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McGaughran A, Dhami MK, Parvizi E, Vaughan AL, Gleeson DM, Hodgins KA, Rollins LA, Tepolt CK, Turner KG, Atsawawaranunt K, Battlay P, Congrains C, Crottini A, Dennis TPW, Lange C, Liu XP, Matheson P, North HL, Popovic I, Rius M, Santure AW, Stuart KC, Tan HZ, Wang C, Wilson J. Genomic Tools in Biological Invasions: Current State and Future Frontiers. Genome Biol Evol 2024; 16:evad230. [PMID: 38109935 PMCID: PMC10776249 DOI: 10.1093/gbe/evad230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/16/2023] [Accepted: 12/12/2023] [Indexed: 12/20/2023] Open
Abstract
Human activities are accelerating rates of biological invasions and climate-driven range expansions globally, yet we understand little of how genomic processes facilitate the invasion process. Although most of the literature has focused on underlying phenotypic correlates of invasiveness, advances in genomic technologies are showing a strong link between genomic variation and invasion success. Here, we consider the ability of genomic tools and technologies to (i) inform mechanistic understanding of biological invasions and (ii) solve real-world issues in predicting and managing biological invasions. For both, we examine the current state of the field and discuss how genomics can be leveraged in the future. In addition, we make recommendations pertinent to broader research issues, such as data sovereignty, metadata standards, collaboration, and science communication best practices that will require concerted efforts from the global invasion genomics community.
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Affiliation(s)
- Angela McGaughran
- 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
- School of Biological Sciences, Waipapa Taumata Rau/University of Auckland, Auckland, New Zealand
| | - 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
| | - Dianne M Gleeson
- Centre for Conservation Ecology and Genomics, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Lee A Rollins
- Evolution and Ecology Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Carolyn K Tepolt
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Kathryn G Turner
- Department of Biological Sciences, Idaho State University, Pocatello, ID, USA
| | - Kamolphat Atsawawaranunt
- School of Biological Sciences, Waipapa Taumata Rau/University of Auckland, Auckland, New Zealand
| | - Paul Battlay
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Carlos Congrains
- Entomology Section, Department of Plant and Environmental Protection Sciences, University of Hawaiʻi at Mānoa, Honolulu, HI 96822, USA
- US Department of Agriculture-Agricultural Research Service, Daniel K. Inouye US Pacific Basin Agricultural Research Center, Hilo, HI 96720, USA
| | - Angelica Crottini
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto 4169–007, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão 4485-661, Portugal
| | - Tristan P W Dennis
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Claudia Lange
- Biocontrol and Molecular Ecology, Manaaki Whenua Landcare Research, Lincoln, New Zealand
| | - Xiaoyue P Liu
- Department of Marine Science, University of Otago, Dunedin, New Zealand
| | - Paige Matheson
- Te Aka Mātuatua/School of Science, University of Waikato, Hamilton, New Zealand
| | - Henry L North
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Iva Popovic
- School of the Environment, University of Queensland, Brisbane, QLD, Australia
| | - Marc Rius
- Centre for Advanced Studies of Blanes (CEAB, CSIC), Accés a la Cala Sant Francesc, Blanes, Spain
- Department of Zoology, Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Johannesburg 2006, South Africa
| | - Anna W Santure
- School of Biological Sciences, Waipapa Taumata Rau/University of Auckland, Auckland, New Zealand
| | - Katarina C Stuart
- School of Biological Sciences, Waipapa Taumata Rau/University of Auckland, Auckland, New Zealand
| | - Hui Zhen Tan
- School of Biological Sciences, Waipapa Taumata Rau/University of Auckland, Auckland, New Zealand
| | - Cui Wang
- The Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Jonathan Wilson
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
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Turner KG, Ostevik KL, Grassa CJ, Rieseberg LH. Genomic Analyses of Phenotypic Differences Between Native and Invasive Populations of Diffuse Knapweed (Centaurea diffusa). Front Ecol Evol 2021. [DOI: 10.3389/fevo.2020.577635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Invasive species represent excellent opportunities to study the evolutionary potential of traits important to success in novel environments. Although some ecologically important traits have been identified in invasive species, little is typically known about the genetic mechanisms that underlie invasion success in non-model species. Here, we use a genome-wide association (GWAS) approach to identify the genetic basis of trait variation in the non-model, invasive, diffuse knapweed [Centaurea diffusa Lam. (Asteraceae)]. To assist with this analysis, we have assembled the first draft genome reference and fully annotated plastome assembly for this species, and one of the first from this large, weedy, genus, which is of major ecological and economic importance. We collected phenotype data from 372 individuals from four native and four invasive populations of C. diffusa grown in a common environment. Using these individuals, we produced reduced-representation genotype-by-sequencing (GBS) libraries and identified 7,058 SNPs. We identify two SNPs associated with leaf width in these populations, a trait which significantly varies between native and invasive populations. In this rosette forming species, increased leaf width is a major component of increased biomass, a common trait in invasive plants correlated with increased fitness. Finally, we use annotations from Arabidopsis thaliana to identify 98 candidate genes that are near the associated SNPs and highlight several good candidates for leaf width variation.
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Turner KG, Lorts CM, Haile AT, Lasky JR. Effects of genomic and functional diversity on stand-level productivity and performance of non-native Arabidopsis. Proc Biol Sci 2020; 287:20202041. [PMID: 33081615 PMCID: PMC7661305 DOI: 10.1098/rspb.2020.2041] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 09/30/2020] [Indexed: 12/25/2022] Open
Abstract
Biodiversity can affect the properties of groups of organisms, such as ecosystem function and the persistence of colonizing populations. Genomic data offer a newly available window to diversity, complementary to other measures like taxonomic or phenotypic diversity. We tested whether native genetic diversity in field experimental stands of Arabidopsis thaliana affected their aboveground biomass and fecundity in their colonized range. We constructed some stands of genotypes that we a priori predicted would differ in performance or show overyielding. We found no relationship between genetic diversity and stand total biomass. However, increasing stand genetic diversity increased fecundity in high-resource conditions. Polyculture (multiple genotype) stands consistently yielded less biomass than expected based on the yields of component genotypes in monoculture. This under-yielding was strongest in stands with late-flowering and high biomass genotypes, potentially due to interference competition by these genotypes. Using a new implementation of association mapping, we identified genetic loci whose diversity was associated with stand-level yield, revealing a major flowering time locus associated with under-yielding of polycultures. Our field experiment supports community ecology studies that find a range of diversity-function relationships. Nevertheless, our results suggest diversity in colonizing propagule pools can enhance population fitness. Furthermore, interference competition among genotypes differing in flowering time might limit the advantages of polyculture.
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Affiliation(s)
- Kathryn G. Turner
- Department of Biology, Pennsylvania State University, USA
- Department of Biological Sciences, Idaho State University, USA
| | | | - Asnake T. Haile
- Department of Biology, Pennsylvania State University, USA
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Ethiopia
| | - Jesse R. Lasky
- Department of Biology, Pennsylvania State University, USA
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Lopez L, Turner KG, Bellis ES, Lasky JR. Genomics of natural history collections for understanding evolution in the wild. Mol Ecol Resour 2020; 20:1153-1160. [DOI: 10.1111/1755-0998.13245] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 08/13/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Lua Lopez
- Department of Biology California State University San Bernardino San Bernardino CaliforniaUSA
- Department of Biology Pennsylvania State University University Park PennsylvaniaUSA
| | - Kathryn G. Turner
- Department of Biology Pennsylvania State University University Park PennsylvaniaUSA
- Department of Biological Sciences Idaho State University Pocatello IdahoUSA
| | - Emily S. Bellis
- Department of Biology Pennsylvania State University University Park PennsylvaniaUSA
- Arkansas Biosciences Institute & Department of Computer Science Arkansas State University Jonesboro ArkansasUSA
| | - Jesse R. Lasky
- Department of Biology Pennsylvania State University University Park PennsylvaniaUSA
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Hedrick BP, Heberling JM, Meineke EK, Turner KG, Grassa CJ, Park DS, Kennedy J, Clarke JA, Cook JA, Blackburn DC, Edwards SV, Davis CC. Digitization and the Future of Natural History Collections. Bioscience 2020. [DOI: 10.1093/biosci/biz163] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Abstract
Natural history collections (NHCs) are the foundation of historical baselines for assessing anthropogenic impacts on biodiversity. Along these lines, the online mobilization of specimens via digitization—the conversion of specimen data into accessible digital content—has greatly expanded the use of NHC collections across a diversity of disciplines. We broaden the current vision of digitization (Digitization 1.0)—whereby specimens are digitized within NHCs—to include new approaches that rely on digitized products rather than the physical specimen (Digitization 2.0). Digitization 2.0 builds on the data, workflows, and infrastructure produced by Digitization 1.0 to create digital-only workflows that facilitate digitization, curation, and data links, thus returning value to physical specimens by creating new layers of annotation, empowering a global community, and developing automated approaches to advance biodiversity discovery and conservation. These efforts will transform large-scale biodiversity assessments to address fundamental questions including those pertaining to critical issues of global change.
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Affiliation(s)
- Brandon P Hedrick
- Department of Cell Biology and Anatomy, Louisiana State University Health Sciences Center, New Orleans, Louisiana
- Department of Organismal and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
| | - J Mason Heberling
- Section of Botany, Carnegie Museum of Natural History, Pittsburgh, Pennsylvania
| | - Emily K Meineke
- Department of Organismal and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
- Harvard University Herbaria, Harvard University, Cambridge, Massachusetts
| | - Kathryn G Turner
- Department of Biological Sciences, Idaho State University, Pocatello
| | | | - Daniel S Park
- Harvard University Herbaria, Harvard University, Cambridge, Massachusetts
| | - Jonathan Kennedy
- Harvard University Herbaria, Harvard University, Cambridge, Massachusetts
| | - Julia A Clarke
- Jackson School of Geosciences, University of Texas at Austin, Austin, Texas
| | - Joseph A Cook
- Department of Biology, University of New Mexico, Albuquerque
| | - David C Blackburn
- Florida Museum of Natural History, University of Florida, Gainesville
| | - Scott V Edwards
- Department of Organismal and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
| | - Charles C Davis
- Harvard University Herbaria, Harvard University, Cambridge, Massachusetts
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Monroe JG, Gill B, Turner KG, McKay JK. Drought regimens predict life history strategies in Heliophila. New Phytol 2019; 223:2054-2062. [PMID: 31087648 DOI: 10.1111/nph.15919] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/01/2019] [Indexed: 06/09/2023]
Abstract
Explaining variation in life history strategies is an enduring goal of evolutionary biology and ecology. Early theory predicted that for plants, annual and perennial life histories reflect adaptations to environments that experience alternative drought regimens. Nevertheless, empirical support for this hypothesis from comparative analyses remains lacking. Here, we test classic life history theory in Heliophila L. (Brassicaceae), a diverse genus of flowering plants native to Africa, controlling for phylogeny and integrating 34 yr of satellite-based drought detection with 2192 herbaria occurrence records. We find that the common ancestor of these species was likely to be an annual, and that perenniality and annuality have repeatedly evolved, an estimated seven and five times, respectively. By comparing historical drought regimens, we show that annuals rather than perennial species occur in environments where droughts are significantly more frequent. We also find evidence that annual plants adapt to predictable drought regimens by escaping drought-prone seasons as seeds. These results yield compelling support for longstanding theoretical predictions by revealing the importance of drought frequency and predictability to explain plant life history. More broadly, this work highlights scalable approaches, integrating herbaria records and remote sensing to address outstanding questions in evolutionary ecology.
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Affiliation(s)
- J Grey Monroe
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, 80521, USA
- College of Agriculture, Colorado State University, Fort Collins, CO, 80521, USA
| | - Brian Gill
- Institute for Environment and Society, Brown University, Providence, RI, 02912, USA
| | - Kathryn G Turner
- Biology Department, Pennsylvania State University, State College, PA, 16802, USA
| | - John K McKay
- College of Agriculture, Colorado State University, Fort Collins, CO, 80521, USA
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Endriss SB, Vahsen ML, Bitume EV, Grey Monroe J, Turner KG, Norton AP, Hufbauer RA. The importance of growing up: juvenile environment influences dispersal of individuals and their neighbours. Ecol Lett 2018; 22:45-55. [PMID: 30450720 DOI: 10.1111/ele.13166] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/03/2018] [Accepted: 08/30/2018] [Indexed: 12/31/2022]
Abstract
Dispersal is a key ecological process that is strongly influenced by both phenotype and environment. Here, we show that juvenile environment influences dispersal not only by shaping individual phenotypes, but also by changing the phenotypes of neighbouring conspecifics, which influence how individuals disperse. We used a model system (Tribolium castaneum, red flour beetles) to test how the past environment of dispersing individuals and their neighbours influences how they disperse in their current environment. We found that individuals dispersed especially far when exposed to a poor environment as adults if their phenotype, or even one-third of their neighbours' phenotypes, were shaped by a poor environment as juveniles. Juvenile environment therefore shapes dispersal both directly, by influencing phenotype, as well as indirectly, by influencing the external social environment. Thus, the juvenile environment of even a minority of individuals in a group can influence the dispersal of the entire group.
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Affiliation(s)
- Stacy B Endriss
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA.,Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA.,Department of Natural Resources, Cornell University, Ithaca, NY, USA
| | - Megan L Vahsen
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA.,Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA.,Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Ellyn V Bitume
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA.,Exotic and Invasive Weeds Research Unit, U.S. Department of Agriculture - Agricultural Research Service, Albany, CA, USA
| | - J Grey Monroe
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA.,Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA
| | - Kathryn G Turner
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA.,Department of Biology, Pennsylvania State University, State College, PA, USA
| | - Andrew P Norton
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA.,Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA
| | - Ruth A Hufbauer
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA.,Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA
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9
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Turner KG, Huang DI, Cronk QCB, Rieseberg LH. Homogenization of Populations in the Wildflower, Texas Bluebonnet (Lupinus texensis). J Hered 2017; 109:152-161. [DOI: 10.1093/jhered/esx094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/26/2017] [Indexed: 11/13/2022] Open
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Turner KG, Fréville H, Rieseberg LH. Adaptive plasticity and niche expansion in an invasive thistle. Ecol Evol 2015; 5:3183-97. [PMID: 26357544 PMCID: PMC4559060 DOI: 10.1002/ece3.1599] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 06/11/2015] [Accepted: 06/14/2015] [Indexed: 01/14/2023] Open
Abstract
Phenotypic differentiation in size and fecundity between native and invasive populations of a species has been suggested as a causal driver of invasion in plants. Local adaptation to novel environmental conditions through a micro-evolutionary response to natural selection may lead to phenotypic differentiation and fitness advantages in the invaded range. Local adaptation may occur along a stress tolerance trade-off, favoring individuals that, in benign conditions, shift resource allocation from stress tolerance to increased vigor and fecundity and, therefore, invasiveness. Alternately, the typically disturbed invaded range may select for a plastic, generalist strategy, making phenotypic plasticity the main driver of invasion success. To distinguish between these hypotheses, we performed a field common garden and tested for genetically based phenotypic differentiation, resource allocation shifts in response to water limitation, and local adaptation to the environmental gradient which describes the source locations for native and invasive populations of diffuse knapweed (Centaurea diffusa). Plants were grown in an experimental field in France (naturalized range) under water addition and limitation conditions. After accounting for phenotypic variation arising from environmental differences among collection locations, we found evidence of genetic variation between the invasive and native populations for most morphological and life-history traits under study. Invasive C. diffusa populations produced larger, later maturing, and therefore potentially fitter individuals than native populations. Evidence for local adaptation along a resource allocation trade-off for water limitation tolerance is equivocal. However, native populations do show evidence of local adaptation to an environmental gradient, a relationship which is typically not observed in the invaded range. Broader analysis of the climatic niche inhabited by the species in both ranges suggests that the physiological tolerances of C. diffusa may have expanded in the invaded range. This observation could be due to selection for plastic, "general-purpose" genotypes with broad environmental tolerances.
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Affiliation(s)
- Kathryn G Turner
- Department of Botany and Biodiversity Research Centre, University of British ColumbiaRoom 3529-6270 University Blvd., Vancouver, British Columbia, V6T 1Z4, Canada
| | - Hélène Fréville
- UMR 1334 AGAP INRA2 place Pierre Viala, Montpellier Cedex 2, 34060, France
- UMR 5175 CEFE CNRS1919 route de Mende, Montpellier Cedex 5, 34293, France
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British ColumbiaRoom 3529-6270 University Blvd., Vancouver, British Columbia, V6T 1Z4, Canada
- Department of Biology, Indiana UniversityBloomington, Indiana, 47405
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Bock DG, Caseys C, Cousens RD, Hahn MA, Heredia SM, Hübner S, Turner KG, Whitney KD, Rieseberg LH. What we still don't know about invasion genetics. Mol Ecol 2015; 24:2277-97. [PMID: 25474505 DOI: 10.1111/mec.13032] [Citation(s) in RCA: 226] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Revised: 11/27/2014] [Accepted: 11/28/2014] [Indexed: 12/12/2022]
Abstract
Publication of The Genetics of Colonizing Species in 1965 launched the field of invasion genetics and highlighted the value of biological invasions as natural ecological and evolutionary experiments. Here, we review the past 50 years of invasion genetics to assess what we have learned and what we still don't know, focusing on the genetic changes associated with invasive lineages and the evolutionary processes driving these changes. We also suggest potential studies to address still-unanswered questions. We now know, for example, that rapid adaptation of invaders is common and generally not limited by genetic variation. On the other hand, and contrary to prevailing opinion 50 years ago, the balance of evidence indicates that population bottlenecks and genetic drift typically have negative effects on invasion success, despite their potential to increase additive genetic variation and the frequency of peak shifts. Numerous unknowns remain, such as the sources of genetic variation, the role of so-called expansion load and the relative importance of propagule pressure vs. genetic diversity for successful establishment. While many such unknowns can be resolved by genomic studies, other questions may require manipulative experiments in model organisms. Such studies complement classical reciprocal transplant and field-based selection experiments, which are needed to link trait variation with components of fitness and population growth rates. We conclude by discussing the potential for studies of invasion genetics to reveal the limits to evolution and to stimulate the development of practical strategies to either minimize or maximize evolutionary responses to environmental change.
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Affiliation(s)
- Dan G Bock
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Room 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
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Hodgins KA, Bock DG, Hahn MA, Heredia SM, Turner KG, Rieseberg LH. Comparative genomics in the Asteraceae reveals little evidence for parallel evolutionary change in invasive taxa. Mol Ecol 2015; 24:2226-40. [PMID: 25439241 DOI: 10.1111/mec.13026] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 11/23/2014] [Accepted: 11/26/2014] [Indexed: 01/12/2023]
Abstract
Asteraceae, the largest family of flowering plants, has given rise to many notorious invasive species. Using publicly available transcriptome assemblies from 35 Asteraceae, including six major invasive species, we examined evidence for micro- and macro-evolutionary genomic changes associated with invasion. To detect episodes of positive selection repeated across multiple introductions, we conducted comparisons between native and introduced genotypes from six focal species and identified genes with elevated rates of amino acid change (dN/dS). We then looked for evidence of positive selection at a broader phylogenetic scale across all taxa. As invasive species may experience founder events during colonization and spread, we also looked for evidence of increased genetic load in introduced genotypes. We rarely found evidence for parallel changes in orthologous genes in the intraspecific comparisons, but in some cases we identified changes in members of the same gene family. Using among-species comparisons, we detected positive selection in 0.003-0.69% and 2.4-7.8% of the genes using site and stochastic branch-site models, respectively. These genes had diverse putative functions, including defence response, stress response and herbicide resistance, although there was no clear pattern in the GO terms. There was no indication that introduced genotypes have a higher proportion of deleterious alleles than native genotypes in the six focal species, suggesting multiple introductions and admixture mitigated the impact of drift. Our findings provide little evidence for common genomic responses in invasive taxa of the Asteraceae and hence suggest that multiple evolutionary pathways may lead to adaptation during introduction and spread in these species.
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Affiliation(s)
- Kathryn A Hodgins
- School of Biological Sciences, Monash University, Clayton, Vic., 3800, Australia
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Abstract
Trade-offs between performance and the ability to tolerate abiotic and biotic stress have been suggested to explain both the success of invasive species and phenotypic differentiation between native and invasive populations. It is critical to sample broadly across both ranges and to account for latitudinal clines and maternal effects when testing this premise. Wild-collected Centaurea diffusa seeds were grown in benign and stressful conditions (drought, flooding, nutrient stress and simulated herbivory), to evaluate whether native and introduced individuals differ in performance or life history phenotypes. A second experiment used glasshouse-grown seeds to evaluate whether patterns remain comparable when maternal environment is consistent. Many traits differed between ranges, and in all cases but one, invasive individuals grew larger, performed better, or matured later. No trade-off in performance with herbivore defense was evident. Invasive populations may have been released from a trade-off between growth and drought tolerance apparent in the native range. Larger individuals with delayed maturity and greater reproductive potential have evolved in invasive populations, a pattern evident across broad population sampling, and after latitude and maternal environment were considered. Release from abiotic stress tolerance trade-offs may be important for the invasion success of Centaurea diffusa.
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Affiliation(s)
- Kathryn G Turner
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Room 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
| | - Ruth A Hufbauer
- Department of Bioagricultural Sciences and Pest Management and Graduate Degree Program in Ecology, Colorado State University, 1177 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Room 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
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Lai Z, Kane NC, Kozik A, Hodgins KA, Dlugosch KM, Barker MS, Matvienko M, Yu Q, Turner KG, Pearl SA, Bell GDM, Zou Y, Grassa C, Guggisberg A, Adams KL, Anderson JV, Horvath DP, Kesseli RV, Burke JM, Michelmore RW, Rieseberg LH. Genomics of Compositae weeds: EST libraries, microarrays, and evidence of introgression. Am J Bot 2012; 99:209-18. [PMID: 22058181 DOI: 10.3732/ajb.1100313] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
PREMISE OF STUDY Weeds cause considerable environmental and economic damage. However, genomic characterization of weeds has lagged behind that of model plants and crop species. Here we describe the development of genomic tools and resources for 11 weeds from the Compositae family that will serve as a basis for subsequent population and comparative genomic analyses. Because hybridization has been suggested as a stimulus for the evolution of invasiveness, we also analyze these genomic data for evidence of hybridization. METHODS We generated 22 expressed sequence tag (EST) libraries for the 11 targeted weeds using Sanger, 454, and Illumina sequencing, compared the coverage and quality of sequence assemblies, and developed NimbleGen microarrays for expression analyses in five taxa. When possible, we also compared the distributions of Ks values between orthologs of congeneric taxa to detect and quantify hybridization and introgression. RESULTS Gene discovery was enhanced by sequencing from multiple tissues, normalization of cDNA libraries, and especially greater sequencing depth. However, assemblies from short sequence reads sometimes failed to resolve close paralogs. Substantial introgression was detected in Centaurea and Helianthus, but not in Ambrosia and Lactuca. CONCLUSIONS Transcriptome sequencing using next-generation platforms has greatly reduced the cost of genomic studies of nonmodel organisms, and the ESTs and microarrays reported here will accelerate evolutionary and molecular investigations of Compositae weeds. Our study also shows how ortholog comparisons can be used to approximately estimate the genome-wide extent of introgression and to identify genes that have been exchanged between hybridizing taxa.
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Affiliation(s)
- Zhao Lai
- Department of Biology and Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana 47405, USA
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Gross BL, Turner KG, Rieseberg LH. Selective sweeps in the homoploid hybrid species Helianthus deserticola: evolution in concert across populations and across origins. Mol Ecol 2008; 16:5246-58. [PMID: 18092993 DOI: 10.1111/j.1365-294x.2007.03574.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The evolution of different populations within a species in response to selective pressures can potentially happen in three different ways. It can occur in parallel, where similar changes occur independently in each population in response to selection; in concert, where the spread of an adaptive mutation across a species' range results in a single allele fixing in each population; or populations can diverge in response to local selective pressures. We explored these possibilities in populations of the homoploid hybrid species Helianthus deserticola relative to its parental species Helianthus annuus and Helianthus petiolaris using an analysis of variation in 96 expressed sequence tag-based microsatellites. A total of nine loci showed evidence consistent with recent selection at either the species or population level, although two of these genes were discarded because the apparent sweep did not occur relative to the parent from which the locus was derived. Between one and five loci showed a putative sweep across the entire species range with the same microsatellite allele fixed in each population. This pattern is consistent with evolution in concert despite geographical isolation and potential independent origins of the populations. Only one population of H. deserticola showed candidate sweeps that were unique compared to the rest of the species, and this population has also potentially experienced recent admixture with the parental species.
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Affiliation(s)
- Briana L Gross
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA.
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Barber JC, Francisco-Ortega J, Santos-Guerra A, Turner KG, Jansen RK. Origin of Macaronesian Sideritis L. (Lamioideae: Lamiaceae) inferred from nuclear and chloroplast sequence datasets. Mol Phylogenet Evol 2002; 23:293-306. [PMID: 12099789 DOI: 10.1016/s1055-7903(02)00018-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Sideritis L. (Lamiaceae) comprises approximately 150 species of annuals and perennials distributed chiefly in the Mediterranean region. The majority of the species belong to the continental subgenus Sideritis which is divided into two perennial (Sideritis and Empedoclea) and two annual (Hesiodia and Burgsdorfia) sections. Twenty-three species are woody perennials endemic to the Macaronesian archipelagos of Madeira and the Canary Islands. In an effort to determine the continental origin of the insular group, we constructed independent phylogenies comprising sequence data from both chloroplast and nuclear markers. Sampling included 7 island taxa drawn from the Macaronesian subgenus Marrubiastrum and 25 continental taxa representing all four sections of subgenus Sideritis. Subgenus Marrubiastrum and the two continental perennial sections form well-supported monophyletic groups in both individual and combined analyses. The annual sections are not monophyletic in any analysis; further sampling of annual taxa is needed to resolve these relationships. All analyses identified Sideritis cossoniana, an annual species from Morocco, as the closest continental relative of the Macaronesian group. This contrasts with the hypothesis of earlier workers who suggested that the insular taxa were most closely related to eastern Mediterranean species of the genus. The phylogenies also demonstrate a distinct increase in woodiness among the Macaronesian species relative to their continental congeners, providing further support for the secondary nature of woodiness in island plants.
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Affiliation(s)
- Janet C Barber
- Department of Biology, University of Missouri, 8001 Natural Bridge Road, St. Louis 63121, USA.
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