema ceranae is a native parasite of the Asian honey bee Apis cerana, which infects epithelial cells of mid-guts. This parasite successfully switched to the European honey bee Apis mellifera, where high virulence has been reported. In this study, we used the parasite N. ceranae and both honey bee species as model organisms to study the impacts of two-host habitat sharing on parasite diversity and virulence. SNVs (Single Nucleotide Variants) were identified from parasites isolated from native and novel hosts from sympatric populations, as well as novel hosts from a parapatric population. Parasites isolated from native hosts showed the highest levels of polymorphism. By comparing the parasites isolated from novel hosts between sympatric and parapatric populations, habitat sharing with the native host significantly enhanced parasite diversity, suggesting there is continuing gene flow of parasites between the two host species in sympatric populations.
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Affiliation(s)
- Li Ke
- Jiangxi Key Laboratory of Honeybee Biology and Beekeeping, Jiangxi Agricultural University, Zhimin Ave. 1101, Nanchang, 330045, China
| | - Wei Yu Yan
- Jiangxi Key Laboratory of Honeybee Biology and Beekeeping, Jiangxi Agricultural University, Zhimin Ave. 1101, Nanchang, 330045, China
| | - Li Zhen Zhang
- Jiangxi Key Laboratory of Honeybee Biology and Beekeeping, Jiangxi Agricultural University, Zhimin Ave. 1101, Nanchang, 330045, China
| | - Zhi Jiang Zeng
- Jiangxi Key Laboratory of Honeybee Biology and Beekeeping, Jiangxi Agricultural University, Zhimin Ave. 1101, Nanchang, 330045, China
| | - Jay D Evans
- USDA-ARS Bee Research Laboratory, BARC-East Building 306, Beltsville, MD, 20705, USA
| | - Qiang Huang
- Jiangxi Key Laboratory of Honeybee Biology and Beekeeping, Jiangxi Agricultural University, Zhimin Ave. 1101, Nanchang, 330045, China.
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31
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van Rees CB, Hand BK, Carter SC, Bargeron C, Cline TJ, Daniel W, Ferrante JA, Gaddis K, Hunter ME, Jarnevich CS, McGeoch MA, Morisette JT, Neilson ME, Roy HE, Rozance MA, Sepulveda A, Wallace RD, Whited D, Wilcox T, Kimball JS, Luikart G. A framework to integrate innovations in invasion science for proactive management. Biol Rev Camb Philos Soc 2022; 97:1712-1735. [PMID: 35451197 DOI: 10.1111/brv.12859] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 11/26/2022]
Abstract
Invasive alien species (IAS) are a rising threat to biodiversity, national security, and regional economies, with impacts in the hundreds of billions of U.S. dollars annually. Proactive or predictive approaches guided by scientific knowledge are essential to keeping pace with growing impacts of invasions under climate change. Although the rapid development of diverse technologies and approaches has produced tools with the potential to greatly accelerate invasion research and management, innovation has far outpaced implementation and coordination. Technological and methodological syntheses are urgently needed to close the growing implementation gap and facilitate interdisciplinary collaboration and synergy among evolving disciplines. A broad review is necessary to demonstrate the utility and relevance of work in diverse fields to generate actionable science for the ongoing invasion crisis. Here, we review such advances in relevant fields including remote sensing, epidemiology, big data analytics, environmental DNA (eDNA) sampling, genomics, and others, and present a generalized framework for distilling existing and emerging data into products for proactive IAS research and management. This integrated workflow provides a pathway for scientists and practitioners in diverse disciplines to contribute to applied invasion biology in a coordinated, synergistic, and scalable manner.
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Affiliation(s)
- Charles B van Rees
- Flathead Lake Biological Station, University of Montana, 32125 Bio Station Lane, Polson, MT, 59860, U.S.A
| | - Brian K Hand
- Flathead Lake Biological Station, University of Montana, 32125 Bio Station Lane, Polson, MT, 59860, U.S.A
| | - Sean C Carter
- Numerical Terradynamic Simulation Group, University of Montana, ISB 415, Missoula, MT, 59812, U.S.A
| | - Chuck Bargeron
- Center for Invasive Species and Ecosystem Health, University of Georgia, 4601 Research Way, Tifton, GA, 31793, U.S.A
| | - Timothy J Cline
- U.S. Geological Survey, Northern Rocky Mountain Science Center, 2327 University Way STE 2, Bozeman MT 59717 & 320 Grinnel Drive, West Glacier, MT, 59936, U.S.A
| | - Wesley Daniel
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, U.S.A
| | - Jason A Ferrante
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, U.S.A
| | - Keith Gaddis
- NASA Biological Diversity and Ecological Forecasting Programs, 300 E St. SW, Washington, DC, 20546, U.S.A
| | - Margaret E Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, U.S.A
| | - Catherine S Jarnevich
- U.S. Geological Survey, Fort Collins Science Center, 2150 Centre Avenue Bldg C, Fort Collins, CO, 80526, U.S.A
| | - Melodie A McGeoch
- Department of Environment and Genetics, La Trobe University, Plenty Road & Kingsbury Drive, Bundoora, Victoria, 3086, Australia
| | - Jeffrey T Morisette
- U.S. Forest Service Rocky Mountain Research Station, 26 Fort Missoula Road, Missoula, 59804, MT, U.S.A
| | - Matthew E Neilson
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, U.S.A
| | - Helen E Roy
- UK Centre for Ecology & Hydrology, MacLean Building, Benson Lane, Crowmarsh Gifford, OX10 8BB, U.K
| | - Mary Ann Rozance
- Northwest Climate Adaptation Science Center, University of Washington, Box 355674, Seattle, WA, 98195, U.S.A
| | - Adam Sepulveda
- U.S. Forest Service Rocky Mountain Research Station, 26 Fort Missoula Road, Missoula, 59804, MT, U.S.A
| | - Rebekah D Wallace
- Center for Invasive Species and Ecosystem Health, University of Georgia, 4601 Research Way, Tifton, GA, 31793, U.S.A
| | - Diane Whited
- Flathead Lake Biological Station, University of Montana, 32125 Bio Station Lane, Polson, MT, 59860, U.S.A
| | - Taylor Wilcox
- U.S. Forest Service Rocky Mountain Research Station, 26 Fort Missoula Road, Missoula, 59804, MT, U.S.A
| | - John S Kimball
- Numerical Terradynamic Simulation Group, University of Montana, ISB 415, Missoula, MT, 59812, U.S.A
| | - Gordon Luikart
- Flathead Lake Biological Station, University of Montana, 32125 Bio Station Lane, Polson, MT, 59860, U.S.A
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32
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Di B, Firn J, Buckley YM, Lomas K, Pausas JG, Smith AL. The impact of roadside burning on genetic diversity in a high‐biomass invasive grass. Evol Appl 2022; 15:790-803. [PMID: 35603028 PMCID: PMC9108304 DOI: 10.1111/eva.13369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 12/06/2021] [Accepted: 02/23/2022] [Indexed: 11/28/2022] Open
Affiliation(s)
- Binyin Di
- School of Agriculture and Food Sciences University of Queensland Gatton 4343 Australia
| | - Jennifer Firn
- School of Biology & Environmental Science Queensland University of Technology Brisbane 4000 Australia
| | - Yvonne M. Buckley
- School of Natural Sciences, Zoology Trinity College Dublin The University of Dublin Dublin 2 Ireland
| | - Kate Lomas
- School of Biology & Environmental Science Queensland University of Technology Brisbane 4000 Australia
| | - Juli G. Pausas
- Centro de Investigaciones sobre Desertificación (CIDE‐CSIC) 46113 Montcada, Valencia Spain
| | - Annabel L. Smith
- School of Agriculture and Food Sciences University of Queensland Gatton 4343 Australia
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33
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Opinion: Nationally reported metrics can't adequately guide transformative change in biodiversity policy. Proc Natl Acad Sci U S A 2022; 119:2117299119. [PMID: 35217615 PMCID: PMC8892539 DOI: 10.1073/pnas.2117299119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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34
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Li Z, Yun L, Gao Z, Wang T, Ren X, Zhao Y. EST-SSR Primer Development and Genetic Structure Analysis of Psathyrostachys juncea Nevski. FRONTIERS IN PLANT SCIENCE 2022; 13:837787. [PMID: 35295628 PMCID: PMC8919075 DOI: 10.3389/fpls.2022.837787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/07/2022] [Indexed: 05/14/2023]
Abstract
Psathyrostachys juncea is a perennial forage grass which plays an important role in soil and water conservation and ecological maintenance in cold and dry areas of temperate regions. In P. juncea, a variety of biotic and abiotic stress related genes have been used in crop improvement, indicating its agronomic, economic, forage, and breeding value. To date, there have been few studies on the genetic structure of P. juncea. Here, the genetic diversity and population structure of P. juncea were analyzed by EST-SSR molecular markers to evaluate the genetic differentiation related to tillering traits in P. juncea germplasm resources. The results showed that 400 simple sequence repeat (SSR) loci were detected in 2,020 differentially expressed tillering related genes. A total of 344 scored bands were amplified using 103 primer pairs, out of which 308 (89.53%) were polymorphic. The Nei's gene diversity of 480 individuals was between 0.092 and 0.449, and the genetic similarity coefficient was between 0.5008 and 0.9111, with an average of 0.6618. Analysis of molecular variance analysis showed that 93% of the variance was due to differences within the population, and the remaining 7% was due to differences among populations. Psathyrostachys juncea materials were clustered into five groups based on population genetic structure, principal coordinate analysis and unweighted pair-group method with arithmetic means (UPGMA) analysis. The results were similar between clustering methods, but a few individual plants were distributed differently by the three models. The clustering results, gene diversity and genetic similarity coefficients showed that the overall genetic relationship of P. juncea individuals was relatively close. A Mantel test, UPGMA and structural analysis also showed a significant correlation between genetic relationship and geographical distribution. These results provide references for future breeding programs, genetic improvement and core germplasm collection of P. juncea.
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Affiliation(s)
- Zhen Li
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Lan Yun
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Grassland Resources Ministry of Education, Hohhot, China
| | - Zhiqi Gao
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Tian Wang
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiaomin Ren
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Yan Zhao
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
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Buckley YM, Puy J. The macroecology of plant populations from local to global scales. THE NEW PHYTOLOGIST 2022; 233:1038-1050. [PMID: 34536970 DOI: 10.1111/nph.17749] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 09/02/2021] [Indexed: 06/13/2023]
Abstract
Population ecologists develop theoretical and pragmatic knowledge of how and why populations change or remain stable, how life histories evolve and devise management strategies for populations of concern. However, forecasting the effects of global change or recommending management strategies is often urgent, requiring ecologists to work without detailed local evidence while using data and models from outside the focal location or species. Here we explore how the comparative ecology of populations, population macroecology, can be used to develop generalisations within and between species across different scales, using available demographic, environmental, life history, occurrence and trait data. We outline the strengths and weaknesses of using broad climatic variables and suitability inferred from probability of occupancy models to represent environmental variation in comparative analyses. We evaluate the contributions of traits, environment and their interaction as drivers of life history strategy. We propose that insights from life history theory, together with the adaptive capacity of populations and individuals, can inform on 'persist in place' vs 'shift in space' responses to changing conditions. As demographic data accumulate at landscape and regional scales for single species, and throughout plant phylogenies, we will have new opportunities for testing macroecological generalities within and across species.
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Affiliation(s)
- Yvonne M Buckley
- School of Natural Sciences, Zoology, Trinity College Dublin, Dublin 2, Ireland
- School of Biological Sciences, The University of Queensland, St Lucia, 4072, QLD, Australia
| | - Javier Puy
- School of Natural Sciences, Zoology, Trinity College Dublin, Dublin 2, Ireland
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36
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Montagnani C, Casazza G, Gentili R, Caronni S, Citterio S. Kudzu in Europe: niche conservatism for a highly invasive plant. Biol Invasions 2022. [DOI: 10.1007/s10530-021-02706-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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37
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Shirsekar G, Devos J, Latorre SM, Blaha A, Queiroz Dias M, González Hernando A, Lundberg DS, Burbano HA, Fenster CB, Weigel D. Multiple Sources of Introduction of North American Arabidopsis thaliana from across Eurasia. Mol Biol Evol 2021; 38:5328-5344. [PMID: 34499163 PMCID: PMC8662644 DOI: 10.1093/molbev/msab268] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Large-scale movement of organisms across their habitable range, or migration, is an important evolutionary process that can shape genetic diversity and influence the adaptive spread of alleles. Although human migrations have been studied in great detail with modern and ancient genomes, recent anthropogenic influence on reducing the biogeographical constraints on the migration of nonnative species has presented opportunities in several study systems to ask the questions about how repeated introductions shape genetic diversity in the introduced range. We present an extensive overview of population structure of North American Arabidopsis thaliana by studying a set of 500 whole-genome sequenced and over 2,800 RAD-seq genotyped individuals in the context of global diversity represented by Afro-Eurasian genomes. We use methods based on haplotype and rare-allele sharing as well as phylogenetic modeling to identify likely sources of introductions of extant N. American A. thaliana from the native range in Africa and Eurasia. We find evidence of admixture among the introduced lineages having increased haplotype diversity and reduced mutational load. We also detect signals of selection in immune-system-related genes that may impart qualitative disease resistance to pathogens of bacterial and oomycete origin. We conclude that multiple introductions to a nonnative range can rapidly enhance the adaptive potential of a colonizing species by increasing haplotypic diversity through admixture. Our results lay the foundation for further investigations into the functional significance of admixture.
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Affiliation(s)
- Gautam Shirsekar
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Jane Devos
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Sergio M Latorre
- Max Planck Institute for Developmental Biology, Tübingen, Germany
- Centre for Life’s Origin and Evolution, University College London, London, United Kingdom
| | - Andreas Blaha
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | | | | | - Derek S Lundberg
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Hernán A Burbano
- Max Planck Institute for Developmental Biology, Tübingen, Germany
- Centre for Life’s Origin and Evolution, University College London, London, United Kingdom
| | - Charles B Fenster
- Oak Lake Field Station, Department of Natural Resource Management, South Dakota State University, Brookings, SD, USA
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Tübingen, Germany
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Morales M, Pasques O, Munné-Bosch S. English plantain deploys stress tolerance mechanisms at various organization levels across an altitudinal gradient in the Pyrenees. PHYSIOLOGIA PLANTARUM 2021; 173:2350-2360. [PMID: 34651706 DOI: 10.1111/ppl.13586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 10/01/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
High-mountain plants must withstand high solar irradiation and low temperatures during winter. Furthermore, climate change is increasing drought events, which pose an additional threat to plants. Here, we studied the stress tolerance mechanisms at various levels of biological organization in English plantain (Plantago lanceolata L.), focusing on photoprotective and antioxidant responses. The response of populations from three different altitudes in the Eastern Pyrenees (1030, 1380, and 1660 m. a.s.l.) was compared during both autumn and winter. Results showed that plants not only suffered from photoinhibition due to very low temperatures at the highest elevation during winter, but also from mild drought stress at the lowest altitude during autumn. Individuals growing at the highest elevation showed reductions in the maximum photochemical efficiency of PSII (Fv /Fm ratio), which might be caused by the lack of an increased induction of tolerance mechanisms at the highest elevation compared to the intermediate one. Although most leaves died at the highest elevation, plants could withstand stress at the organism level by generating new leaves once the stress ceased. Drought at the lowest elevation during autumn caused mild stress with small decreases in the Fv /Fm ratio, along with an increase in abscisic acid and jasmonic acid content. This study underlines the great capacity of English plantain to adapt to high elevation by activating not only photo- and antioxidant protection mechanisms and adjustments in stress-related phytohormones, but also by fully regenerating its aboveground biomass through renewed growth once the stress has ceased.
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Affiliation(s)
- Melanie Morales
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca en Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Ot Pasques
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Barcelona, Spain
| | - Sergi Munné-Bosch
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca en Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
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The phytosanitary risks posed by seeds for sowing trade networks. PLoS One 2021; 16:e0259912. [PMID: 34847168 PMCID: PMC8631629 DOI: 10.1371/journal.pone.0259912] [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: 07/06/2021] [Accepted: 10/28/2021] [Indexed: 11/22/2022] Open
Abstract
When successful, the operation of local and international networks of crop seed distribution or “seed systems” ensures farmer access to seed and impacts rural livelihoods and food security. Farmers are both consumers and producers in seed systems and benefit from access to global markets. However, phytosanitary measures and seed purity tests are also needed to maintain seed quality and prevent the spread of costly weeds, pests and diseases, in some countries regulatory controls have been in place since the 1800s. Nevertheless, seed contaminants are internationally implicated in between 7% and 37% of the invasive plant species and many of the agricultural pests and diseases. We assess biosecurity risk across international seed trade networks of forage crops using models of contaminant spread that integrate network connectivity and trade volume. To stochastically model hypothetical contaminants through global seed trade networks, realistic dispersal probabilities were estimated from quarantine weed seed detections and incursions from border security interception data in New Zealand. For our test case we use contaminants linked to the global trade of ryegrass and clover seed. Between 2014 and 2018 only four quarantine weed species (222 species and several genera are on the quarantine schedule) warranting risk mitigation were detected at the border. Quarantine weeds were rare considering that average import volumes were over 190 tonnes for ryegrass and clover, but 105 unregulated contaminant species were allowed in. Ryegrass and clover seed imports each led to one post-border weed incursion response over 20 years. Trade reports revealed complex global seed trade networks spanning >134 (ryegrass) and >110 (clover) countries. Simulations showed contaminants could disperse to as many as 50 (clover) or 80 (ryegrass) countries within 10 time-steps. Risk assessed via network models differed 18% (ryegrass) or 48% (clover) of the time compared to risk assessed on trade volumes. We conclude that biosecurity risk is driven by network position, the number of trading connections and trade volume. Risk mitigation measures could involve the use of more comprehensive lists of regulated species, comprehensive inspection protocols, or the addition of field surveillance at farms where seed is planted.
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Borokini IT, Klingler KB, Peacock MM. Life in the desert: The impact of geographic and environmental gradients on genetic diversity and population structure of Ivesia webberi. Ecol Evol 2021; 11:17537-17556. [PMID: 34938528 PMCID: PMC8668734 DOI: 10.1002/ece3.8389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 10/25/2021] [Accepted: 11/05/2021] [Indexed: 11/11/2022] Open
Abstract
For range-restricted species with disjunct populations, it is critical to characterize population genetic structure, gene flow, and factors that influence functional connectivity among populations in order to design effective conservation programs. In this study, we genotyped 314 individuals from 16 extant populations of Ivesia webberi, a United States federally threatened Great Basin Desert using six microsatellite loci. We assessed the effects of Euclidean distance, landscape features, and ecological dissimilarity on the pairwise genetic distance of the sampled populations, while also testing for a potential relationship between I. webberi genetic diversity and diversity in the vegetative communities. The results show low levels of genetic diversity overall (H e = 0.200-0.441; H o = 0.192-0.605) and high genetic differentiation among populations. Genetic diversity was structured along a geographic gradient, congruent with patterns of isolation by distance. Populations near the species' range core have relatively high genetic diversity, supporting in part a central-marginal pattern, while also showing some evidence for a metapopulation dynamic. Peripheral populations have lower genetic diversity, significantly higher genetic distances, and higher relatedness. Genotype cluster admixture results suggest a complex dispersal pattern among populations with dispersal direction and distance varying on the landscape. Pairwise genetic distance strongly correlates with elevation, actual evapotranspiration, and summer seasonal precipitation, indicating a role for isolation by environment, which the observed phenological mismatches among the populations also support. The significant correlation between pairwise genetic distance and floristic dissimilarity in the germinated soil seed bank suggests that annual regeneration in the plant communities contribute to the maintenance of genetic diversity in I. webberi.
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Affiliation(s)
- Israel T. Borokini
- Ecology, Evolution and Conservation Biology Graduate ProgramDepartment of BiologyUniversity of Nevada, RenoRenoNevadaUSA
- University and Jepson HerbariaDepartment of Integrative BiologyUniversity of California, BerkeleyBerkeleyCaliforniaUSA
| | - Kelly B. Klingler
- Department of Environmental ConservationUniversity of MassachusettsAmherstMassachusettsUSA
| | - Mary M. Peacock
- Ecology, Evolution and Conservation Biology Graduate ProgramDepartment of BiologyUniversity of Nevada, RenoRenoNevadaUSA
- Department of BiologyUniversity of Nevada, RenoRenoNevadaUSA
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41
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Addressing context dependence in ecology. Trends Ecol Evol 2021; 37:158-170. [PMID: 34756764 DOI: 10.1016/j.tree.2021.09.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 09/05/2021] [Accepted: 09/21/2021] [Indexed: 12/26/2022]
Abstract
Context dependence is widely invoked to explain disparate results in ecology. It arises when the magnitude or sign of a relationship varies due to the conditions under which it is observed. Such variation, especially when unexplained, can lead to spurious or seemingly contradictory conclusions, which can limit understanding and our ability to transfer findings across studies, space, and time. Using examples from biological invasions, we identify two types of context dependence resulting from four sources: mechanistic context dependence arises from interaction effects; and apparent context dependence can arise from the presence of confounding factors, problems of statistical inference, and methodological differences among studies. Addressing context dependence is a critical challenge in ecology, essential for increased understanding and prediction.
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Sofi IA, Rashid I, Lone JY, Tyagi S, Reshi ZA, Mir RR. Genetic diversity may help evolutionary rescue in a clonal endemic plant species of Western Himalaya. Sci Rep 2021; 11:19595. [PMID: 34599214 PMCID: PMC8486807 DOI: 10.1038/s41598-021-98648-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 08/25/2021] [Indexed: 02/08/2023] Open
Abstract
Habitat loss due to climate change may cause the extinction of the clonal species with a limited distribution range. Thus, determining the genetic diversity required for adaptability by these species in sensitive ecosystems can help infer the chances of their survival and spread in changing climate. We studied the genetic diversity and population structure of Sambucus wightiana-a clonal endemic plant species of the Himalayan region for understanding its possible survival chances in anticipated climate change. Eight polymorphic microsatellite markers were used to study the allelic/genetic diversity and population structure. In addition, ITS1-ITS4 Sanger sequencing was used for phylogeny and SNP detection. A total number of 73 alleles were scored for 37 genotypes at 17 loci for 8 SSRs markers. The population structural analysis using the SSR marker data led to identifying two sub-populations in our collection of 37 S. wightiana genotypes, with 11 genotypes having mixed ancestry. The ITS sequence data show a specific allele in higher frequency in a particular sub-population, indicating variation in different S. wightiana accessions at the sequence level. The genotypic data of SSR markers and trait data of 11 traits of S. wightiana, when analyzed together, revealed five significant Marker-Trait Associations (MTAs) through Single Marker Analysis (SMA) or regression analysis. Most of the SSR markers were found to be associated with more than one trait, indicating the usefulness of these markers for working out marker-trait associations. Moderate to high genetic diversity observed in the present study may provide insurance against climate change to S. wightiana and help its further spread.
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Affiliation(s)
- Irshad Ahmad Sofi
- grid.412997.00000 0001 2294 5433Department of Botany, University of Kashmir, Srinagar, Jammu and Kashmir 190006 India
| | - Irfan Rashid
- grid.412997.00000 0001 2294 5433Department of Botany, University of Kashmir, Srinagar, Jammu and Kashmir 190006 India
| | - Javaid Yousuf Lone
- grid.412997.00000 0001 2294 5433Department of Botany, University of Kashmir, Srinagar, Jammu and Kashmir 190006 India
| | - Sandhya Tyagi
- grid.418196.30000 0001 2172 0814Department of Plant Physiology, Indian Agricultural Research Institute, New Delhi, Delhi 110012 India
| | - Zafar A. Reshi
- grid.412997.00000 0001 2294 5433Department of Botany, University of Kashmir, Srinagar, Jammu and Kashmir 190006 India
| | - Reyazul Rouf Mir
- grid.444725.40000 0004 0500 6225Division of Genetics and Plant Breeding, Faculty of Agriculture, SKUAST-Kashmir, Wadura Campus, Sopore, Jammu and Kashmir 193201 India
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G Campoy J, Lema M, Fenollosa E, Munné-Bosch S, Retuerto R. Functional responses to climate change may increase invasive potential of Carpobrotus edulis. AMERICAN JOURNAL OF BOTANY 2021; 108:1902-1916. [PMID: 34636413 DOI: 10.1002/ajb2.1745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Biological invasions and climate change are major threats to biodiversity. It is therefore important to anticipate how the climate changes projected for Southern Europe would affect the ecophysiological performance of the invasive South African plant, Carpobrotus edulis (ice plant or sour fig), and its capacity to undergo rapid adaptive evolution. METHODS We manipulated the climate conditions in a field plot located on the island of Sálvora (northwest of the Iberian Peninsula) to establish a full factorial experiment with C. edulis plants transplanted from four native (southern African) and four invasive (northwestern Iberian Peninsula) populations. Throughout 14 months we measured growth and functional traits of this species under two temperatures (control vs. increased), and two rainfall levels (control vs. reduced). RESULTS Temperature increased photochemical efficiency and relative growth rate of C. edulis. Rainfall modulated some of the effects of temperature on C and N isotopic composition, and pigment contents. Invasive populations showed lower root mass allocation and higher survival rates, as well as increased water use efficiency, lipid peroxidation, chlorophyll, and xanthophyll cycle pigment contents than native populations. CONCLUSIONS The increased growth and physiological performances observed under our experimental conditions suggest that the expected climate changes would further promote the invasion of C. edulis. Differences between native and invasive genotypes in survival and functional traits revealed that populations have diverged during the process of invasion, what gives support to the invasiveness hypothesis. Our findings highlight the importance of analyzing intraspecific variability in functional responses to better predict how invasive species will respond to environmental changes.
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Affiliation(s)
- Josefina G Campoy
- Departamento de Bioloxía Funcional, Facultade de Bioloxía, Universidade de Santiago de Compostela, Santiago de Compostela, A Coruña, 15782, Spain
| | - Margarita Lema
- Departamento de Bioloxía Funcional, Facultade de Bioloxía, Universidade de Santiago de Compostela, Santiago de Compostela, A Coruña, 15782, Spain
| | - Erola Fenollosa
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Barcelona, Spain
- Biodiversity Research Institute (IrBio), Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Sergi Munné-Bosch
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Barcelona, Spain
- Biodiversity Research Institute (IrBio), Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Rubén Retuerto
- Departamento de Bioloxía Funcional, Facultade de Bioloxía, Universidade de Santiago de Compostela, Santiago de Compostela, A Coruña, 15782, Spain
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Unrestricted gene flow between two subspecies of translocated brushtail possums (Trichosurus vulpecula) in Aotearoa New Zealand. Biol Invasions 2021. [DOI: 10.1007/s10530-021-02635-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
AbstractTwo lineages of brushtail possums (Trichosurus vulpecula) were historically introduced to Aotearoa New Zealand, and these two subspecies have different phenotypic forms. Despite over 100 years of potential interbreeding, they appear to retain morphological differences, which may indicate reproductive isolation. We examined this using population samples from a confined landscape and scored each specimen for phenotype using a number of fur colour traits. This resulted in a bimodal trait distribution expected for segregated grey and black lineages. We also sought evidence for genetic partitioning based on spatial and temporal effects. Genetic structure and rates of genetic mixing were determined using seven neutral, species-specific nuclear microsatellite markers and mitochondrial DNA control region sequence. Genotype analyses indicated high levels of variation and mtDNA sequences formed two major haplogroups. Pairwise tests for population differentiation of these markers found no evidence of subdivision, indicating that these brushtail possums behave as a single randomly mating unit. Despite maintenance of two main colour phenotypes with relatively few intermediates, previous inference of assortative mating and anecdotes of distinct races, our data indicate that New Zealand brushtail possums can freely interbreed, and that in some locations they have formed completely mixed populations where neutral genetic markers are unrelated to phenotype. This has implications for effective pest management towards eradication.
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Fountain-Jones NM, Kozakiewicz CP, Forester BR, Landguth EL, Carver S, Charleston M, Gagne RB, Greenwell B, Kraberger S, Trumbo DR, Mayer M, Clark NJ, Machado G. MrIML: Multi-response interpretable machine learning to model genomic landscapes. Mol Ecol Resour 2021; 21:2766-2781. [PMID: 34448358 DOI: 10.1111/1755-0998.13495] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 08/01/2021] [Accepted: 08/23/2021] [Indexed: 12/29/2022]
Abstract
We introduce a new R package "MrIML" ("Mister iml"; Multi-response Interpretable Machine Learning). MrIML provides a powerful and interpretable framework that enables users to harness recent advances in machine learning to quantify multilocus genomic relationships, to identify loci of interest for future landscape genetics studies, and to gain new insights into adaptation across environmental gradients. Relationships between genetic variation and environment are often nonlinear and interactive; these characteristics have been challenging to address using traditional landscape genetic approaches. Our package helps capture this complexity and offers functions that fit and interpret a wide range of highly flexible models that are routinely used for single-locus landscape genetics studies but are rarely extended to estimate response functions for multiple loci. To demonstrate the package's broad functionality, we test its ability to recover landscape relationships from simulated genomic data. We also apply the package to two empirical case studies. In the first, we model genetic variation of North American balsam poplar (Populus balsamifera, Salicaceae) populations across environmental gradients. In the second case study, we recover the landscape and host drivers of feline immunodeficiency virus genetic variation in bobcats (Lynx rufus). The ability to model thousands of loci collectively and compare models from linear regression to extreme gradient boosting, within the same analytical framework, has the potential to be transformative. The MrIML framework is also extendable and not limited to modelling genetic variation; for example, it can quantify the environmental drivers of microbiomes and coinfection dynamics.
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Affiliation(s)
| | | | - Brenna R Forester
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Erin L Landguth
- School of Public and Community Health Sciences, University of Montana, Missoula, Montana, USA
| | - Scott Carver
- School of Natural Sciences, University of Tasmania, Hobart, Tas., Australia
| | - Michael Charleston
- School of Natural Sciences, University of Tasmania, Hobart, Tas., Australia
| | - Roderick B Gagne
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, USA
| | - Brandon Greenwell
- Department of Operations, Business Analytics, and Information Systems, University of Cincinnati, Cincinnati, Ohio, USA
| | - Simona Kraberger
- Biodesign Center for Fundamental & Applied Microbiomics, Arizona State University, Tempe, Arizona, USA
| | - Daryl R Trumbo
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Michael Mayer
- Actuarial Department, La Mobilière, Bern, Switzerland
| | - Nicholas J Clark
- UQ Spatial Epidemiology Laboratory, School of Veterinary Science, The University of Queensland, Gatton, Qld., Australia
| | - Gustavo Machado
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
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Ruan X, Wang Z, Su Y, Wang T. Population Genomics Reveals Gene Flow and Adaptive Signature in Invasive Weed Mikania micrantha. Genes (Basel) 2021; 12:1279. [PMID: 34440453 PMCID: PMC8394975 DOI: 10.3390/genes12081279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/15/2021] [Accepted: 08/18/2021] [Indexed: 11/28/2022] Open
Abstract
A long-standing and unresolved issue in invasion biology concerns the rapid adaptation of invaders to nonindigenous environments. Mikania micrantha is a notorious invasive weed that causes substantial economic losses and negative ecological consequences in southern China. However, the contributions of gene flow, environmental variables, and functional genes, all generally recognized as important factors driving invasive success, to its successful invasion of southern China are not fully understood. Here, we utilized a genotyping-by-sequencing approach to sequence 306 M. micrantha individuals from 21 invasive populations. Based on the obtained genome-wide single nucleotide polymorphism (SNP) data, we observed that all the populations possessed similar high levels of genetic diversity that were not constrained by longitude and latitude. Mikania micrantha was introduced multiple times and subsequently experienced rapid-range expansion with recurrent high gene flow. Using FST outliers, a latent factor mixed model, and the Bayesian method, we identified 38 outlier SNPs associated with environmental variables. The analysis of these outlier SNPs revealed that soil composition, temperature, precipitation, and ecological variables were important determinants affecting the invasive adaptation of M. micrantha. Candidate genes with outlier signatures were related to abiotic stress response. Gene family clustering analysis revealed 683 gene families unique to M. micrantha which may have significant implications for the growth, metabolism, and defense responses of M. micrantha. Forty-one genes showing significant positive selection signatures were identified. These genes mainly function in binding, DNA replication and repair, signature transduction, transcription, and cellular components. Collectively, these findings highlight the contribution of gene flow to the invasion and spread of M. micrantha and indicate the roles of adaptive loci and functional genes in invasive adaptation.
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Affiliation(s)
- Xiaoxian Ruan
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (X.R.); (Z.W.)
| | - Zhen Wang
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (X.R.); (Z.W.)
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (X.R.); (Z.W.)
- Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen 518057, China
| | - Ting Wang
- College of Life Sciences, South China Agricultural University, Guangzhou 510641, China
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47
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Villellas J, Ehrlén J, Crone EE, Csergő AM, Garcia MB, Laine AL, Roach DA, Salguero-Gómez R, Wardle GM, Childs DZ, Elderd BD, Finn A, Munné-Bosch S, Bachelot B, Bódis J, Bucharova A, Caruso CM, Catford JA, Coghill M, Compagnoni A, Duncan RP, Dwyer JM, Ferguson A, Fraser LH, Griffoul E, Groenteman R, Hamre LN, Helm A, Kelly R, Laanisto L, Lonati M, Münzbergová Z, Nuche P, Olsen SL, Oprea A, Pärtel M, Petry WK, Ramula S, Rasmussen PU, Enri SR, Roeder A, Roscher C, Schultz C, Skarpaas O, Smith AL, Tack AJM, Töpper JP, Vesk PA, Vose GE, Wandrag E, Wingler A, Buckley YM. PHENOTYPIC PLASTICITY MASKS RANGE-WIDE GENETIC DIFFERENTIATION FOR VEGETATIVE BUT NOT REPRODUCTIVE TRAITS IN A SHORT-LIVED PLANT. Ecol Lett 2021; 24:2378-2393. [PMID: 34355467 DOI: 10.1111/ele.13858] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 05/13/2021] [Accepted: 05/19/2021] [Indexed: 12/12/2022]
Abstract
Genetic differentiation and phenotypic plasticity jointly shape intraspecific trait variation, but their roles differ among traits. In short-lived plants, reproductive traits may be more genetically determined due to their impact on fitness, whereas vegetative traits may show higher plasticity to buffer short-term perturbations. Combining a multi-treatment greenhouse experiment with observational field data throughout the range of a widespread short-lived herb, Plantago lanceolata, we (1) disentangled genetic and plastic responses of functional traits to a set of environmental drivers and (2) assessed how genetic differentiation and plasticity shape observational trait-environment relationships. Reproductive traits showed distinct genetic differentiation that largely determined observational patterns, but only when correcting traits for differences in biomass. Vegetative traits showed higher plasticity and opposite genetic and plastic responses, masking the genetic component underlying field-observed trait variation. Our study suggests that genetic differentiation may be inferred from observational data only for the traits most closely related to fitness.
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Affiliation(s)
- Jesus Villellas
- Departamento de Biodiversidad, Ecología y Evolución, Universidad Complutense de Madrid, Madrid, Spain.,School of Natural Sciences, Zoology, Trinity College Dublin, Dublin, Ireland
| | - Johan Ehrlén
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Elizabeth E Crone
- Department of Biology, Tufts University, Medford, Massachusetts, USA
| | - Anna Mária Csergő
- School of Natural Sciences, Zoology, Trinity College Dublin, Dublin, Ireland.,Department of Botany and Soroksár Botanical Garden, Szent István University, Budapest, Hungary
| | - Maria B Garcia
- Department of Biodiversity Conservation and Ecosystem Restoration, Pyrenean Institute of Ecology (CSIC), Zaragoza, Spain
| | - Anna-Liisa Laine
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,Organismal & Evolutionary Biology Research Program, Faculty of Biological & Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Deborah A Roach
- Department of Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Roberto Salguero-Gómez
- Department of Zoology, University of Oxford, Oxford, UK.,Max Planck Institute for Demographic Research, Rostock, Germany.,School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Glenda M Wardle
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Dylan Z Childs
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Bret D Elderd
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Alain Finn
- School of Natural Sciences, Zoology, Trinity College Dublin, Dublin, Ireland
| | - Sergi Munné-Bosch
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Barcelona, Spain.,Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
| | - Benedicte Bachelot
- Department of Plant Biology, Ecology and Evolution, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Judit Bódis
- Department of Plant Sciences and Biotechnology, Georgikon Faculty, University of Pannonia, Keszthely, Hungary
| | - Anna Bucharova
- Biodiversity and Ecosystem Research Group, Institut of Landscape Ecology, University of Münster, Germany.,Plant Evolutionary Ecology, Institut of Evolution and Ecology, University of Tübingen, Tübingen, Germany
| | - Christina M Caruso
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Jane A Catford
- Department of Geography, King's College London, London, UK.,Biological Sciences, University of Southampton, Southampton, UK
| | - Matthew Coghill
- Department of Natural Resource Sciences, Thompson Rivers University, Kamloops, British Columbia, Canada
| | - Aldo Compagnoni
- Institute of Biology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Richard P Duncan
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia
| | - John M Dwyer
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia.,CSIRO Land & Water, EcoSciences Precinct, Dutton Park, Queensland, Australia
| | | | - Lauchlan H Fraser
- Department of Natural Resource Sciences, Thompson Rivers University, Kamloops, British Columbia, Canada
| | | | | | - Liv Norunn Hamre
- Department of Environmental Sciences, Western Norway University of Applied Sciences, Sogndal, Norway
| | - Aveliina Helm
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Ruth Kelly
- School of Natural Sciences, Zoology, Trinity College Dublin, Dublin, Ireland.,Agri-Food and Biosciences Institute, Belfast, Northern Ireland, UK
| | - Lauri Laanisto
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Michele Lonati
- Department of Agriculture, Forest and Food Science, University of Torino, Grugliasco, Italy
| | - Zuzana Münzbergová
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.,Department of Population Ecology, Institute of Botany, Czech Academy of Sciences, Prague, Czech Republic
| | - Paloma Nuche
- School of Natural Sciences, Zoology, Trinity College Dublin, Dublin, Ireland
| | | | - Adrian Oprea
- Botanic Garden "Anastasie Fatu", University "Alexandru Ioan Cuza" Iaşi, Romania
| | - Meelis Pärtel
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - William K Petry
- Department of Plant & Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Satu Ramula
- Department of Biology, University of Turku, Turku, Finland
| | - Pil U Rasmussen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden.,The National Research Centre for the Working Environment, Copenhagen, Denmark
| | - Simone Ravetto Enri
- Department of Agriculture, Forest and Food Science, University of Torino, Grugliasco, Italy
| | - Anna Roeder
- Department of Physiological Diversity, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Christiane Roscher
- Department of Physiological Diversity, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Cheryl Schultz
- School of Biological Sciences, Washington State University, Vancouver, Washington, USA
| | - Olav Skarpaas
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Annabel L Smith
- School of Natural Sciences, Zoology, Trinity College Dublin, Dublin, Ireland.,School of Agriculture and Food Sciences, University of Queensland, Gatton, Queensland, Australia
| | - Ayco J M Tack
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | | | - Peter A Vesk
- School of BioSciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Gregory E Vose
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Elizabeth Wandrag
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia.,Department of Biology, University of York, York, UK
| | - Astrid Wingler
- School of Biological, Earth & Environmental Sciences and Environmental Research Institute, University College Cork, Cork, Ireland
| | - Yvonne M Buckley
- School of Natural Sciences, Zoology, Trinity College Dublin, Dublin, Ireland.,School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
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48
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Adhikari S, Revolinski SR, Eigenbrode SD, Burke IC. Genetic diversity and population structure of a global invader Mayweed chamomile ( Anthemis cotula): management implications. AOB PLANTS 2021; 13:plab049. [PMID: 34466213 PMCID: PMC8403231 DOI: 10.1093/aobpla/plab049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
Mayweed chamomile (Anthemis cotula) is a globally invasive, troublesome annual weed but knowledge of its genetic diversity, population structure in invaded regions and invasion patterns remains unstudied. Therefore, germplasm from 19 A. cotula populations (sites) from three geographically distinct invaded regions: the Walla Walla Basin (located in southern Washington) and the Palouse (located in both northern Idaho and eastern Washington), Pacific Northwest, USA and Kashmir Valley, India were grown in the greenhouse for DNA extraction and sequencing. A total of 18 829 single-nucleotide polymorphisms were called and filtered for each of 89 samples. Pairwise F ST, Nei's genetic distance, heterozygosity, Wright's inbreeding coefficient (F) and self-fertilization rates were estimated for populations within and among the three regions with a total of 19 populations comprised of 89 individuals. Overall measurements of genetic variation were low but significant among regions, populations and individuals. Despite the weak genetic structure, two main genetic clusters were evident, one comprised of populations from Palouse and Kashmir Valley, the other comprised of populations from the Walla Walla Basin. Significant selfing was observed in populations from the Walla Walla Basin and Palouse but not from Kashmir Valley, indicating that Mayweed chamomile in the Pacific Northwest, USA could persist with low pollinator or pollen donor densities. Although F ST values between the regions indicate Palouse populations are more closely related to Kashmir Valley than to Walla Walla Basin populations, based on Migrate-n analysis, panmixis was the most likely model, suggesting an unrestricted gene flow among all three regions. Our study indicated that Kashmir Valley populations either originated from or shared the origin with the Palouse populations, suggesting human-mediated migration of A. cotula between regions.
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Affiliation(s)
- Subodh Adhikari
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, 875 Perimeter Drive MS 2329, Moscow, ID 83844, USA
- Department of Crop and Soil Sciences, Washington State University, Johnson Hall Rm. 115, PO Box 646420, Pullman, WA 99164, USA
| | - Samuel R Revolinski
- Department of Crop and Soil Sciences, Washington State University, Johnson Hall Rm. 115, PO Box 646420, Pullman, WA 99164, USA
| | - Sanford D Eigenbrode
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, 875 Perimeter Drive MS 2329, Moscow, ID 83844, USA
| | - Ian C Burke
- Department of Crop and Soil Sciences, Washington State University, Johnson Hall Rm. 115, PO Box 646420, Pullman, WA 99164, USA
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49
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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: 5] [Impact Index Per Article: 1.7] [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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50
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Safdari P, Höckerstedt L, Brosche M, Salojärvi J, Laine AL. Genotype-Specific Expression and NLR Repertoire Contribute to Phenotypic Resistance Diversity in Plantago lanceolata. FRONTIERS IN PLANT SCIENCE 2021; 12:675760. [PMID: 34322142 PMCID: PMC8311189 DOI: 10.3389/fpls.2021.675760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
High levels of phenotypic variation in resistance appears to be nearly ubiquitous across natural host populations. Molecular processes contributing to this variation in nature are still poorly known, although theory predicts resistance to evolve at specific loci driven by pathogen-imposed selection. Nucleotide-binding leucine-rich repeat (NLR) genes play an important role in pathogen recognition, downstream defense responses and defense signaling. Identifying the natural variation in NLRs has the potential to increase our understanding of how NLR diversity is generated and maintained, and how to manage disease resistance. Here, we sequenced the transcriptomes of five different Plantago lanceolata genotypes when inoculated by the same strain of obligate fungal pathogen Podosphaera plantaginis. A de novo transcriptome assembly of RNA-sequencing data yielded 24,332 gene models with N50 value of 1,329 base pairs and gene space completeness of 66.5%. The gene expression data showed highly varying responses where each plant genotype demonstrated a unique expression profile in response to the pathogen, regardless of the resistance phenotype. Analysis on the conserved NB-ARC domain demonstrated a diverse NLR repertoire in P. lanceolata consistent with the high phenotypic resistance diversity in this species. We find evidence of selection generating diversity at some of the NLR loci. Jointly, our results demonstrate that phenotypic resistance diversity results from a crosstalk between different defense mechanisms. In conclusion, characterizing the architecture of resistance in natural host populations may shed unprecedented light on the potential of evolution to generate variation.
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Affiliation(s)
- Pezhman Safdari
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Layla Höckerstedt
- Climate System Research, Finnish Meteorological Institute, Helsinki, Finland
| | - Mikael Brosche
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Jarkko Salojärvi
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Anna-Liisa Laine
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
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