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Du L, Oduor AMO, Zuo W, Liu H, Li J. Directional and stabilizing selection shaped morphological, reproductive, and physiological traits of the invader Solidago canadensis. Ecol Evol 2023; 13:e10410. [PMID: 37636867 PMCID: PMC10450839 DOI: 10.1002/ece3.10410] [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: 01/05/2023] [Revised: 07/01/2023] [Accepted: 07/25/2023] [Indexed: 08/29/2023] Open
Abstract
Trait evolution in invasive plant species is important because it can impact demographic parameters key to invasion success. Invasive plant species often show phenotypic clines along geographic and climatic gradients. However, the relative contributions of natural selection and neutral evolutionary processes to phenotypic trait variation among populations of invasive plants remain unclear. A common method to assess whether a trait has been shaped by natural selection or neutral evolutionary processes is to compare the geographical pattern for the trait of interest to the divergence in neutral genetic loci (i.e., Q ST -F ST comparisons). Subsequently, a redundancy analysis (RDA) can facilitate identification of putative agents of natural selection on the trait. Here, we employed both a Q ST -F ST comparisons approach and RDA to infer whether natural selection shaped traits of invasive populations of Solidago canadensis in China and identify the potential environmental drivers of natural selection. We addressed two questions: (1) Did natural selection drive phenotypic trait variation among S. canadensis populations? (2) Did climatic, latitudinal, longitudinal, and altitudinal gradients drive patterns of genetic variation among S. canadensis populations? We found significant directional selection for several morphological and reproductive traits (i.e., Q ST > F ST) and stabilizing selection for physiological traits (i.e., Q ST < F ST). The RDA showed that stem biomass of S. canadensis was strongly positively correlated with longitude, while leaf width ratio and specific leaf area were significantly positively correlated with the mean diurnal range. Stem biomass had a strong negative correlation with annual precipitation. Moreover, height of S. canadensis individuals was strongly positively correlated with altitude and precipitation of the wettest quarter. A longitudinal shift in precipitation seasonality likely selected for larger stem biomass in S. canadensis. Overall, these results suggest that longitudinal and altitudinal clines in climate exerted strong selection pressures that shaped the phenotypic traits of S. canadensis.
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Affiliation(s)
- Leshan Du
- State Key Laboratory of Environmental Criteria and Risk AssessmentChinese Research Academy of Environmental SciencesBeijingChina
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and ConservationTaizhou UniversityTaizhouChina
| | - Ayub M. O. Oduor
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and ConservationTaizhou UniversityTaizhouChina
- Department of Applied BiologyTechnical University of KenyaNairobiKenya
| | - Wei Zuo
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and ConservationTaizhou UniversityTaizhouChina
- Sanofi (Hangzhou) Pharmaceuticals Co. Ltd.HangzhouChina
| | - Haiyan Liu
- State Key Laboratory of Environmental Criteria and Risk AssessmentChinese Research Academy of Environmental SciencesBeijingChina
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and ConservationTaizhou UniversityTaizhouChina
| | - Jun‐Min Li
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and ConservationTaizhou UniversityTaizhouChina
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2
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Oduor AMO, Adomako MO, Yuan Y, Li JM. Older populations of the invader Solidago canadensis exhibit stronger positive plant-soil feedbacks and competitive ability in China. AMERICAN JOURNAL OF BOTANY 2022; 109:1230-1241. [PMID: 35819013 DOI: 10.1002/ajb2.16034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
PREMISE The enemy release hypothesis predicts that release from natural enemies, including soil-borne pathogens, liberates invasive plants from a negative regulating force. Nevertheless, invasive plants may acquire novel enemies and mutualists in the introduced range, which may cause variable effects on invader growth. However, how soil microorganisms may influence competitive ability of invasive plants along invasion chronosequences has been little explored. METHODS Using the invasive plant Solidago canadensis, we tested whether longer residence times are associated with stronger negative plant-soil feedbacks and thus weaker competitive abilities at the individual level. We grew S. canadensis individuals from 36 populations with different residence times across southeastern China in competition versus no competition and in three different types of soils: (1) conspecific rhizospheric soils; (2) soils from uninvaded patches; and (3) sterilized soil. For our competitor treatments, we constructed synthetic communities of four native species (Bidens parviflora, Solanum nigrum, Kalimeris indica, and Mosla scabra), which naturally co-occur with Solidago canadensis in the field. RESULTS Solidago canadensis populations with longer residence times experienced stronger positive plant-soil feedbacks and had greater competitive responses (i.e., produced greater above-ground biomass and grew taller) in conspecific rhizospheric soils than in sterilized or uninvaded soils. Moreover, S. canadensis from older populations significantly suppressed above-ground biomass of the native communities in rhizospheric and uninvaded soils but not in sterilized soil. CONCLUSIONS The present results suggest that older populations of S. canadensis experience stronger positive plant-soil feedbacks, which may enhance their competitive ability against native plant communities.
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Affiliation(s)
- Ayub M O Oduor
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, 318000, China
- Department of Applied Biology, Technical University of Kenya, P.O. Box, 52428, Nairobi, Kenya
| | - Michael Opoku Adomako
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, 318000, China
| | - Yongge Yuan
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, 318000, China
| | - Jun-Min Li
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, 318000, China
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3
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Innes SG, Santangelo JS, Kooyers NJ, Olsen KM, Johnson MTJ. Evolution in response to climate in the native and introduced ranges of a globally distributed plant. Evolution 2022; 76:1495-1511. [PMID: 35589013 DOI: 10.1111/evo.14514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 03/23/2022] [Accepted: 04/04/2022] [Indexed: 01/22/2023]
Abstract
The extent to which species can adapt to spatiotemporal climatic variation in their native and introduced ranges remains unresolved. To address this, we examined how clines in cyanogenesis (hydrogen cyanide [HCN] production-an antiherbivore defense associated with decreased tolerance to freezing) have shifted in response to climatic variation in space and time over a 60-year period in both the native and introduced ranges of Trifolium repens. HCN production is a polymorphic trait controlled by variation at two Mendelian loci (Ac and Li). Using phenotypic assays, we estimated within-population frequencies of HCN production and dominant alleles at both loci (i.e., Ac and Li) from 10,575 plants sampled from 131 populations on five continents, and then compared these frequencies to those from historical data collected in the 1950s. There were no clear relationships between changes in the frequency of HCN production, Ac, or Li and changes in temperature between contemporary and historical samples. We did detect evidence of continued evolution to temperature gradients in the introduced range, whereby the slope of contemporary clines for HCN and Ac in relation to winter temperature became steeper than historical clines and more similar to native clines. These results suggest that cyanogenesis clines show no clear changes through time in response to global warming, but introduced populations continue to adapt to their contemporary environments.
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Affiliation(s)
- Simon G Innes
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada.,Department of Biology, University of Louisiana, Lafayette, Louisiana, 70504
| | - James S Santangelo
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
| | - Nicholas J Kooyers
- Department of Biology, University of Louisiana, Lafayette, Louisiana, 70504
| | - Kenneth M Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130
| | - Marc T J Johnson
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
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4
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Liu W, Chen X, Wang J, Zhang Y. Does the effect of flowering time on biomass allocation across latitudes differ between invasive and native salt marsh grass
Spartina alterniflora
? Ecol Evol 2022; 12:e8681. [PMID: 35309742 PMCID: PMC8901870 DOI: 10.1002/ece3.8681] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 01/26/2022] [Accepted: 02/07/2022] [Indexed: 12/29/2022] Open
Abstract
Parallel latitudinal clines in flowering time have been documented in both the invasive and native ranges of plants. Furthermore, flowering time has been found to affect biomass at maturity. Therefore, understanding how these flowering times affect biomass accumulation across latitudes is essential to understanding plant adaptations and distributions. We investigated and compared trends in first flowering day (FFD), aboveground biomass (AGB), belowground biomass (BGB), and BGB:AGB ratio of the salt marsh grass Spartina alterniflora along latitudinal gradients from the invasive (China, 19–40°N) and native range (United States, 27–43°N) in a greenhouse common garden experiment, and tested whether FFD would drive these divergences between invasive and native ranges. The invasive populations produced more (~20%, ~19%) AGB and BGB than native populations, but there were no significant differences in the FFD and BGB:AGB ratio. We found significant parallel latitudinal clines in FFD in both invasive and native ranges. In addition, the BGB:AGB ratio was negatively correlated with the FFD in both the invasive and native ranges but nonsignificant in invasive populations. In contrast, AGB and BGB increased with latitude in the invasive range, but declined with latitude in the native range. Most interestingly, we found AGB and BGB positively correlated with the FFD in the native range, but no significant relationships in the invasive range. Our results indirectly support the evolution of increased competitive ability hypothesis (EICA) that S. alterniflora has evolved to produce greater AGB and BGB in China, but the flowering and allocation pattern of native populations is maintained in the invasive range. Our results also suggest that invasive S. alterniflora in China is not constrained by the trade‐off of earlier flowering with smaller size, and that flowering time has played an important role in biomass allocation across latitudes.
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Affiliation(s)
- Wenwen Liu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems College of the Environment and Ecology Xiamen University Fujian China
| | - Xincong Chen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems College of the Environment and Ecology Xiamen University Fujian China
| | - Jiayu Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems College of the Environment and Ecology Xiamen University Fujian China
| | - Yihui Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems College of the Environment and Ecology Xiamen University Fujian China
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5
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Kreiner JM, Caballero A, Wright SI, Stinchcombe JR. Selective ancestral sorting and de novo evolution in the agricultural invasion of Amaranthus tuberculatus. Evolution 2021; 76:70-85. [PMID: 34806764 DOI: 10.1111/evo.14404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 10/12/2021] [Accepted: 10/24/2021] [Indexed: 12/16/2022]
Abstract
The relative role of hybridization, de novo evolution, and standing variation in weed adaptation to agricultural environments is largely unknown. In Amaranthus tuberculatus, a widespread North American agricultural weed, adaptation is likely influenced by recent secondary contact and admixture of two previously isolated lineages. We characterized the extent of adaptation and phenotypic differentiation accompanying the spread of A. tuberculatus into agricultural environments and the contribution of ancestral divergence. We generated phenotypic and whole-genome sequence data from a manipulative common garden experiment, using paired samples from natural and agricultural populations. We found strong latitudinal, longitudinal, and sex differentiation in phenotypes, and subtle differences among agricultural and natural environments that were further resolved with ancestry inference. The transition into agricultural environments has favored southwestern var. rudis ancestry that leads to higher biomass and treatment-specific phenotypes: increased biomass and earlier flowering under reduced water availability, and reduced plasticity in fitness-related traits. We also detected de novo adaptation in individuals from agricultural habitats independent of ancestry effects, including marginally higher biomass, later flowering, and treatment-dependent divergence in time to germination. Therefore, the invasion of A. tuberculatus into agricultural environments has drawn on adaptive variation across multiple timescales-through both preadaptation via the preferential sorting of var. rudis ancestry and de novo local adaptation.
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Affiliation(s)
- Julia M Kreiner
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, V6T 1Z4, Canada.,Current Address: Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.,Current Address: Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Amalia Caballero
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, V6T 1Z4, Canada
| | - John R Stinchcombe
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, V6T 1Z4, Canada.,Koffler Scientific Reserve, University of Toronto, King City, ON, L7B 1K5, Canada
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6
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Weng ML, Ågren J, Imbert E, Nottebrock H, Rutter MT, Fenster CB. Fitness effects of mutation in natural populations of Arabidopsis thaliana reveal a complex influence of local adaptation. Evolution 2020; 75:330-348. [PMID: 33340094 DOI: 10.1111/evo.14152] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 08/21/2020] [Accepted: 09/13/2020] [Indexed: 12/22/2022]
Abstract
Little is empirically known about the contribution of mutations to fitness in natural environments. However, Fisher's Geometric Model (FGM) provides a conceptual foundation to consider the influence of the environment on mutational effects. To quantify mutational properties in the field, we established eight sets of MA lines (7-10 generations) derived from eight founders collected from natural populations of Arabidopsis thaliana from French and Swedish sites, representing the range margins of the species in Europe. We reciprocally planted the MA lines and their founders at French and Swedish sites, allowing us to test predictions of FGM under naturally occurring environmental conditions. The performance of the MA lines relative to each other and to their respective founders confirmed some and contradicted other predictions of the FGM: the contribution of mutation to fitness variance increased when the genotype was in an environment where its fitness was low, that is, in the away environment, but mutations were more likely to be beneficial when the genotype was in its home environment. Consequently, environmental context plays a large role in the contribution of mutations to the evolutionary process and local adaptation does not guarantee that a genotype is at or close to its optimum.
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Affiliation(s)
- Mao-Lun Weng
- Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota, USA.,Current address: Department of Biology, Westfield State University, Westfield, Massachusettes, USA
| | - Jon Ågren
- Plant Ecology and Evolution, Department of Ecology and Genetics, EBC, Uppsala University, Uppsala, Sweden
| | - Eric Imbert
- Institut des Sciences de la Évolution, Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, France
| | - Henning Nottebrock
- Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota, USA.,Current address: Plant Ecology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Universitätsstrasse 30, Bayreuth, Germany
| | - Matthew T Rutter
- Department of Biology, College of Charleston, South Carolina, USA
| | - Charles B Fenster
- Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota, USA.,Oak Lake Field Station, South Dakota State University, Brookings, South Dakota, USA
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7
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Homola JJ, Loftin CS, Cammen KM, Helbing CC, Birol I, Schultz TF, Kinnison MT. Replicated Landscape Genomics Identifies Evidence of Local Adaptation to Urbanization in Wood Frogs. J Hered 2020; 110:707-719. [PMID: 31278891 PMCID: PMC6785938 DOI: 10.1093/jhered/esz041] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 06/28/2019] [Indexed: 12/20/2022] Open
Abstract
Native species that persist in urban environments may benefit from local adaptation to novel selection factors. We used double-digest restriction-side associated DNA (RAD) sequencing to evaluate shifts in genome-wide genetic diversity and investigate the presence of parallel evolution associated with urban-specific selection factors in wood frogs (Lithobates sylvaticus). Our replicated paired study design involved 12 individuals from each of 4 rural and urban populations to improve our confidence that detected signals of selection are indeed associated with urbanization. Genetic diversity measures were less for urban populations; however, the effect size was small, suggesting little biological consequence. Using an FST outlier approach, we identified 37 of 8344 genotyped single nucleotide polymorphisms with consistent evidence of directional selection across replicates. A genome-wide association study analysis detected modest support for an association between environment type and 12 of the 37 FST outlier loci. Discriminant analysis of principal components using the 37 FST outlier loci produced correct reassignment for 87.5% of rural samples and 93.8% of urban samples. Eighteen of the 37 FST outlier loci mapped to the American bullfrog (Rana [Lithobates] catesbeiana) genome, although none were in coding regions. This evidence of parallel evolution to urban environments provides a powerful example of the ability of urban landscapes to direct evolutionary processes.
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Affiliation(s)
- Jared J Homola
- School of Biology and Ecology, University of Maine, Orono, ME.,Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI
| | - Cynthia S Loftin
- the US Geological Survey, Maine Cooperative Fish and Wildlife Research Unit, Orono, ME
| | | | - Caren C Helbing
- the Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Inanc Birol
- the Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Thomas F Schultz
- the Division of Marine Science and Conservation, Nicholas School of the Environment, Duke University, Beaufort, NC
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8
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Chong VK, Stinchcombe JR. Evaluating Population Genomic Candidate Genes Underlying Flowering Time in Arabidopsis thaliana Using T-DNA Insertion Lines. J Hered 2020; 110:445-454. [PMID: 31158286 DOI: 10.1093/jhered/esz026] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 04/16/2019] [Indexed: 12/14/2022] Open
Abstract
Population genomic scans have emerged as a powerful tool to detect regions of the genome that are potential targets of selection. Despite the success of genomic scans in identifying novel lists of loci potentially underlying adaptation, few studies proceed to validate the function of these candidate genes. In this study, we used transfer-DNA (T-DNA) insertion lines to evaluate the effects of 27 candidate genes on flowering time in North American accessions of Arabidopsis thaliana. We compared the flowering time of T-DNA insertion lines that knock out the function of a candidate gene obtained from population genomic studies to a wild type under long- and short-day conditions. We also did the same for a collection of randomly chosen genes that had not been identified as candidates. We validated the well-known effect of long-day conditions in accelerating flowering time and found that gene disruption caused by insertional mutagenesis tends to delay flowering. Surprisingly, we found that knockouts in random genes were just as likely to produce significant phenotypic effects as knockouts in candidate genes. T-DNA insertions at a handful of candidate genes that had previously been identified as outlier loci showed significant delays in flowering time under both long and short days, suggesting that they are promising candidates for future investigation.
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Affiliation(s)
- Veronica K Chong
- 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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9
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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] [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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10
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Murren CJ, Alt CHS, Kohler C, Sancho G. Natural variation on whole-plant form in the wild is influenced by multivariate soil nutrient characteristics: natural selection acts on root traits. AMERICAN JOURNAL OF BOTANY 2020; 107:319-328. [PMID: 32002983 DOI: 10.1002/ajb2.1420] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 09/23/2019] [Indexed: 05/22/2023]
Abstract
PREMISE In the complex soil nutrient environments of wild populations of annual plants, in general, low nutrient availability restricts growth and alters root-shoot relationships. However, our knowledge of natural selection on roots in field settings is limited. We sought to determine whether selection acts directly on root traits and to identify which components of the soil environment were potential agents of selection. METHODS We studied wild native populations of Arabidopsis thaliana across 4 years, measuring aboveground and belowground traits and analyzing soil nutrients. Using multivariate methods, we examined patterns of natural selection and identified soil attributes that contributed to whole-plant form. In a common garden experiment at two field sites with contrasting soil texture, we examined patterns of selection on root and shoot traits. RESULTS In wild populations, we uncovered selection for above- and belowground size and architectural traits. We detected variation through time and identified soil components that influenced fruit production. In the garden experiment, we detected a distinct positive selection for total root length at the site with greater water-holding capacity and negative selection for measures of root architecture at the field site with reduced nutrient availability and water holding capacity. CONCLUSIONS Patterns of natural selection on belowground traits varied through time, across field sites and experimental gardens. Simultaneous investigations of above- and belowground traits reveal trait functional relationships on which natural selection can act, highlighting the influence of edaphic features on evolutionary processes in wild annual plant populations.
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Affiliation(s)
- Courtney J Murren
- Department of Biology, College of Charleston, Charleston, SC, 29424, USA
| | - Claudia H S Alt
- Department of Biology, College of Charleston, Charleston, SC, 29424, USA
- Department of Earth Sciences, University of Bristol, Bristol, UK
| | - Clare Kohler
- Department of Biology, College of Charleston, Charleston, SC, 29424, USA
- Environmental Sciences Initiative, CUNY ASRC, New York, NY, 10031, USA
| | - Gorka Sancho
- Department of Biology, College of Charleston, Charleston, SC, 29424, USA
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11
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Rutter MT, Murren CJ, Callahan HS, Bisner AM, Leebens-Mack J, Wolyniak MJ, Strand AE. Distributed phenomics with the unPAK project reveals the effects of mutations. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:199-211. [PMID: 31155775 DOI: 10.1111/tpj.14427] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 05/01/2019] [Accepted: 05/10/2019] [Indexed: 06/09/2023]
Abstract
Determining how genes are associated with traits in plants and other organisms is a major challenge in modern biology. The unPAK project - undergraduates phenotyping Arabidopsis knockouts - has generated phenotype data for thousands of non-lethal insertion mutation lines within a single Arabidopsis thaliana genomic background. The focal phenotypes examined by unPAK are complex macroscopic fitness-related traits, which have ecological, evolutionary and agricultural importance. These phenotypes are placed in the context of the wild-type and also natural accessions (phytometers), and standardized for environmental differences between assays. Data from the unPAK project are used to describe broad patterns in the phenotypic consequences of insertion mutation, and to identify individual mutant lines with distinct phenotypes as candidates for further study. Inclusion of undergraduate researchers is at the core of unPAK activities, and an important broader impact of the project is providing students an opportunity to obtain research experience.
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Affiliation(s)
- Matthew T Rutter
- Department of Biology, College of Charleston, 66 George Street, Charleston, SC, 29424, USA
| | - Courtney J Murren
- Department of Biology, College of Charleston, 66 George Street, Charleston, SC, 29424, USA
| | - Hilary S Callahan
- Department of Biology, Barnard College, 3009 Broadway, New York, NY, 10027, USA
| | - April M Bisner
- Department of Biology, College of Charleston, 66 George Street, Charleston, SC, 29424, USA
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, 120 Carlton St, Athens, GA, 30602, USA
| | | | - Allan E Strand
- Department of Biology, College of Charleston, 66 George Street, Charleston, SC, 29424, USA
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12
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Large-effect flowering time mutations reveal conditionally adaptive paths through fitness landscapes in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2019; 116:17890-17899. [PMID: 31420516 PMCID: PMC6731683 DOI: 10.1073/pnas.1902731116] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Mutations are often assumed to be largely detrimental to fitness, but they may also be beneficial, and mutations with large phenotypic effects can persist in nature. One explanation for these observations is that mutations may be beneficial in specific environments because these conditions shift trait expression toward higher fitness. This hypothesis is rarely tested due to the difficulty of replicating mutants in multiple natural environments and measuring their phenotypes. We did so by planting Arabidopsis thaliana genotypes with large-effect flowering time mutations in field sites across the species’ European climate range. We quantified the adaptive value of mutant traits, finding that certain mutations increased fitness in some environments but not in others. Contrary to previous assumptions that most mutations are deleterious, there is increasing evidence for persistence of large-effect mutations in natural populations. A possible explanation for these observations is that mutant phenotypes and fitness may depend upon the specific environmental conditions to which a mutant is exposed. Here, we tested this hypothesis by growing large-effect flowering time mutants of Arabidopsis thaliana in multiple field sites and seasons to quantify their fitness effects in realistic natural conditions. By constructing environment-specific fitness landscapes based on flowering time and branching architecture, we observed that a subset of mutations increased fitness, but only in specific environments. These mutations increased fitness via different paths: through shifting flowering time, branching, or both. Branching was under stronger selection, but flowering time was more genetically variable, pointing to the importance of indirect selection on mutations through their pleiotropic effects on multiple phenotypes. Finally, mutations in hub genes with greater connectedness in their regulatory networks had greater effects on both phenotypes and fitness. Together, these findings indicate that large-effect mutations may persist in populations because they influence traits that are adaptive only under specific environmental conditions. Understanding their evolutionary dynamics therefore requires measuring their effects in multiple natural environments.
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13
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Samis KE, Stinchcombe JR, Murren CJ. Population climatic history predicts phenotypic responses in novel environments for Arabidopsis thaliana in North America. AMERICAN JOURNAL OF BOTANY 2019; 106:1068-1080. [PMID: 31364776 DOI: 10.1002/ajb2.1334] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 05/28/2019] [Indexed: 05/28/2023]
Abstract
PREMISE Determining how species perform in novel climatic environments is essential for understanding (1) responses to climate change and (2) evolutionary consequences of biological invasions. For the vast majority of species, the number of population characteristics that will predict performance and patterns of natural selection in novel locations in the wild remains limited. METHODS We evaluated phenological, vegetative, architectural, and fitness-related traits in experimental gardens in contrasting climates (Ontario, Canada, and South Carolina, USA) in the North American non-native distribution of Arabidopsis thaliana. We assessed the effects of climatic distance, geographic distance, and genetic features of history on performance and patterns of natural selection in the novel garden settings. RESULTS We found that plants had greater survivorship, flowered earlier, were larger, and produced more fruit in the south, and that genotype-by-environment interactions were significant between gardens. However, our analyses revealed similar patterns of natural selection between gardens in distinct climate zones. After accounting for genetic ancestry, we also detected that population climatic distance best predicted performance within gardens. CONCLUSIONS These data suggest that colonization success in novel, non-native environments is determined by a combination of climate and genetic history. When performance at novel sites was assessed with seed sources from geographically and genetically disparate, established non-native populations, proximity to the garden alone was insufficient to predict performance. Our study highlights the need to evaluate seed sources from diverse origins to describe comprehensively phenotypic responses to novel environments, particularly for taxa in which many source populations may contribute to colonization.
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Affiliation(s)
- Karen E Samis
- Department of Biology, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - John R Stinchcombe
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
- Koffler Scientific Reserve at Joker's Hill, University of Toronto, Toronto, Ontario, Canada
| | - Courtney J Murren
- Department of Biology, College of Charleston, Charleston, South Carolina, 29424, USA
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14
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Does adaptation to historical climate shape plant responses to future rainfall patterns? A rainfall manipulation experiment with common ragweed. Oecologia 2019; 190:941-953. [DOI: 10.1007/s00442-019-04463-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 07/02/2019] [Indexed: 01/30/2023]
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15
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Santangelo JS, Johnson MTJ, Ness RW. Modern spandrels: the roles of genetic drift, gene flow and natural selection in the evolution of parallel clines. Proc Biol Sci 2019; 285:rspb.2018.0230. [PMID: 29743253 DOI: 10.1098/rspb.2018.0230] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/12/2018] [Indexed: 11/12/2022] Open
Abstract
Urban environments offer the opportunity to study the role of adaptive and non-adaptive evolutionary processes on an unprecedented scale. While the presence of parallel clines in heritable phenotypic traits is often considered strong evidence for the role of natural selection, non-adaptive evolutionary processes can also generate clines, and this may be more likely when traits have a non-additive genetic basis due to epistasis. In this paper, we use spatially explicit simulations modelled according to the cyanogenesis (hydrogen cyanide, HCN) polymorphism in white clover (Trifolium repens) to examine the formation of phenotypic clines along urbanization gradients under varying levels of drift, gene flow and selection. HCN results from an epistatic interaction between two Mendelian-inherited loci. Our results demonstrate that the genetic architecture of this trait makes natural populations susceptible to decreases in HCN frequencies via drift. Gradients in the strength of drift across a landscape resulted in phenotypic clines with lower frequencies of HCN in strongly drifting populations, giving the misleading appearance of deterministic adaptive changes in the phenotype. Studies of heritable phenotypic change in urban populations should generate null models of phenotypic evolution based on the genetic architecture underlying focal traits prior to invoking selection's role in generating adaptive differentiation.
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Affiliation(s)
- James S Santangelo
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada L5L 1C6 .,Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada L5L 1C6.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada M5S 3B2
| | - Marc T J Johnson
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada L5L 1C6.,Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada L5L 1C6.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada M5S 3B2
| | - Rob W Ness
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada L5L 1C6.,Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada L5L 1C6.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada M5S 3B2
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16
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Helliwell EE, Faber‐Hammond J, Lopez ZC, Garoutte A, Wettberg E, Friesen ML, Porter SS. Rapid establishment of a flowering cline in
Medicago polymorpha
after invasion of North America. Mol Ecol 2018; 27:4758-4774. [DOI: 10.1111/mec.14898] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 10/01/2018] [Accepted: 10/03/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Emily E. Helliwell
- School of Biological Sciences Washington State University Vancouver Washington
| | | | - Zoie C. Lopez
- School of Biological Sciences Washington State University Vancouver Washington
| | - Aaron Garoutte
- Department of Plant Biology Michigan State University East Lansing Michigan
| | - Eric Wettberg
- Department of Plant and Soil Science The University of Vermont Burlington Vermont
| | - Maren L. Friesen
- Department of Plant Biology Michigan State University East Lansing Michigan
- Department of Plant Pathology Washington State University Pullman Washington
- Department of Crop and Soil Sciences Washington State University Pullman Washington
| | - Stephanie S. Porter
- School of Biological Sciences Washington State University Vancouver Washington
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17
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Ozaki H, Oguchi R, Hikosaka K. Dependence of functional traits related to growth rates and their CO 2 response on multiple habitat climate factors across Arabidopsis thaliana populations. JOURNAL OF PLANT RESEARCH 2018; 131:987-999. [PMID: 30046937 DOI: 10.1007/s10265-018-1058-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 07/06/2018] [Indexed: 06/08/2023]
Abstract
The values of many plant traits are often different even within a species as a result of local adaptation. Here, we studied how multiple climate variables influence trait values in Arabidopsis thaliana grown under common conditions. We examined 9 climate variables and 29 traits related to vegetative growth rate in 44 global A. thaliana accessions grown at ambient or elevated CO2 concentration ([CO2]) and applied a multiple regression analysis. We found that genetic variations in the traits related to growth rates were associated with various climate variables. At ambient [CO2], plant size was positively correlated with precipitation in the original habitat. This may be a result of larger biomass investment in roots at the initial stage in plants adapting to a lower precipitation. Stomatal conductance and photosynthetic nitrogen use efficiency were negatively correlated with vapor pressure deficit, probably as a result of the trade-off between photosynthetic water- and nitrogen-use efficiency. These results suggest that precipitation and air humidity influence belowground and aboveground traits, respectively. Elevated [CO2] altered climate dependences in some of the studied traits. The CO2 response of relative growth rate was negatively correlated with altitude, indicating that plants inhabiting a higher altitude have less plasticity to changing [CO2]. These results are useful not only for understanding evolutionary process but also to predict the plant species that are favored under future global change.
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Affiliation(s)
- Hiroshi Ozaki
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8578, Japan.
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan.
| | - Riichi Oguchi
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8578, Japan
| | - Kouki Hikosaka
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8578, Japan
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18
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Olatoye MO, Hu Z, Maina F, Morris GP. Genomic Signatures of Adaptation to a Precipitation Gradient in Nigerian Sorghum. G3 (BETHESDA, MD.) 2018; 8:3269-3281. [PMID: 30097471 PMCID: PMC6169398 DOI: 10.1534/g3.118.200551] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 08/04/2018] [Indexed: 02/05/2023]
Abstract
Evolution of plants under climatic gradients may lead to clinal adaptation. Understanding the genomic basis of clinal adaptation in crops species could facilitate breeding for climate resilience. We investigated signatures of clinal adaptation in the cereal crop sorghum (Sorghum bicolor L. [Moench]) to the precipitation gradient in West Africa using a panel (n = 607) of sorghum accessions from diverse agroclimatic zones of Nigeria. Significant correlations were observed between common-garden phenotypes of three putative climate-adaptive traits (flowering time, plant height, and panicle length) and climatic variables. The panel was characterized at >400,000 single nucleotide polymorphisms (SNPs) using genotyping-by-sequencing (GBS). Redundancy analysis indicated that a small proportion of SNP variation can be explained by climate (1%), space (1%), and climate collinear with space (3%). Discriminant analysis of principal components identified three genetic groups that are distributed differently along the precipitation gradient. Genome-wide association studies were conducted with phenotypes and three climatic variables (annual mean precipitation, precipitation in the driest quarter, and annual mean temperature). There was no overall enrichment of associations near a priori candidate genes implicated in flowering time, height, and inflorescence architecture in cereals, but several significant associations were found near a priori candidates including photoperiodic flowering regulators SbCN12 and Ma6 Together, the findings suggest that a small (3%) but significant proportion of nucleotide variation in Nigerian sorghum landraces reflects clinal adaptation along the West African precipitation gradient.
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Affiliation(s)
- Marcus O Olatoye
- Department of Agronomy, Kansas State University, Manhattan KS 66506
| | - Zhenbin Hu
- Department of Agronomy, Kansas State University, Manhattan KS 66506
| | - Fanna Maina
- Department of Agronomy, Kansas State University, Manhattan KS 66506
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19
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Tabas-Madrid D, Méndez-Vigo B, Arteaga N, Marcer A, Pascual-Montano A, Weigel D, Xavier Picó F, Alonso-Blanco C. Genome-wide signatures of flowering adaptation to climate temperature: Regional analyses in a highly diverse native range of Arabidopsis thaliana. PLANT, CELL & ENVIRONMENT 2018; 41:1806-1820. [PMID: 29520809 DOI: 10.1111/pce.13189] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/02/2018] [Accepted: 03/02/2018] [Indexed: 05/25/2023]
Abstract
Current global change is fueling an interest to understand the genetic and molecular mechanisms of plant adaptation to climate. In particular, altered flowering time is a common strategy for escape from unfavourable climate temperature. In order to determine the genomic bases underlying flowering time adaptation to this climatic factor, we have systematically analysed a collection of 174 highly diverse Arabidopsis thaliana accessions from the Iberian Peninsula. Analyses of 1.88 million single nucleotide polymorphisms provide evidence for a spatially heterogeneous contribution of demographic and adaptive processes to geographic patterns of genetic variation. Mountains appear to be allele dispersal barriers, whereas the relationship between flowering time and temperature depended on the precise temperature range. Environmental genome-wide associations supported an overall genome adaptation to temperature, with 9.4% of the genes showing significant associations. Furthermore, phenotypic genome-wide associations provided a catalogue of candidate genes underlying flowering time variation. Finally, comparison of environmental and phenotypic genome-wide associations identified known (Twin Sister of FT, FRIGIDA-like 1, and Casein Kinase II Beta chain 1) and new (Epithiospecifer Modifier 1 and Voltage-Dependent Anion Channel 5) genes as candidates for adaptation to climate temperature by altered flowering time. Thus, this regional collection provides an excellent resource to address the spatial complexity of climate adaptation in annual plants.
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Affiliation(s)
- Daniel Tabas-Madrid
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049, Madrid, Spain
| | - Belén Méndez-Vigo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049, Madrid, Spain
| | - Noelia Arteaga
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049, Madrid, Spain
| | - Arnald Marcer
- CREAF, 08193, Cerdanyola del Vallès, Spain
- Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Spain
| | - Alberto Pascual-Montano
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049, Madrid, Spain
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany
| | - F Xavier Picó
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), 41092, Sevilla, Spain
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049, Madrid, Spain
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20
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Rutter MT, Roles AJ, Fenster CB. Quantifying natural seasonal variation in mutation parameters with mutation accumulation lines. Ecol Evol 2018; 8:5575-5585. [PMID: 29938075 PMCID: PMC6010865 DOI: 10.1002/ece3.4085] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 03/19/2018] [Indexed: 12/13/2022] Open
Abstract
Mutations create novel genetic variants, but their contribution to variation in fitness and other phenotypes may depend on environmental conditions. Furthermore, natural environments may be highly heterogeneous. We assessed phenotypes associated with survival and reproductive success in over 30,000 plants representing 100 mutation accumulation lines of Arabidopsis thaliana across four temporal environments at a single field site. In each of the four assays, environmental variance was substantially larger than mutational variance. For some traits, whether mutational variance was significantly varied between seasons. The founder genotype had mean trait values near the mean of the distribution of the mutation accumulation lines in all field experiments. New mutations also contributed more phenotypic variation than would be predicted, given phenotypic and sequence‐level divergence among natural populations of A. thaliana. The combination of large environmental variance with a mean effect of mutation near zero suggests that mutations could contribute substantially to standing genetic variation.
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Affiliation(s)
- Matthew T Rutter
- Department of Biology College of Charleston Charleston South Carolina
| | | | - Charles B Fenster
- Department of Biology and Microbiology South Dakota State University Brookings South Dakota
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21
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Frachon L, Bartoli C, Carrère S, Bouchez O, Chaubet A, Gautier M, Roby D, Roux F. A Genomic Map of Climate Adaptation in Arabidopsis thaliana at a Micro-Geographic Scale. FRONTIERS IN PLANT SCIENCE 2018; 9:967. [PMID: 30042773 PMCID: PMC6048436 DOI: 10.3389/fpls.2018.00967] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 06/15/2018] [Indexed: 05/21/2023]
Abstract
Understanding the genetic bases underlying climate adaptation is a key element to predict the potential of species to face climate warming. Although substantial climate variation is observed at a micro-geographic scale, most genomic maps of climate adaptation have been established at broader geographical scales. Here, by using a Pool-Seq approach combined with a Bayesian hierarchical model that control for confounding by population structure, we performed a genome-environment association (GEA) analysis to investigate the genetic basis of adaptation to six climate variables in 168 natural populations of Arabidopsis thaliana distributed in south-west of France. Climate variation among the 168 populations represented up to 24% of climate variation among 521 European locations where A. thaliana inhabits. We identified neat and strong peaks of association, with most of the associated SNPs being significantly enriched in likely functional variants and/or in the extreme tail of genetic differentiation among populations. Furthermore, genes involved in transcriptional mechanisms appear predominant in plant functions associated with local climate adaptation. Globally, our results suggest that climate adaptation is an important driver of genomic variation in A. thaliana at a small spatial scale and mainly involves genome-wide changes in fundamental mechanisms of gene regulation. The identification of climate-adaptive genetic loci at a micro-geographic scale also highlights the importance to include within-species genetic diversity in ecological niche models for projecting potential species distributional shifts over short geographic distances.
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Affiliation(s)
- Léa Frachon
- Laboratoire des Interactions Plantes-Microorganismes, Université de Toulouse, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Castanet-Tolosan, France
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Naples, Italy
- Department of Systematic and Evolutionary Botany, University of Zurich, Zürich, Switzerland
| | - Claudia Bartoli
- Laboratoire des Interactions Plantes-Microorganismes, Université de Toulouse, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Castanet-Tolosan, France
| | - Sébastien Carrère
- Laboratoire des Interactions Plantes-Microorganismes, Université de Toulouse, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Castanet-Tolosan, France
| | - Olivier Bouchez
- Institut National de la Recherche Agronomique, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Adeline Chaubet
- Institut National de la Recherche Agronomique, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Mathieu Gautier
- Centre de Biologie pour la Gestion des Populations, Institut National de la Recherche Agronomique, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Institut de Recherche pour le Développement, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Dominique Roby
- Laboratoire des Interactions Plantes-Microorganismes, Université de Toulouse, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Castanet-Tolosan, France
| | - Fabrice Roux
- Laboratoire des Interactions Plantes-Microorganismes, Université de Toulouse, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Castanet-Tolosan, France
- *Correspondence: Fabrice Roux,
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22
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Wright SJ, Cui Zhou D, Kuhle A, Olsen KM. Continent-Wide Climatic Variation Drives Local Adaptation in North American White Clover. J Hered 2017; 109:78-89. [PMID: 28992131 DOI: 10.1093/jhered/esx060] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 07/13/2017] [Indexed: 12/19/2022] Open
Abstract
Climate-associated clines in adaptive polymorphisms are commonly cited as evidence of local adaptation within species. However, the contribution of the clinally varying trait to overall fitness is often unknown. To address this question, we examined survival, vegetative growth, and reproductive output in a central US common garden experiment using 161 genotypes of white clover (Trifolium repens L.) originating from 15 locations across North America. White clover is polymorphic for cyanogenesis (hydrogen cyanide release upon tissue damage), a chemical defense against generalist herbivores, and climate-associated cyanogenesis clines have repeatedly evolved across the species range. Over a 12-month experiment, we observed striking correlations between the population of origin and plant performance in the common garden, with climatic distance from the common garden site predicting fitness more accurately than geographic distance. Assessments of herbivore leaf damage over the 2015 growing season indicated marginally lower herbivory on cyanogenic plants; however, this effect did not result in increased fitness in the common garden location. Linear mixed modeling suggested that while cyanogenesis variation had little predictive value for vegetative growth, it is as important as climatic variation for predicting reproductive output in the central United States. Together, our findings suggest that knowledge of climate similarity, as well as knowledge of locally favored adaptive traits, will help to inform transplantation strategies for restoration ecology and other conservation efforts in the face of climate change.
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Affiliation(s)
- Sara J Wright
- Department of Biology, Washington University, St. Louis, MO 63130-4899
| | - Daniel Cui Zhou
- Department of Biology, Washington University, St. Louis, MO 63130-4899
| | | | - Kenneth M Olsen
- Department of Biology, Washington University, St. Louis, MO 63130-4899
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23
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Cousins EA, Murren CJ. Edaphic history over seedling characters predicts integration and plasticity of integration across geologically variable populations of Arabidopsis thaliana. AMERICAN JOURNAL OF BOTANY 2017; 104:1802-1815. [PMID: 29196342 DOI: 10.3732/ajb.1700220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 09/28/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF THE STUDY Studies on phenotypic plasticity and plasticity of integration have uncovered functionally linked modules of aboveground traits and seedlings of Arabidopsis thaliana, but we lack details about belowground variation in adult plants. Functional modules can be comprised of additional suites of traits that respond to environmental variation. We assessed whether shoot and root responses to nutrient environments in adult A. thaliana were predictable from seedling traits or population-specific geologic soil characteristics at the site of origin. METHODS We compared 17 natural accessions from across the native range of A. thaliana using 14-day-old seedlings grown on agar or sand and plants grown to maturity across nutrient treatments in sand. We measured aboveground size, reproduction, timing traits, root length, and root diameter. Edaphic characteristics were obtained from a global-scale dataset and related to field data. KEY RESULTS We detected significant among-population variation in root traits of seedlings and adults and in plasticity in aboveground and belowground traits of adult plants. Phenotypic integration of roots and shoots varied by population and environment. Relative integration was greater in roots than in shoots, and integration was predicted by edaphic soil history, particularly organic carbon content, whereas seedling traits did not predict later ontogenetic stages. CONCLUSIONS Soil environment of origin has significant effects on phenotypic plasticity in response to nutrients, and on phenotypic integration of root modules and shoot modules. Root traits varied among populations in reproductively mature individuals, indicating potential for adaptive and integrated functional responses of root systems in annuals.
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Affiliation(s)
- Elsa A Cousins
- Department of Biology, College of Charleston, Charleston, South Carolina 29424, USA
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, Massachusetts 01002, USA
| | - Courtney J Murren
- Department of Biology, College of Charleston, Charleston, South Carolina 29424, USA
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24
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Taylor MA, Cooper MD, Sellamuthu R, Braun P, Migneault A, Browning A, Perry E, Schmitt J. Interacting effects of genetic variation for seed dormancy and flowering time on phenology, life history, and fitness of experimental Arabidopsis thaliana populations over multiple generations in the field. THE NEW PHYTOLOGIST 2017; 216:291-302. [PMID: 28752957 DOI: 10.1111/nph.14712] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 06/19/2017] [Indexed: 06/07/2023]
Abstract
Major alleles for seed dormancy and flowering time are well studied, and can interact to influence seasonal timing and fitness within generations. However, little is known about how this interaction controls phenology, life history, and population fitness across multiple generations in natural seasonal environments. To examine how seed dormancy and flowering time shape annual plant life cycles over multiple generations, we established naturally dispersing populations of recombinant inbred lines of Arabidopsis thaliana segregating early and late alleles for seed dormancy and flowering time in a field experiment. We recorded seasonal phenology and fitness of each genotype over 2 yr and several generations. Strong seed dormancy suppressed mid-summer germination in both early- and late-flowering genetic backgrounds. Strong dormancy and late-flowering genotypes were both necessary to confer a winter annual life history; other genotypes were rapid-cycling. Strong dormancy increased within-season fecundity in an early-flowering background, but decreased it in a late-flowering background. However, there were no detectable differences among genotypes in population growth rates. Seasonal phenology, life history, and cohort fitness over multiple generations depend strongly upon interacting genetic variation for dormancy and flowering. However, similar population growth rates across generations suggest that different life cycle genotypes can coexist in natural populations.
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Affiliation(s)
- Mark A Taylor
- University of California at Davis, Davis, CA, 95616, USA
| | | | | | - Peter Braun
- Brown University, Providence, RI, 02912, USA
- California State University at San Bernardino, San Bernardino, CA, 92407, USA
| | | | | | - Emily Perry
- Brown University, Providence, RI, 02912, USA
| | - Johanna Schmitt
- University of California at Davis, Davis, CA, 95616, USA
- Brown University, Providence, RI, 02912, USA
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25
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Stearns FW, Fenster CB. The effect of induced mutations on quantitative traits in Arabidopsis thaliana: Natural versus artificial conditions. Ecol Evol 2016; 6:8366-8374. [PMID: 28031789 PMCID: PMC5167040 DOI: 10.1002/ece3.2558] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 09/09/2016] [Accepted: 09/15/2016] [Indexed: 12/04/2022] Open
Abstract
Mutations are the ultimate source of all genetic variations. New mutations are expected to affect quantitative traits differently depending on the extent to which traits contribute to fitness and the environment in which they are tested. The dogma is that the preponderance of mutations affecting fitness will be skewed toward deleterious while their effects on nonfitness traits will be bidirectionally distributed. There are mixed views on the role of stress in modulating these effects. We quantify mutation effects by inducing mutations in Arabidopsis thaliana (Columbia accession) using the chemical ethylmethane sulfonate. We measured the effects of new mutations relative to a premutation founder for fitness components under both natural (field) and artificial (growth room) conditions. Additionally, we measured three other quantitative traits, not expected to contribute directly to fitness, under artificial conditions. We found that induced mutations were equally as likely to increase as decrease a trait when that trait was not closely related to fitness (traits that were neither survivorship nor reproduction). We also found that new mutations were more likely to decrease fitness or fitness‐related traits under more stressful field conditions than under relatively benign artificial conditions. In the benign condition, the effect of new mutations on fitness components was similar to traits not as closely related to fitness. These results highlight the importance of measuring the effects of new mutations on fitness and other traits under a range of conditions.
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Affiliation(s)
- Frank W Stearns
- Department of Biology Biology-Psychology Building University of Maryland College Park MD USA
| | - Charles B Fenster
- Department of Biology Biology-Psychology Building University of Maryland College Park MD USA
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26
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Kleine S, Weissinger L, Müller C. Impact of drought on plant populations of native and invasive origins. Oecologia 2016; 183:9-20. [PMID: 27568026 DOI: 10.1007/s00442-016-3706-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 08/13/2016] [Indexed: 11/28/2022]
Abstract
Invasive populations often shift phenotypically during introduction. Moreover, they are postulated to show an increased phenotypic plasticity compared with their native counterparts, which could be advantageous. However, less is known about trait selection across populations along the invasion gradient in response to environmental factors, such as increasing drought caused by climate change. In this study, we investigated the impacts of drought on growth, regrowth, and various leaf traits in plants of different origin. Therefore, seeds of 18 populations of the perennial Tanacetum vulgare were collected along the invasion gradient (North America, invasive; West Europe, archaeophyte; East Europe, native) and grown in competition with the grass Poa pratensis under control or dry conditions in a common garden. Above-ground biomass was cut once and the regrowth was measured as an indicator for tolerance over a second growth period. Initially, drought had little effects on growth of T. vulgare, but after cutting, plants grew more vigorously. Against expectations, phenotypic plasticity was not higher in invasive populations, but even reduced in one trait, which may be attributable to ecological constraints imposed by multiple stress conditions. Trait responses reflected the range expansion and invasion gradient and were influenced by the latitudinal origin of populations. Populations of invaded ranges may be subject to faster and more extensive genetic mixing or had less time to undergo and reflect selective processes.
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Affiliation(s)
- Sandra Kleine
- Department of Chemical Ecology, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
| | - Lisa Weissinger
- Department of Chemical Ecology, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
| | - Caroline Müller
- Department of Chemical Ecology, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany.
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Gould BA, Stinchcombe JR. Population genomic scans suggest novel genes underlie convergent flowering time evolution in the introduced range of Arabidopsis thaliana. Mol Ecol 2016; 26:92-106. [PMID: 27064998 DOI: 10.1111/mec.13643] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 04/06/2016] [Accepted: 04/08/2016] [Indexed: 01/08/2023]
Abstract
A long-standing question in evolutionary biology is whether the evolution of convergent phenotypes results from selection on the same heritable genetic components. Using whole-genome sequencing and genome scans, we tested whether the evolution of parallel longitudinal flowering time clines in the native and introduced ranges of Arabidopsis thaliana has a similar genetic basis. We found that common variants of large effect on flowering time in the native range do not appear to have been under recent strong selection in the introduced range. We identified a set of 38 new candidate genes that are putatively linked to the evolution of flowering time. A high degree of conditional neutrality of flowering time variants between the native and introduced range may preclude parallel evolution at the level of genes. Overall, neither gene pleiotropy nor available standing genetic variation appears to have restricted the evolution of flowering time to high-frequency variants from the native range or to known flowering time pathway genes.
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Affiliation(s)
- Billie A Gould
- Department of Plant Biology, Michigan State University, 612 Wilson Rd, East Lansing, MI, 48823, USA
| | - John R Stinchcombe
- Department of Plant Biology, Michigan State University, 612 Wilson Rd, East Lansing, MI, 48823, USA
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28
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Vidigal DS, Marques ACSS, Willems LAJ, Buijs G, Méndez-Vigo B, Hilhorst HWM, Bentsink L, Picó FX, Alonso-Blanco C. Altitudinal and climatic associations of seed dormancy and flowering traits evidence adaptation of annual life cycle timing in Arabidopsis thaliana. PLANT, CELL & ENVIRONMENT 2016; 39:1737-1748. [PMID: 26991665 DOI: 10.1111/pce.12734] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 03/04/2016] [Accepted: 03/06/2016] [Indexed: 06/05/2023]
Abstract
The temporal control or timing of the life cycle of annual plants is presumed to provide adaptive strategies to escape harsh environments for survival and reproduction. This is mainly determined by the timing of germination, which is controlled by the level of seed dormancy, and of flowering initiation. However, the environmental factors driving the evolution of plant life cycles remain largely unknown. To address this question we have analysed nine quantitative life history traits, in a native regional collection of 300 wild accessions of Arabidopsis thaliana. Seed dormancy and flowering time were negatively correlated, indicating that these traits have coevolved. In addition, environmental-phenotypic analyses detected strong altitudinal and climatic clines for most life history traits. Overall, accessions showing life cycles with early flowering, small seeds, high seed dormancy and slow germination rate were associated with locations exposed to high temperature, low summer precipitation and high radiation. Furthermore, we analysed the expression level of the positive regulator of seed dormancy DELAY OF GERMINATION 1 (DOG1), finding similar but weaker altitudinal and climatic patterns than seed dormancy. Therefore, DOG1 regulatory mutations are likely to provide a quantitative molecular mechanism for the adaptation of A. thaliana life cycle to altitude and climate.
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Affiliation(s)
- Deborah S Vidigal
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Alexandre C S S Marques
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Leo A J Willems
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Gonda Buijs
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Belén Méndez-Vigo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - Henk W M Hilhorst
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Leónie Bentsink
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - F Xavier Picó
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, 41092, Spain
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
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Adams WW, Stewart JJ, Cohu CM, Muller O, Demmig-Adams B. Habitat Temperature and Precipitation of Arabidopsis thaliana Ecotypes Determine the Response of Foliar Vasculature, Photosynthesis, and Transpiration to Growth Temperature. FRONTIERS IN PLANT SCIENCE 2016; 7:1026. [PMID: 27504111 PMCID: PMC4959142 DOI: 10.3389/fpls.2016.01026] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 06/30/2016] [Indexed: 05/20/2023]
Abstract
Acclimatory adjustments of foliar vascular architecture, photosynthetic capacity, and transpiration rate in Arabidopsis thaliana ecotypes (Italian, Polish [Col-0], Swedish) were characterized in the context of habitat of origin. Temperatures of the habitat of origin decreased linearly with increasing habitat latitude, but habitat precipitation was greatest in Italy, lowest in Poland, and intermediate in Sweden. Plants of the three ecotypes raised under three different growth temperature regimes (low, moderate, and high) exhibited highest photosynthetic capacities, greatest leaf thickness, highest chlorophyll a/b ratio and levels of β-carotene, and greatest levels of wall ingrowths in phloem transfer cells, and, in the Col-0 and Swedish ecotypes, of phloem per minor vein in plants grown at the low temperature. In contrast, vein density and minor vein tracheary to sieve element ratio increased with increasing growth temperature - most strongly in Col-0 and least strongly in the Italian ecotype - and transpirational water loss correlated with vein density and number of tracheary elements per minor vein. Plotting of these vascular features as functions of climatic conditions in the habitat of origin suggested that temperatures during the evolutionary history of the ecotypes determined acclimatory responses of the foliar phloem and photosynthesis to temperature in this winter annual that upregulates photosynthesis in response to lower temperature, whereas the precipitation experienced during the evolutionary history of the ecotypes determined adjustment of foliar vein density, xylem, and transpiration to temperature. In particular, whereas photosynthetic capacity, leaf thickness, and foliar minor vein phloem features increased linearly with increasing latitude and decreasing temperature of the habitats of origin in response to experimental growth at low temperature, transpiration rate, foliar vein density, and minor vein tracheary element numbers and cross-sectional areas increased linearly with decreasing precipitation level in the habitats of origin in response to experimental growth at high temperature. This represents a situation where temperature acclimation of the apparent capacity for water flux through the xylem and transpiration rate in a winter annual responded differently from that of photosynthetic capacity, in contrast to previous reports of strong relationships between hydraulic conductance and photosynthesis in other studies.
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Affiliation(s)
- William W. Adams
- Department of Ecology and Evolutionary Biology, University of Colorado BoulderBoulder, CO, USA
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Burgarella C, Chantret N, Gay L, Prosperi J, Bonhomme M, Tiffin P, Young ND, Ronfort J. Adaptation to climate through flowering phenology: a case study in
Medicago truncatula. Mol Ecol 2016; 25:3397-415. [DOI: 10.1111/mec.13683] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 04/26/2016] [Accepted: 04/27/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Concetta Burgarella
- UMR 232 DIADE/DYNADIV Institut de Recherche pour le Developpement (IRD) 911 avenue Agropolis BP 64501, 34394 Montpellier France
- UMR AGAP, Equipe Génomique évolutive et gestion des populations Institut national de Recherche Agronomique (INRA) 34060 Montpellier France
| | - Nathalie Chantret
- UMR AGAP, Equipe Génomique évolutive et gestion des populations Institut national de Recherche Agronomique (INRA) 34060 Montpellier France
| | - Laurène Gay
- UMR AGAP, Equipe Génomique évolutive et gestion des populations Institut national de Recherche Agronomique (INRA) 34060 Montpellier France
| | - Jean‐Marie Prosperi
- UMR AGAP, Equipe Génomique évolutive et gestion des populations Institut national de Recherche Agronomique (INRA) 34060 Montpellier France
| | - Maxime Bonhomme
- UPS Laboratoire de Recherche en Sciences Végétales Université de Toulouse BP42617, Auzeville F‐31326 Castanet‐Tolosan France
- Laboratoire de Recherche en Sciences Végétales CNRS BP42617, Auzeville F‐31326 Castanet‐Tolosan France
| | - Peter Tiffin
- Department of Plant Biology University of Minnesota St. Paul MN 55108 USA
| | - Nevin D. Young
- Department of Plant Biology University of Minnesota St. Paul MN 55108 USA
- Department of Plant Pathology University of Minnesota St. Paul MN 55108 USA
| | - Joelle Ronfort
- UMR AGAP, Equipe Génomique évolutive et gestion des populations Institut national de Recherche Agronomique (INRA) 34060 Montpellier France
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Comparative Transcriptomics Indicates a Role for SHORT VEGETATIVE PHASE (SVP) Genes in Mimulus guttatus Vernalization Response. G3-GENES GENOMES GENETICS 2016; 6:1239-49. [PMID: 26921300 PMCID: PMC4856076 DOI: 10.1534/g3.115.026468] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The timing of reproduction in response to variable environmental conditions is critical to plant fitness, and is a major driver of taxon differentiation. In the yellow monkey flower, Mimulus guttatus, geographically distinct North American populations vary in their photoperiod and chilling (vernalization) requirements for flowering, suggesting strong local adaptation to their surroundings. Previous analyses revealed quantitative trait loci (QTL) underlying short-day mediated vernalization responsiveness using two annual M. guttatus populations that differed in their vernalization response. To narrow down candidate genes responsible for this variation, and to reveal potential downstream genes, we conducted comparative transcriptomics and quantitative PCR (qPCR) in shoot apices of parental vernalization responsive IM62, and unresponsive LMC24 inbred lines grown under different photoperiods and temperatures. Our study identified several metabolic, hormone signaling, photosynthetic, stress response, and flowering time genes that are differentially expressed between treatments, suggesting a role for their protein products in short-day-mediated vernalization responsiveness. Only a small subset of these genes intersected with candidate genes from the previous QTL study, and, of the main candidates tested with qPCR under nonpermissive conditions, only SHORT VEGETATIVE PHASE (SVP) gene expression met predictions for a population-specific short-day-repressor of flowering that is repressed by cold.
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Méndez-Vigo B, Savic M, Ausín I, Ramiro M, Martín B, Picó FX, Alonso-Blanco C. Environmental and genetic interactions reveal FLOWERING LOCUS C as a modulator of the natural variation for the plasticity of flowering in Arabidopsis. PLANT, CELL & ENVIRONMENT 2016; 39:282-94. [PMID: 26173848 DOI: 10.1111/pce.12608] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 06/30/2015] [Accepted: 07/02/2015] [Indexed: 05/12/2023]
Abstract
The timing of flowering initiation depends strongly on the environment, a property termed as the plasticity of flowering. Such plasticity determines the adaptive potential of plants because it provides phenotypic buffer against environmental changes, and its natural variation contributes to evolutionary adaptation. We addressed the genetic mechanisms of the natural variation for this plasticity in Arabidopsis thaliana by analysing a population of recombinant inbred lines derived from Don-0 and Ler accessions collected from distinct climates. Quantitative trait locus (QTL) mapping in four environmental conditions differing in photoperiod, vernalization treatment and ambient temperature detected the folllowing: (i) FLOWERING LOCUS C (FLC) as a large effect QTL affecting flowering time differentially in all environments; (ii) numerous QTL displaying smaller effects specifically in some conditions; and (iii) significant genetic interactions between FLC and other loci. Hence, the variation for the plasticity of flowering is determined by a combination of environmentally sensitive and specific QTL, and epistasis. Analysis of FLC from Don identified a new and more active allele likely caused by a cis-regulatory deletion covering the non-coding RNA COLDAIR. Further characterization of four FLC natural alleles showed different environmental and genetic interactions. Thus, FLC appears as a major modulator of the natural variation for the plasticity of flowering to multiple environmental factors.
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Affiliation(s)
- Belén Méndez-Vigo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - Marija Savic
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - Israel Ausín
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - Mercedes Ramiro
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - Beatriz Martín
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - F Xavier Picó
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Sevilla, 41092, Spain
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
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33
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Nagler M, Nukarinen E, Weckwerth W, Nägele T. Integrative molecular profiling indicates a central role of transitory starch breakdown in establishing a stable C/N homeostasis during cold acclimation in two natural accessions of Arabidopsis thaliana. BMC PLANT BIOLOGY 2015; 15:284. [PMID: 26628055 PMCID: PMC4667452 DOI: 10.1186/s12870-015-0668-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 11/23/2015] [Indexed: 05/21/2023]
Abstract
BACKGROUND The variation of growth and cold tolerance of two natural Arabidopsis accessions, Cvi (cold sensitive) and Rschew (cold tolerant), was analysed on a proteomic, phosphoproteomic and metabolomic level to derive characteristic information about genotypically distinct strategies of metabolic reprogramming and growth maintenance during cold acclimation. RESULTS Growth regulation before and after a cold acclimation period was monitored by recording fresh weight of leaf rosettes. Significant differences in the shoot fresh weight of Cvi and Rschew were detected both before and after acclimation to low temperature. During cold acclimation, starch levels were found to accumulate to a significantly higher level in Cvi compared to Rschew. Concomitantly, statistical analysis revealed a cold-induced decrease of beta-amylase 3 (BAM3; AT4G17090) in Cvi but not in Rschew. Further, only in Rschew we observed an increase of the protein level of the debranching enzyme isoamylase 3 (ISA3; AT4G09020). Additionally, the cold response of both accessions was observed to severely affect ribosomal complexes, but only Rschew showed a pronounced accumulation of carbon and nitrogen compounds. The abundance of the Cold Regulated (COR) protein COR78 (AT5G52310) as well as its phosphorylation was observed to be positively correlated with the acclimation state of both accessions. In addition, transcription factors being involved in growth and developmental regulation were found to characteristically separate the cold sensitive from the cold tolerant accession. Predicted protein-protein interaction networks (PPIN) of significantly changed proteins during cold acclimation allowed for a differentiation between both accessions. The PPIN revealed the central role of carbon/nitrogen allocation and ribosomal complex formation to establish a new cold-induced metabolic homeostasis as also observed on the level of the metabolome and proteome. CONCLUSION Our results provide evidence for a comprehensive multi-functional molecular interaction network orchestrating growth regulation and cold acclimation in two natural accessions of Arabidopsis thaliana. The differential abundance of beta-amylase 3 and isoamylase 3 indicates a central role of transitory starch degradation in the coordination of growth regulation and the development of stress tolerance. Finally, our study indicates naturally occurring differential patterns of C/N balance and protein synthesis during cold acclimation.
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Affiliation(s)
- Matthias Nagler
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstr. 14, 1090, Vienna, Austria.
| | - Ella Nukarinen
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstr. 14, 1090, Vienna, Austria.
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstr. 14, 1090, Vienna, Austria.
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstr. 14, 1090, Vienna, Austria.
| | - Thomas Nägele
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstr. 14, 1090, Vienna, Austria.
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstr. 14, 1090, Vienna, Austria.
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Gilabert A, Dedryver CA, Stoeckel S, Plantegenest M, Simon JC. Longitudinal clines in the frequency distribution of 'super-clones' in an aphid crop pest. BULLETIN OF ENTOMOLOGICAL RESEARCH 2015; 105:694-703. [PMID: 26278064 DOI: 10.1017/s0007485315000619] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Parthenogenesis is the main mode of reproduction of aphids. Their populations are therefore composed of clones whose frequency distribution varies in space and time. Previous population genetic studies on aphids have highlighted the existence of highly abundant clones ('super-clones'), distributed over large geographic areas and persisting over time. Whether the abundance of 'super-clones' results from their ecological success or from stochastic forces, such as drift and migration, is an open question. Here, we looked for the existence of clines in clonal frequency along a climatic gradient in the cereal aphid Rhopalosiphum padi (Linnaeus, 1758) and examined the possible influence of geographical distance and environmental variables in the buildup and maintenance of such clonal clines. We investigated the spatial distribution of the commonest genotypes of R. padi by sampling populations along an east-west transect in maize fields in the northern half of France in both spring and late summer. Individual aphids were genotyped at several polymorphic loci, allowing the assessment of frequency distributions of multilocus genotypes (MLGs) across the cropping season. We found several MLGs showing longitudinal clines in their frequency distribution in both spring and summer. In particular, two dominant asexual genotypes of R. padi showed inverted geographical clines, which could suggest divergent adaptations to environmental conditions. We concluded that while the distribution of some 'super-clones' of R. padi seems most likely driven by the action of migration and genetic drift, selection could be also involved in the establishment of longitudinal clines of others.
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Affiliation(s)
- A Gilabert
- INRA UMR 1349 IGEPP,Domaine de la Motte,F-35653 Le Rheu,France
| | - C-A Dedryver
- INRA UMR 1349 IGEPP,Domaine de la Motte,F-35653 Le Rheu,France
| | - S Stoeckel
- INRA UMR 1349 IGEPP,Domaine de la Motte,F-35653 Le Rheu,France
| | - M Plantegenest
- Agrocampus-ouest UMR 1349 IGEPP,65 rue de Saint-Brieuc,F-35042 Rennes,France
| | - J-C Simon
- INRA UMR 1349 IGEPP,Domaine de la Motte,F-35653 Le Rheu,France
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Root architecture, plant size and soil nutrient variation in natural populations of Arabidopsis thaliana. Evol Ecol 2015. [DOI: 10.1007/s10682-015-9808-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Stock AJ, McGoey BV, Stinchcombe JR. Water availability as an agent of selection in introduced populations of Arabidopsis thaliana: impacts on flowering time evolution. PeerJ 2015; 3:e898. [PMID: 25909038 PMCID: PMC4406364 DOI: 10.7717/peerj.898] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 03/28/2015] [Indexed: 01/13/2023] Open
Abstract
Flowering is one of the most influential events in the life history of a plant and one of the main determinants of reproductive investment and lifetime fitness. It is also a highly complex trait controlled by dozens of genes. Understanding the selective pressures influencing time to flowering, and being able to reliably predict how it will evolve in novel environments, are unsolved challenges for plant evolutionary geneticists. Using the model plant species, Arabidopsis thaliana, we examined the impact of simulated high and low winter precipitation levels on the flowering time of naturalized lines from across the eastern portion of the introduced North American range, and the fitness consequences of early versus late flowering. Flowering time order was significantly correlated across two environments-in a previous common garden experiment and in environmental chambers set to mimic mid-range photoperiod and temperature conditions. Plants in low water flowered earlier, had fewer basal branches and produced fewer fruits. Selection in both treatments favored earlier flowering and more basal branches. Our analyses revealed an interaction between flowering time and water treatment for fitness, where flowering later was more deleterious for fitness in the low water treatment. Our results are consistent with the hypothesis that differences in winter precipitation levels are one of the selective agents underlying a flowering time cline in introduced A. thaliana populations.
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Affiliation(s)
- Amanda J. Stock
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Brechann V. McGoey
- 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
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
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Fabian DK, Lack JB, Mathur V, Schlötterer C, Schmidt PS, Pool JE, Flatt T. Spatially varying selection shapes life history clines among populations of Drosophila melanogaster from sub-Saharan Africa. J Evol Biol 2015; 28:826-40. [PMID: 25704153 DOI: 10.1111/jeb.12607] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 02/12/2015] [Accepted: 02/17/2015] [Indexed: 01/31/2023]
Abstract
Clines in life history traits, presumably driven by spatially varying selection, are widespread. Major latitudinal clines have been observed, for example, in Drosophila melanogaster, an ancestrally tropical insect from Africa that has colonized temperate habitats on multiple continents. Yet, how geographic factors other than latitude, such as altitude or longitude, affect life history in this species remains poorly understood. Moreover, most previous work has been performed on derived European, American and Australian populations, but whether life history also varies predictably with geography in the ancestral Afro-tropical range has not been investigated systematically. Here, we have examined life history variation among populations of D. melanogaster from sub-Saharan Africa. Viability and reproductive diapause did not vary with geography, but body size increased with altitude, latitude and longitude. Early fecundity covaried positively with altitude and latitude, whereas lifespan showed the opposite trend. Examination of genetic variance-covariance matrices revealed geographic differentiation also in trade-off structure, and QST -FST analysis showed that life history differentiation among populations is likely shaped by selection. Together, our results suggest that geographic and/or climatic factors drive adaptive phenotypic differentiation among ancestral African populations and confirm the widely held notion that latitude and altitude represent parallel gradients.
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Affiliation(s)
- D K Fabian
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria; Vienna Graduate School of Population Genetics, Vienna, Austria
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Hamilton JA, Okada M, Korves T, Schmitt J. The role of climate adaptation in colonization success inArabidopsis thaliana. Mol Ecol 2015; 24:2253-63. [DOI: 10.1111/mec.13099] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 01/15/2015] [Accepted: 01/19/2015] [Indexed: 12/25/2022]
Affiliation(s)
- Jill A. Hamilton
- Department of Evolution and Ecology; University of California; Davis CA 95616 USA
| | - Miki Okada
- Department of Evolution and Ecology; University of California; Davis CA 95616 USA
| | - Tonia Korves
- Data Analytics Department; The MITRE Corporation; 202 Burlington Rd, Bedford MA 01730 USA
| | - Johanna Schmitt
- Department of Evolution and Ecology; University of California; Davis CA 95616 USA
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Stock AJ, Campitelli BE, Stinchcombe JR. Quantitative genetic variance and multivariate clines in the Ivyleaf morning glory, Ipomoea hederacea. Philos Trans R Soc Lond B Biol Sci 2015; 369:20130259. [PMID: 25002704 DOI: 10.1098/rstb.2013.0259] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Clinal variation is commonly interpreted as evidence of adaptive differentiation, although clines can also be produced by stochastic forces. Understanding whether clines are adaptive therefore requires comparing clinal variation to background patterns of genetic differentiation at presumably neutral markers. Although this approach has frequently been applied to single traits at a time, we have comparatively fewer examples of how multiple correlated traits vary clinally. Here, we characterize multivariate clines in the Ivyleaf morning glory, examining how suites of traits vary with latitude, with the goal of testing for divergence in trait means that would indicate past evolutionary responses. We couple this with analysis of genetic variance in clinally varying traits in 20 populations to test whether past evolutionary responses have depleted genetic variance, or whether genetic variance declines approaching the range margin. We find evidence of clinal differentiation in five quantitative traits, with little evidence of isolation by distance at neutral loci that would suggest non-adaptive or stochastic mechanisms. Within and across populations, the traits that contribute most to population differentiation and clinal trends in the multivariate phenotype are genetically variable as well, suggesting that a lack of genetic variance will not cause absolute evolutionary constraints. Our data are broadly consistent theoretical predictions of polygenic clines in response to shallow environmental gradients. Ecologically, our results are consistent with past findings of natural selection on flowering phenology, presumably due to season-length variation across the range.
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Affiliation(s)
- Amanda J Stock
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada M5S 3B2
| | - Brandon E Campitelli
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada M5S 3B2
| | - John R Stinchcombe
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada M5S 3B2 Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada M5S 3B2
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40
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Neuheimer AB, MacKenzie BR. Explaining life history variation in a changing climate across a species' range. Ecology 2014. [DOI: 10.1890/13-2370.1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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41
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Li XM, She DY, Zhang DY, Liao WJ. Life history trait differentiation and local adaptation in invasive populations of Ambrosia artemisiifolia in China. Oecologia 2014; 177:669-677. [PMID: 25362583 DOI: 10.1007/s00442-014-3127-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 10/18/2014] [Indexed: 10/24/2022]
Abstract
Local adaptation has been suggested to play an important role in range expansion, particularly among invasive species. However, the extent to which local adaptation affects the success of an invasive species and the factors that contribute to local adaptation are still unclear. This study aimed to investigate a case of population divergence that may have contributed to the local adaptation of invasive populations of Ambrosia artemisiifolia in China. Common garden experiments in seven populations indicated clinal variations along latitudinal gradients, with plants from higher latitudes exhibiting earlier flowering and smaller sizes at flowering. In reciprocal transplant experiments, plants of a northern Beijing origin produced more seeds at their home site than plants of a southern Wuhan origin, and the Wuhan-origin plants had grown taller at flowering than the Beijing-origin plants in Wuhan, which is believed to facilitate pollen dispersal. These results suggest that plants of Beijing origin may be locally adapted through female fitness and plants from Wuhan possibly locally adapted through male fitness. Selection and path analysis suggested that the phenological and growth traits of both populations have been influenced by natural selection and that flowering time has played an important role through its direct and indirect effects on the relative fitness of each individual. This study evidences the life history trait differentiation and local adaptation during range expansion of invasive A. artemisiifolia in China.
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Affiliation(s)
- Xiao-Meng Li
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, Beijing Normal University, Beijing, 100875, China
| | - Deng-Ying She
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, Beijing Normal University, Beijing, 100875, China
| | - Da-Yong Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, Beijing Normal University, Beijing, 100875, China
| | - Wan-Jin Liao
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, Beijing Normal University, Beijing, 100875, China.
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42
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Kooyers NJ, Olsen KM. Adaptive cyanogenesis clines evolve recurrently through geographical sorting of existing gene deletions. J Evol Biol 2014; 27:2554-8. [DOI: 10.1111/jeb.12466] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 06/15/2014] [Accepted: 07/22/2014] [Indexed: 11/30/2022]
Affiliation(s)
- N. J. Kooyers
- Department of Biology; Washington University in St. Louis; St. Louis MO USA
| | - K. M. Olsen
- Department of Biology; Washington University in St. Louis; St. Louis MO USA
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43
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Preston JC, Jorgensen SA, Jha SG. Functional characterization of duplicated Suppressor of Overexpression of Constans 1-like genes in petunia. PLoS One 2014; 9:e96108. [PMID: 24787903 PMCID: PMC4006870 DOI: 10.1371/journal.pone.0096108] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 04/03/2014] [Indexed: 12/31/2022] Open
Abstract
Flowering time is strictly controlled by a combination of internal and external signals that match seed set with favorable environmental conditions. In the model plant species Arabidopsis thaliana (Brassicaceae), many of the genes underlying development and evolution of flowering have been discovered. However, much remains unknown about how conserved the flowering gene networks are in plants with different growth habits, gene duplication histories, and distributions. Here we functionally characterize three homologs of the flowering gene Suppressor Of Overexpression of Constans 1 (SOC1) in the short-lived perennial Petunia hybrida (petunia, Solanaceae). Similar to A. thaliana soc1 mutants, co-silencing of duplicated petunia SOC1-like genes results in late flowering. This phenotype is most severe when all three SOC1-like genes are silenced. Furthermore, expression levels of the SOC1-like genes Unshaven (UNS) and Floral Binding Protein 21 (FBP21), but not FBP28, are positively correlated with developmental age. In contrast to A. thaliana, petunia SOC1-like gene expression did not increase with longer photoperiods, and FBP28 transcripts were actually more abundant under short days. Despite evidence of functional redundancy, differential spatio-temporal expression data suggest that SOC1-like genes might fine-tune petunia flowering in response to photoperiod and developmental stage. This likely resulted from modification of SOC1-like gene regulatory elements following recent duplication, and is a possible mechanism to ensure flowering under both inductive and non-inductive photoperiods.
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Affiliation(s)
- Jill C. Preston
- Department of Plant Biology, The University of Vermont, Burlington, Vermont, United States of America
| | - Stacy A. Jorgensen
- Department of Plant Biology, The University of Vermont, Burlington, Vermont, United States of America
| | - Suryatapa G. Jha
- Department of Plant Biology, The University of Vermont, Burlington, Vermont, United States of America
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44
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Weinig C, Ewers BE, Welch SM. Ecological genomics and process modeling of local adaptation to climate. CURRENT OPINION IN PLANT BIOLOGY 2014; 18:66-72. [PMID: 24631846 DOI: 10.1016/j.pbi.2014.02.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 01/23/2014] [Accepted: 02/14/2014] [Indexed: 06/03/2023]
Abstract
Locally adapted genotypes have higher fitness in their native site in comparison to foreign genotypes. Recent studies have demonstrated both local adaptation to and genomic associations with a range of climate variables. For climate adaptation, the most common genomic pattern is conditional neutrality, as proven by weak across-environment correlations, frequent SNP×environment interactions, and the topology of some developmental and physiological pathways potentially involved in local adaptation. Genomic association approaches readily translate to non-model systems, and genetically explicit climate envelope models will predict future species' distributions under changing climates. Here, we review recent evidence for local adaptation to climate, focusing primarily on the model system, Arabidopsis thaliana, and on studies incorporating genomic tools into field studies or climate analyses.
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Affiliation(s)
- Cynthia Weinig
- Department of Botany, University of Wyoming, Laramie, WY 82071, USA; Program in Ecology, University of Wyoming, Laramie, WY 82071, USA; Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA.
| | - Brent E Ewers
- Department of Botany, University of Wyoming, Laramie, WY 82071, USA; Program in Ecology, University of Wyoming, Laramie, WY 82071, USA
| | - Stephen M Welch
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
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45
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Kooyers NJ, Gage LR, Al-Lozi A, Olsen KM. Aridity shapes cyanogenesis cline evolution in white clover (Trifolium repens L.). Mol Ecol 2014; 23:1053-70. [PMID: 24438087 DOI: 10.1111/mec.12666] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 12/31/2013] [Accepted: 01/09/2014] [Indexed: 01/14/2023]
Abstract
Adaptive differentiation between populations is often proposed to be the product of multiple interacting selective pressures, although empirical support for this is scarce. In white clover, populations show adaptive differentiation in frequencies of cyanogenesis, the ability to produce hydrogen cyanide after tissue damage. This polymorphism arises through independently segregating polymorphisms for the presence/absence of two required cyanogenic components, cyanogenic glucosides and their hydrolysing enzyme. White clover populations worldwide have evolved a series of recurrent, climate-associated clines, with higher frequencies of cyanogenic plants in warmer locations. These clines have traditionally been hypothesized to reflect a fitness trade-off between chemical defence in herbivore-rich areas (warmer climates) and energetic costs of producing cyanogenic components in areas of low herbivore pressure (cooler climates). Recent observational studies suggest that cyanogenic components may also be beneficial in water-stressed environments. We investigated fitness trade-offs associated with temperature-induced water stress in the cyanogenesis system using manipulative experiments in growth chambers and population surveys across a longitudinal precipitation gradient in the central United States. We find that plants producing cyanogenic glucosides have higher relative fitness in treatments simulating a moderate, persistent drought stress. In water-neutral treatments, there are energetic costs to producing cyanogenic components, but only in treatments with nutrient stress. These fitness trade-offs are consistent with cyanogenesis frequencies in natural populations, where we find clinal variation in the proportion of plants producing cyanogenic glucosides along the precipitation gradient. These results suggest that multiple selective pressures interact to maintain this adaptive polymorphism and that modelling adaptation will require knowledge of environment-specific fitness effects.
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Affiliation(s)
- Nicholas J Kooyers
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA
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46
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Lee YW, Gould BA, Stinchcombe JR. Identifying the genes underlying quantitative traits: a rationale for the QTN programme. AOB PLANTS 2014; 6:plu004. [PMID: 24790125 PMCID: PMC4038433 DOI: 10.1093/aobpla/plu004] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Accepted: 01/01/2014] [Indexed: 05/19/2023]
Abstract
The goal of identifying the genes or even nucleotides underlying quantitative and adaptive traits has been characterized as the 'QTN programme' and has recently come under severe criticism. Part of the reason for this criticism is that much of the QTN programme has asserted that finding the genes and nucleotides for adaptive and quantitative traits is a fundamental goal, without explaining why it is such a hallowed goal. Here we outline motivations for the QTN programme that offer general insight, regardless of whether QTNs are of large or small effect, and that aid our understanding of the mechanistic dynamics of adaptive evolution. We focus on five areas: (i) vertical integration of insight across different levels of biological organization, (ii) genetic parallelism and the role of pleiotropy in shaping evolutionary dynamics, (iii) understanding the forces maintaining genetic variation in populations, (iv) distinguishing between adaptation from standing variation and new mutation, and (v) the role of genomic architecture in facilitating adaptation. We argue that rather than abandoning the QTN programme, we should refocus our efforts on topics where molecular data will be the most effective for testing hypotheses about phenotypic evolution.
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Affiliation(s)
- Young Wha Lee
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON, CanadaM5S 3B2
| | - Billie A. Gould
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON, CanadaM5S 3B2
| | - John R. Stinchcombe
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON, CanadaM5S 3B2
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, CanadaM5S 3B2
- Corresponding author's e-mail address:
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47
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Stearns FW, Fenster CB. Evidence for parallel adaptation to climate across the natural range of Arabidopsis thaliana. Ecol Evol 2013; 3:2241-50. [PMID: 23919166 PMCID: PMC3728961 DOI: 10.1002/ece3.622] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 04/30/2013] [Accepted: 05/06/2013] [Indexed: 11/23/2022] Open
Abstract
How organisms adapt to different climate habitats is a key question in evolutionary ecology and biological conservation. Species distributions are often determined by climate suitability. Consequently, the anthropogenic impact on earth's climate is of key concern to conservation efforts because of our relatively poor understanding of the ability of populations to track and evolve to climate change. Here, we investigate the ability of Arabidopsis thaliana to occupy climate space by quantifying the extent to which different climate regimes are accessible to different A. thaliana genotypes using publicly available data from a large-scale genotyping project and from a worldwide climate database. The genetic distance calculated from 149 single-nucleotide polymorphisms (SNPs) among 60 lineages of A. thaliana was compared to the corresponding climate distance among collection localities calculated from nine different climatic factors. A. thaliana was found to be highly labile when adapting to novel climate space, suggesting that populations may experience few constraints when adapting to changing climates. Our results also provide evidence of a parallel or convergent evolution on the molecular level supporting recent generalizations regarding the genetics of adaptation.
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Affiliation(s)
- Frank W Stearns
- Department of Biology, Biology-Psychology Building, University of Maryland College Park, Maryland, 20742
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48
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Debieu M, Tang C, Stich B, Sikosek T, Effgen S, Josephs E, Schmitt J, Nordborg M, Koornneef M, de Meaux J. Co-variation between seed dormancy, growth rate and flowering time changes with latitude in Arabidopsis thaliana. PLoS One 2013; 8:e61075. [PMID: 23717385 DOI: 10.1371/journal.pone.0061075.s002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 03/05/2013] [Indexed: 05/25/2023] Open
Abstract
Life-history traits controlling the duration and timing of developmental phases in the life cycle jointly determine fitness. Therefore, life-history traits studied in isolation provide an incomplete view on the relevance of life-cycle variation for adaptation. In this study, we examine genetic variation in traits covering the major life history events of the annual species Arabidopsis thaliana: seed dormancy, vegetative growth rate and flowering time. In a sample of 112 genotypes collected throughout the European range of the species, both seed dormancy and flowering time follow a latitudinal gradient independent of the major population structure gradient. This finding confirms previous studies reporting the adaptive evolution of these two traits. Here, however, we further analyze patterns of co-variation among traits. We observe that co-variation between primary dormancy, vegetative growth rate and flowering time also follows a latitudinal cline. At higher latitudes, vegetative growth rate is positively correlated with primary dormancy and negatively with flowering time. In the South, this trend disappears. Patterns of trait co-variation change, presumably because major environmental gradients shift with latitude. This pattern appears unrelated to population structure, suggesting that changes in the coordinated evolution of major life history traits is adaptive. Our data suggest that A. thaliana provides a good model for the evolution of trade-offs and their genetic basis.
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Affiliation(s)
- Marilyne Debieu
- Laboratoire des Interactions Plantes-Microorganismes, CNRS UMR2594, Castanet-Tolosan, France.
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49
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Co-variation between seed dormancy, growth rate and flowering time changes with latitude in Arabidopsis thaliana. PLoS One 2013; 8:e61075. [PMID: 23717385 PMCID: PMC3662791 DOI: 10.1371/journal.pone.0061075] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 03/05/2013] [Indexed: 01/20/2023] Open
Abstract
Life-history traits controlling the duration and timing of developmental phases in the life cycle jointly determine fitness. Therefore, life-history traits studied in isolation provide an incomplete view on the relevance of life-cycle variation for adaptation. In this study, we examine genetic variation in traits covering the major life history events of the annual species Arabidopsis thaliana: seed dormancy, vegetative growth rate and flowering time. In a sample of 112 genotypes collected throughout the European range of the species, both seed dormancy and flowering time follow a latitudinal gradient independent of the major population structure gradient. This finding confirms previous studies reporting the adaptive evolution of these two traits. Here, however, we further analyze patterns of co-variation among traits. We observe that co-variation between primary dormancy, vegetative growth rate and flowering time also follows a latitudinal cline. At higher latitudes, vegetative growth rate is positively correlated with primary dormancy and negatively with flowering time. In the South, this trend disappears. Patterns of trait co-variation change, presumably because major environmental gradients shift with latitude. This pattern appears unrelated to population structure, suggesting that changes in the coordinated evolution of major life history traits is adaptive. Our data suggest that A. thaliana provides a good model for the evolution of trade-offs and their genetic basis.
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50
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Méndez-Vigo B, Gomaa NH, Alonso-Blanco C, Xavier Picó F. Among- and within-population variation in flowering time of Iberian Arabidopsis thaliana estimated in field and glasshouse conditions. THE NEW PHYTOLOGIST 2013; 197:1332-1343. [PMID: 23252608 DOI: 10.1111/nph.12082] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 11/05/2012] [Indexed: 05/08/2023]
Abstract
The study of the evolutionary and population genetics of quantitative traits requires the assessment of within- and among-population patterns of variation. We carried out experiments including eight Iberian Arabidopsis thaliana populations (10 individuals per population) in glasshouse and field conditions. We quantified among- and within-population variation for flowering time and for several field life-history traits. Individuals were genotyped with microsatellites, single nucleotide polymorphisms and four well-known flowering genes (FRI, FLC, CRY2 and PHYC). Phenotypic and genotypic data were used to conduct Q(ST)-F(ST) comparisons. Life-history traits varied significantly among- and within-populations. Flowering time also showed substantial within- and among-population variation as well as significant genotype × environment interactions among the various conditions. Individuals bearing FRI truncations exhibited reduced recruitment in field conditions and differential flowering time behavior across experimental conditions, suggesting that FRI contributes to the observed significant genotype × environment interactions. Flowering time estimated in field conditions was the only trait showing significantly higher quantitative genetic differentiation than neutral genetic differentiation values. Overall, our results show that these A. thaliana populations are genetically more differentiated for flowering time than for neutral markers, suggesting that flowering time is likely to be under divergent selection.
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Affiliation(s)
- Belén Méndez-Vigo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049, Madrid, Spain
| | - Nasr H Gomaa
- Department of Botany, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049, Madrid, Spain
| | - F Xavier Picó
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), 41092, Sevilla, Spain
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