1
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Whiting JR, Booker TR, Rougeux C, Lind BM, Singh P, Lu M, Huang K, Whitlock MC, Aitken SN, Andrew RL, Borevitz JO, Bruhl JJ, Collins TL, Fischer MC, Hodgins KA, Holliday JA, Ingvarsson PK, Janes JK, Khandaker M, Koenig D, Kreiner JM, Kremer A, Lascoux M, Leroy T, Milesi P, Murray KD, Pyhäjärvi T, Rellstab C, Rieseberg LH, Roux F, Stinchcombe JR, Telford IRH, Todesco M, Tyrmi JS, Wang B, Weigel D, Willi Y, Wright SI, Zhou L, Yeaman S. The genetic architecture of repeated local adaptation to climate in distantly related plants. Nat Ecol Evol 2024:10.1038/s41559-024-02514-5. [PMID: 39187610 DOI: 10.1038/s41559-024-02514-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 07/22/2024] [Indexed: 08/28/2024]
Abstract
Closely related species often use the same genes to adapt to similar environments. However, we know little about why such genes possess increased adaptive potential and whether this is conserved across deeper evolutionary lineages. Adaptation to climate presents a natural laboratory to test these ideas, as even distantly related species must contend with similar stresses. Here, we re-analyse genomic data from thousands of individuals from 25 plant species as diverged as lodgepole pine and Arabidopsis (~300 Myr). We test for genetic repeatability based on within-species associations between allele frequencies in genes and variation in 21 climate variables. Our results demonstrate significant statistical evidence for genetic repeatability across deep time that is not expected under randomness, identifying a suite of 108 gene families (orthogroups) and gene functions that repeatedly drive local adaptation to climate. This set includes many orthogroups with well-known functions in abiotic stress response. Using gene co-expression networks to quantify pleiotropy, we find that orthogroups with stronger evidence for repeatability exhibit greater network centrality and broader expression across tissues (higher pleiotropy), contrary to the 'cost of complexity' theory. These gene families may be important in helping wild and crop species cope with future climate change, representing important candidates for future study.
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Affiliation(s)
- James R Whiting
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.
| | - Tom R Booker
- Department of Zoology, Faculty of Science, University of British Columbia, Vancouver, British Colombia, Canada
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Clément Rougeux
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Brandon M Lind
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Pooja Singh
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Mengmeng Lu
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Kaichi Huang
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael C Whitlock
- Department of Zoology, Faculty of Science, University of British Columbia, Vancouver, British Colombia, Canada
| | - Sally N Aitken
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rose L Andrew
- School of Environmental and Rural Science, University of New England, Armidale, New South Wales, Australia
| | - Justin O Borevitz
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Jeremy J Bruhl
- School of Environmental and Rural Science, University of New England, Armidale, New South Wales, Australia
| | - Timothy L Collins
- Department of Planning and Environment, Queanbeyan, New South Wales, Australia
- Department of Climate Change, Energy, the Environment and Water, Queanbeyan, New South Wales, Australia
| | - Martin C Fischer
- ETH Zurich: Institute of Integrative Biology (IBZ), ETH Zurich, Zurich, Switzerland
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Jason A Holliday
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, VA, USA
| | - Pär K Ingvarsson
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jasmine K Janes
- Biology Department, Vancouver Island University, Nanaimo, British Columbia, Canada
- Department of Ecosystem Science and Management, University of Northern British Columbia, Prince George, British Columbia, Canada
- Species Survival Commission, Orchid Specialist Group, IUCN North America, Washington, DC, USA
| | - Momena Khandaker
- School of Environmental and Rural Science, University of New England, Armidale, New South Wales, Australia
| | - Daniel Koenig
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
- Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Julia M Kreiner
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Antoine Kremer
- UMR BIOGECO, INRAE, Université de Bordeaux; 69 Route d'Arcachon, Cestas, France
| | - Martin Lascoux
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Thibault Leroy
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | - Pascal Milesi
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Kevin D Murray
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Tanja Pyhäjärvi
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | | | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Fabrice Roux
- Laboratoire des Interactions Plantes-Microbes-Environnement, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - John R Stinchcombe
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Ian R H Telford
- School of Environmental and Rural Science, University of New England, Armidale, New South Wales, Australia
| | - Marco Todesco
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biology, University of British Columbia, Kelowna, British Columbia, Canada
| | - Jaakko S Tyrmi
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Baosheng Wang
- South China National Botanical Garden, Guangzhou, China
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Yvonne Willi
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Stephen I Wright
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Lecong Zhou
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, VA, USA
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.
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2
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Hartfield M, Glémin S. Polygenic selection to a changing optimum under self-fertilisation. PLoS Genet 2024; 20:e1011312. [PMID: 39018328 DOI: 10.1371/journal.pgen.1011312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 07/29/2024] [Accepted: 05/21/2024] [Indexed: 07/19/2024] Open
Abstract
Many traits are polygenic, affected by multiple genetic variants throughout the genome. Selection acting on these traits involves co-ordinated allele-frequency changes at these underlying variants, and this process has been extensively studied in random-mating populations. Yet many species self-fertilise to some degree, which incurs changes to genetic diversity, recombination and genome segregation. These factors cumulatively influence how polygenic selection is realised in nature. Here, we use analytical modelling and stochastic simulations to investigate to what extent self-fertilisation affects polygenic adaptation to a new environment. Our analytical solutions show that while selfing can increase adaptation to an optimum, it incurs linkage disequilibrium that can slow down the initial spread of favoured mutations due to selection interference, and favours the fixation of alleles with opposing trait effects. Simulations show that while selection interference is present, high levels of selfing (at least 90%) aids adaptation to a new optimum, showing a higher long-term fitness. If mutations are pleiotropic then only a few major-effect variants fix along with many neutral hitchhikers, with a transient increase in linkage disequilibrium. These results show potential advantages to self-fertilisation when adapting to a new environment, and how the mating system affects the genetic composition of polygenic selection.
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Affiliation(s)
- Matthew Hartfield
- Institute of Ecology and Evolution, The University of Edinburgh, Edinburgh, United Kingdom
| | - Sylvain Glémin
- Université de Rennes, Centre National de la Recherche Scientifique (CNRS), ECOBIO (Ecosystèmes, Biodiversité, Evolution) - Unité Mixte de Recherche (UMR) 6553, Rennes, France
- Department of Ecology and Evolution, Evolutionary Biology Center, Uppsala University, Uppsala, Sweden
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3
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Ahrens CW, Murray K, Mazanec RA, Ferguson S, Jones A, Tissue DT, Byrne M, Borevitz JO, Rymer PD. Genomic determinants, architecture, and constraints in drought-related traits in Corymbia calophylla. BMC Genomics 2024; 25:640. [PMID: 38937661 PMCID: PMC11209971 DOI: 10.1186/s12864-024-10531-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 06/14/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND Drought adaptation is critical to many tree species persisting under climate change, however our knowledge of the genetic basis for trees to adapt to drought is limited. This knowledge gap impedes our fundamental understanding of drought response and application to forest production and conservation. To improve our understanding of the genomic determinants, architecture, and trait constraints, we assembled a reference genome and detected ~ 6.5 M variants in 432 phenotyped individuals for the foundational tree Corymbia calophylla. RESULTS We found 273 genomic variants determining traits with moderate heritability (h2SNP = 0.26-0.64). Significant variants were predominantly in gene regulatory elements distributed among several haplotype blocks across all chromosomes. Furthermore, traits were constrained by frequent epistatic and pleiotropic interactions. CONCLUSIONS Our results on the genetic basis for drought traits in Corymbia calophylla have several implications for the ability to adapt to climate change: (1) drought related traits are controlled by complex genomic architectures with large haplotypes, epistatic, and pleiotropic interactions; (2) the most significant variants determining drought related traits occurred in regulatory regions; and (3) models incorporating epistatic interactions increase trait predictions. Our findings indicate that despite moderate heritability drought traits are likely constrained by complex genomic architecture potentially limiting trees response to climate change.
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Affiliation(s)
- Collin W Ahrens
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia.
- Cesar Australia, Brunswick, VIC, 3058, Australia.
| | - Kevin Murray
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Richard A Mazanec
- Biodiversity and Conservation Science, Western Australian Department of Biodiversity, Conservation and Attractions, Kensington, WA, 6151, Australia
| | - Scott Ferguson
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Ashley Jones
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - David T Tissue
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Margaret Byrne
- Biodiversity and Conservation Science, Western Australian Department of Biodiversity, Conservation and Attractions, Kensington, WA, 6151, Australia
| | - Justin O Borevitz
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Paul D Rymer
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
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4
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Hämälä T, Moore C, Cowan L, Carlile M, Gopaulchan D, Brandrud MK, Birkeland S, Loose M, Kolář F, Koch MA, Yant L. Impact of whole-genome duplications on structural variant evolution in Cochlearia. Nat Commun 2024; 15:5377. [PMID: 38918389 PMCID: PMC11199601 DOI: 10.1038/s41467-024-49679-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 06/14/2024] [Indexed: 06/27/2024] Open
Abstract
Polyploidy, the result of whole-genome duplication (WGD), is a major driver of eukaryote evolution. Yet WGDs are hugely disruptive mutations, and we still lack a clear understanding of their fitness consequences. Here, we study whether WGDs result in greater diversity of genomic structural variants (SVs) and how they influence evolutionary dynamics in a plant genus, Cochlearia (Brassicaceae). By using long-read sequencing and a graph-based pangenome, we find both negative and positive interactions between WGDs and SVs. Masking of recessive mutations due to WGDs leads to a progressive accumulation of deleterious SVs across four ploidal levels (from diploids to octoploids), likely reducing the adaptive potential of polyploid populations. However, we also discover putative benefits arising from SV accumulation, as more ploidy-specific SVs harbor signals of local adaptation in polyploids than in diploids. Together, our results suggest that SVs play diverse and contrasting roles in the evolutionary trajectories of young polyploids.
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Affiliation(s)
- Tuomas Hämälä
- School of Life Sciences, University of Nottingham, Nottingham, UK.
- Production Systems, Natural Resources Institute Finland, Jokioinen, Finland.
| | | | - Laura Cowan
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Matthew Carlile
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | | | | | - Siri Birkeland
- Natural History Museum, University of Oslo, Oslo, Norway
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Matthew Loose
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czech Republic
| | - Marcus A Koch
- Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
| | - Levi Yant
- School of Life Sciences, University of Nottingham, Nottingham, UK.
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.
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5
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Martin RA, Tate AT. Pleiotropy alleviates the fitness costs associated with resource allocation trade-offs in immune signalling networks. Proc Biol Sci 2024; 291:20240446. [PMID: 38835275 DOI: 10.1098/rspb.2024.0446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 05/03/2024] [Indexed: 06/06/2024] Open
Abstract
Many genes and signalling pathways within plant and animal taxa drive the expression of multiple organismal traits. This form of genetic pleiotropy instigates trade-offs among life-history traits if a mutation in the pleiotropic gene improves the fitness contribution of one trait at the expense of another. Whether or not pleiotropy gives rise to conflict among traits, however, likely depends on the resource costs and timing of trait deployment during organismal development. To investigate factors that could influence the evolutionary maintenance of pleiotropy in gene networks, we developed an agent-based model of co-evolution between parasites and hosts. Hosts comprise signalling networks that must faithfully complete a developmental programme while also defending against parasites, and trait signalling networks could be independent or share a pleiotropic component as they evolved to improve host fitness. We found that hosts with independent developmental and immune networks were significantly more fit than hosts with pleiotropic networks when traits were deployed asynchronously during development. When host genotypes directly competed against each other, however, pleiotropic hosts were victorious regardless of trait synchrony because the pleiotropic networks were more robust to parasite manipulation, potentially explaining the abundance of pleiotropy in immune systems despite its contribution to life history trade-offs.
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Affiliation(s)
- Reese A Martin
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Ann T Tate
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
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6
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Venkataraman P, Nagendra P, Ahlawat N, Brajesh RG, Saini S. Convergent genetic adaptation of Escherichia coli in minimal media leads to pleiotropic divergence. Front Mol Biosci 2024; 11:1286824. [PMID: 38660375 PMCID: PMC11039892 DOI: 10.3389/fmolb.2024.1286824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 02/15/2024] [Indexed: 04/26/2024] Open
Abstract
Adaptation in an environment can either be beneficial, neutral or disadvantageous in another. To test the genetic basis of pleiotropic behaviour, we evolved six lines of E. coli independently in environments where glucose and galactose were the sole carbon sources, for 300 generations. All six lines in each environment exhibit convergent adaptation in the environment in which they were evolved. However, pleiotropic behaviour was observed in several environmental contexts, including other carbon environments. Genome sequencing reveals that mutations in global regulators rpoB and rpoC cause this pleiotropy. We report three new alleles of the rpoB gene, and one new allele of the rpoC gene. The novel rpoB alleles confer resistance to Rifampicin, and alter motility. Our results show how single nucleotide changes in the process of adaptation in minimal media can lead to wide-scale pleiotropy, resulting in changes in traits that are not under direct selection.
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Affiliation(s)
| | | | | | | | - Supreet Saini
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
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7
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Piatkowski B, Weston DJ, Aguero B, Duffy A, Imwattana K, Healey AL, Schmutz J, Shaw AJ. Divergent selection and climate adaptation fuel genomic differentiation between sister species of Sphagnum (peat moss). ANNALS OF BOTANY 2023; 132:499-512. [PMID: 37478307 PMCID: PMC10666999 DOI: 10.1093/aob/mcad104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/24/2023] [Indexed: 07/23/2023]
Abstract
BACKGROUND AND AIMS New plant species can evolve through the reinforcement of reproductive isolation via local adaptation along habitat gradients. Peat mosses (Sphagnaceae) are an emerging model system for the study of evolutionary genomics and have well-documented niche differentiation among species. Recent molecular studies have demonstrated that the globally distributed species Sphagnum magellanicum is a complex of morphologically cryptic lineages that are phylogenetically and ecologically distinct. Here, we describe the architecture of genomic differentiation between two sister species in this complex known from eastern North America: the northern S. diabolicum and the largely southern S. magniae. METHODS We sampled plant populations from across a latitudinal gradient in eastern North America and performed whole genome and restriction-site associated DNA sequencing. These sequencing data were then analyzed computationally. KEY RESULTS Using sliding-window population genetic analyses we find that differentiation is concentrated within 'islands' of the genome spanning up to 400 kb that are characterized by elevated genetic divergence, suppressed recombination, reduced nucleotide diversity and increased rates of non-synonymous substitution. Sequence variants that are significantly associated with genetic structure and bioclimatic variables occur within genes that have functional enrichment for biological processes including abiotic stress response, photoperiodism and hormone-mediated signalling. Demographic modelling demonstrates that these two species diverged no more than 225 000 generations ago with secondary contact occurring where their ranges overlap. CONCLUSIONS We suggest that this heterogeneity of genomic differentiation is a result of linked selection and reflects the role of local adaptation to contrasting climatic zones in driving speciation. This research provides insight into the process of speciation in a group of ecologically important plants and strengthens our predictive understanding of how plant populations will respond as Earth's climate rapidly changes.
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Affiliation(s)
- Bryan Piatkowski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Blanka Aguero
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Aaron Duffy
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Karn Imwattana
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Adam L Healey
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - A Jonathan Shaw
- Department of Biology, Duke University, Durham, NC 27708, USA
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8
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Feng S, DeGrey SP, Guédot C, Schoville SD, Pool JE. Genomic Diversity Illuminates the Environmental Adaptation of Drosophila suzukii. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.03.547576. [PMID: 37461625 PMCID: PMC10349955 DOI: 10.1101/2023.07.03.547576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Biological invasions carry substantial practical and scientific importance, and represent natural evolutionary experiments on contemporary timescales. Here, we investigated genomic diversity and environmental adaptation of the crop pest Drosophila suzukii using whole-genome sequencing data and environmental metadata for 29 population samples from its native and invasive range. Through a multifaceted analysis of this population genomic data, we increase our understanding of the D. suzukii genome, its diversity and its evolution, and we identify an appropriate genotype-environment association pipeline for our data set. Using this approach, we detect genetic signals of local adaptation associated with nine distinct environmental factors related to altitude, wind speed, precipitation, temperature, and human land use. We uncover unique functional signatures for each environmental variable, such as a prevalence of cuticular genes associated with annual precipitation. We also infer biological commonalities in the adaptation to diverse selective pressures, particularly in terms of the apparent contribution of nervous system evolution to enriched processes (ranging from neuron development to circadian behavior) and to top genes associated with all nine environmental variables. Our findings therefore depict a finer-scale adaptive landscape underlying the rapid invasion success of this agronomically important species.
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Affiliation(s)
- Siyuan Feng
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Samuel P. DeGrey
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
| | - Christelle Guédot
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
| | - Sean D. Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
| | - John E. Pool
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
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9
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Martin R, Tate AT. Pleiotropy alleviates the fitness costs associated with resource allocation trade-offs in immune signaling networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.06.561276. [PMID: 37873469 PMCID: PMC10592669 DOI: 10.1101/2023.10.06.561276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Many genes and signaling pathways within plant and animal taxa drive the expression of multiple organismal traits. This form of genetic pleiotropy instigates trade-offs among life-history traits if a mutation in the pleiotropic gene improves the fitness contribution of one trait at the expense of another. Whether or not pleiotropy gives rise to conflict among traits, however, likely depends on the resource costs and timing of trait deployment during organismal development. To investigate factors that could influence the evolutionary maintenance of pleiotropy in gene networks, we developed an agent-based model of co-evolution between parasites and hosts. Hosts comprise signaling networks that must faithfully complete a developmental program while also defending against parasites, and trait signaling networks could be independent or share a pleiotropic component as they evolved to improve host fitness. We found that hosts with independent developmental and immune networks were significantly more fit than hosts with pleiotropic networks when traits were deployed asynchronously during development. When host genotypes directly competed against each other, however, pleiotropic hosts were victorious regardless of trait synchrony because the pleiotropic networks were more robust to parasite manipulation, potentially explaining the abundance of pleiotropy in immune systems despite its contribution to life history trade-offs.
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Affiliation(s)
- Reese Martin
- Department of Biological Sciences, Vanderbilt University, Nashville TN, 37235
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
| | - Ann T Tate
- Department of Biological Sciences, Vanderbilt University, Nashville TN, 37235
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
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10
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Petak C, Frati L, Brennan RS, Pespeni MH. Whole-Genome Sequencing Reveals That Regulatory and Low Pleiotropy Variants Underlie Local Adaptation to Environmental Variability in Purple Sea Urchins. Am Nat 2023; 202:571-586. [PMID: 37792925 DOI: 10.1086/726013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
AbstractOrganisms experience environments that vary across both space and time. Such environmental heterogeneity shapes standing genetic variation and may influence species' capacity to adapt to rapid environmental change. However, we know little about the kind of genetic variation that is involved in local adaptation to environmental variability. To address this gap, we sequenced the whole genomes of 140 purple sea urchins (Strongylocentrotus purpuratus) from seven populations that vary in their degree of pH variability. Despite no evidence of global population structure, we found a suite of single-nucleotide polymorphisms (SNPs) tightly correlated with local pH variability (outlier SNPs), which were overrepresented in regions putatively involved in gene regulation (long noncoding RNA and enhancers), supporting the idea that variation in regulatory regions is important for local adaptation to variability. In addition, outliers in genes were found to be (i) enriched for biomineralization and ion homeostasis functions related to low pH response, (ii) less central to the protein-protein interaction network, and (iii) underrepresented among genes highly expressed during early development. Taken together, these results suggest that loci that underlie local adaptation to pH variability in purple sea urchins fall in regions with potentially low pleiotropic effects (based on analyses involving regulatory regions, network centrality, and expression time) involved in low pH response (based on functional enrichment).
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11
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Miao L, Jiang L, Tang B, Sham PC, Li M. Dissecting the high-resolution genetic architecture of complex phenotypes by accurately estimating gene-based conditional heritability. Am J Hum Genet 2023; 110:1534-1548. [PMID: 37633278 PMCID: PMC10502872 DOI: 10.1016/j.ajhg.2023.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 08/10/2023] [Accepted: 08/10/2023] [Indexed: 08/28/2023] Open
Abstract
Despite extensive research on global heritability estimation for complex traits, few methods accurately dissect local heritability. A precise local heritability estimate is crucial for high-resolution mapping in genetics. Here, we report the effective heritability estimator (EHE) that can use p values from genome-wide association studies (GWASs) for local heritability estimation by directly converting marginal heritability estimates of SNPs to a non-redundant heritability estimate of a gene or a small genomic region. EHE provides higher accuracy and precision for local heritability estimation among seven compared methods. Importantly, EHE can be applied to estimate the conditional heritability of nearby genes, where redundant heritability among the genes can also be removed further. The conditional estimation can be guided by tissue-specific expression profiles (or other functional scores) to prioritize and quantify more functionally important genes of complex phenotypes. Applying EHE to 42 complex phenotypes from the UK Biobank, we revealed the existence of two types of distinct genetic architectures for various complex phenotypes and found that highly pleiotropic genes are not enriched for more heritability compared to other candidate susceptibility genes. EHE provides an accurate and robust way to dissect the genetic architecture of complex phenotypes.
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Affiliation(s)
- Lin Miao
- Research Center of Medical Sciences, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Lin Jiang
- Research Center of Medical Sciences, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Bin Tang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Pak Chung Sham
- State Key Laboratory of Brain and Cognitive Sciences, the University of Hong Kong, Hong Kong SAR 999077, China; Department of Psychiatry, the University of Hong Kong, Hong Kong SAR 999077, China
| | - Miaoxin Li
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China; Department of Psychiatry, the University of Hong Kong, Hong Kong SAR 999077, China; Center for Precision Medicine, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China.
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12
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Ruelens P, Wynands T, de Visser JAGM. Interaction between mutation type and gene pleiotropy drives parallel evolution in the laboratory. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220051. [PMID: 37004729 PMCID: PMC10067263 DOI: 10.1098/rstb.2022.0051] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 12/30/2022] [Indexed: 04/04/2023] Open
Abstract
What causes evolution to be repeatable is a fundamental question in evolutionary biology. Pleiotropy, i.e. the effect of an allele on multiple traits, is thought to enhance repeatability by constraining the number of available beneficial mutations. Additionally, pleiotropy may promote repeatability by allowing large fitness benefits of single mutations via adaptive combinations of phenotypic effects. Yet, this latter evolutionary potential may be reaped solely by specific types of mutations able to realize optimal combinations of phenotypic effects while avoiding the costs of pleiotropy. Here, we address the interaction of gene pleiotropy and mutation type on evolutionary repeatability in a meta-analysis of experimental evolution studies with Escherichia coli. We hypothesize that single nucleotide polymorphisms (SNPs) are principally able to yield large fitness benefits by targeting highly pleiotropic genes, whereas indels and structural variants (SVs) provide smaller benefits and are restricted to genes with lower pleiotropy. By using gene connectivity as proxy for pleiotropy, we show that non-disruptive SNPs in highly pleiotropic genes yield the largest fitness benefits, since they contribute more to parallel evolution, especially in large populations, than inactivating SNPs, indels and SVs. Our findings underscore the importance of considering genetic architecture together with mutation type for understanding evolutionary repeatability. This article is part of the theme issue 'Interdisciplinary approaches to predicting evolutionary biology'.
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Affiliation(s)
- Philip Ruelens
- Laboratory of Genetics, Wageningen University and Research, Wageningen 6708PB, The Netherlands
- Laboratory of Socioecology and Social Evolution, KU Leuven, Leuven 3000, Belgium
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven 3000, Belgium
| | - Thomas Wynands
- Laboratory of Genetics, Wageningen University and Research, Wageningen 6708PB, The Netherlands
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13
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Li B, Gschwend AR, Hovick SM, Gutek A, McHale L, Harrison SK, Regnier EE. Evolution of weedy giant ragweed ( Ambrosia trifida): Multiple origins and gene expression variability facilitates weediness. Ecol Evol 2022; 12:e9590. [PMID: 36514541 PMCID: PMC9731915 DOI: 10.1002/ece3.9590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 11/16/2022] [Indexed: 12/13/2022] Open
Abstract
Agricultural weeds may originate from wild populations, but the origination patterns and genetics underlying this transition remain largely unknown. Analysis of weedy-wild paired populations from independent locations may provide evidence to identify key genetic variation contributing to this adaptive shift. We performed genetic variation and expression analyses on transcriptome data from 67 giant ragweed samples collected from different locations in Ohio, Iowa, and Minnesota and found geographically separated weedy populations likely originated independently from their adjacent wild populations, but subsequent spreading of weedy populations also occurred locally. By using eight closely related weedy-wild paired populations, we identified thousands of unique transcripts in weedy populations that reflect shared or specific functions corresponding, respectively, to both convergently evolved and population-specific weediness processes. In addition, differential expression of specific groups of genes was detected between weedy and wild giant ragweed populations using gene expression diversity and gene co-expression network analyses. Our study suggests an integrated route of weedy giant ragweed origination, consisting of independent origination combined with the subsequent spreading of certain weedy populations, and provides several lines of evidence to support the hypothesis that gene expression variability plays a key role in the evolution of weedy species.
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Affiliation(s)
- Bo Li
- Department of Horticulture and Crop SciencesThe Ohio State UniversityColumbusOhioUSA
| | - Andrea R. Gschwend
- Department of Horticulture and Crop SciencesThe Ohio State UniversityColumbusOhioUSA
| | - Stephen M. Hovick
- Department of Evolution, Ecology and Organismal BiologyThe Ohio State UniversityColumbusOhioUSA
| | - Amanda Gutek
- Department of Horticulture and Crop SciencesThe Ohio State UniversityColumbusOhioUSA
| | - Leah McHale
- Department of Horticulture and Crop SciencesThe Ohio State UniversityColumbusOhioUSA
| | - S. Kent Harrison
- Department of Horticulture and Crop SciencesThe Ohio State UniversityColumbusOhioUSA
| | - Emilie E. Regnier
- Department of Horticulture and Crop SciencesThe Ohio State UniversityColumbusOhioUSA
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14
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Gorton AJ, Benning JW, Tiffin P, Moeller DA. The spatial scale of adaptation in a native annual plant and its implications for responses to climate change. Evolution 2022; 76:2916-2929. [PMID: 35880454 DOI: 10.1111/evo.14583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 07/04/2022] [Accepted: 07/08/2022] [Indexed: 01/22/2023]
Abstract
Spatial patterns of adaptation provide important insights into agents of selection and expected responses of populations to climate change. Robust inference into the spatial scale of adaptation can be gained through reciprocal transplant experiments that combine multiple source populations and common gardens. Here, we examine the spatial scale of local adaptation of the North American annual plant common ragweed, Ambrosia artemisiifolia, using data from four common gardens with 22 source populations sampled from across a ∼1200 km latitudinal gradient within the native range. We found evidence of local adaptation at the northernmost common garden, but maladaptation at the two southern gardens, where more southern source populations outperformed local populations. Overall, the spatial scale of adaptation was large-at the three gardens where distance between source populations and gardens explained variation in fitness, it took an average of 820 km for fitness to decline to 50% of its predicted maximum. Taken together, these results suggest that climate change has already caused maladaptation, especially across the southern portion of the range, and may result in northward range contraction over time.
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Affiliation(s)
- Amanda J Gorton
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, 55108
| | - John W Benning
- Department of Botany, University of Wyoming, Laramie, Wyoming, 82071
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, 55108
| | - David A Moeller
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, 55108
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15
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Hämälä T, Ning W, Kuittinen H, Aryamanesh N, Savolainen O. Environmental response in gene expression and DNA methylation reveals factors influencing the adaptive potential of Arabidopsis lyrata. eLife 2022; 11:e83115. [PMID: 36306157 PMCID: PMC9616567 DOI: 10.7554/elife.83115] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/12/2022] [Indexed: 11/13/2022] Open
Abstract
Understanding what factors influence plastic and genetic variation is valuable for predicting how organisms respond to changes in the selective environment. Here, using gene expression and DNA methylation as molecular phenotypes, we study environmentally induced variation among Arabidopsis lyrata plants grown at lowland and alpine field sites. Our results show that gene expression is highly plastic, as many more genes are differentially expressed between the field sites than between populations. These environmentally responsive genes evolve under strong selective constraint - the strength of purifying selection on the coding sequence is high, while the rate of adaptive evolution is low. We find, however, that positive selection on cis-regulatory variants has likely contributed to the maintenance of genetically variable environmental responses, but such variants segregate only between distantly related populations. In contrast to gene expression, DNA methylation at genic regions is largely insensitive to the environment, and plastic methylation changes are not associated with differential gene expression. Besides genes, we detect environmental effects at transposable elements (TEs): TEs at the high-altitude field site have higher expression and methylation levels, suggestive of a broad-scale TE activation. Compared to the lowland population, plants native to the alpine environment harbor an excess of recent TE insertions, and we observe that specific TE families are enriched within environmentally responsive genes. Our findings provide insight into selective forces shaping plastic and genetic variation. We also highlight how plastic responses at TEs can rapidly create novel heritable variation in stressful conditions.
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Affiliation(s)
- Tuomas Hämälä
- Department of Ecology and Genetics, University of OuluOuluFinland
| | - Weixuan Ning
- Department of Ecology and Genetics, University of OuluOuluFinland
| | - Helmi Kuittinen
- Department of Ecology and Genetics, University of OuluOuluFinland
| | - Nader Aryamanesh
- Department of Ecology and Genetics, University of OuluOuluFinland
| | - Outi Savolainen
- Department of Ecology and Genetics, University of OuluOuluFinland
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16
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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] [Abstract] [Key Words] [Grants] [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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17
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Abstract
The rediscovery of Mendel’s work showing that the heredity of phenotypes is controlled by discrete genes was followed by the reconciliation of Mendelian genetics with evolution by natural selection in the middle of the last century with the Modern Synthesis. In the past two decades, dramatic advances in genomic methods have facilitated the identification of the loci, genes, and even individual mutations that underlie phenotypic variants that are the putative targets of natural selection. Moreover, these methods have also changed how we can study adaptation by flipping the problem around, allowing us to first examine what loci show evidence of having been under selection, and then connecting these genetic variants to phenotypic variation. As a result, we now have an expanding list of actual genetic changes that underlie potentially adaptive phenotypic variation. Here, we synthesize how considering the effects of these adaptive loci in the context of cellular environments, genomes, organisms, and populations has provided new insights to the genetic architecture of adaptation.
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18
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Rennison DJ, Peichel CL. Pleiotropy facilitates parallel adaptation in sticklebacks. Mol Ecol 2022; 31:1476-1486. [PMID: 34997980 PMCID: PMC9306781 DOI: 10.1111/mec.16335] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 10/27/2021] [Accepted: 12/20/2021] [Indexed: 11/27/2022]
Abstract
Highly pleiotropic genes are predicted to be used less often during adaptation, as mutations in these loci are more likely to have negative fitness consequences. Following this logic, we tested whether pleiotropy impacts the probability that a locus will be used repeatedly in adaptation. We used two proxies to estimate pleiotropy: number of phenotypic traits affected by a given genomic region and gene connectivity. We first surveyed 16 independent stream‐lake and three independent benthic‐limnetic ecotype pairs of threespine stickleback to estimate genome‐wide patterns in parallel genomic differentiation. Our analysis revealed parallel divergence across the genome; 30%–37% of outlier regions were shared between at least two independent pairs in either the stream‐lake or benthic‐limnetic comparisons. We then tested whether parallel genomic regions are less pleiotropic than nonparallel regions. Counter to our a priori prediction, parallel genomic regions contained genes with significantly more pleiotropy; that is, influencing a greater number of traits and more highly connected. The increased pleiotropy of parallel regions could not be explained by other genomic factors, as there was no significant difference in mean gene count, mutation or recombination rates between parallel and nonparallel regions. Interestingly, although nonparallel regions contained genes that were less connected and influenced fewer mapped traits on average than parallel regions, they also tended to contain the genes that were predicted to be the most pleiotropic. Taken together, our findings are consistent with the idea that pleiotropy only becomes constraining at high levels and that low or intermediate levels of pleiotropy may be beneficial for adaptation.
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Affiliation(s)
- Diana J Rennison
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012, Bern, Switzerland
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012, Bern, Switzerland
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19
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Wright SJ, Goad DM, Gross BL, Muñoz PR, Olsen KM. Genetic trade-offs underlie divergent life history strategies for local adaptation in white clover. Mol Ecol 2021; 31:3742-3760. [PMID: 34532899 DOI: 10.1111/mec.16180] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/25/2021] [Accepted: 09/02/2021] [Indexed: 01/26/2023]
Abstract
Local adaptation is common in plants, yet characterization of its underlying genetic basis is rare in herbaceous perennials. Moreover, while many plant species exhibit intraspecific chemical defence polymorphisms, their importance for local adaptation remains poorly understood. We examined the genetic architecture of local adaptation in a perennial, obligately-outcrossing herbaceous legume, white clover (Trifolium repens). This widespread species displays a well-studied chemical defence polymorphism for cyanogenesis (HCN release following tissue damage) and has evolved climate-associated cyanogenesis clines throughout its range. Two biparental F2 mapping populations, derived from three parents collected in environments spanning the U.S. latitudinal species range (Duluth, MN, St. Louis, MO and Gainesville, FL), were grown in triplicate for two years in reciprocal common garden experiments in the parental environments (6,012 total plants). Vegetative growth and reproductive fitness traits displayed trade-offs across reciprocal environments, indicating local adaptation. Genetic mapping of fitness traits revealed a genetic architecture characterized by allelic trade-offs between environments, with 100% and 80% of fitness QTL in the two mapping populations showing significant QTL×E interactions, consistent with antagonistic pleiotropy. Across the genome there were three hotspots of QTL colocalization. Unexpectedly, we found little evidence that the cyanogenesis polymorphism contributes to local adaptation. Instead, divergent life history strategies in reciprocal environments were major fitness determinants: selection favoured early investment in flowering at the cost of multiyear survival in the southernmost site versus delayed flowering and multiyear persistence in the northern environments. Our findings demonstrate that multilocus genetic trade-offs contribute to contrasting life history characteristics that allow for local adaptation in this outcrossing herbaceous perennial.
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Affiliation(s)
- Sara J Wright
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | - David M Goad
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | - Briana L Gross
- Biology Department, University of Minnesota-Duluth, Duluth, Minnesota, USA
| | - Patricio R Muñoz
- Horticultural Science Department, University of Florida, Gainesville, Florida, USA
| | - Kenneth M Olsen
- Department of Biology, Washington University, St. Louis, Missouri, USA
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20
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Correlational selection in the age of genomics. Nat Ecol Evol 2021; 5:562-573. [PMID: 33859374 DOI: 10.1038/s41559-021-01413-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 02/11/2021] [Indexed: 02/01/2023]
Abstract
Ecologists and evolutionary biologists are well aware that natural and sexual selection do not operate on traits in isolation, but instead act on combinations of traits. This long-recognized and pervasive phenomenon is known as multivariate selection, or-in the particular case where it favours correlations between interacting traits-correlational selection. Despite broad acknowledgement of correlational selection, the relevant theory has often been overlooked in genomic research. Here, we discuss theory and empirical findings from ecological, quantitative genetic and genomic research, linking key insights from different fields. Correlational selection can operate on both discrete trait combinations and quantitative characters, with profound implications for genomic architecture, linkage, pleiotropy, evolvability, modularity, phenotypic integration and phenotypic plasticity. We synthesize current knowledge and discuss promising research approaches that will enable us to understand how correlational selection shapes genomic architecture, thereby linking quantitative genetic approaches with emerging genomic methods. We suggest that research on correlational selection has great potential to integrate multiple fields in evolutionary biology, including developmental and functional biology, ecology, quantitative genetics, phenotypic polymorphisms, hybrid zones and speciation processes.
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21
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Lu M, Feau N, Vidakovic DO, Ukrainetz N, Wong B, Aitken SN, Hamelin RC, Yeaman S. Comparative Gene Expression Analysis Reveals Mechanism of Pinus contorta Response to the Fungal Pathogen Dothistroma septosporum. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:397-409. [PMID: 33258711 DOI: 10.1094/mpmi-10-20-0282-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Many conifers have distributions that span wide ranges in both biotic and abiotic conditions, but the basis of response to biotic stress has received much less attention than response to abiotic stress. In this study, we investigated the gene expression response of lodgepole pine (Pinus contorta) to attack by the fungal pathogen Dothistroma septosporum, which causes Dothistroma needle blight, a disease that has caused severe climate-related outbreaks in northwestern British Columbia. We inoculated tolerant and susceptible pines with two D. septosporum isolates and analyzed the differentially expressed genes (DEGs), differential exon usage, and coexpressed gene modules using RNA-sequencing data. We found a rapid and strong transcriptomic response in tolerant lodgepole pine samples inoculated with one D. septosporum isolate, and a late and weak response in susceptible samples inoculated with another isolate. We mapped 43 of the DEG- or gene module-identified genes to the reference plant-pathogen interaction pathway deposited in the Kyoto Encyclopedia of Genes and Genomes database. These genes are present in PAMP-triggered and effector-triggered immunity pathways. Genes comprising pathways and gene modules had signatures of strong selective constraint, while the highly expressed genes in tolerant samples appear to have been favored by selection to counterattack the pathogen. We identified candidate resistance genes that may respond to D. septosporum effectors. Taken together, our results show that gene expression response to D. septosporum infection in lodgepole pine varies both among tree genotypes and pathogen strains and involves both known candidate genes and a number of genes with previously unknown functions.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Mengmeng Lu
- Department of Biological Sciences, University of Calgary, 507 Campus Drive NW, Calgary, Canada
| | - Nicolas Feau
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, Canada
| | - Dragana Obreht Vidakovic
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, Canada
| | - Nicholas Ukrainetz
- Forest Improvement and Research Management Branch, Ministry of Forests, Lands and Natural Resource Operations & Rural Development, 18793-32nd Ave., Surrey, Canada
| | - Barbara Wong
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Pavillon Charles-Eugène-Marchand 1030, avenue de la Médecine, Québec, Canada
| | - Sally N Aitken
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, Canada
| | - Richard C Hamelin
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Pavillon Charles-Eugène-Marchand 1030, avenue de la Médecine, Québec, Canada
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, 507 Campus Drive NW, Calgary, Canada
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22
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Kostanecki A, Gorton AJ, Moeller DA. An urban–rural spotlight: evolution at small spatial scales among urban and rural populations of common ragweed. JOURNAL OF URBAN ECOLOGY 2021. [DOI: 10.1093/jue/juab004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Abstract
Urbanization produces similar environmental changes across cities relative to their neighboring rural environments. However, there may be high environmental heterogeneity across an urban–rural gradient. Previous research in Minneapolis, MN, USA, found mixed evidence that urban and rural plant populations of common ragweed have locally adapted and that urban populations exhibit greater among-population divergence in ecologically-important traits. To investigate whether there are parallel patterns of urban–rural trait divergence across different urban areas, we examined trait variation across an urban–rural gradient in a second city, St. Louis, MO, USA. We used growth chamber and greenhouse common environments to investigate variation in six traits within and among 16 populations of common ragweed (eight from each urban and rural area). Urban and rural plants diverged significantly in three of five traits, with rural plants having lower percent germination, greater height and lower leaf dissection index. We also found greater variance in plant height among urban compared to rural populations, potentially driven by heterogeneity in human management practices on urban populations. Patterns of urban-rural trait divergence (e.g. in flowering time) differ substantially from those found previously in the reciprocal transplant experiment in Minneapolis, contradicting the hypothesis of parallel evolution across different metropolitan areas. The results of this study suggest that there is considerable population variation in ecologically-important traits, but that urban populations do not consistently differ from neighboring rural populations.
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Affiliation(s)
- Adam Kostanecki
- Department of Plant and Microbial Biology, University of Minnesota, 1479 Gortner Avenue, St. Paul, MN 55108, USA
| | - Amanda J Gorton
- Department of Ecology, Evolution and Behavior, University of Minnesota, 1479 Gortner Avenue, St. Paul, MN 55108, USA
| | - David A Moeller
- Department of Plant and Microbial Biology, University of Minnesota, 1479 Gortner Avenue, St. Paul, MN 55108, USA
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23
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Yuan M, Stinchcombe JR. Population genomics of parallel adaptation. Mol Ecol 2020; 29:4033-4036. [PMID: 32997363 DOI: 10.1111/mec.15659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 09/22/2020] [Indexed: 11/29/2022]
Abstract
Parallel evolution is one of the striking patterns in nature. The presence of repeated evolution of the same phenotypes, suites of traits, and adaptations suggests a strong role for natural selection in shaping biological diversity. The reasoning is straightforward: each instance of repeated evolution makes it less likely that these features evolved neutrally or due to stochastic forces in each population or species. With the growing sequencing capability, we are now poised to examine the genetic basis of parallel evolution in model and nonmodel systems. On pages 4102-4117 of this issue of Molecular Ecology, van Boheemen and Hodgins (2020) provide an exemplar study of this kind, using common ragweed (Ambrosia artemisiifolia; Figure 1a). Their study is noteworthy and ambitious in many respects, and we think will serve as a model for studying parallel adaptation, even in nonmodel species.
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Affiliation(s)
- Meng Yuan
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - John R Stinchcombe
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
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