1
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Gallegos C, Hodgins KA, Monro K. Temperature and sex shape reproductive barriers in a climate change hotspot. Evolution 2024; 78:906-918. [PMID: 38332537 DOI: 10.1093/evolut/qpae012] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/01/2024] [Accepted: 02/07/2024] [Indexed: 02/10/2024]
Abstract
Climate change is altering species ranges and reproductive interactions in existing ranges, offering species new scope to mate and hybridize. The outcomes will depend on how environmental factors shape reproductive barriers across life stages, yet this is rarely assessed across the environments that species encounter in nature. We assess prezygotic and postzygotic barriers, and their dependence on temperature and parental sex, in species of a reef-building tubeworm (Galeolaria) from a fast-warming biodiversity hotspot in southern Australia. By replicating pure and reciprocal hybrid crosses across 5 temperatures spanning species' thermal ranges, we estimate thermal tolerance curves (defining niches) for crosses and reproductive isolation at each temperature. By also replicating crosses at 3 life stages, we partition the contributions of prezygotic barriers at fertilization, postzygotic barriers at embryogenesis, and postzygotic barriers at larval development to reproductive isolation. We show that barriers are weaker at fertilization and embryogenesis, but stronger and more temperature sensitive at larval development, as species diverge in thermal niche. Asymmetry of barriers between parental sexes, moreover, suggests a complex interplay between niche differentiation and maternal inheritance. Our findings point to a key role for temperature in reproductive isolation, but also challenges for predicting the fate of isolation in future climates.
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Affiliation(s)
- Cristóbal Gallegos
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Keyne Monro
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
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2
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Caizergues AE, Santangelo JS, Ness RW, Angeoletto F, Anstett DN, Anstett J, Baena-Diaz F, Carlen EJ, Chaves JA, Comerford MS, Dyson K, Falahati-Anbaran M, Fellowes MDE, Hodgins KA, Hood GR, Iñiguez-Armijos C, Kooyers NJ, Lázaro-Lobo A, Moles AT, Munshi-South J, Paule J, Porth IM, Santiago-Rosario LY, Whitney KS, Tack AJM, Johnson MTJ. Does urbanisation lead to parallel demographic shifts across the world in a cosmopolitan plant? Mol Ecol 2024; 33:e17311. [PMID: 38468155 DOI: 10.1111/mec.17311] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 12/08/2023] [Accepted: 01/30/2024] [Indexed: 03/13/2024]
Abstract
Urbanisation is occurring globally, leading to dramatic environmental changes that are altering the ecology and evolution of species. In particular, the expansion of human infrastructure and the loss and fragmentation of natural habitats in cities is predicted to increase genetic drift and reduce gene flow by reducing the size and connectivity of populations. Alternatively, the 'urban facilitation model' suggests that some species will have greater gene flow into and within cities leading to higher diversity and lower differentiation in urban populations. These alternative hypotheses have not been contrasted across multiple cities. Here, we used the genomic data from the GLobal Urban Evolution project (GLUE), to study the effects of urbanisation on non-adaptive evolutionary processes of white clover (Trifolium repens) at a global scale. We found that white clover populations presented high genetic diversity and no evidence of reduced Ne linked to urbanisation. On the contrary, we found that urban populations were less likely to experience a recent decrease in effective population size than rural ones. In addition, we found little genetic structure among populations both globally and between urban and rural populations, which showed extensive gene flow between habitats. Interestingly, white clover displayed overall higher gene flow within urban areas than within rural habitats. Our study provides the largest comprehensive test of the demographic effects of urbanisation. Our results contrast with the common perception that heavily altered and fragmented urban environments will reduce the effective population size and genetic diversity of populations and contribute to their isolation.
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Affiliation(s)
- Aude E Caizergues
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - James S Santangelo
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, USA
| | - Rob W Ness
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Fabio Angeoletto
- Programa de Pós-Graduação em Gestão e Tecnologia Ambiental da Universidade Federal de Rondonópolis, Rondonópolis, Brasil
| | - Daniel N Anstett
- Department of Plant Biology, Department of Entomology, Plant Resilience Institute, Michigan State University, East Lansing, Michigan, USA
| | - Julia Anstett
- Genomic Sciences and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Elizabeth J Carlen
- Living Earth Collaborative, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Jaime A Chaves
- Universidad San Francisco de Quito, Ecuador, Quito
- San Francisco State University, San Francisco, California, USA
| | - Mattheau S Comerford
- Department of Biology, University of Massachusetts Boston, Boston, Massachusetts, USA
| | | | | | | | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Glen Ray Hood
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Carlos Iñiguez-Armijos
- Laboratorio de Ecología Tropical y Servicios Ecosistémicos (EcoSs-Lab), Universidad Técnica Particular de Loja, Loja, Ecuador
| | | | - Adrián Lázaro-Lobo
- Biodiversity Research Institute (IMIB), CSIC-University of Oviedo-Principality of Asturias, Mieres, Spain
| | - Angela T Moles
- Evolution & Ecology Research Centre, UNSW-University of New South Wales, Sydney, New South Wales, Australia
| | - Jason Munshi-South
- Department of Biology and Louis Calder Center, Fordham University, New York City, New York, USA
| | - Juraj Paule
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Berlin, Germany
| | - Ilga M Porth
- Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, Quebec, Canada
| | - Luis Y Santiago-Rosario
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, USA
| | - Kaitlin Stack Whitney
- Science, Technology & Society Department, Rochester Institute of Technology, Rochester, New York, USA
| | - Ayko J M Tack
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Marc T J Johnson
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
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3
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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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4
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Putra AR, Hodgins KA, Fournier‐Level A. Assessing the invasive potential of different source populations of ragweed ( Ambrosia artemisiifolia L.) through genomically informed species distribution modelling. Evol Appl 2024; 17:e13632. [PMID: 38283606 PMCID: PMC10810254 DOI: 10.1111/eva.13632] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 01/30/2024] Open
Abstract
The genetic composition of founding populations is likely to play a key role in determining invasion success. Individual genotypes may differ in habitat preference and environmental tolerance, so their ability to colonize novel environments can be highly variable. Despite the importance of genetic variation on invasion success, its influence on the potential distribution of invaders is rarely investigated. Here, we integrate population genomics and ecological niche models (ENMs) into a single framework to predict the distribution of globally invasive common ragweed (Ambrosia artemisiifolia) in Australia. We identified three genetic clusters for ragweed and used these to construct cluster-specific ENMs and characterize within-species niche differentiation. The potential range of ragweed in Australia depended on the genetic composition and continent of origin of the introduced population. Invaders originating from warmer, wetter climates had a broader potential distribution than those from cooler, drier ones. By quantifying this change, we identified source populations most likely to expand the ragweed distribution. As prevention remains the most effective method of invasive species management, our work provides a valuable way of ranking the threat posed by different populations to better inform management decisions.
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Affiliation(s)
- Andhika R. Putra
- School of BioSciencesThe University of MelbourneParkvilleVictoriaAustralia
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5
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Kim AS, Kreiner JM, Hernández F, Bock DG, Hodgins KA, Rieseberg LH. Temporal collections to study invasion biology. Mol Ecol 2023; 32:6729-6742. [PMID: 37873879 DOI: 10.1111/mec.17176] [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: 08/22/2023] [Revised: 10/07/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023]
Abstract
Biological invasions represent an extraordinary opportunity to study evolution. This is because accidental or deliberate species introductions have taken place for centuries across large geographical scales, frequently prompting rapid evolutionary transitions in invasive populations. Until recently, however, the utility of invasions as evolutionary experiments has been hampered by limited information on the makeup of populations that were part of earlier invasion stages. Now, developments in ancient and historical DNA technologies, as well as the quickening pace of digitization for millions of specimens that are housed in herbaria and museums globally, promise to help overcome this obstacle. In this review, we first introduce the types of temporal data that can be used to study invasions, highlighting the timescale captured by each approach and their respective limitations. We then discuss how ancient and historical specimens as well as data available from prior invasion studies can be used to answer questions on mechanisms of (mal)adaptation, rates of evolution, or community-level changes during invasions. By bridging the gap between contemporary and historical invasive populations, temporal data can help us connect pattern to process in invasion science. These data will become increasingly important if invasions are to achieve their full potential as experiments of evolution in nature.
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Affiliation(s)
- Amy S Kim
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Julia M Kreiner
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Fernando Hernández
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Dan G Bock
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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6
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Santangelo JS, Battlay P, Hendrickson BT, Kuo WH, Olsen KM, Kooyers NJ, Johnson MTJ, Hodgins KA, Ness RW. Haplotype-Resolved, Chromosome-Level Assembly of White Clover (Trifolium repens L., Fabaceae). Genome Biol Evol 2023; 15:evad146. [PMID: 37542471 PMCID: PMC10433932 DOI: 10.1093/gbe/evad146] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/24/2023] [Accepted: 07/29/2023] [Indexed: 08/07/2023] Open
Abstract
White clover (Trifolium repens L.; Fabaceae) is an important forage and cover crop in agricultural pastures around the world and is increasingly used in evolutionary ecology and genetics to understand the genetic basis of adaptation. Historically, improvements in white clover breeding practices and assessments of genetic variation in nature have been hampered by a lack of high-quality genomic resources for this species, owing in part to its high heterozygosity and allotetraploid hybrid origin. Here, we use PacBio HiFi and chromosome conformation capture (Omni-C) technologies to generate a chromosome-level, haplotype-resolved genome assembly for white clover totaling 998 Mbp (scaffold N50 = 59.3 Mbp) and 1 Gbp (scaffold N50 = 58.6 Mbp) for haplotypes 1 and 2, respectively, with each haplotype arranged into 16 chromosomes (8 per subgenome). We additionally provide a functionally annotated haploid mapping assembly (968 Mbp, scaffold N50 = 59.9 Mbp), which drastically improves on the existing reference assembly in both contiguity and assembly accuracy. We annotated 78,174 protein-coding genes, resulting in protein BUSCO completeness scores of 99.6% and 99.3% against the embryophyta_odb10 and fabales_odb10 lineage datasets, respectively.
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Affiliation(s)
- James S Santangelo
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Paul Battlay
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | | | - Wen-Hsi Kuo
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Kenneth M Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Nicholas J Kooyers
- Department of Biology, University of Louisiana, Lafayette, Louisiana, USA
| | - Marc T J Johnson
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Rob W Ness
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
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7
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Battlay P, Wilson J, Bieker VC, Lee C, Prapas D, Petersen B, Craig S, van Boheemen L, Scalone R, de Silva NP, Sharma A, Konstantinović B, Nurkowski KA, Rieseberg LH, Connallon T, Martin MD, Hodgins KA. Large haploblocks underlie rapid adaptation in the invasive weed Ambrosia artemisiifolia. Nat Commun 2023; 14:1717. [PMID: 36973251 PMCID: PMC10042993 DOI: 10.1038/s41467-023-37303-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 03/11/2023] [Indexed: 03/29/2023] Open
Abstract
Adaptation is the central feature and leading explanation for the evolutionary diversification of life. Adaptation is also notoriously difficult to study in nature, owing to its complexity and logistically prohibitive timescale. Here, we leverage extensive contemporary and historical collections of Ambrosia artemisiifolia-an aggressively invasive weed and primary cause of pollen-induced hayfever-to track the phenotypic and genetic causes of recent local adaptation across its native and invasive ranges in North America and Europe, respectively. Large haploblocks-indicative of chromosomal inversions-contain a disproportionate share (26%) of genomic regions conferring parallel adaptation to local climates between ranges, are associated with rapidly adapting traits, and exhibit dramatic frequency shifts over space and time. These results highlight the importance of large-effect standing variants in rapid adaptation, which have been critical to A. artemisiifolia's global spread across vast climatic gradients.
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Affiliation(s)
- Paul Battlay
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Jonathan Wilson
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Vanessa C Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Christopher Lee
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Diana Prapas
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Bent Petersen
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), AIMST University, 08100, Bedong, Kedah, Malaysia
| | - Sam Craig
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Lotte van Boheemen
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Romain Scalone
- Department of Crop Production Ecology, Uppsala Ecology Center, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Grapevine Breeding, Hochschule Geisenheim University, Geisenheim, Germany
| | - Nissanka P de Silva
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Amit Sharma
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Bojan Konstantinović
- Department of Environmental and Plant Protection, Faculty of Agriculture, University of Novi Sad, Novi Sad, Serbia
| | - Kristin A Nurkowski
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Tim Connallon
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia.
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8
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Gallegos C, Hodgins KA, Monro K. Climate adaptation and vulnerability of foundation species in a global change hotspot. Mol Ecol 2023; 32:1990-2004. [PMID: 36645732 DOI: 10.1111/mec.16848] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 01/05/2023] [Indexed: 01/17/2023]
Abstract
Climate change is altering species ranges, and relative abundances within ranges, as populations become differentially adapted and vulnerable to the climates they face. Understanding present species ranges, whether species harbour and exchange adaptive variants, and how variants are distributed across landscapes undergoing rapid change, is therefore crucial to predicting responses to future climates and informing conservation strategies. Such insights are nonetheless lacking for most species of conservation concern. We assess genomic patterns of neutral variation, climate adaptation and climate vulnerability (offsets in predicted distributions of putatively adaptive variants across present and future landscapes) for sister foundation species, the marine tubeworms Galeolaria caespitosa and Galeolaria gemineoa, in a sentinel region for climate change impacts. We find that species are genetically isolated despite uncovering sympatry in their ranges, show parallel and nonparallel signals of thermal adaptation on spatial scales smaller than gene flow across their ranges, and are predicted to face different risks of maladaptation under future temperatures across their ranges. Our findings have implications for understanding local adaptation in the face of gene flow, and generate spatially explicit predictions for climatic disruption of adaptation and species distributions in coastal ecosystems that could guide experimental validation and conservation planning.
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Affiliation(s)
- Cristóbal Gallegos
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Keyne Monro
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
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9
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De Silva NP, Lee C, Battlay P, Fournier-Level A, Moore JL, Hodgins KA. Genome assembly of an Australian native grass species reveals a recent whole-genome duplication and biased gene retention of genes involved in stress response. Gigascience 2022; 12:giad034. [PMID: 37171129 PMCID: PMC10176504 DOI: 10.1093/gigascience/giad034] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 01/04/2023] [Accepted: 04/24/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND The adaptive significance of polyploidy has been extensively debated, and chromosome-level genome assemblies of polyploids can provide insight into this. The Australian grass Bothriochloa decipiens belongs to the BCD clade, a group with a complex history of hybridization and polyploid. This is the first genome assembly and annotation of a species that belongs to this fascinating yet complex group. FINDINGS Using Illumina short reads, 10X Genomics linked reads, and Hi-C sequencing data, we assembled a highly contiguous genome of B. decipiens, with a total length of 1,218.22 Mb and scaffold N50 of 42.637 Mb. Comparative analysis revealed that the species experienced a relatively recent whole-genome duplication. We clustered the 20 major scaffolds, representing the 20 chromosomes, into the 2 subgenomes of the parental species using unique repeat signatures. We found evidence of biased fractionation and differences in the activity of transposable elements between the subgenomes prior to hybridization. Duplicates were enriched for genes involved in transcription and response to external stimuli, supporting a biased retention of duplicated genes following whole-genome duplication. CONCLUSIONS Our results support the hypotheses of a biased retention of duplicated genes following polyploidy and point to differences in repeat activity associated with subgenome dominance. B. decipiens is a widespread species with the ability to establish across many soil types, making it a prime candidate for climate change- resilient ecological restoration of Australian grasslands. This reference genome is a valuable resource for future population genomic research on Australian grasses.
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Affiliation(s)
- Nissanka P De Silva
- School of Biological Sciences, Monash University, Clayton, 3800 Victoria, Australia
| | - Christopher Lee
- School of Biological Sciences, Monash University, Clayton, 3800 Victoria, Australia
| | - Paul Battlay
- School of Biological Sciences, Monash University, Clayton, 3800 Victoria, Australia
| | - A Fournier-Level
- School of BioSciences, University of Melbourne, Melbourne, 3010 Victoria, Australia
| | - Joslin L Moore
- School of Biological Sciences, Monash University, Clayton, 3800 Victoria, Australia
- Arthur Rylah Institute for Environment Research, Heidelberg, 3084 Victoria, Australia
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Clayton, 3800 Victoria, Australia
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10
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Bieker VC, Battlay P, Petersen B, Sun X, Wilson J, Brealey JC, Bretagnolle F, Nurkowski K, Lee C, Barreiro FS, Owens GL, Lee JY, Kellner FL, van Boheeman L, Gopalakrishnan S, Gaudeul M, Mueller-Schaerer H, Lommen S, Karrer G, Chauvel B, Sun Y, Kostantinovic B, Dalén L, Poczai P, Rieseberg LH, Gilbert MTP, Hodgins KA, Martin MD. Uncovering the genomic basis of an extraordinary plant invasion. Sci Adv 2022; 8:eabo5115. [PMID: 36001672 PMCID: PMC9401624 DOI: 10.1126/sciadv.abo5115] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 07/11/2022] [Indexed: 05/31/2023]
Abstract
Invasive species are a key driver of the global biodiversity crisis, but the drivers of invasiveness, including the role of pathogens, remain debated. We investigated the genomic basis of invasiveness in Ambrosia artemisiifolia (common ragweed), introduced to Europe in the late 19th century, by resequencing 655 ragweed genomes, including 308 herbarium specimens collected up to 190 years ago. In invasive European populations, we found selection signatures in defense genes and lower prevalence of disease-inducing plant pathogens. Together with temporal changes in population structure associated with introgression from closely related Ambrosia species, escape from specific microbial enemies likely favored the plant's remarkable success as an invasive species.
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Affiliation(s)
- Vanessa C. Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Paul Battlay
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Bent Petersen
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), AIMST University, 08100 Kedah, Malaysia
| | - Xin Sun
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Jonathan Wilson
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Jaelle C. Brealey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - François Bretagnolle
- UMR CNRS/uB 6282 Biogéosciences, Université de Bourgogne-Franche-Comté, Dijon, France
| | - Kristin Nurkowski
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Chris Lee
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Fátima Sánchez Barreiro
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Jacqueline Y. Lee
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Fabian L. Kellner
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | | | - Shyam Gopalakrishnan
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Myriam Gaudeul
- Institut de Systématique Evolution Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, SU, EPHE, UA, National Herbarium (P), 57 rue Cuvier, CP39, 75005 Paris, France
| | | | - Suzanne Lommen
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Institute of Biology, Section Plant Ecology and Phytochemistry, Leiden University, P.O. Box 9505, 2300 RA Leiden, Netherlands
- Koppert Biological Systems, Department R&D Macrobiology, Veilingweg 14, 2651 BE Berkel en Rodenrijs, Netherlands
| | - Gerhard Karrer
- Department of Integrative Biology and Biodiversity Research, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Bruno Chauvel
- UMR Agroécologie, Institut Agro, INRAE, Univ. Bourgogne, Univ. Bourgogne-Franche-Comté, F-21000 Dijon, France
| | - Yan Sun
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Bojan Kostantinovic
- Department of Environmental and Plant Protection, Faculty of Agriculture, University of Novi Sad, Novi Sad, Serbia
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Péter Poczai
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Institute of Advanced Studies Kőszeg (iASK), Kőszeg, Hungary
| | - Loren H. Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - M. Thomas P. Gilbert
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Michael D. Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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11
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Prapas D, Scalone R, Lee J, Nurkowski KA, Bou‐assi S, Rieseberg L, Battlay P, Hodgins KA. Quantitative trait loci mapping reveals an oligogenic architecture of a rapidly adapting trait during the European invasion of common ragweed. Evol Appl 2022; 15:1249-1263. [PMID: 36051461 PMCID: PMC9423086 DOI: 10.1111/eva.13453] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 06/05/2022] [Accepted: 06/30/2022] [Indexed: 01/09/2023] Open
Abstract
Biological invasions offer a unique opportunity to investigate evolution over contemporary timescales. Rapid adaptation to local climates during range expansion can be a major determinant of invasion success, yet fundamental questions remain about its genetic basis. This study sought to investigate the genetic basis of climate adaptation in invasive common ragweed (Ambrosia artemisiifolia). Flowering time adaptation is key to this annual species' invasion success, so much so that it has evolved repeated latitudinal clines in size and phenology across its native and introduced ranges despite high gene flow among populations. Here, we produced a high-density linkage map (4493 SNPs) and paired this with phenotypic data from an F2 mapping population (n = 336) to identify one major and two minor quantitative trait loci (QTL) underlying flowering time and height differentiation in this species. Within each QTL interval, several candidate flowering time genes were also identified. Notably, the major flowering time QTL detected in this study was found to overlap with a previously identified haploblock (putative inversion). Multiple genetic maps of this region identified evidence of suppressed recombination in specific genotypes, consistent with inversions. These discoveries support the expectation that a concentrated genetic architecture with fewer, larger, and more tightly linked alleles should underlie rapid local adaptation during invasion, particularly when divergently adapting populations experience high levels of gene flow.
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Affiliation(s)
- Diana Prapas
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia
| | - Romain Scalone
- Department of Crop Production Ecology, Uppsala Ecology CenterSwedish University of Agricultural SciencesUppsalaSweden,Department of Grapevine BreedingHochschule Geisenheim UniversityGeisenheimGermany
| | - Jacqueline Lee
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia
| | - Kristin A. Nurkowski
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia,Department of Botany and Biodiversity Research CentreUniversity of British ColumbiaVancouverCanada
| | - Sarah Bou‐assi
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia
| | - Loren Rieseberg
- Department of Botany and Biodiversity Research CentreUniversity of British ColumbiaVancouverCanada
| | - Paul Battlay
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia
| | - Kathryn A. Hodgins
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia
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12
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Jalali T, Rosinger HS, Hodgins KA, Fournier‐Level AJ. Pollen competition in hybridizing Cakile species: How does a latecomer win the race? Am J Bot 2022; 109:1290-1304. [PMID: 35844035 PMCID: PMC9544311 DOI: 10.1002/ajb2.16035] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 06/10/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
PREMISE Hybridization between cross-compatible species depends on the extent of competition between alternative mates. Even if stigmatic compatibility allows for hybridization, hybridization requires the heterospecific pollen to be competitive. Here, we determined whether conspecific pollen has an advantage in the race to fertilize ovules and the potential handicap to be overcome by heterospecific pollen in invasive Cakile species. METHODS We used fluorescence microscopy to measure pollen tube growth after conspecific and heterospecific hand-pollination treatments. We then determined siring success in the progeny relative to the timing of heterospecific pollen arrival on the stigma using CAPS markers. RESULTS In the absence of pollen competition, pollination time and pollen recipient species had a significant effect on the ratio of pollen tube growth. In long-styled C. maritima (outcrosser), pollen tubes grew similarly in both directions. In short-styled C. edentula (selfer), conspecific and heterospecific pollen tubes grew differently. Cakile edentula pollen produced more pollen tubes, revealing the potential for a mating asymmetry whereby C. edentula pollen had an advantage relative to C. maritima. In the presence of pollen competition, siring success was equivalent when pollen deposition was synchronous. However, a moderate 1-h advantage in the timing of conspecific pollination resulted in almost complete assortative mating, while an equivalent delay in conspecific pollination resulted in substantial hybrid formation. CONCLUSIONS Hybridization can aid the establishment of invasive species through the transfer of adaptive alleles from cross-compatible species, but also lead to extinction through demographic or genetic swamping. Time of pollen arrival on the stigma substantially affected hybridization rate, pointing to the importance of pollination timing in driving introgression and genetic swamping.
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Affiliation(s)
- Tara Jalali
- School of BiosciencesThe University of MelbourneParkvilleVictoria3010Australia
| | - Hanna S. Rosinger
- School of Biological SciencesMonash UniversityClaytonVictoria3800Australia
| | - Kathryn A. Hodgins
- School of Biological SciencesMonash UniversityClaytonVictoria3800Australia
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13
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Santangelo JS, Ness RW, Cohan B, Fitzpatrick CR, Innes SG, Koch S, Miles LS, Munim S, Peres-Neto PR, Prashad C, Tong AT, Aguirre WE, Akinwole PO, Alberti M, Álvarez J, Anderson JT, Anderson JJ, Ando Y, Andrew NR, Angeoletto F, Anstett DN, Anstett J, Aoki-Gonçalves F, Arietta AZA, Arroyo MTK, Austen EJ, Baena-Díaz F, Barker CA, Baylis HA, Beliz JM, Benitez-Mora A, Bickford D, Biedebach G, Blackburn GS, Boehm MMA, Bonser SP, Bonte D, Bragger JR, Branquinho C, Brans KI, Bresciano JC, Brom PD, Bucharova A, Burt B, Cahill JF, Campbell KD, Carlen EJ, Carmona D, Castellanos MC, Centenaro G, Chalen I, Chaves JA, Chávez-Pesqueira M, Chen XY, Chilton AM, Chomiak KM, Cisneros-Heredia DF, Cisse IK, Classen AT, Comerford MS, Fradinger CC, Corney H, Crawford AJ, Crawford KM, Dahirel M, David S, De Haan R, Deacon NJ, Dean C, Del-Val E, Deligiannis EK, Denney D, Dettlaff MA, DiLeo MF, Ding YY, Domínguez-López ME, Dominoni DM, Draud SL, Dyson K, Ellers J, Espinosa CI, Essi L, Falahati-Anbaran M, Falcão JCF, Fargo HT, Fellowes MDE, Fitzpatrick RM, Flaherty LE, Flood PJ, Flores MF, Fornoni J, Foster AG, Frost CJ, Fuentes TL, Fulkerson JR, Gagnon E, Garbsch F, Garroway CJ, Gerstein AC, Giasson MM, Girdler EB, Gkelis S, Godsoe W, Golemiec AM, Golemiec M, González-Lagos C, Gorton AJ, Gotanda KM, Granath G, Greiner S, Griffiths JS, Grilo F, Gundel PE, Hamilton B, Hardin JM, He T, Heard SB, Henriques AF, Hernández-Poveda M, Hetherington-Rauth MC, Hill SJ, Hochuli DF, Hodgins KA, Hood GR, Hopkins GR, Hovanes KA, Howard AR, Hubbard SC, Ibarra-Cerdeña CN, Iñiguez-Armijos C, Jara-Arancio P, Jarrett BJM, Jeannot M, Jiménez-Lobato V, Johnson M, Johnson O, Johnson PP, Johnson R, Josephson MP, Jung MC, Just MG, Kahilainen A, Kailing OS, Kariñho-Betancourt E, Karousou R, Kirn LA, Kirschbaum A, Laine AL, LaMontagne JM, Lampei C, Lara C, Larson EL, Lázaro-Lobo A, Le JH, Leandro DS, Lee C, Lei Y, León CA, Lequerica Tamara ME, Levesque DC, Liao WJ, Ljubotina M, Locke H, Lockett MT, Longo TC, Lundholm JT, MacGillavry T, Mackin CR, Mahmoud AR, Manju IA, Mariën J, Martínez DN, Martínez-Bartolomé M, Meineke EK, Mendoza-Arroyo W, Merritt TJS, Merritt LEL, Migiani G, Minor ES, Mitchell N, Mohammadi Bazargani M, Moles AT, Monk JD, Moore CM, Morales-Morales PA, Moyers BT, Muñoz-Rojas M, Munshi-South J, Murphy SM, Murúa MM, Neila M, Nikolaidis O, Njunjić I, Nosko P, Núñez-Farfán J, Ohgushi T, Olsen KM, Opedal ØH, Ornelas C, Parachnowitsch AL, Paratore AS, Parody-Merino AM, Paule J, Paulo OS, Pena JC, Pfeiffer VW, Pinho P, Piot A, Porth IM, Poulos N, Puentes A, Qu J, Quintero-Vallejo E, Raciti SM, Raeymaekers JAM, Raveala KM, Rennison DJ, Ribeiro MC, Richardson JL, Rivas-Torres G, Rivera BJ, Roddy AB, Rodriguez-Muñoz E, Román JR, Rossi LS, Rowntree JK, Ryan TJ, Salinas S, Sanders NJ, Santiago-Rosario LY, Savage AM, Scheepens JF, Schilthuizen M, Schneider AC, Scholier T, Scott JL, Shaheed SA, Shefferson RP, Shepard CA, Shykoff JA, Silveira G, Smith AD, Solis-Gabriel L, Soro A, Spellman KV, Whitney KS, Starke-Ottich I, Stephan JG, Stephens JD, Szulc J, Szulkin M, Tack AJM, Tamburrino Í, Tate TD, Tergemina E, Theodorou P, Thompson KA, Threlfall CG, Tinghitella RM, Toledo-Chelala L, Tong X, Uroy L, Utsumi S, Vandegehuchte ML, VanWallendael A, Vidal PM, Wadgymar SM, Wang AY, Wang N, Warbrick ML, Whitney KD, Wiesmeier M, Wiles JT, Wu J, Xirocostas ZA, Yan Z, Yao J, Yoder JB, Yoshida O, Zhang J, Zhao Z, Ziter CD, Zuellig MP, Zufall RA, Zurita JE, Zytynska SE, Johnson MTJ. Global urban environmental change drives adaptation in white clover. Science 2022; 375:1275-1281. [PMID: 35298255 DOI: 10.1126/science.abk0989] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban-rural gradients were associated with the evolution of clines in defense in 47% of cities throughout the world. Variation in the strength of clines was explained by environmental changes in drought stress and vegetation cover that varied among cities. Sequencing 2074 genomes from 26 cities revealed that the evolution of urban-rural clines was best explained by adaptive evolution, but the degree of parallel adaptation varied among cities. Our results demonstrate that urbanization leads to adaptation at a global scale.
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Affiliation(s)
- James S Santangelo
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada.,Centre for Urban Environments, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Rob W Ness
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada.,Centre for Urban Environments, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Beata Cohan
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
| | | | - Simon G Innes
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada.,Department of Biology, University of Louisiana, Lafayette, LA, USA
| | - Sophie Koch
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Lindsay S Miles
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada.,Centre for Urban Environments, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Samreen Munim
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada.,Department of Biology, Queen's University, Kingston, ON, Canada
| | | | - Cindy Prashad
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Alex T Tong
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Windsor E Aguirre
- Department of Biological Sciences, DePaul University, Chicago, IL, USA
| | | | - Marina Alberti
- Department of Urban Design and Planning, University of Washington, Seattle, WA, USA
| | - Jackie Álvarez
- Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Jill T Anderson
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Joseph J Anderson
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Yoshino Ando
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Nigel R Andrew
- Natural History Museum, Zoology, University of New England, Armidale, NSW, Australia
| | - Fabio Angeoletto
- Programa de Pós-Graduação em Geografia da UFMT, campus de Rondonópolis, Cuiabá, Brazil
| | - Daniel N Anstett
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Julia Anstett
- Graduate Program in Genome Sciences and Technology, Genome Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | - Mary T K Arroyo
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.,Instituto de Ecología y Biodiversidad, Universidad de Chile, Santiago, Chile
| | - Emily J Austen
- Department of Biology, Mount Allison University, Sackville, NB, Canada
| | | | - Cory A Barker
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Howard A Baylis
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Julia M Beliz
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA.,Department of Biology, University of Miami, Miami, FL, USA
| | - Alfonso Benitez-Mora
- Centro de Investigación en Recursos Naturales y Sustentabilidad (CIRENYS), Universidad Bernardo O'Higgins, Santiago, Chile
| | - David Bickford
- Department of Biology, University of La Verne, La Verne, CA, USA
| | | | - Gwylim S Blackburn
- Département des sciences du bois et de la forêt, Université Laval, Quebec, QC, Canada
| | - Mannfred M A Boehm
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Stephen P Bonser
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Dries Bonte
- Department of Biology, Ghent University, Ghent, Belgium
| | - Jesse R Bragger
- Department of Biology, Monmouth University, West Long Branch, NJ, USA
| | - Cristina Branquinho
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | | | - Jorge C Bresciano
- School of Agriculture and Environment, Wildlife and Ecology group, Massey University, Palmerston North, Manawatu, New Zealand
| | - Peta D Brom
- Department of Biological Sciences, University of Cape Town, Cape Town, South Africa
| | - Anna Bucharova
- Institute of Landscape Ecology, University of Münster, Münster, Germany
| | - Briana Burt
- Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA
| | - James F Cahill
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | | | - Elizabeth J Carlen
- Louis Calder Center and Department of Biological Sciences, Fordham University, Armonk, NY, USA
| | - Diego Carmona
- Departamento de Ecología Tropical, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | | | - Giada Centenaro
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Izan Chalen
- Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Ecuador.,iBIOTROP Instituto de Biodiversidad Tropical, Universidad San Francisco de Quito, Quito, Ecuador
| | - Jaime A Chaves
- Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Ecuador.,Department of Biology, San Francisco State University, San Francisco, CA, USA
| | - Mariana Chávez-Pesqueira
- Unidad de Recursos Naturales, Centro de Investigación Científica de Yucatán AC, Mérida, Yucatán, México
| | - Xiao-Yong Chen
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China.,Shanghai Engineering Research Center of Sustainable Plant Innovation, Shanghai 200231, China
| | - Angela M Chilton
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Kristina M Chomiak
- Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA
| | - Diego F Cisneros-Heredia
- Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Ecuador.,iBIOTROP Instituto de Biodiversidad Tropical, Universidad San Francisco de Quito, Quito, Ecuador
| | - Ibrahim K Cisse
- Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA
| | - Aimée T Classen
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Hannah Corney
- Biology Department, Saint Mary's University, Halifax, NS, Canada
| | - Andrew J Crawford
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Kerri M Crawford
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Maxime Dahirel
- ECOBIO (Ecosystèmes, biodiversité, évolution), Université de Rennes, Rennes, France
| | - Santiago David
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Robert De Haan
- Department of Environmental Studies, Dordt University, Sioux Center, IA, USA
| | - Nicholas J Deacon
- Department of Biology, Minneapolis Community and Technical College, Minneapolis, MN, USA
| | - Clare Dean
- Department of Natural Sciences, Ecology and Environment Research Centre, Manchester Metropolitan University, Manchester, UK
| | - Ek Del-Val
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, UNAM, Morelia, Mexico
| | | | - Derek Denney
- Department of Genetics, University of Georgia, Athens, GA, USA
| | | | - Michelle F DiLeo
- Faculty of Biological and Environmental Science, Organismal & Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Yuan-Yuan Ding
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Moisés E Domínguez-López
- Corporación Científica Ingeobosque, Medellín, Antioquia, Colombia.,GTA Colombia S.A.S. Envigado, Antioquia, Colombia
| | - Davide M Dominoni
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, Scotland, UK
| | | | - Karen Dyson
- Department of Urban Design and Planning, University of Washington, Seattle, WA, USA
| | - Jacintha Ellers
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Carlos I Espinosa
- Departamento de Ciencias Biológicas y Agropecuarias, Universidad Técnica Particular de Loja, Loja, Ecuador
| | - Liliana Essi
- Departamento de Biologia, Universidade Federal de Santa Maria (UFSM), Santa Maria, Rio Grande do Sul, Brazil
| | - Mohsen Falahati-Anbaran
- Department of Plant Sciences, School of Biology, College of Science, University of Tehran, Tehran, Iran.,NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Jéssica C F Falcão
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C., Xalapa, Mexico
| | - Hayden T Fargo
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Mark D E Fellowes
- School of Biological Sciences, University of Reading, Whiteknights Park, Reading, Berkshire, UK
| | | | - Leah E Flaherty
- Department of Biological Sciences, MacEwan University, Edmonton, AB, Canada
| | - Pádraic J Flood
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - María F Flores
- Instituto de Ecología y Biodiversidad, Universidad de Chile, Santiago, Chile
| | - Juan Fornoni
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Amy G Foster
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | - Tracy L Fuentes
- Department of Urban Design and Planning, University of Washington, Seattle, WA, USA
| | - Justin R Fulkerson
- Alaska Center for Conservation Science, University of Alaska Anchorage, Anchorage, AK, USA
| | - Edeline Gagnon
- Tropical Diversity, Royal Botanical Garden of Edinburgh, Edinburgh, UK.,Département de biologie, Université de Moncton, Moncton, New Brunswick, Canada
| | - Frauke Garbsch
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Colin J Garroway
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Aleeza C Gerstein
- Departments of Microbiology & Statistics, University of Manitoba, Winnipeg, MB, Canada
| | - Mischa M Giasson
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | | | - Spyros Gkelis
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - William Godsoe
- BioProtection Research Centre, Lincoln University, Lincoln, Canterbury, New Zealand
| | | | - Mireille Golemiec
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - César González-Lagos
- Centro de Investigación en Recursos Naturales y Sustentabilidad (CIRENYS), Universidad Bernardo O'Higgins, Santiago, Chile.,Departamento de Ciencias, Facultad de Artes Liberales, Universidad Adolfo Ibáñez, Santiago, Chile
| | - Amanda J Gorton
- Department of Ecology, Evolution, and Behaviour University of Minnesota, Minneapolis, MN, USA
| | - Kiyoko M Gotanda
- Department of Zoology, University of Cambridge, Cambridge, UK.,Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada
| | - Gustaf Granath
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Stephan Greiner
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Joanna S Griffiths
- Department of Environmental Toxicology, University of California, Davis, CA, USA
| | - Filipa Grilo
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - Pedro E Gundel
- IFEVA, Universidad de Buenos Aires, CONICET, Facultad de Agronomía, Buenos Aires, Argentina.,ICB - University of Talca, Chile
| | - Benjamin Hamilton
- Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA
| | | | - Tianhua He
- School of Molecular and Life Science, Curtin University, Perth, Australia.,College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Stephen B Heard
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | - André F Henriques
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | | | | | - Sarah J Hill
- Natural History Museum, Zoology, University of New England, Armidale, NSW, Australia
| | - Dieter F Hochuli
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Glen R Hood
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Gareth R Hopkins
- Department of Biology, Western Oregon University, Monmouth, OR, USA
| | - Katherine A Hovanes
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, USA
| | - Ava R Howard
- Department of Biology, Western Oregon University, Monmouth, OR, USA
| | | | | | - Carlos Iñiguez-Armijos
- Departamento de Ciencias Biológicas y Agropecuarias, Universidad Técnica Particular de Loja, Loja, Ecuador
| | - Paola Jara-Arancio
- Departamento de Ciencias Biológicas y Departamento de Ecología y Biodiversidad, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile.,Institute of Ecology and Biodiversity (IEB), Chile
| | - Benjamin J M Jarrett
- Department of Zoology, University of Cambridge, Cambridge, UK.,Department of Biology, Lund University, Lund, Sweden
| | - Manon Jeannot
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Vania Jiménez-Lobato
- Escuela Superiro de Desarrollo Sustentable, Universidad Autónoma de Guerrero -CONACYT, Las Tunas, Mexico
| | - Mae Johnson
- Clarkson Secondary School, Peel District School Board, Mississauga, ON, Canada
| | - Oscar Johnson
- Homelands Sr. Public School, Peel District School Board, Mississauga, ON, Canada
| | - Philip P Johnson
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Reagan Johnson
- St. James Catholic Global Learning Centre, Dufferin-Peel Catholic District School Board, Mississauga ON, Canada
| | | | - Meen Chel Jung
- Department of Urban Design and Planning, University of Washington, Seattle, WA, USA
| | - Michael G Just
- Ecological Processes Branch, U.S. Army ERDC-CERL, Champaign, IL, USA
| | - Aapo Kahilainen
- Faculty of Biological and Environmental Science, Organismal & Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Otto S Kailing
- Department of Biology, Oberlin College, Oberlin, OH, USA
| | | | - Regina Karousou
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Lauren A Kirn
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Anna Kirschbaum
- Institute of Evolution and Ecology, University of Tübingen, Tübingen, Germany
| | - Anna-Liisa Laine
- Faculty of Biological and Environmental Science, Organismal & Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse, Zurich, Switzerland
| | - Jalene M LaMontagne
- Department of Biological Sciences, DePaul University, Chicago, IL, USA.,Urban Wildlife Institute, Department of Conservation and Science, Lincoln Park Zoo, Chicago, IL, USA
| | - Christian Lampei
- Institute of Landscape Ecology, University of Münster, Münster, Germany
| | - Carlos Lara
- Departamento de Ecología, Universidad Católica de la Santísima Concepción, Concepción, Chile
| | - Erica L Larson
- Department of Biological Sciences, University of Denver, Denver, CO, USA
| | - Adrián Lázaro-Lobo
- Department of Biological Sciences, Mississippi State University, Starkville, MS, USA
| | - Jennifer H Le
- Department of Biology, Center for Computational & Integrative Biology, Rutgers University-Camden, Camden, NJ, USA
| | - Deleon S Leandro
- Programa de Pós-Graduação em Geografia da UFMT, campus de Rondonópolis, Brasil
| | - Christopher Lee
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Yunting Lei
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Carolina A León
- Centro de Investigación en Recursos Naturales y Sustentabilidad (CIRENYS), Universidad Bernardo O'Higgins, Santiago, Chile
| | | | - Danica C Levesque
- Department of Chemistry & Biochemistry, Laurentian University, Sudbury, ON, Canada
| | - Wan-Jin Liao
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Megan Ljubotina
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Hannah Locke
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Martin T Lockett
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
| | - Tiffany C Longo
- Department of Biology, Monmouth University, West Long Branch, NJ, USA
| | | | - Thomas MacGillavry
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, Scotland, UK
| | | | - Alex R Mahmoud
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Isaac A Manju
- Department of Biology, Western Oregon University, Monmouth, OR, USA
| | - Janine Mariën
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - D Nayeli Martínez
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, UNAM, Morelia, Mexico.,Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Coyoacán, Mexico City, 04510, Mexico
| | - Marina Martínez-Bartolomé
- Department of Biological Sciences, Mississippi State University, Starkville, MS, USA.,Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Emily K Meineke
- Department of Entomology and Nematology, University of California, Davis, CA, USA
| | | | - Thomas J S Merritt
- Department of Chemistry & Biochemistry, Laurentian University, Sudbury, ON, Canada
| | | | - Giuditta Migiani
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, Scotland, UK
| | - Emily S Minor
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Nora Mitchell
- Department of Biology, University of New Mexico, Albuquerque, NM, USA.,Department of Biology, University of Wisconsin - Eau Claire, Eau Claire, WI 54701
| | - Mitra Mohammadi Bazargani
- Agriculture Institute, Iranian Research Organization for Science and Technology (IROST), Tehran, Iran
| | - Angela T Moles
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Julia D Monk
- School of the Environment, Yale University, New Haven, CT, USA
| | | | | | - Brook T Moyers
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA.,Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Miriam Muñoz-Rojas
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, Australia.,Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Av. Reina Mercedes s/n, 41012 Sevilla, Spain
| | - Jason Munshi-South
- Louis Calder Center and Department of Biological Sciences, Fordham University, Armonk, NY, USA
| | - Shannon M Murphy
- Department of Biological Sciences, University of Denver, Denver, CO, USA
| | - Maureen M Murúa
- Facultad de Estudios Interdisciplinarios, Centro GEMA- Genómica, Ecología y Medio Ambiente, Universidad Mayor, Santiago, Chile
| | - Melisa Neila
- Centro de Investigación en Recursos Naturales y Sustentabilidad (CIRENYS), Universidad Bernardo O'Higgins, Santiago, Chile
| | - Ourania Nikolaidis
- Department of Biology, Center for Computational & Integrative Biology, Rutgers University-Camden, Camden, NJ, USA
| | - Iva Njunjić
- Evolutionary Ecology Group, Naturalis Biodiversity Center, Leiden, Netherlands
| | - Peter Nosko
- Department of Biology and Chemistry, Nipissing University, North Bay, ON, Canada
| | - Juan Núñez-Farfán
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Takayuki Ohgushi
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
| | - Kenneth M Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | | | - Cristina Ornelas
- Bonanza Creek Long Term Ecological Research Program, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Amy L Parachnowitsch
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.,Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | - Aaron S Paratore
- Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA
| | - Angela M Parody-Merino
- School of Agriculture and Environment, Wildlife and Ecology group, Massey University, Palmerston North, Manawatu, New Zealand
| | - Juraj Paule
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
| | - Octávio S Paulo
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - João Carlos Pena
- Departamento de Biodiversidade, Instituto de Biociências, Univ Estadual Paulista - UNESP, Rio Claro, São Paulo, Brazil
| | - Vera W Pfeiffer
- Nelson Institute for Environmental Studies, University of Wisconsin-Madison, Madison, WI, USA
| | - Pedro Pinho
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - Anthony Piot
- Département des sciences du bois et de la forêt, Université Laval, Quebec, QC, Canada
| | - Ilga M Porth
- Département des sciences du bois et de la forêt, Université Laval, Quebec, QC, Canada
| | - Nicholas Poulos
- Department of Biology, California State University, Northridge, Los Angeles, CA, USA
| | - Adriana Puentes
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jiao Qu
- Department of Biology, Ghent University, Ghent, Belgium
| | | | - Steve M Raciti
- Department of Biology, Hofstra University, Long Island, NY, USA
| | | | - Krista M Raveala
- Faculty of Biological and Environmental Science, Organismal & Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Diana J Rennison
- Division of Biological Sciences, University of California San Diego, San Diego, CA, USA
| | - Milton C Ribeiro
- Departamento de Biodiversidade, Instituto de Biociências, Univ Estadual Paulista - UNESP, Rio Claro, São Paulo, Brazil
| | | | - Gonzalo Rivas-Torres
- Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Ecuador.,Estación de Biodiversidad Tiputini, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | | | - Adam B Roddy
- Department of Biological Sciences, Institute of Environment, Florida International University, Miami, FL, USA
| | | | | | - Laura S Rossi
- Department of Biology and Chemistry, Nipissing University, North Bay, ON, Canada
| | - Jennifer K Rowntree
- Department of Natural Sciences, Ecology and Environment Research Centre, Manchester Metropolitan University, Manchester, UK
| | - Travis J Ryan
- Department of Biological Sciences and Center for Urban Ecology and Sustainability, Butler University, Indianapolis, IN, USA
| | | | - Nathan J Sanders
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | | | - Amy M Savage
- Department of Biology, Center for Computational & Integrative Biology, Rutgers University-Camden, Camden, NJ, USA
| | - J F Scheepens
- Institute of Evolution and Ecology, University of Tübingen, Tübingen, Germany.,Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Adam C Schneider
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada.,Department of Biology, Hendrix College, Conway, AR, USA
| | - Tiffany Scholier
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Jared L Scott
- Department of Biology, University of Louisville, Louisville, KY, USA
| | - Summer A Shaheed
- Department of Biology, Monmouth University, West Long Branch, NJ, USA
| | - Richard P Shefferson
- Organization for Programs on Environmental Science, University of Tokyo, Tokyo, Japan
| | | | - Jacqui A Shykoff
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique et Evolution, 91405, Orsay, France
| | | | - Alexis D Smith
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Lizet Solis-Gabriel
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, UNAM, Morelia, Mexico
| | - Antonella Soro
- General Zoology, Institute for Biology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Katie V Spellman
- Bonanza Creek Long Term Ecological Research Program, University of Alaska Fairbanks, Fairbanks, AK, USA.,International Arctic Research Center, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Kaitlin Stack Whitney
- Science, Technology and Society Department, Rochester Institute of Technology, Rochester, NY, USA
| | - Indra Starke-Ottich
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
| | - Jörg G Stephan
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.,SLU Swedish Species Information Centre, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Justyna Szulc
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Marta Szulkin
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Ayco J M Tack
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Ítalo Tamburrino
- Instituto de Ecología y Biodiversidad, Universidad de Chile, Santiago, Chile
| | - Tayler D Tate
- Department of Biology, Western Oregon University, Monmouth, OR, USA
| | | | - Panagiotis Theodorou
- General Zoology, Institute for Biology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Ken A Thompson
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.,Department of Biology, Stanford University, Stanford, CA, USA
| | - Caragh G Threlfall
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | | | | | - Xin Tong
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Léa Uroy
- ECOBIO (Ecosystèmes, biodiversité, évolution), Université de Rennes, Rennes, France.,UMR 0980 BAGAP, Agrocampus Ouest-ESA-INRA, Rennes, France
| | - Shunsuke Utsumi
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Martijn L Vandegehuchte
- Department of Biology, Ghent University, Ghent, Belgium.,Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Acer VanWallendael
- Plant Biology Department, Michigan State University, East Lansing, MI, USA
| | - Paula M Vidal
- Instituto de Ecología y Biodiversidad, Universidad de Chile, Santiago, Chile
| | | | - Ai-Ying Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Nian Wang
- College of Horticulture and Forestry Sciences/ Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, China, Hubei, China
| | - Montana L Warbrick
- Department of Biology and Chemistry, Nipissing University, North Bay, ON, Canada
| | - Kenneth D Whitney
- Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Miriam Wiesmeier
- School of Life Sciences, Technical University of Munich, Munich, Germany
| | | | - Jianqiang Wu
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zoe A Xirocostas
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Zhaogui Yan
- College of Horticulture and Forestry Sciences/ Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, China, Hubei, China
| | - Jiahe Yao
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jeremy B Yoder
- Department of Biology, California State University, Northridge, Los Angeles, CA, USA
| | - Owen Yoshida
- Biology Department, Saint Mary's University, Halifax, NS, Canada
| | - Jingxiong Zhang
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zhigang Zhao
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Carly D Ziter
- Department of Biology, Concordia University, Montreal, QC, Canada
| | - Matthew P Zuellig
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Rebecca A Zufall
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Juan E Zurita
- Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Sharon E Zytynska
- School of Life Sciences, Technical University of Munich, Munich, Germany.,Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool, UK
| | - Marc T J Johnson
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada.,Centre for Urban Environments, University of Toronto Mississauga, Mississauga, ON, Canada
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14
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Crombie TA, Battlay P, Tanny RE, Evans KS, Buchanan CM, Cook DE, Dilks CM, Stinson LA, Zdraljevic S, Zhang G, Roberto NM, Lee D, Ailion M, Hodgins KA, Andersen EC. Local adaptation and spatiotemporal patterns of genetic diversity revealed by repeated sampling of Caenorhabditis elegans across the Hawaiian Islands. Mol Ecol 2022; 31:2327-2347. [PMID: 35167162 PMCID: PMC9306471 DOI: 10.1111/mec.16400] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 10/15/2021] [Revised: 01/23/2022] [Accepted: 02/03/2022] [Indexed: 11/28/2022]
Abstract
The nematode Caenorhabditis elegans is among the most widely studied organisms, but relatively little is known about its natural ecology. Genetic diversity is low across much of the globe but high in the Hawaiian Islands and across the Pacific Rim. To characterize the niche and genetic diversity of C. elegans on the Hawaiian Islands and to explore how genetic diversity might be influenced by local adaptation, we repeatedly sampled nematodes over a three‐year period, measured various environmental parameters at each sampling site, and whole‐genome sequenced the C. elegans isolates that we identified. We found that the typical Hawaiian C. elegans niche comprises moderately moist native forests at high elevations (500–1,500 m) where ambient air temperatures are cool (15–20°C). Compared to other Caenorhabditis species found on the Hawaiian Islands (e.g., Caenorhabditis briggsae and Caenorhabditis tropicalis), we found that C. elegans were enriched in native habitats. We measured levels of genetic diversity and differentiation among Hawaiian C. elegans and found evidence of seven genetically distinct groups distributed across the islands. Then, we scanned these genomes for signatures of local adaptation and identified 18 distinct regions that overlap with hyper‐divergent regions, which may be maintained by balancing selection and are enriched for genes related to environmental sensing, xenobiotic detoxification, and pathogen resistance. These results provide strong evidence of local adaptation among Hawaiian C. elegans and contribute to our understanding of the forces that shape genetic diversity on the most remote volcanic archipelago in the world.
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Affiliation(s)
- Timothy A Crombie
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Paul Battlay
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Robyn E Tanny
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Kathryn S Evans
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Claire M Buchanan
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Daniel E Cook
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - Clayton M Dilks
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - Loraina A Stinson
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - Stefan Zdraljevic
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - Gaotian Zhang
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Nicole M Roberto
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Daehan Lee
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Michael Ailion
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
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15
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Abstract
Over most of the 20th century, evolutionary biologists predominantly subscribed to a strong form of "micro-mutationism," in which adaptive phenotypic divergence arises from allele frequency changes at many loci, each with a small effect on the phenotype. To be sure, there were well-known examples of large-effect alleles contributing to adaptation, yet such cases were generally regarded as atypical and unrepresentative of evolutionary change in general. In 1998, Allen Orr published a landmark theoretical paper in Evolution, which showed that both small- and large-effect mutations are likely to contribute to "adaptive walks" of a population to an optimum. Coupled with a growing set of empirical examples of large-effect alleles contributing to divergence (e.g., from QTL studies), Orr's paper provided a mathematical formalism that converted many evolutionary biologists from micro-mutationism to a more pluralistic perspective on the genetic basis of evolutionary change. We revisit the theoretical insights emerging from Orr's paper within the historical context leading up to 1998, and track the influence of this paper on the field of evolutionary biology through an examination of its citations over the last two decades and an analysis of the extensive body of theoretical and empirical research that Orr's pioneering paper inspired.
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Affiliation(s)
- Tim Connallon
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, Australia
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16
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Rosinger HS, Geraldes A, Nurkowski KA, Battlay P, Cousens RD, Rieseberg LH, Hodgins KA. The tip of the iceberg: Genome wide marker analysis reveals hidden hybridization during invasion. Mol Ecol 2021; 30:810-825. [PMID: 33296112 DOI: 10.1111/mec.15768] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 11/29/2020] [Accepted: 12/03/2020] [Indexed: 12/12/2022]
Abstract
Biological invasions are accelerating, and invasive species can have large economic impacts as well as severe consequences for biodiversity. During invasions, species can interact, potentially resulting in hybridization. Here, we examined two Cakile species, C. edentula and C. maritima (Brassicaceae), that co-occur and may hybridize during range expansion in separate regions of the globe. Cakile edentula invaded each location first, while C. maritima established later, apparently replacing the former. We assessed the evidence for hybridization in western North America and Australia, where both species have been introduced, and identified source populations with 4561 SNPs using Genotype-by-Sequencing. Our results indicate that C. edentula in Australia originated from one region of eastern North America while in western North America it is probably from multiple sources. Cakile maritima in Australia is derived from at least two different parts of Europe while the introduction in western North America is from one. Although morphological evidence of hybridization is generally limited to mixed species populations in Australia and virtually absent elsewhere, our genetic analysis revealed relatively high levels of hybridization in Australia (58% hybrids using Admixture) and supported the presence of hybrids in western North America (16% hybrids using Admixture) and New Zealand. Hybrids might be commonly overlooked in invaders, as identification based solely on morphological traits may represent only the tip of the iceberg. Our study reveals a repeated pattern of invasion, hybridization and apparent replacement of one species by another, which offers an opportunity to investigate the role of hybridization and introgression during invasion.
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Affiliation(s)
- Hanna S Rosinger
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Armando Geraldes
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada.,Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Kristin A Nurkowski
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia.,Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Paul Battlay
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Roger D Cousens
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
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17
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Hodgins KA, Guggisberg A, Nurkowski K, Rieseberg LH. Genetically Based Trait Differentiation but Lack of Trade-offs between Stress Tolerance and Performance in Introduced Canada Thistle. Plant Commun 2020; 1:100116. [PMID: 33367269 PMCID: PMC7748015 DOI: 10.1016/j.xplc.2020.100116] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 10/16/2020] [Accepted: 10/23/2020] [Indexed: 06/12/2023]
Abstract
Trade-offs between performance and tolerance of abiotic and biotic stress have been proposed to explain both the success of invasive species and frequently observed size differences between native and introduced populations. Canada thistle seeds collected from across the introduced North American and the native European range were grown in benign and stressful conditions (nutrient stress, shading, simulated herbivory, drought, and mowing), to evaluate whether native and introduced individuals differ in performance or stress tolerance. An additional experiment assessed the strength of maternal effects by comparing plants derived from field-collected seeds with those derived from clones grown in the glasshouse. Introduced populations tended to be larger in size, but no trade-off of stress tolerance with performance was detected; introduced populations had either superior performance or equivalent trait values and survivorship in the treatment common gardens. We also detected evidence of parallel latitudinal clines of some traits in both the native and introduced ranges and associations with climate variables in some treatments, consistent with recent climate adaptation within the introduced range. Our results are consistent with rapid adaptation of introduced populations, but, contrary to predictions, the evolution of invasive traits did not come at the cost of reduced stress tolerance.
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Affiliation(s)
- Kathryn A. Hodgins
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Alessia Guggisberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Kristin Nurkowski
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Loren H. Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
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Marden E, Abbott RJ, Austerlitz F, Ortiz-Barrientos D, Baucom RS, Bongaerts P, Bonin A, Bonneaud C, Browne L, Alex Buerkle C, Caicedo AL, Coltman DW, Cruzan MB, Davison A, DeWoody JA, Dumbrell AJ, Emerson BC, Fountain-Jones NM, Gillespie R, Giraud T, Hansen MM, Hodgins KA, Heuertz M, Hirase S, Hooper R, Hohenlohe P, Kane NC, Kelley JL, Kinziger AP, McKenzie VJ, Moreau CS, Nazareno AG, Pelletier TA, Pemberton JM, Qu Y, Renaut S, Riginos C, Rodríguez-Ezpeleta N, Rogers SM, Russell JA, Schoville SD, Shi S, Smith M, Sork VL, Stone GN, Taberlet P, Videvall E, Waits L, Warschefsky E, Wayne RK, Whibley A, Willoughby J, Yoder JB, Zinger L, Sibbett B, Narum S, Rieseberg LH. Sharing and reporting benefits from biodiversity research. Mol Ecol 2020; 30:1103-1107. [PMID: 33159357 DOI: 10.1111/mec.15702] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 10/19/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Emily Marden
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | | | - Frédéric Austerlitz
- UMR 7206 Eco-Anthropologie, CNRS/MNHN/Université de Paris, Musée de l'Homme, Paris, France
| | | | - Regina S Baucom
- Ecology and Evolutionary Biology Department, University of Michigan, Ann Arbor, MI, USA
| | - Pim Bongaerts
- California Academy of Sciences, San Francisco, CA, USA
| | - Aurélie Bonin
- Laboratoire d'Ecologie Alpine, CNRS, Université Grenoble Alpes, Grenoble, France
| | - Camille Bonneaud
- Biosciences, College of Life and Environmental Science, University of Exeter, Cornwall, UK
| | - Luke Browne
- School of the Environment, Yale University, New Haven, CT, USA
| | - C Alex Buerkle
- Department of Botany, University of Wyoming, Laramie, WY, USA
| | - Ana L Caicedo
- Biology Department, University of Massachusetts, Amherst, MA, USA
| | - David W Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | | | - Angus Davison
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - J Andrew DeWoody
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, USA
| | | | - Brent C Emerson
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), La Laguna, Spain
| | | | - Rosemary Gillespie
- Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - Tatiana Giraud
- Ecologie Systematique Evolution, CNRS, Université Paris-Saclay, Orsay, France
| | | | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | | | - Shotaro Hirase
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Shizuoka, Japan
| | - Rebecca Hooper
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - Paul Hohenlohe
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, USA
| | - Nolan C Kane
- Department of Ecology and Evolutionary Biology, The University of Colorado, Boulder, CO, USA
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Andrew P Kinziger
- Department of Fisheries Biology, Humboldt State University, Arcata, CA, USA
| | - Valerie J McKenzie
- Department of Ecology and Evolutionary Biology, The University of Colorado, Boulder, CO, USA
| | - Corrie S Moreau
- Departments of Entomology and Ecology & Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Alison G Nazareno
- Department of Genetics, Ecology and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | - Josephine M Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Yanhua Qu
- Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | | | - Cynthia Riginos
- School of Biological Sciences, University of Queensland, Saint Lucia, QLD, Australia
| | | | - Sean M Rogers
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Jacob A Russell
- Department of Biology, Drexel University, Philadelphia, PA, USA
| | - Sean D Schoville
- Department of Entomology, University of Wisconsin, Madison, WI, USA
| | - Suhua Shi
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Megan Smith
- Department of Biology and Department of Computer Science, Indiana University, Bloomington, IN, USA
| | - Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Graham N Stone
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine, CNRS, Université Grenoble Alpes, Grenoble, France
| | - Elin Videvall
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Washington, DC, USA
| | - Lisette Waits
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA
| | - Emily Warschefsky
- Department of Ecology and Evolutionary Biology, The University of Colorado, Boulder, CO, USA.,William L. Brown Center, Missouri Botanical Garden, St. Louis, MO, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Janna Willoughby
- School of Forestry and Wildlife Sciences, Auburn University, Auburn, AL, USA
| | - Jeremy B Yoder
- Department of Biology, California State University, Northridge, CA, USA
| | - Lucie Zinger
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Benjamin Sibbett
- John Wiley & Sons, Atrium Southern Gate, Chichester, West Sussex, UK
| | - Shawn Narum
- Hagerman Genetics Laboratory, Columbia River Inter-Tribal Fish Commission, Hagerman, ID, USA
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
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19
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McGoey BV, Hodgins KA, Stinchcombe JR. Parallel flowering time clines in native and introduced ragweed populations are likely due to adaptation. Ecol Evol 2020; 10:4595-4608. [PMID: 32551046 PMCID: PMC7297792 DOI: 10.1002/ece3.6163] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 12/04/2019] [Accepted: 12/06/2019] [Indexed: 01/06/2023] Open
Abstract
As introduced species expand their ranges, they often encounter differences in climate which are often correlated with geography. For introduced species, encountering a geographically variable climate sometimes leads to the re-establishment of clines seen in the native range. However, clines can also be caused by neutral processes, and so it is important to gather additional evidence that population differentiation is the result of selection as opposed to nonadaptive processes. Here, we examine phenotypic and genetic differences in ragweed from the native (North America) and introduced (European) ranges. We used a common garden to assess phenotypic differentiation in size and flowering time in ragweed populations. We found significant parallel clines in flowering time in both North America and Europe. Height and branch number had significant clines in North America, and, while not statistically significant, the patterns in Europe were the same. We used SNP data to assess population structure in both ranges and to compare phenotypic differentiation to neutral genetic variation. We failed to detect significant patterns of isolation by distance, geographic patterns in population structure, or correlations between the major axes of SNP variation and phenotypes or latitude of origin. We conclude that the North American clines in size and the parallel clines seen for flowering time are most likely the result of adaptation.
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Affiliation(s)
- Brechann V. McGoey
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONCanada
| | | | - John R. Stinchcombe
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONCanada
- Koffler Scientific ReserveUniversity of TorontoTorontoONCanada
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20
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Uesugi A, Baker DJ, de Silva N, Nurkowski K, Hodgins KA. A lack of genetically compatible mates constrains the spread of an invasive weed. New Phytol 2020; 226:1864-1872. [PMID: 32083724 DOI: 10.1111/nph.16496] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 10/18/2019] [Accepted: 01/31/2020] [Indexed: 06/10/2023]
Abstract
Introduced populations often experience lag times before invasion, but the mechanisms constraining rapid expansions of introduced populations are unclear. Solidago altissima is a North American native plant with highly invasive Japanese populations and introduced Australian populations that are not invasive despite the climatic and ecological suitability of the region. By contrasting Australian with Japanese populations, we tested the hypothesis that Australian population growth is limited by a lack of long-distance dispersal via seeds owing to a limited number of compatible mates. In the field, Australian populations rarely produced viable seeds. A cross-pollination experiment found that Australian plants are fertile, yet lack compatible mates within Australia. Genetic analysis revealed that Australian individuals descend from a small set of self-incompatible genetic clones, which explains the negligible seed set within Australia. Our results show that low genetic diversity, leading to mate incompatibility, inhibits invasiveness of Australian S. altissima, and provides compelling evidence for genetic, rather than ecological, factors constraining invasion in Australia.
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Affiliation(s)
- Akane Uesugi
- School of Biological Sciences, Monash University, Building 18, Clayton, Vic., 3800, Australia
| | - David J Baker
- School of Biological Sciences, Monash University, Building 18, Clayton, Vic., 3800, Australia
| | - Nissanka de Silva
- School of Biological Sciences, Monash University, Building 18, Clayton, Vic., 3800, Australia
| | - Kristin Nurkowski
- School of Biological Sciences, Monash University, Building 18, Clayton, Vic., 3800, Australia
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Building 18, Clayton, Vic., 3800, Australia
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21
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van Boheemen LA, Hodgins KA. Rapid repeatable phenotypic and genomic adaptation following multiple introductions. Mol Ecol 2020; 29:4102-4117. [PMID: 32246535 DOI: 10.1111/mec.15429] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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: 07/13/2019] [Revised: 03/19/2020] [Accepted: 03/25/2020] [Indexed: 12/25/2022]
Abstract
Uncovering the genomic basis of repeated adaption can provide important insights into the constraints and biases that limit the diversity of genetic responses. Demographic processes such as admixture or bottlenecks affect genetic variation underlying traits experiencing selection. The impact of these processes on the genetic basis of adaptation remains, however, largely unexamined empirically. We here test repeatability in phenotypes and genotypes along parallel climatic clines within the native North American and introduced European and Australian Ambrosia artemisiifolia ranges. To do this, we combined multiple lines of evidence from phenotype-environment associations, FST -like outlier tests, genotype-environment associations and genotype-phenotype associations. We used 853 individuals grown in common garden from 84 sampling locations, targeting 19 phenotypes, >83 k SNPs and 22 environmental variables. We found that 17%-26% of loci with adaptive signatures were repeated among ranges, despite alternative demographic histories shaping genetic variation and genetic associations. Our results suggest major adaptive changes can occur on short timescales, with seemingly minimum impacts due to demographic changes linked to introduction. These patterns reveal some predictability of evolutionary change during range expansion, key in a world facing ongoing climate change, and rapid invasive spread.
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Affiliation(s)
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Clayton, Vic., Australia
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22
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Hodgins KA, Yeaman S. Mating system impacts the genetic architecture of adaptation to heterogeneous environments. New Phytol 2019; 224:1201-1214. [PMID: 31505030 DOI: 10.1111/nph.16186] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 08/27/2019] [Indexed: 06/10/2023]
Abstract
Self-fertilisation has consequences for variation across the genome as it reduces effective population size, effect recombination rates and pollen flow, with implications for local adaptation. We conducted simulations of divergent stabilising selection on a quantitative trait with drift, pollen flow, mutation, recombination and different outcrossing rates. We quantified trait divergence and the genetic architecture of adaptation. We conducted an FST outlier analysis to identify candidate loci and quantified the impact of mating system on detectability. Selfing promoted trait divergence mainly through reductions in pollen flow. Moreover, trait architecture became more diffuse with selfing. Average effect size of trait loci was lower, while the number of loci, and their clustering distance increased. The genetic architecture of selfers was also more diffuse than outcrossers for equivalent migration rates. However, when deleterious alleles were included, architectures became more concentrated in selfers, likely to be because of reductions in population size caused by mutational meltdown and impacts of background selection on Ne . Our simulations demonstrate that mating system has important impacts on adaptive divergence of traits and the genetic landscape underlying that divergence. Selfing has a significant effect on detectability of regions of the genome important for adaptation because of neutral divergence and diffuse trait architecture.
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Affiliation(s)
- Kathryn A Hodgins
- School of Biological Sciences, Monash University - Clayton Campus, Building 17, Wellington Road, Clayton, Victoria, 3800, Australia
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, 507 Campus Drive NW, Calgary, AB, T2N 4S8, Canada
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23
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van Boheemen LA, Bou‐Assi S, Uesugi A, Hodgins KA. Rapid growth and defence evolution following multiple introductions. Ecol Evol 2019; 9:7942-7956. [PMID: 31380062 PMCID: PMC6662289 DOI: 10.1002/ece3.5275] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 01/16/2019] [Revised: 04/23/2019] [Accepted: 05/04/2019] [Indexed: 01/02/2023] Open
Abstract
Rapid adaptation can aid invasive populations in their competitive success. Resource allocation trade-off hypotheses predict higher resource availability or the lack of natural enemies in introduced ranges allow for increased growth and reproduction, thus contributing to invasive success. Evidence for such hypotheses is however equivocal and tests among multiple ranges over productivity gradients are required to provide a better understanding of the general applicability of these theories.Using common gardens, we investigated the adaptive divergence of various constitutive and inducible defence-related traits between the native North American and introduced European and Australian ranges, while controlling for divergence due to latitudinal trait clines, individual resource budgets, and population differentiation, using >11,000 SNPs.Rapid, repeated clinal adaptation in defence-related traits was apparent despite distinct demographic histories. We also identified divergence among ranges in some defence-related traits, although differences in energy budgets among ranges may explain some, but not all, defence-related trait divergence. We do not identify a general reduction in defence in concert with an increase in growth among the multiple introduced ranges as predicted trade-off hypotheses. Synthesis: The rapid spread of invasive species is affected by a multitude of factors, likely including adaptation to climate and escape from natural enemies. Unravelling the mechanisms underlying invasives' success enhances understanding of eco-evolutionary theory and is essential to inform management strategies in the face of ongoing climate change. OPEN RESEARCH BADGES This article has been awarded Open Materials, Open Data, Preregistered Research Designs Badges. All materials and data are publicly accessible via the Open Science Framework at https://doi.org/10.6084/m9.figshare.8028875.v1, https://github.com/lotteanna/defence_adaptation,https://doi.org/10.1101/435271.
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Affiliation(s)
| | - Sarah Bou‐Assi
- School of Biological SciencesMonash UniversityClaytonVictoriaAustralia
| | - Akane Uesugi
- School of Biological SciencesMonash UniversityClaytonVictoriaAustralia
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24
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Lu M, Hodgins KA, Degner JC, Yeaman S. Purifying selection does not drive signatures of convergent local adaptation of lodgepole pine and interior spruce. BMC Evol Biol 2019; 19:110. [PMID: 31138118 PMCID: PMC6537219 DOI: 10.1186/s12862-019-1438-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 05/15/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Lodgepole pine (Pinus contorta) and interior spruce (Picea glauca, Picea engelmannii, and their hybrids) are distantly related conifer species. Previous studies identified 47 genes containing variants associated with environmental variables in both species, providing evidence of convergent local adaptation. However, if the intensity of purifying selection varies with the environment, clines in nucleotide diversity could evolve through linked (background) selection that would yield allele frequency-environment signatures resembling local adaptation. If similar geographic patterns in the strength of purifying selection occur in these species, this could result in the convergent signatures of local adaptation, especially if the landscape of recombination is conserved. In the present study, we investigated whether spatially/environmentally varying purifying selection could give rise to the convergent signatures of local adaptation that had previously reported. RESULTS We analyzed 86 lodgepole pine and 50 interior spruce natural populations spanning heterogeneous environments in western Canada where previous analyses had found signatures of convergent local adaptation. We estimated nucleotide diversity and Tajima's D for each gene within each population and calculated the strength of correlations between nucleotide diversity and environmental variables. Overall, these estimates in the genes with previously identified convergent local adaptation signatures had no similar pattern between pine and spruce. Clines in nucleotide diversity along environmental variables were found for interior spruce, but not for lodgepole pine. In spruce, genes with convergent adaption signatures showed a higher strength of correlations than genes without convergent adaption signatures, but there was no such disparity in pine, which suggests the pattern in spruce may have arisen due to a combination of selection and hybridization. CONCLUSIONS The results rule out purifying/background selection as a driver of convergent local adaption signatures in lodgepole pine and interior spruce.
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Affiliation(s)
- Mengmeng Lu
- Department of Biological Sciences, University of Calgary, 507 Campus Drive NW, Calgary, T2N 4S8, Canada.
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University - Clayton Campus, Building 17, Wellington Road, Melbourne, 3800, Australia
| | - Jon C Degner
- Department of Forest and Conservation Sciences, Forest Sciences Centre 3041, University of British Columbia, 2424 Main Mall, Vancouver, V6T 1Z4, Canada
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, 507 Campus Drive NW, Calgary, T2N 4S8, Canada
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25
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van Boheemen LA, Atwater DZ, Hodgins KA. Rapid and repeated local adaptation to climate in an invasive plant. New Phytol 2019; 222:614-627. [PMID: 30367474 DOI: 10.1111/nph.15564] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 10/18/2018] [Indexed: 06/08/2023]
Abstract
Biological invasions provide opportunities to study evolutionary processes occurring over contemporary timescales. To explore the speed and repeatability of adaptation, we examined the divergence of life-history traits to climate, using latitude as a proxy, in the native North American and introduced European and Australian ranges of the annual plant Ambrosia artemisiifolia. We explored niche changes following introductions using climate niche dynamic models. In a common garden, we examined trait divergence by growing seeds collected across three ranges with highly distinct demographic histories. Heterozygosity-fitness associations were used to explore the effect of invasion history on potential success. We accounted for nonadaptive population differentiation using 11 598 single nucleotide polymorphisms. We revealed a centroid shift to warmer, wetter climates in the introduced ranges. We identified repeated latitudinal divergence in life-history traits, with European and Australian populations positioned at either end of the native clines. Our data indicate rapid and repeated adaptation to local climates despite the recent introductions and a bottleneck limiting genetic variation in Australia. Centroid shifts in the introduced ranges suggest adaptation to more productive environments, potentially contributing to trait divergence between the ranges.
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Affiliation(s)
- Lotte A van Boheemen
- School of Biological Sciences, Monash University, Clayton, Vic., 3800, Australia
| | - Daniel Z Atwater
- Department of Biology, Earlham College, Richmond, IN, 47374, USA
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Clayton, Vic., 3800, Australia
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26
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Lee-Yaw JA, Zenni RD, Hodgins KA, Larson BMH, Cousens R, Webber BL. Range shifts and local adaptation: integrating data and theory towards a new understanding of species' distributions in the Anthropocene. New Phytol 2019; 221:644-647. [PMID: 30569613 DOI: 10.1111/nph.15554] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- Julie A Lee-Yaw
- Department of Botany, University of British Columbia, 6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
| | - Rafael D Zenni
- Department of Biology, Federal University of Lavras, Av. Central, S/N Campus Universitário, Lavras, Minas Gerais, 37200-000, Brazil
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Clayton, Vic, 3800, Australia
| | - Brendon M H Larson
- School of Environment, Resources and Sustainability, University of Waterloo, 200 University Avenue W., Waterloo, ON, N2L 3G1, Canada
| | - Roger Cousens
- School of BioSciences, The University of Melbourne, Melbourne, Vic, 3010, Australia
| | - Bruce L Webber
- CSIRO Land and Water, Centre for Environment and Life Sciences, 147 Underwood Ave, Floreat, WA, 6014, Australia
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
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27
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Yeaman S, Gerstein AC, Hodgins KA, Whitlock MC. Quantifying how constraints limit the diversity of viable routes to adaptation. PLoS Genet 2018; 14:e1007717. [PMID: 30296265 PMCID: PMC6193742 DOI: 10.1371/journal.pgen.1007717] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 10/18/2018] [Accepted: 09/26/2018] [Indexed: 12/25/2022] Open
Abstract
Convergent adaptation occurs at the genome scale when independently evolving lineages use the same genes to respond to similar selection pressures. These patterns of genetic repeatability provide insights into the factors that facilitate or constrain the diversity of genetic responses that contribute to adaptive evolution. A first step in studying such factors is to quantify the observed amount of repeatability relative to expectations under a null hypothesis. Here, we formulate a novel index to quantify the constraints driving the observed amount of repeated adaptation in pairwise contrasts based on the hypergeometric distribution, and then generalize this for simultaneous analysis of multiple lineages. This index is explicitly based on the probability of observing a given amount of repeatability by chance under a given null hypothesis and is readily compared among different species and types of trait. We also formulate an index to quantify the effective proportion of genes in the genome that have the potential to contribute to adaptation. As an example of how these indices can be used to draw inferences, we assess the amount of repeatability observed in existing datasets on adaptation to stress in yeast and climate in conifers. This approach provides a method to test a wide range of hypotheses about how different kinds of factors can facilitate or constrain the diversity of genetic responses observed during adaptive evolution. How many ways can evolution solve the same adaptive problem? While convergent adaptation is evident in many organisms at the phenotypic level, we are only beginning to understand how commonly this convergence extends to the genome scale. Quantifying the repeatability of adaptation at the genome scale is therefore critical for assessing how constraints affect the diversity of viable genetic responses. Here, we develop probability-based indices to quantify the deviation between observed repeatability and expectations under a range of null hypotheses, and an estimator of the proportion of loci in the genome that can contribute to adaptation. We demonstrate the usage of these indices with individual-based simulations and example datasets from yeast and conifers and discuss how they differ from previously developed approaches to studying repeatability. Because these indices are unitless, they provide a general approach to quantifying and comparing how constraints drive convergence at the genome scale across a wide range of traits and taxa.
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Affiliation(s)
- Sam Yeaman
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
- * E-mail:
| | - Aleeza C. Gerstein
- Department of Microbiology & Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Kathryn A. Hodgins
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Michael C. Whitlock
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
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28
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Lotterhos KE, Yeaman S, Degner J, Aitken S, Hodgins KA. Modularity of genes involved in local adaptation to climate despite physical linkage. Genome Biol 2018; 19:157. [PMID: 30290843 PMCID: PMC6173883 DOI: 10.1186/s13059-018-1545-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 09/18/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Linkage among genes experiencing different selection pressures can make natural selection less efficient. Theory predicts that when local adaptation is driven by complex and non-covarying stresses, increased linkage is favored for alleles with similar pleiotropic effects, with increased recombination favored among alleles with contrasting pleiotropic effects. Here, we introduce a framework to test these predictions with a co-association network analysis, which clusters loci based on differing associations. We use this framework to study the genetic architecture of local adaptation to climate in lodgepole pine, Pinus contorta, based on associations with environments. RESULTS We identify many clusters of candidate genes and SNPs associated with distinct environments, including aspects of aridity and freezing, and discover low recombination rates among some candidate genes in different clusters. Only a few genes contain SNPs with effects on more than one distinct aspect of climate. There is limited correspondence between co-association networks and gene regulatory networks. We further show how associations with environmental principal components can lead to misinterpretation. Finally, simulations illustrate both benefits and caveats of co-association networks. CONCLUSIONS Our results support the prediction that different selection pressures favor the evolution of distinct groups of genes, each associating with a different aspect of climate. But our results went against the prediction that loci experiencing different sources of selection would have high recombination among them. These results give new insight into evolutionary debates about the extent of modularity, pleiotropy, and linkage in the evolution of genetic architectures.
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Affiliation(s)
- Katie E Lotterhos
- Department of Marine and Environmental Sciences, Northeastern Marine Science Center, 430 Nahant Rd, Nahant, MA, 01908, USA.
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N1N4, Canada
| | - Jon Degner
- Department of Forest and Conservation Sciences, Faculty of Forestry, Vancouver, BC, V6T 1Z4, Canada
| | - Sally Aitken
- Department of Forest and Conservation Sciences, Faculty of Forestry, Vancouver, BC, V6T 1Z4, Canada
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Wellington Rd, Clayton, Melbourne, VIC, 3800, Australia
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Conte GL, Hodgins KA, Yeaman S, Degner JC, Aitken SN, Rieseberg LH, Whitlock MC. Bioinformatically predicted deleterious mutations reveal complementation in the interior spruce hybrid complex. BMC Genomics 2017; 18:970. [PMID: 29246191 PMCID: PMC5731209 DOI: 10.1186/s12864-017-4344-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [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: 05/25/2017] [Accepted: 11/21/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Mutation load is expected to be reduced in hybrids via complementation of deleterious alleles. While local adaptation of hybrids confounds phenotypic tests for reduced mutation load, it may be possible to assess variation in load by analyzing the distribution of putatively deleterious alleles. Here, we use this approach in the interior spruce (Picea glauca x P. engelmannii) hybrid complex, a group likely to suffer from high mutation load and in which hybrids exhibit local adaptation to intermediate conditions. We used PROVEAN to bioinformatically predict whether non-synonymous alleles are deleterious, based on conservation of the position and abnormality of the amino acid change. RESULTS As expected, we found that predicted deleterious alleles were at lower average allele frequencies than alleles not predicted to be deleterious. We were unable to detect a phenotypic effect on juvenile growth rate of the many rare alleles predicted to be deleterious. Both the proportion of alleles predicted to be deleterious and the proportion of loci homozygous for predicted deleterious alleles were higher in P. engelmannii (Engelmann spruce) than in P. glauca (white spruce), due to higher diversity and frequencies of rare alleles in Engelmann. Relative to parental species, the proportion of alleles predicted to be deleterious was intermediate in hybrids, and the proportion of loci homozygous for predicted deleterious alleles was lowest. CONCLUSION Given that most deleterious alleles are recessive, this suggests that mutation load is reduced in hybrids due to complementation of deleterious alleles. This effect may enhance the fitness of hybrids.
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Affiliation(s)
- Gina L Conte
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada. .,Department of Botany, University of British Columbia, 3200-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada.
| | - Kathryn A Hodgins
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada.,Present Address: School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, 3800, Australia
| | - Sam Yeaman
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada.,Present Address: Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, AB, T2N 1N4, Canada
| | - Jon C Degner
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Sally N Aitken
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Loren H Rieseberg
- Department of Botany, University of British Columbia, 3200-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
| | - Michael C Whitlock
- Department of Zoology, University of British Columbia, 4200-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
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van Boheemen LA, Lombaert E, Nurkowski KA, Gauffre B, Rieseberg LH, Hodgins KA. Multiple introductions, admixture and bridgehead invasion characterize the introduction history of Ambrosia artemisiifolia
in Europe and Australia. Mol Ecol 2017; 26:5421-5434. [DOI: 10.1111/mec.14293] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 08/05/2017] [Indexed: 01/16/2023]
Affiliation(s)
| | - Eric Lombaert
- UMR 1355 ISA; INRA; Sophia-Antipolis France
- UMR ISA; Université de Nice Sophia Antipolis; Sophia-Antipolis France
- UMR 7254 ISA; CNRS; Sophia-Antipolis France
| | | | - Bertrand Gauffre
- School of Biological Sciences; Monash University; Clayton VIC Australia
- UMR 7372; Centre d'Etudes Biologiques de Chizé; CNRS - Université de La Rochelle; Villiers-en-Bois France
- USC1339; Centre d'Etudes Biologiques de Chizé; INRA; Villiers-en-Bois France
| | - Loren H. Rieseberg
- Department of Botany; University of British Columbia; Vancouver BC Canada
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Hodgins KA, Moore JL. Adapting to a warming world: Ecological restoration, climate change, and genomics. Am J Bot 2016; 103:590-592. [PMID: 27022008 DOI: 10.3732/ajb.1600049] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 03/02/2016] [Indexed: 06/05/2023]
Affiliation(s)
- Kathryn A Hodgins
- School of Biological Sciences, Building 18, Monash University, Melbourne, Victoria, Australia, 3800
| | - Joslin L Moore
- School of Biological Sciences, Building 18, Monash University, Melbourne, Victoria, Australia, 3800
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32
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Hodgins KA, Yeaman S, Nurkowski KA, Rieseberg LH, Aitken SN. Expression Divergence Is Correlated with Sequence Evolution but Not Positive Selection in Conifers. Mol Biol Evol 2016; 33:1502-16. [PMID: 26873578 DOI: 10.1093/molbev/msw032] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The evolutionary and genomic determinants of sequence evolution in conifers are poorly understood, and previous studies have found only limited evidence for positive selection. Using RNAseq data, we compared gene expression profiles to patterns of divergence and polymorphism in 44 seedlings of lodgepole pine (Pinus contorta) and 39 seedlings of interior spruce (Picea glauca × engelmannii) to elucidate the evolutionary forces that shape their genomes and their plastic responses to abiotic stress. We found that rapidly diverging genes tend to have greater expression divergence, lower expression levels, reduced levels of synonymous site diversity, and longer proteins than slowly diverging genes. Similar patterns were identified for the untranslated regions, but with some exceptions. We found evidence that genes with low expression levels had a larger fraction of nearly neutral sites, suggesting a primary role for negative selection in determining the association between evolutionary rate and expression level. There was limited evidence for differences in the rate of positive selection among genes with divergent versus conserved expression profiles and some evidence supporting relaxed selection in genes diverging in expression between the species. Finally, we identified a small number of genes that showed evidence of site-specific positive selection using divergence data alone. However, estimates of the proportion of sites fixed by positive selection (α) were in the range of other plant species with large effective population sizes suggesting relatively high rates of adaptive divergence among conifers.
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Affiliation(s)
- Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Sam Yeaman
- Department of Botany, University of British Columbia, Vancouver, BC, Canada Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | | | - Loren H Rieseberg
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Sally N Aitken
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
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Abstract
Stressors and heterogeneity are ubiquitous features of natural environments, and theory suggests that when environmental qualities alter flowering schedules through phenotypic plasticity, assortative mating can result that promotes evolutionary divergence. Therefore, it is important to determine whether common ecological stressors induce similar changes in flowering time. We review previous studies to determine whether two important stressors, water restriction and herbivory, induce consistent flowering time responses among species; for example, how often do water restriction and herbivory both delay flowering? We focus on the direction of change in flowering time, which affects the potential for divergence in heterogeneous environments. We also tested whether these stressors influenced time to flowering and nonphenology traits using Mimulus guttatus. The literature review suggests that water restriction has variable effects on flowering time, whereas herbivory delays flowering with exceptional consistency. In the Mimulus experiment, low water and herbivory advanced and delayed flowering, respectively. Overall, our results temper theoretical predictions for evolutionary divergence due to habitat‐induced changes in flowering time; in particular, we discuss how accounting for variation in the direction of change in flowering time can either increase or decrease the potential for divergence. In addition, we caution against adaptive interpretations of stress‐induced phenology shifts.
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Affiliation(s)
- Crispin Y Jordan
- Department of Zoology University of British Columbia Vancouver British Columbia V6T 1Z4 Canada
| | - Dilara Ally
- Department of Zoology University of British Columbia Vancouver British Columbia V6T 1Z4 Canada
| | - Kathryn A Hodgins
- Department of Zoology University of British Columbia Vancouver British Columbia 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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Chown SL, Hodgins KA, Griffin PC, Oakeshott JG, Byrne M, Hoffmann AA. Biological invasions, climate change and genomics. Evol Appl 2015; 8:23-46. [PMID: 25667601 PMCID: PMC4310580 DOI: 10.1111/eva.12234] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [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: 09/02/2014] [Accepted: 10/24/2014] [Indexed: 12/13/2022] Open
Abstract
The rate of biological invasions is expected to increase as the effects of climate change on biological communities become widespread. Climate change enhances habitat disturbance which facilitates the establishment of invasive species, which in turn provides opportunities for hybridization and introgression. These effects influence local biodiversity that can be tracked through genetic and genomic approaches. Metabarcoding and metagenomic approaches provide a way of monitoring some types of communities under climate change for the appearance of invasives. Introgression and hybridization can be followed by the analysis of entire genomes so that rapidly changing areas of the genome are identified and instances of genetic pollution monitored. Genomic markers enable accurate tracking of invasive species' geographic origin well beyond what was previously possible. New genomic tools are promoting fresh insights into classic questions about invading organisms under climate change, such as the role of genetic variation, local adaptation and climate pre-adaptation in successful invasions. These tools are providing managers with often more effective means to identify potential threats, improve surveillance and assess impacts on communities. We provide a framework for the application of genomic techniques within a management context and also indicate some important limitations in what can be achieved.
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Affiliation(s)
- Steven L Chown
- School of Biological Sciences, Monash UniversityClayton, Vic., Australia
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash UniversityClayton, Vic., Australia
| | - Philippa C Griffin
- Department of Genetics, Bio21 Institute, The University of MelbourneParkville, Vic., Australia
| | - John G Oakeshott
- CSIRO Land and Water Flagship, Black Mountain LaboratoriesCanberra, ACT, Australia
| | - Margaret Byrne
- Science and Conservation Division, Department of Parks and Wildlife, Bentley Delivery CentreBentley, WA, Australia
| | - Ary A Hoffmann
- Departments of Zoology and Genetics, Bio21 Institute, The University of MelbourneParkville, Vic., Australia
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36
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Yeaman S, Hodgins KA, Suren H, Nurkowski KA, Rieseberg LH, Holliday JA, Aitken SN. Conservation and divergence of gene expression plasticity following c. 140 million years of evolution in lodgepole pine (Pinus contorta) and interior spruce (Picea glauca×Picea engelmannii). New Phytol 2014; 203:578-591. [PMID: 24750196 DOI: 10.1111/nph.12819] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [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: 01/27/2014] [Accepted: 03/20/2014] [Indexed: 06/03/2023]
Abstract
Species respond to environmental stress through a combination of genetic adaptation and phenotypic plasticity, both of which may be important for survival in the face of climatic change. By characterizing the molecular basis of plastic responses and comparing patterns among species, it is possible to identify how such traits evolve. Here, we used de novo transcriptome assembly and RNAseq to explore how patterns of gene expression differ in response to temperature, moisture, and light regime treatments in lodgepole pine (Pinus contorta) and interior spruce (a natural hybrid population of Picea glauca and Picea engelmannii). We found wide evidence for an effect of treatment on expression within each species, with 6413 and 11,658 differentially expressed genes identified in spruce and pine, respectively. Comparing patterns of expression among these species, we found that 74% of all orthologs with differential expression had a pattern that was conserved in both species, despite 140 million yr of evolution. We also found that the specific treatments driving expression patterns differed between genes with conserved versus diverged patterns of expression. We conclude that natural selection has probably played a role in shaping plastic responses to environment in these species.
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Affiliation(s)
- Sam Yeaman
- Department of Botany, 6270 University Blvd, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Kathryn A Hodgins
- Department of Botany, 6270 University Blvd, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
- School of Biological Sciences, Monash University, Building 18, Melbourne, Vic., 3800, Australia
| | - Haktan Suren
- Department of Forest Resources and Environmental Conservation, Virginia Polytechnic Institute and State University, 304 Cheatham Hall, Blacksburg, VA, 24061, USA
- Genetics, Bioinformatics and Computational Biology Program, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Kristin A Nurkowski
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Loren H Rieseberg
- Department of Botany, 6270 University Blvd, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Jason A Holliday
- Department of Forest Resources and Environmental Conservation, Virginia Polytechnic Institute and State University, 304 Cheatham Hall, Blacksburg, VA, 24061, USA
| | - Sally N Aitken
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
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Hodgins KA, Lai Z, Oliveira LO, Still DW, Scascitelli M, Barker MS, Kane NC, Dempewolf H, Kozik A, Kesseli RV, Burke JM, Michelmore RW, Rieseberg LH. Genomics of Compositae crops: reference transcriptome assemblies and evidence of hybridization with wild relatives. Mol Ecol Resour 2013; 14:166-77. [DOI: 10.1111/1755-0998.12163] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 08/14/2013] [Accepted: 08/15/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Kathryn A. Hodgins
- Department of Botany and Biodiversity Research Centre; University of British Columbia; Vancouver BC V6T 1Z4 Canada
| | - Zhao Lai
- Department of Biology and Center for Genomics and Bioinformatics; Indiana University; Bloomington IN 47405 USA
| | - Luiz O. Oliveira
- Departamento de Bioquímica e Biologia Molecular; Universidade Federal de Viçosa; 36570-000 Viçosa Brazil
| | - David W. Still
- Department of Plant Sciences; Cal Poly Pomona; Pomona CA 91768 USA
| | - Moira Scascitelli
- Department of Botany and Biodiversity Research Centre; University of British Columbia; Vancouver BC V6T 1Z4 Canada
| | - Michael S. Barker
- Department of Ecology and Evolutionary Biology; University of Arizona; Tucson AZ 85721 USA
| | - Nolan C. Kane
- Department of Ecology and Evolutionary Biology; University of Colorado Boulder; Boulder CO 80309 USA
| | - Hannes Dempewolf
- Department of Botany and Biodiversity Research Centre; University of British Columbia; Vancouver BC V6T 1Z4 Canada
| | - Alex Kozik
- The Genome Center; University of California; Davis CA 95616 USA
| | | | - John M. Burke
- Department of Plant Biology; University of Georgia; Athens GA 30602 USA
| | - Richard W. Michelmore
- The Genome Center; University of California; Davis CA 95616 USA
- Departments of Plant Sciences, Molecular & Cellular Biology, and Medical Microbiology & Immunology; University of California; Davis CA 95616 USA
| | - Loren H. Rieseberg
- Department of Botany and Biodiversity Research Centre; University of British Columbia; Vancouver BC V6T 1Z4 Canada
- Department of Biology and Center for Genomics and Bioinformatics; Indiana University; Bloomington IN 47405 USA
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Hodgins KA, Lai Z, Nurkowski K, Huang J, Rieseberg LH. The molecular basis of invasiveness: differences in gene expression of native and introduced common ragweed (Ambrosia artemisiifolia) in stressful and benign environments. Mol Ecol 2013; 22:2496-510. [PMID: 23294156 DOI: 10.1111/mec.12179] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Revised: 11/14/2012] [Accepted: 11/21/2012] [Indexed: 11/28/2022]
Abstract
Although the evolutionary and ecological processes that contribute to plant invasion have been the focus of much research, investigation into the molecular basis of invasion is just beginning. Common ragweed (Ambrosia artemisiifolia) is an annual weed native to North America and has been introduced to Europe where it has become invasive. Using a custom-designed NimbleGen oligoarray, we examined differences in gene expression between five native and six introduced populations of common ragweed in three different environments (control, light stress and nutrient stress), as well as two different time points. We identified candidate genes that may contribute to invasiveness in common ragweed based on differences in expression between native and introduced populations from Europe. Specifically, we found 180 genes where range explained a significant proportion of the variation in gene expression and a further 103 genes with a significant range by treatment interaction. Several of these genes are potentially involved in the metabolism of secondary compounds, stress response and the detoxification of xenobiotics. Previously, we found more rapid growth and greater reproductive success in introduced populations, particularly in benign and competitive (light stress) environments, and many of these candidate genes potentially underlie these growth differences. We also found expression differences among populations within each range, reflecting either local adaptation or neutral processes, although no associations with climate or latitude were identified. These data provide a first step in identifying genes that are involved with introduction success in an aggressive annual weed.
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Affiliation(s)
- Kathryn A Hodgins
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.
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Dempewolf H, Hodgins KA, Rummell SE, Ellstrand NC, Rieseberg LH. Reproductive isolation during domestication. Plant Cell 2012; 24:2710-7. [PMID: 22773750 PMCID: PMC3426109 DOI: 10.1105/tpc.112.100115] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 04/30/2012] [Accepted: 06/18/2012] [Indexed: 05/02/2023]
Abstract
It has been hypothesized that reproductive isolation should facilitate evolution under domestication. However, a systematic comparison of reproductive barrier strength between crops and their progenitors has not been conducted to test this hypothesis. Here, we present a systematic survey of reproductive barriers between 32 economically important crop species and their progenitors to better understand the role of reproductive isolation during the domestication process. We took a conservative approach, avoiding those types of reproductive isolation that are poorly known for these taxa (e.g., differences in flowering time). We show that the majority of crops surveyed are isolated from their progenitors by one or more reproductive barriers, despite the fact that the most important reproductive barrier in natural systems, geographical isolation, was absent, at least in the initial stages of domestication for most species. Thus, barriers to reproduction between crops and wild relatives are closely associated with domestication and may facilitate it, thereby raising the question whether reproductive isolation could be viewed as a long-overlooked "domestication trait." Some of the reproductive barriers observed (e.g., polyploidy and uniparental reproduction), however, may have been favored for reasons other than, or in addition to, their effects on gene flow.
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Affiliation(s)
- Hannes Dempewolf
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Kathryn A. Hodgins
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Sonja E. Rummell
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Norman C. Ellstrand
- Department of Botany and Plant Sciences and Center for Conservation Biology, University of California, Riverside, California 92521
| | - Loren H. Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Biology, Indiana University, Bloomington, Indiana 47405
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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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Abstract
Invasive plants cause substantial environmental damage and economic loss. Here, we explore the possibility that a selfish genetic element found in plants called cytoplasmic male sterility (CMS) could be exploited for weed control. CMS is caused by mutations in the mitochondrial genome that sterilize male reproductive organs. We developed an analytical model and a spatial simulation to assess the use of CMS alleles to manage weed populations. Specifically, we examined how fertility, selfing, pollen limitation and dispersal influenced extinction rate and time until extinction in populations where CMS arises. We found that the introduction of a CMS allele can cause rapid population extinction, but only under a restricted set of conditions. Both models suggest that the CMS strategy will be appropriate for species where pollen limitation is negligible, inbreeding depression is high and the fertility advantage of females over hermaphrodites is substantial. In general, spatial structure did not have a strong influence on the simulation outcome, although low pollen dispersal and intermediate levels of seed dispersal tended to reduce population extinction rates. Given these results, the introduction of CMS alleles into a population of invasive plants probably represents an effective control method for only a select number of species.
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Affiliation(s)
- Kathryn A Hodgins
- Department of Botany, University of British Columbia Vancouver, BC, Canada
| | - Loren Rieseberg
- Department of Botany, University of British Columbia Vancouver, BC, Canada
| | - Sarah P Otto
- Department of Zoology, University of British Columbia Vancouver, BC, Canada
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Hodgins KA, Barrett SCH. Natural selection on floral traits through male and female function in wild populations of the heterostylous daffodil Narcissus triandrus. Evolution 2008; 62:1751-1763. [PMID: 18419752 DOI: 10.1111/j.1558-5646.2008.00404.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Measurements of natural selection in hermaphrodite populations require the analysis of performance through both female and male sex functions. Here, we investigate selection on three floral traits: flower number, flower length, and corona width through both sex functions in natural populations of the tristylous daffodil Narcissus triandrus. Selection through female function was examined in six populations, and in two of these we also estimated male selection gradients using multilocus microsatellite genotyping of parents and offspring. We detected significant directional selection for flower number through female function, and significant stabilizing selection for corona width and flower length through male function. Variation in male reproductive success was strongly influenced by the distance between mates and was significantly higher than variation in female reproductive success in one population, a result consistent with Bateman's principle. However, variation through both sex functions was similar in the other population and there was a significant negative correlation between female and male fitness indicating sex-specific trade-offs in reproductive success. Selection on floral design in N. triandrus was stronger through male than female function probably because floral morphology plays an important role in promoting effective cross-pollen transfer in populations of this heterostylous species.
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Affiliation(s)
- Kathryn A Hodgins
- Department of Ecology & Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, Canada.
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Hodgins KA, Barrett SCH. Geographic variation in floral morphology and style-morph ratios in a sexually polymorphic daffodil. Am J Bot 2008; 95:185-195. [PMID: 21632344 DOI: 10.3732/ajb.95.2.185] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Narcissus triandrus is a tristylous daffodil from the Iberian Peninsula that has striking geographical variation in floral morphology and style-morph ratios. Here, we investigate the relation between this variation and ecological factors to understand mechanisms governing morph ratios. We estimated morph ratios in 124 populations throughout the range of N. triandrus and measured 13 morphological traits in 35-78 populations. Sampling of morph ratios conducted over 2-10-yr intervals demonstrated strong temporal stability. Variation in floral and vegetative traits enabled statistical prediction of morph-frequency variation among populations. Latitudinal gradients in precipitation and temperature were correlated with plant and flower size, with larger flowers in northern populations associated with bumblebee visitation and stylar dimorphism. Flowers of the L- and M-morphs differed significantly from the S-morph in several size-related characters, unlike other tristylous species. This pattern and the similarity in anther positions of the L- and M-morphs suggest that the M-morph of N. triandrus originated through genetic modifiers that shortened styles of the L-morph. Our findings support the hypothesis that geographical variation in style-morph ratios is largely governed by climatic gradients in the Iberian Peninsula, which influence the floral morphology and pollination biology of N. triandrus populations.
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Affiliation(s)
- Kathryn A Hodgins
- Department of Ecology & Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario M5S 3B2 Canada
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Hodgins KA, Barrett SCH. Population structure and genetic diversity in tristylous Narcissus triandrus: insights from microsatellite and chloroplast DNA variation. Mol Ecol 2007; 16:2317-32. [PMID: 17561893 DOI: 10.1111/j.1365-294x.2007.03314.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [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: 10/23/2022]
Abstract
We investigated cpDNA sequence and nuclear microsatellite variation among populations of the wild daffodil Narcissus triandrus to examine the role of historical vs. contemporary forces in shaping population structure, morphological differentiation and sexual-system evolution. This wide-ranging heterostylous species of the Iberian Peninsula is largely composed of two allopatric varieties (vars. cernuus and triandrus), and populations with either stylar trimorphism or dimorphism. Dimorphic populations only occur in var. triandrus, are mainly restricted to the northwestern portion of the species range, and uniformly lack the mid-styled morph (M-morph). Chloroplast DNA (cpDNA) sequence variation revealed strong geographical structuring and evidence for a fragmentation event associated with differentiation of the two varieties. In var. triandrus, population fragmentation, restricted gene flow and isolation-by-distance were also inferred. Significant differences in genetic diversity and population structure between the two varieties likely reflect historical and contemporary differences in demography and gene flow among populations. Discordance between cpDNA markers and both microsatellite and morphological variation indicate that hybridization has occurred between the two varieties at contact zones. There were no differences in genetic diversity or population structure between dimorphic and trimorphic populations, and chloroplast haplotypes were not associated with either sexual system, indicating transitions in morph structure within each maternal lineage. M-morph frequencies were positively correlated with differentiation at microsatellite loci, indicating that the evolutionary processes influencing these neutral markers also influence alleles controlling the style morphs.
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Affiliation(s)
- Kathryn A Hodgins
- Department of Ecology & Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada.
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Abstract
Mating patterns in plant populations are influenced by interactions between reproductive traits and ecological conditions, both factors that are likely to vary geographically. Narcissus triandrus, a wide-ranging heterostylous herb, exhibits populations with either two (dimorphic) or three (trimorphic) style morphs and displays substantial geographical variation in demographic attributes and floral morphology. Here, we investigate this variation to determine if demography, morphology, and mating system differ between the two sexual systems. Our surveys in Portugal and NW Spain indicated that dimorphic populations were less dense, of smaller size, and had larger plants and flowers compared to trimorphic populations. Outcrossing rates estimated using allozyme markers revealed similar outcrossing rates in dimorphic and trimorphic populations (t(m) dimorphic=0.759; t(m) trimorphic=0.710). All populations experienced significant inbreeding in progeny (mean F=0.143). In contrast, parental estimates of inbreeding were not significantly different from zero (mean F=0.062), implying that few inbred offspring survive to reproductive maturity due to inbreeding depression. Although the majority of inbreeding results from selfing, significant levels of biparental inbreeding were also detected in eight of the nine populations (mean s(s)-s(m)=0.081). Density was negatively associated with levels of selfing but positively associated with biparental inbreeding. Population size was positively associated with outcrossing but not biparental inbreeding. There were no consistent differences among the style morphs in outcrossing or biparental inbreeding indicating that the maintenance of trimorphism vs dimorphism is unlikely to be associated with inbreeding of maternal parents.
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Affiliation(s)
- K A Hodgins
- Department of Botany, University of Toronto, 25 Willcocks Street, Toronto, ON, Canada M5S 3B2.
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Abstract
In tristylous populations, mating-type frequencies are governed by negative frequency-dependent selection typically resulting in equal morph ratios at equilibrium. However, Narcissus triandrus generally exhibits long-styled (L)-biased populations with a deficiency of the mid-styled (M)-morph. Here we used a pollen-transfer model and measurements of female fertility in natural populations to investigate whether these uneven morph ratios were associated with variation in female reproductive success. Our theoretical analysis demonstrated that morph ratio bias can result from maternal fitness differences among the morphs, and that these effects were magnified by asymmetrical mating. In nine out of 15 populations of N. triandrus, seed set differed significantly among the morphs, but pollen limitation occurred in only two of 11 populations investigated. Average seed set of the M-morph was positively associated with its frequency in populations. Flower size was negatively correlated with the seed set of the M-morph. Our results suggest that interactions between mating patterns and female fertility are responsible for variation in morph frequencies and loss of the M-morph from tristylous populations of N. triandrus.
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Affiliation(s)
- Kathryn A Hodgins
- Department of Botany, University of Toronto, 25 Willcocks Street, Toronto, Ontario M5S 3B2, Canada.
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