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Ensing DJ, Eckert CG. Interannual variation in season length is linked to strong co-gradient plasticity of phenology in a montane annual plant. THE NEW PHYTOLOGIST 2019; 224:1184-1200. [PMID: 31225910 DOI: 10.1111/nph.16009] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 06/10/2019] [Indexed: 06/09/2023]
Abstract
Species are commonly distributed along latitudinal and elevational gradients of growing season length to which they might respond via phenotypic plasticity and/or adaptive genetic differentiation. However, the relative contribution of these processes and whether plasticity, if it occurs, facilitates expansion along season-length gradients remain unclear, but are important for predicting species fates during anthropogenic change. We quantified phenological trait variation in the montane annual Rhinanthus minor for three generations at 12 sites across 900 m of elevation in the Canadian Rocky Mountains and conducted a reciprocal transplant experiment for two generations among nine sites. We compared clines and interannual variation of phenological traits between natural and transplanted individuals. Season length declined by c. 37% along our elevational gradient and, as expected, plants emerged, reached first flower and made their first seed in c. 41% fewer growing degree days under shorter growing seasons. Although reciprocal transplants revealed modest genetic differentiation across elevation, trait clines primarily were due to striking co-gradient plasticity that paralleled genetic differentiation. Co-gradient plasticity likely evolved in response to considerable interannual variation in season length across our elevational transect, and should prepare R. minor to make adaptive changes to phenology in response to ongoing climate change predicted for montane environments.
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Affiliation(s)
- David J Ensing
- Department of Biology, Queen's University, Kingston, ON, K7L 3N6, Canada
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52
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Kooyers NJ, Colicchio JM, Greenlee AB, Patterson E, Handloser NT, Blackman BK. Lagging Adaptation to Climate Supersedes Local Adaptation to Herbivory in an Annual Monkeyflower. Am Nat 2019; 194:541-557. [DOI: 10.1086/702312] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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53
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Dickman EE, Pennington LK, Franks SJ, Sexton JP. Evidence for adaptive responses to historic drought across a native plant species range. Evol Appl 2019; 12:1569-1582. [PMID: 31462915 PMCID: PMC6708426 DOI: 10.1111/eva.12803] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 03/15/2019] [Accepted: 03/19/2019] [Indexed: 01/03/2023] Open
Abstract
As climatic conditions change, species will be forced to move or adapt to avoid extinction. Exacerbated by ongoing climate change, California recently experienced a severe and exceptional drought from 2011 to 2017. To investigate whether an adaptive response occurred during this event, we conducted a "resurrection" study of the cutleaf monkeyflower (Mimulus laciniatus), an annual plant, by comparing trait means and variances of ancestral seed collections ("pre-drought") with contemporary descendant collections ("drought"). Plants were grown under common conditions to test whether this geographically restricted species has the capacity to respond evolutionarily to climate stress across its range. We examined if traits shifted in response to the recent, severe drought and included populations across an elevation gradient, including populations at the low- and high-elevation edges of the species range. We found that time to seedling emergence in the drought generation was significantly earlier than in the pre-drought generation, a response consistent with drought adaptation. Additionally, trait variation in days to emergence was reduced in the drought generation, which suggests selection or bottleneck events. Days to first flower increased significantly by elevation, consistent with climate adaptation across the species range. Drought generation plants were larger and had greater reproduction, which was likely a carryover effect of earlier germination. These results demonstrate that rapid shifts in trait means and variances consistent with climate adaptation are occurring within populations, including peripheral populations at warm and cold climate limits, of a plant species with a relatively restricted range that has so far not shifted its elevation distribution during contemporary climate change. Thus, rapid evolution may mitigate, at least temporarily, range shifts under global climate change. This study highlights the need for better understanding rapid adaptation as a means for plant communities to cope with extraordinary climate events.
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Affiliation(s)
- Erin E. Dickman
- Department of Life and Environmental SciencesUniversity of CaliforniaMercedCalifornia
- Yosemite National ParkEl PortalCalifornia
| | - Lillie K. Pennington
- Department of Life and Environmental SciencesUniversity of CaliforniaMercedCalifornia
| | - Steven J. Franks
- Department of Biological SciencesFordham UniversityBronxNew York
| | - Jason P. Sexton
- Department of Life and Environmental SciencesUniversity of CaliforniaMercedCalifornia
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Mantel SJ, Sweigart AL. Divergence in drought-response traits between sympatric species of Mimulus. Ecol Evol 2019; 9:10291-10304. [PMID: 31632643 PMCID: PMC6787937 DOI: 10.1002/ece3.5549] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 07/19/2019] [Accepted: 07/24/2019] [Indexed: 12/26/2022] Open
Abstract
Differential adaptation to local environmental conditions is thought to be an important driver of speciation. Plants, whose sedentary lifestyle necessitates fine-tuned adaptation to edaphic conditions such as water availability, are often distributed based on these conditions. Populations occupying water-limited habitats may employ a variety of strategies, involving numerous phenotypes, to prevent and withstand desiccation. In sympatry, two closely related Mimulus species-M. guttatus and M. nasutus-occupy distinct microhabitats that differ in seasonal water availability. In a common garden experiment, we characterized natural variation within and between sympatric M. guttatus and M. nasutus in the ability to successfully set seed under well-watered and drought conditions. We also measured key phenotypes for drought adaptation, including developmental timing, plant size, flower size, and stomatal density. Consistent with their microhabitat associations in nature, M. nasutus set seed much more successfully than M. guttatus under water-limited conditions. This divergence in reproductive output under drought was due to differences in mortality after the onset of flowering, with M. nasutus surviving at a much higher rate than M. guttatus. Higher seed set in M. nasutus was mediated, at least in part, by a plastic increase in the rate of late-stage development (i.e., fruit maturation), consistent with the ability of this species to inhabit more ephemeral habitats in the field. Our results suggest adaptation to water availability may be an important factor in species maintenance of these Mimulus taxa in sympatry.
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55
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Kooyers N. Are drought resistance strategies associated with life history strategy? A commentary on: 'Arabidopsis species deploy distinct strategies to cope with drought stress'. ANNALS OF BOTANY 2019; 124:vi-viii. [PMID: 31373618 PMCID: PMC6676376 DOI: 10.1093/aob/mcz096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
This article comments on: M. Bouzid, F. He, G. Schmitz, R. E. Häusler, A. P. M. Weber, T. Mettler-Altmann and J. de Meaux. 2019. Arabidopsis species deploy distinct strategies to cope with drought stress. Annals of Botany 124(1): 27–40.
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Affiliation(s)
- Nicholas Kooyers
- Department of Biology, University of Louisiana, Lafayette, LA, USA
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56
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Ferguson J, Meyer R, Edwards K, Humphry M, Brendel O, Bechtold U. Accelerated flowering time reduces lifetime water use without penalizing reproductive performance in Arabidopsis. PLANT, CELL & ENVIRONMENT 2019; 42:1847-1867. [PMID: 30707443 PMCID: PMC6563486 DOI: 10.1111/pce.13527] [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: 04/30/2018] [Accepted: 01/14/2019] [Indexed: 05/30/2023]
Abstract
Natural selection driven by water availability has resulted in considerable variation for traits associated with drought tolerance and leaf-level water-use efficiency (WUE). In Arabidopsis, little is known about the variation of whole-plant water use (PWU) and whole-plant WUE (transpiration efficiency). To investigate the genetic basis of PWU, we developed a novel proxy trait by combining flowering time and rosette water use to estimate lifetime PWU. We validated its usefulness for large-scale screening of mapping populations in a subset of ecotypes. This parameter subsequently facilitated the screening of water use and drought tolerance traits in a recombinant inbred line population derived from two Arabidopsis accessions with distinct water-use strategies, namely, C24 (low PWU) and Col-0 (high PWU). Subsequent quantitative trait loci mapping and validation through near-isogenic lines identified two causal quantitative trait loci, which showed that a combination of weak and nonfunctional alleles of the FRIGIDA (FRI) and FLOWERING LOCUS C (FLC) genes substantially reduced plant water use due to their control of flowering time. Crucially, we observed that reducing flowering time and consequently water use did not penalize reproductive performance, as such water productivity (seed produced per unit of water transpired) improved. Natural polymorphisms of FRI and FLC have previously been elucidated as key determinants of natural variation in intrinsic WUE (δ13 C). However, in the genetic backgrounds tested here, drought tolerance traits, stomatal conductance, δ13 C. and rosette water use were independent of allelic variation at FRI and FLC, suggesting that flowering is critical in determining lifetime PWU but not always leaf-level traits.
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Affiliation(s)
- John N. Ferguson
- School of Biological SciencesUniversity of EssexColchesterUK
- Institute for Genomic BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
| | - Rhonda C. Meyer
- Department of Molecular GeneticsLeibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
| | - Kieron D. Edwards
- Sibelius Natural Products Health Wellness and FitnessOxfordUK
- Advanced Technologies CambridgeCambridgeUK
| | - Matt Humphry
- Advanced Technologies CambridgeCambridgeUK
- Quantitative GeneticsBritish American TobaccoCambridgeUK
| | - Oliver Brendel
- Université de LorraineAgroParisTech, INRA, SilvaNancyFrance
| | - Ulrike Bechtold
- School of Biological SciencesUniversity of EssexColchesterUK
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57
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Khasanova A, Lovell JT, Bonnette J, Weng X, Jenkins J, Yoshinaga Y, Schmutz J, Juenger TE. The Genetic Architecture of Shoot and Root Trait Divergence Between Mesic and Xeric Ecotypes of a Perennial Grass. FRONTIERS IN PLANT SCIENCE 2019; 10:366. [PMID: 31019518 PMCID: PMC6458277 DOI: 10.3389/fpls.2019.00366] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 03/08/2019] [Indexed: 05/16/2023]
Abstract
Environmental heterogeneity can drive patterns of functional trait variation and lead to the formation of locally adapted ecotypes. Plant ecotypes are often differentiated by suites of correlated root and shoot traits that share common genetic, developmental, and physiological relationships. For instance, although plant water loss is largely governed by shoot systems, root systems determine water access and constrain shoot water status. To evaluate the genetic basis of root and shoot trait divergence, we developed a recombinant inbred population derived from mesic and xeric ecotypes of the perennial grass Panicum hallii. Our study sheds light on the genetic architecture underlying the relationships between root and shoot traits. We identified several genomic "hotspots" which control suites of correlated root and shoot traits, thus indicating genetic coordination between plant organ systems in the process of ecotypic divergence. Genomic regions of colocalized quantitative trait locus (QTL) for the majority of shoot and root growth related traits were independent of colocalized QTL for shoot and root resource acquisition traits. The allelic effects of individual QTL underscore ecological specialization for drought adaptation between ecotypes and reveal possible hybrid breakdown through epistatic interactions. These results have implications for understanding the factors constraining or facilitating local adaptation in plants.
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Affiliation(s)
- Albina Khasanova
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, United States
| | - John T. Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Jason Bonnette
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, United States
| | - Xiaoyu Weng
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, United States
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Yuko Yoshinaga
- United States Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Thomas E. Juenger
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, United States
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58
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Nelson TC, Jones MR, Velotta JP, Dhawanjewar AS, Schweizer RM. UNVEILing connections between genotype, phenotype, and fitness in natural populations. Mol Ecol 2019; 28:1866-1876. [PMID: 30830713 PMCID: PMC6525050 DOI: 10.1111/mec.15067] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/12/2019] [Accepted: 02/27/2019] [Indexed: 12/29/2022]
Abstract
Understanding the links between genetic variation and fitness in natural populations is a central goal of evolutionary genetics. This monumental task spans the fields of classical and molecular genetics, population genetics, biochemistry, physiology, developmental biology, and ecology. Advances to our molecular and developmental toolkits are facilitating integrative approaches across these traditionally separate fields, providing a more complete picture of the genotype-phenotype map in natural and non-model systems. Here, we summarize research presented at the first annual symposium of the UNVEIL Network, an NSF-funded collaboration between the University of Montana and the University of Nebraska, Lincoln, which took place from the 1st to the 3rd of June, 2018. We discuss how this body of work advances basic evolutionary science, what it implies for our ability to predict evolutionary change, and how it might inform novel conservation strategies.
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Affiliation(s)
- Thomas C Nelson
- Division of Biological Sciences, University of Montana, 32 Campus Dr HS 104, Missoula, MT, 59812
| | - Matthew R Jones
- Division of Biological Sciences, University of Montana, 32 Campus Dr HS 104, Missoula, MT, 59812
| | - Jonathan P Velotta
- Division of Biological Sciences, University of Montana, 32 Campus Dr HS 104, Missoula, MT, 59812
| | | | - Rena M Schweizer
- Division of Biological Sciences, University of Montana, 32 Campus Dr HS 104, Missoula, MT, 59812
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59
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Yuan YW. Monkeyflowers (Mimulus): new model for plant developmental genetics and evo-devo. THE NEW PHYTOLOGIST 2019; 222:694-700. [PMID: 30471231 DOI: 10.1111/nph.15560] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/18/2018] [Indexed: 06/09/2023]
Abstract
Contents Summary 694 I. Introduction 694 II. The system 695 III. Regulation of carotenoid pigmentation 695 IV. Formation of periodic pigmentation patterns 696 V. Developmental genetics of corolla tube formation and elaboration 697 VI. Molecular basis of floral trait variation underlying pollinator shift 698 VII. Outlook 699 Acknowledgements 699 References 699 SUMMARY: Monkeyflowers (Mimulus) have long been recognized as a classic ecological and evolutionary model system. However, only recently has it been realized that this system also holds great promise for studying the developmental genetics and evo-devo of important plant traits that are not found in well-established model systems such as Arabidopsis. Here, I review recent progress in four different areas of plant research enabled by this new model, including transcriptional regulation of carotenoid biosynthesis, formation of periodic pigmentation patterns, developmental genetics of corolla tube formation and elaboration, and the molecular basis of floral trait divergence underlying pollinator shift. These examples suggest that Mimulus offers ample opportunities to make exciting discoveries in plant development and evolution.
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Affiliation(s)
- Yao-Wu Yuan
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269, USA
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60
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Ware IM, Van Nuland ME, Schweitzer JA, Yang Z, Schadt CW, Sidak-Loftis LC, Stone NE, Busch JD, Wagner DM, Bailey JK. Climate-driven reduction of genetic variation in plant phenology alters soil communities and nutrient pools. GLOBAL CHANGE BIOLOGY 2019; 25:1514-1528. [PMID: 30659721 DOI: 10.1111/gcb.14553] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 12/07/2018] [Indexed: 06/09/2023]
Abstract
We examined the hypothesis that climate-driven evolution of plant traits will influence associated soil microbiomes and ecosystem function across the landscape. Using a foundation tree species, Populus angustifolia, observational and common garden approaches, and a base population genetic collection that spans 17 river systems in the western United States, from AZ to MT, we show that (a) as mean annual temperature (MAT) increases, genetic and phenotypic variation for bud break phenology decline; (b) soil microbiomes, soil nitrogen (N), and soil carbon (C) vary in response to MAT and conditioning by trees; and (c) with losses of genetic variation due to warming, population-level regulation of community and ecosystem functions strengthen. These results demonstrate a relationship between the potential evolutionary response of populations and subsequent shifts in ecosystem function along a large temperature gradient.
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Affiliation(s)
- Ian M Ware
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee
| | | | - Jennifer A Schweitzer
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee
| | - Zamin Yang
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Christopher W Schadt
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee
| | | | - Nathan E Stone
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona
| | - Joseph D Busch
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona
| | - David M Wagner
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona
| | - Joseph K Bailey
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee
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61
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Rubin MJ, Schmid KM, Friedman J. Assortative mating by flowering time and its effect on correlated traits in variable environments. Ecol Evol 2019; 9:471-481. [PMID: 30680129 PMCID: PMC6342113 DOI: 10.1002/ece3.4765] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/13/2018] [Accepted: 11/13/2018] [Indexed: 11/10/2022] Open
Abstract
Reproductive timing is a key life-history trait that impacts the pool of available mates, the environment experienced during flowering, and the expression of other traits through genetic covariation. Selection on phenology, and its consequences on other life-history traits, has considerable implications in the context of ongoing climate change and shifting growing seasons. To test this, we grew field-collected seed from the wildflower Mimulus guttatus in a greenhouse to assess the standing genetic variation for flowering time and covariation with other traits. We then created full-sib families through phenological assortative mating and grew offspring in three photoperiod treatments representing seasonal variation in daylength. We find substantial quantitative genetic variation for the onset of flowering time, which covaried with vegetative traits. The assortatively-mated offspring varied in their critical photoperiod by over two hours, so that families differed in their probability of flowering across treatments Allocation to flowering and vegetative growth changed across the daylength treatments, with consistent direction and magnitude of covariation among flowering time and other traits. Our results suggest that future studies of flowering time evolution should consider the joint evolution of correlated traits and shifting seasonal selection to understand how environmental variation influences life histories.
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62
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Johnson KM, Jordan GJ, Brodribb TJ. Wheat leaves embolized by water stress do not recover function upon rewatering. PLANT, CELL & ENVIRONMENT 2018; 41:2704-2714. [PMID: 29981153 DOI: 10.1111/pce.13397] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 06/26/2018] [Accepted: 06/27/2018] [Indexed: 05/14/2023]
Abstract
New techniques now make it possible to precisely and accurately determine the failure threshold of the plant vascular system during water stress. This creates an opportunity to understand the vulnerability of species to drought, but first, it must be determined whether damage to leaf function associated with xylem cavitation is reparable or permanent. This question is particularly relevant in crop plants such as wheat, which may have the capacity to repair xylem embolism with positive root pressure. Using wheat (Triticum aestivum, Heron), we employed non-invasive imaging to find the water potential causing 50% xylem embolism (-2.87 ± 0.52 MPa) in leaves. Replicate plants were water-stressed to varying degrees to induce embolism ranging from minimal to substantial. Plants were then rewatered to determine the reversibility of xylem damage and photosynthetic inhibition in glasshouse conditions. Rewatering after drought-induced xylem cavitation did not induce visible refilling of embolized xylem, and embolized leaves showed photosynthetic impairment upon rewatering. This impairment was significant even after only 10-20% of leaf veins were embolized, and leaves accumulating >20% embolism died upon rewatering in 7/10 individuals. Photosynthetic damage and hydraulic decline occurred concurrently as wheat leaves dehydrated, and leaf shrinkage during drying was the best predictor of photosynthetic recovery.
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Affiliation(s)
- Kate M Johnson
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Gregory J Jordan
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Timothy J Brodribb
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania, Australia
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63
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Bertel C, Rešetnik I, Frajman B, Erschbamer B, Hülber K, Schönswetter P. Natural selection drives parallel divergence in the mountain plant Heliosperma pusillum
s.l. OIKOS 2018. [DOI: 10.1111/oik.05364] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Clara Bertel
- Dept. of Botany; Univ. of Innsbruck, Sternwartestraße 15; AT-6020 Innsbruck Austria
| | | | - Božo Frajman
- Dept. of Botany; Univ. of Innsbruck, Sternwartestraße 15; AT-6020 Innsbruck Austria
| | - Brigitta Erschbamer
- Dept. of Botany; Univ. of Innsbruck, Sternwartestraße 15; AT-6020 Innsbruck Austria
| | - Karl Hülber
- Dept of Botany and Biodiversity Research; Univ. of Vienna; Vienna Austria
| | - Peter Schönswetter
- Dept. of Botany; Univ. of Innsbruck, Sternwartestraße 15; AT-6020 Innsbruck Austria
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64
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Campbell DR, Faidiga A, Trujillo G. Clines in traits compared over two decades in a plant hybrid zone. ANNALS OF BOTANY 2018; 122:315-324. [PMID: 29800076 PMCID: PMC6070099 DOI: 10.1093/aob/mcy072] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 04/17/2018] [Indexed: 05/30/2023]
Abstract
Background and Aims Clines in traits across hybrid zones reflect a balance between natural selection and gene flow. Changes over time in average values for traits, and especially the shapes of their clines, are rarely investigated in plants, but could result from evolution in an unstable hybrid zone. Differences in clines between floral and vegetative traits could indicate different strengths of divergent selection. Methods Five floral and two vegetative traits were measured in 12 populations along an elevational gradient spanning a natural hybrid zone between Ipomopsis aggregata and Ipomopsis tenuituba. We compared clines in the floral traits with those measured 25 years ago. Observed changes in mean trait values were compared with predictions based on prior estimates of natural selection. We also compared the steepness and position of clines between the floral and vegetative traits. Key Results Corolla length has increased over five generations to an extent that matches predictions from measurements of phenotypic selection and heritability. The shape of its cline, and that of other traits, has not changed detectably. Clines varied across traits, but not all floral traits showed steeper clines than did vegetative traits. Both suites of morphological traits had steeper clines than did neutral molecular markers. Conclusions The increase in corolla length provides a rare example of a match between predicted and observed evolution of a plant trait in natural populations. The clinal properties are consistent with the hypothesis that habitat-mediated divergent selection on vegetative traits and pollinator-mediated selection on floral traits both maintain species differences across the hybrid zone.
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Affiliation(s)
- Diane R Campbell
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
- Rocky Mountain Biological Laboratory, Crested Butte, CO 81224, USA
| | | | - Gabriel Trujillo
- Rocky Mountain Biological Laboratory, Crested Butte, CO 81224, USA
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65
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Pantoja PO, Paine CET, Vallejo-Marín M. Natural selection and outbreeding depression suggest adaptive differentiation in the invasive range of a clonal plant. Proc Biol Sci 2018; 285:20181091. [PMID: 30051824 PMCID: PMC6053932 DOI: 10.1098/rspb.2018.1091] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 06/14/2018] [Indexed: 11/12/2022] Open
Abstract
Analyses of phenotypic selection and demography in field populations are powerful ways to establishing the potential role of natural selection in shaping evolution during biological invasions. Here we use experimental F2 crosses between native and introduced populations of Mimulus guttatus to estimate the pattern of natural selection in part of its introduced range, and to seek evidence of outbreeding depression of colonists. The F2s combined the genome of an introduced population with the genome of either native or introduced populations. We found that the introduced × introduced cross had the fastest population growth rate owing to increased winter survival, clonality and seed production. Our analysis also revealed that selection through sexual fitness favoured large floral displays, large vegetative and flower size, lateral spread and early flowering. Our results indicate a source-of-origin effect, consistent with outbreeding depression exposed by mating between introduced and native populations. Our findings suggest that well-established non-native populations may pay a high fitness cost during subsequent bouts of admixture with native populations, and reveal that processes such as local adaptation in the invasive range can mediate the fitness consequences of admixture.
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Affiliation(s)
- Pauline O Pantoja
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
| | - C E Timothy Paine
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
| | - Mario Vallejo-Marín
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
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66
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Ferris KG, Willis JH. Differential adaptation to a harsh granite outcrop habitat between sympatric
Mimulus
species. Evolution 2018; 72:1225-1241. [DOI: 10.1111/evo.13476] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 02/20/2018] [Accepted: 02/28/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Kathleen G. Ferris
- Department of Biology Duke University 125 Science Drive Durham North Carolina 27705
- Current Address: Center for Population Biology, 2320 Storer Hall University of California Davis One Shields Avenue Davis California 95616
| | - John H. Willis
- Department of Biology Duke University 125 Science Drive Durham North Carolina 27705
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67
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Vaidya P, McDurmon A, Mattoon E, Keefe M, Carley L, Lee CR, Bingham R, Anderson JT. Ecological causes and consequences of flower color polymorphism in a self-pollinating plant (Boechera stricta). THE NEW PHYTOLOGIST 2018; 218:380-392. [PMID: 29369384 DOI: 10.1111/nph.14998] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 12/12/2017] [Indexed: 05/21/2023]
Abstract
Intraspecific variation in flower color is often attributed to pollinator-mediated selection, yet this mechanism cannot explain flower color polymorphisms in self-pollinating species. Indirect selection mediated via biotic and abiotic stresses could maintain flower color variation in these systems. The selfing forb, Boechera stricta, typically displays white flowers, but some individuals produce purple flowers. We quantified environmental correlates of flower color in natural populations. To disentangle plasticity from genotypic variation, we performed a multiyear field experiment in five gardens. In controlled conditions, we evaluated herbivore preferences and the effects of drought stress and soil pH on flower color expression. In natural populations, purple-flowered individuals experienced lower foliar herbivory than did their white-flowered counterparts. This pattern also held in the common gardens. Additionally, low-elevation environments induced pigmented flowers (plasticity), and the likelihood of floral pigmentation decreased with source elevation of maternal families (genetic cline). Viability selection favored families with pigmented flowers. In the laboratory, herbivores exerted greater damage on tissue derived from white- vs purple-flowered individuals. Furthermore, drought induced pigmentation in white-flowered lineages, and white-flowered plants had a fecundity advantage in the well-watered control. Flower color variation in selfing species is probably maintained by herbivory, drought stress, and other abiotic factors that vary spatially.
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Affiliation(s)
- Priya Vaidya
- The Rocky Mountain Biological Laboratory, Crested Butte, CO, 81224, USA
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Ansley McDurmon
- The Rocky Mountain Biological Laboratory, Crested Butte, CO, 81224, USA
| | - Emily Mattoon
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Michaela Keefe
- The Rocky Mountain Biological Laboratory, Crested Butte, CO, 81224, USA
- Department of Natural and Environmental Sciences, Western State Colorado University, Gunnison, CO, 81231, USA
| | - Lauren Carley
- The Rocky Mountain Biological Laboratory, Crested Butte, CO, 81224, USA
- Department of Biology, Duke University, Durham, NC, 27708, USA
- University Program in Ecology, Duke University, Durham, NC, 27708, USA
| | - Cheng-Ruei Lee
- Institute of Ecology and Evolutionary Biology & Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
| | - Robin Bingham
- The Rocky Mountain Biological Laboratory, Crested Butte, CO, 81224, USA
- Department of Natural and Environmental Sciences, Western State Colorado University, Gunnison, CO, 81231, USA
| | - Jill T Anderson
- The Rocky Mountain Biological Laboratory, Crested Butte, CO, 81224, USA
- Department of Genetics and Odum School of Ecology, University of Georgia, Athens, GA, 30602, USA
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68
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Molina-Montenegro MA, Acuña-Rodríguez IS, Flores TSM, Hereme R, Lafon A, Atala C, Torres-Díaz C. Is the Success of Plant Invasions the Result of Rapid Adaptive Evolution in Seed Traits? Evidence from a Latitudinal Rainfall Gradient. FRONTIERS IN PLANT SCIENCE 2018; 9:208. [PMID: 29535741 PMCID: PMC5835042 DOI: 10.3389/fpls.2018.00208] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 02/05/2018] [Indexed: 05/29/2023]
Abstract
It has been widely suggested that invasion success along broad environmental gradients may be partially due to phenotypic plasticity, but rapid evolution could also be a relevant factor for invasions. Seed and fruit traits can be relevant for plant invasiveness since they are related to dispersal, germination, and fitness. Some seed traits vary along environmental gradients and can be heritable, with the potential to evolve by means of natural selection. Utilizing cross-latitude and reciprocal-transplant experiments, we evaluated the adaptive value of seed thickness as assessed by survival and biomass accumulation in Taraxacum officinale plants. In addition, thickness of a seed and Endosperm to Seed Coat Proportion (ESCP) in a second generation (F2) was measured to evaluate the heritability of this seed trait. On the other hand, we characterized the genetic variability of the sampled individuals with amplified fragment length polymorphism (AFLP) markers, analyzing its spatial distribution and population structure. Overall, thickness of seed coat (plus wall achene) decreases with latitude, indicating that individuals of T. officinale from northern populations have a thicker seed coat than those from southern populations. Germination increased with greater addition of water and seeds from southern localities germinated significantly more than those from the north. Additionally, reciprocal transplants showed significant differences in survival percentage and biomass accumulation among individuals from different localities and moreover, the high correlation between maternal plants and their offspring can be suggesting a high grade of heritability of this trait. Although genetic differentiation was found when was considered all populations, there was no significant differentiation when only was compared the northernmost populations which inhabit in the driest climate conditions. Our results suggest that climatic conditions could affect both, the ESCP and the genetic variability in the invasive T. officinale, suggesting that this seed trait could be indicative of adaptive selection. Thus, colonization along broad geographical gradients in many cases may be the result -in part- for the presence of functional traits as shown in invasive plant species with rapid adaptive capacity.
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Affiliation(s)
- Marco A. Molina-Montenegro
- Centro de Estudios Avanzados en Ecología Molecular y Funcional, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
- Centro de Estudios Avanzados en Zonas Áridas, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile
- Research Program “Adaptation of the Agriculture to Climate Change” PIEI A2C2, Universidad de Talca, Talca, Chile
| | - Ian S. Acuña-Rodríguez
- Centro de Estudios Avanzados en Ecología Molecular y Funcional, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Tomás S. M. Flores
- Centro de Estudios Avanzados en Zonas Áridas, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile
| | - Rasme Hereme
- Centro de Estudios Avanzados en Ecología Molecular y Funcional, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Alejandra Lafon
- Centro de Investigación en Ecosistemas de la Patagonia, Coyhaique, Chile
| | - Cristian Atala
- Laboratorio de Anatomía y Ecología Funcional de Plantas, Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Cristian Torres-Díaz
- Grupo de Biodiversidad y Cambio Global, Departamento de Ciencias Básicas, Universidad del Bío-Bío, Chillan, Chile
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69
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Muir CD, Angert AL. Grow with the flow: a latitudinal cline in physiology is associated with more variable precipitation in Erythranthe cardinalis. J Evol Biol 2017; 30:2189-2203. [PMID: 28977720 DOI: 10.1111/jeb.13184] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 09/24/2017] [Accepted: 09/28/2017] [Indexed: 01/19/2023]
Abstract
Local adaptation is commonly observed in nature: organisms perform well in their natal environment, but poorly outside it. Correlations between traits and latitude, or latitudinal clines, are among the most common pieces of evidence for local adaptation, but identifying the traits under selection and the selective agents is challenging. Here, we investigated a latitudinal cline in growth and photosynthesis across 16 populations of the perennial herb Erythranthe cardinalis (Phrymaceae). Using machine learning methods, we identify interannual variation in precipitation as a likely selective agent: southern populations from more variable environments had higher photosynthetic rates and grew faster. We hypothesize that selection may favour a more annualized life history - grow now rather than save for next year - in environments where severe droughts occur more often. Thus, our study provides insight into how species may adapt if Mediterranean climates become more variable due to climate change.
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Affiliation(s)
- C D Muir
- Biodiversity Research Centre and Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - A L Angert
- Biodiversity Research Centre and Department of Botany, University of British Columbia, Vancouver, BC, Canada.,Department of Zoology, University of British Columbia, Vancouver, BC, Canada
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70
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Aeschbacher S, Selby JP, Willis JH, Coop G. Population-genomic inference of the strength and timing of selection against gene flow. Proc Natl Acad Sci U S A 2017; 114:7061-7066. [PMID: 28634295 PMCID: PMC5502586 DOI: 10.1073/pnas.1616755114] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The interplay of divergent selection and gene flow is key to understanding how populations adapt to local environments and how new species form. Here, we use DNA polymorphism data and genome-wide variation in recombination rate to jointly infer the strength and timing of selection, as well as the baseline level of gene flow under various demographic scenarios. We model how divergent selection leads to a genome-wide negative correlation between recombination rate and genetic differentiation among populations. Our theory shows that the selection density (i.e., the selection coefficient per base pair) is a key parameter underlying this relationship. We then develop a procedure for parameter estimation that accounts for the confounding effect of background selection. Applying this method to two datasets from Mimulus guttatus, we infer a strong signal of adaptive divergence in the face of gene flow between populations growing on and off phytotoxic serpentine soils. However, the genome-wide intensity of this selection is not exceptional compared with what M. guttatus populations may typically experience when adapting to local conditions. We also find that selection against genome-wide introgression from the selfing sister species M. nasutus has acted to maintain a barrier between these two species over at least the last 250 ky. Our study provides a theoretical framework for linking genome-wide patterns of divergence and recombination with the underlying evolutionary mechanisms that drive this differentiation.
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Affiliation(s)
- Simon Aeschbacher
- Department of Evolution and Ecology, University of California, Davis, CA 95616;
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | | | - John H Willis
- Department of Biology, Duke University, Durham, NC 27708
| | - Graham Coop
- Department of Evolution and Ecology, University of California, Davis, CA 95616
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71
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Pfennigwerth AA, Bailey JK, Schweitzer JA. Trait variation along elevation gradients in a dominant woody shrub is population-specific and driven by plasticity. AOB PLANTS 2017; 9:plx027. [PMID: 28721188 PMCID: PMC5509947 DOI: 10.1093/aobpla/plx027] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 06/15/2017] [Indexed: 05/24/2023]
Abstract
Elevation gradients are frequently used as space-for-time substitutions to infer species' trait responses to climate change. However, studies rarely investigate whether trait responses to elevation are widespread or population-specific within a species, and the relative genetic and plastic contributions to such trait responses may not be well understood. Here, we examine plant trait variation in the dominant woody shrub, Rhododendron maximum, along elevation gradients in three populations in the South Central Appalachian Mountains, USA, in both field and common garden environments. We ask the following: (i) do plant traits vary along elevation? (ii) do trait responses to elevation differ across populations, and if so, why? and (iii) does genetic differentiation or phenotypic plasticity drive trait variation within and among populations? We found that internode length, shoot length, leaf dry mass, and leaf area varied along elevation, but that these responses were generally unique to one population, suggesting that trait responses to environmental gradients are population-specific. A common garden experiment identified no genetic basis to variation along elevation or among populations in any trait, suggesting that plasticity drives local and regional trait variation and may play a key role in the persistence of plant species such as R. maximum with contemporary climate change. Overall, our findings highlight the importance of examining multiple locations in future elevation studies and indicate that, for a given plant species, the magnitude of trait responses to global climate change may vary by location.
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Affiliation(s)
- Alix A. Pfennigwerth
- Department of Ecology and Evolutionary Biology, University of Tennessee, 569 Dabney Hall, Knoxville, TN 37996-0001, USA
| | - Joseph K. Bailey
- Department of Ecology and Evolutionary Biology, University of Tennessee, 569 Dabney Hall, Knoxville, TN 37996-0001, USA
| | - Jennifer A. Schweitzer
- Department of Ecology and Evolutionary Biology, University of Tennessee, 569 Dabney Hall, Knoxville, TN 37996-0001, USA
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72
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Kooyers NJ, Blackman BK, Holeski LM. Optimal defense theory explains deviations from latitudinal herbivory defense hypothesis. Ecology 2017; 98:1036-1048. [DOI: 10.1002/ecy.1731] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 12/19/2016] [Accepted: 12/20/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Nicholas J. Kooyers
- Department of Biology University of Virginia Charlottesville Virginia 22904 USA
- Department of Integrative Biology University of South Florida Tampa Florida 33620 USA
- Department of Plant and Microbial Biology University of California Berkeley California 94720 USA
| | - Benjamin K. Blackman
- Department of Biology University of Virginia Charlottesville Virginia 22904 USA
- Department of Integrative Biology University of South Florida Tampa Florida 33620 USA
| | - Liza M. Holeski
- Department of Biological Sciences Northern Arizona University Flagstaff Arizona 86011 USA
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73
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Des Marais DL, Lasky JR, Verslues PE, Chang TZ, Juenger TE. Interactive effects of water limitation and elevated temperature on the physiology, development and fitness of diverse accessions of Brachypodium distachyon. THE NEW PHYTOLOGIST 2017; 214:132-144. [PMID: 27864966 DOI: 10.1111/nph.14316] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 10/03/2016] [Indexed: 05/21/2023]
Abstract
An enduring question in plant physiology and evolution is how single genotypes of plants optimize performance in diverse, often highly variable, environments. We grew 35 natural accessions of the grass Brachypodium distachyon in four environments in the glasshouse, contrasting soil water deficit, elevated temperature and their interaction. We modeled treatment, genotype and interactive effects on leaf-level and whole-plant traits, including fecundity. We also assessed the relationship between glasshouse-measured traits and parameters related to climate at the place of origin. We found abundant genetic variation in both constitutive and induced traits related to plant-water relations. Most traits showed strong interaction between temperature and water availability, and we observed genotype-by-environment interaction for several traits. Notably, leaf free proline abundance showed a strong effect of genotype × temperature × water. We found strong associations between phenology, biomass and water use efficiency (WUE) with parameters describing climate of origin. Plants respond to multiple stressors in ways not directly predictable from single stressors, underscoring the complex and trait-specific mechanisms of environmental response. Climate-trait correlations support a role for WUE and phenology in local adaptation to climate in B. distachyon.
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Affiliation(s)
- David L Des Marais
- Department of Integrative Biology and Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Jesse R Lasky
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Paul E Verslues
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Trent Z Chang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Thomas E Juenger
- Department of Integrative Biology and Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, USA
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74
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Kooyers NJ, James B, Blackman BK. Competition drives trait evolution and character displacement between Mimulus species along an environmental gradient. Evolution 2017; 71:1205-1221. [PMID: 28186619 DOI: 10.1111/evo.13200] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 01/24/2017] [Accepted: 01/27/2017] [Indexed: 01/31/2023]
Abstract
Closely related species may evolve to coexist stably in sympatry through niche differentiation driven by in situ competition, a process termed character displacement. Alternatively, past evolution in allopatry may have already sufficiently reduced niche overlap to permit establishment in sympatry, a process called ecological sorting. The relative importance of each process to niche differentiation is contentious even though they are not mutually exclusive and are both mediated via multivariate trait evolution. We explore how competition has impacted niche differentiation in two monkeyflowers, Mimulus alsinoides and M. guttatus, which often co-occur. Through field observations, common gardens, and competition experiments, we demonstrate that M. alsinoides is restricted to marginal habitats in sympatry and that the impacts of character displacement on niche differentiation are complex. Competition with M. guttatus alters selection gradients and has favored taller M. alsinoides with earlier seasonal flowering at low elevation and floral shape divergence at high elevation. However, no trait exhibits the pattern typically associated with character displacement, higher divergence between species in sympatry than allopatry. Thus, although character displacement was unlikely the process driving initial divergence along niche axes necessary for coexistence, we conclude that competition in sympatry has likely driven trait evolution along additional niche axes.
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Affiliation(s)
- Nicholas J Kooyers
- Department of Biology, University of Virginia, Charlottesville, Virginia, 22904.,Department of Plant and Microbial Biology, University of California, Berkeley, California, 94720.,Department of Integrative Biology, University of South Florida, Tampa, Florida, 33620
| | - Brooke James
- Department of Biology, University of Virginia, Charlottesville, Virginia, 22904
| | - Benjamin K Blackman
- Department of Biology, University of Virginia, Charlottesville, Virginia, 22904.,Department of Plant and Microbial Biology, University of California, Berkeley, California, 94720
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75
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Greenham K, Lou P, Puzey JR, Kumar G, Arnevik C, Farid H, Willis JH, McClung CR. Geographic Variation of Plant Circadian Clock Function in Natural and Agricultural Settings. J Biol Rhythms 2017; 32:26-34. [PMID: 27920227 DOI: 10.1177/0748730416679307] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
The increasing demand for improved agricultural production will require more efficient breeding for traits that maintain yield under heterogeneous environments. The internal circadian oscillator is essential for perceiving and coordinating environmental cues such as day length, temperature, and abiotic stress responses within physiological processes. To investigate the contribution of the circadian clock to local adaptability, we have analyzed circadian period by leaf movement in natural populations of Mimulus guttatus and domesticated cultivars of Glycine max. We detected consistent variation in circadian period along a latitudinal gradient in annual populations of the wild plant and the selectively bred crop, and this provides novel evidence of natural and artificial selection for circadian performance. These findings provide new support that the circadian clock acts as a central regulator of plant adaptability and further highlight the potential of applying circadian clock gene variation to marker-assisted breeding programs in crops.
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Affiliation(s)
- Kathleen Greenham
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire
| | - Ping Lou
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire
| | - Joshua R Puzey
- Biology Department, College of William and Mary, Williamsburg, Virginia
| | | | | | - Hany Farid
- Department of Computer Science, Dartmouth College, Hanover, New Hampshire
| | - John H Willis
- Biology Department, Duke University, Durham, North Carolina
| | - C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire
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76
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Puzey JR, Willis JH, Kelly JK. Population structure and local selection yield high genomic variation in Mimulus guttatus. Mol Ecol 2017; 26:519-535. [PMID: 27859786 PMCID: PMC5274581 DOI: 10.1111/mec.13922] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 09/30/2016] [Accepted: 11/07/2016] [Indexed: 12/30/2022]
Abstract
Across western North America, Mimulus guttatus exists as many local populations adapted to site-specific environmental challenges. Gene flow between locally adapted populations will affect genetic diversity both within demes and across the larger metapopulation. Here, we analyse 34 whole-genome sequences from the intensively studied Iron Mountain population (IM) in conjunction with sequences from 22 Mimulus individuals sampled from across western North America. Three striking features of these data address hypotheses about migration and selection in a locally adapted population. First, we find very high levels of intrapopulation polymorphism (synonymous π = 0.033). Variation outside of genes is likely even higher but difficult to estimate because excessive divergence reduces the efficiency of read mapping. Second, IM exhibits a significantly positive genomewide average for Tajima's D. This indicates allele frequencies are typically more intermediate than expected from neutrality, opposite the pattern observed in many other species. Third, IM exhibits a distinctive haplotype structure with a genomewide excess of positive associations between rarer alleles at linked loci. This suggests an important effect of gene flow from other Mimulus populations, although a residual effect of population founding might also contribute. The combination of multiple analyses, including a novel tree-based analytic method, illustrates how the balance of local selection, limited dispersal and metapopulation dynamics manifests across the genome. The overall genomic pattern of sequence diversity suggests successful gene flow of divergent immigrant genotypes into IM. However, many loci show patterns indicative of local adaptation, particularly at SNPs associated with chromosomal inversions.
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Affiliation(s)
- Joshua R. Puzey
- Department of Biology, College of William and Mary, Williamsburg, Virginia, 23187
- Department of Biology, Duke University, Durham, North Carolina, 27708
| | - John H. Willis
- Department of Biology, Duke University, Durham, North Carolina, 27708
| | - John K. Kelly
- Department of Ecology and Evolution, University of Kansas, Lawrence, Kansas, 27708
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77
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McAssey EV, Corbi J, Burke JM. Range-wide phenotypic and genetic differentiation in wild sunflower. BMC PLANT BIOLOGY 2016; 16:249. [PMID: 27829377 PMCID: PMC5103407 DOI: 10.1186/s12870-016-0937-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 10/28/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND Divergent phenotypes and genotypes are key signals for identifying the targets of natural selection in locally adapted populations. Here, we used a combination of common garden phenotyping for a variety of growth, plant architecture, and seed traits, along with single-nucleotide polymorphism (SNP) genotyping to characterize range-wide patterns of diversity in 15 populations of wild sunflower (Helianthus annuus L.) sampled along a latitudinal gradient in central North America. We analyzed geographic patterns of phenotypic diversity, quantified levels of within-population SNP diversity, and also determined the extent of population structure across the range of this species. We then used these data to identify significantly over-differentiated loci as indicators of genomic regions that likely contribute to local adaptation. RESULTS Traits including flowering time, plant height, and seed oil composition (i.e., percentage of saturated fatty acids) were significantly correlated with latitude, and thus differentiated northern vs. southern populations. Average pairwise FST was found to be 0.21, and a STRUCTURE analysis identified two significant clusters that largely separated northern and southern individuals. The significant FST outliers included a SNP in HaFT2, a flowering time gene that has been previously shown to co-localize with flowering time QTL, and which exhibits a known cline in gene expression. CONCLUSIONS Latitudinal differentiation in both phenotypic traits and SNP allele frequencies is observed across wild sunflower populations in central North America. Such differentiation may play an important adaptive role across the range of this species, and could facilitate adaptation to a changing climate.
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Affiliation(s)
- Edward V. McAssey
- Department of Plant Biology, University of Georgia, Miller Plant Sciences Building, Athens, GA 30602 USA
- University of Georgia, Center for Applied Genetic Technologies, 111 Riverbend Road, Athens, GA 30602 USA
| | - Jonathan Corbi
- Department of Plant Biology, University of Georgia, Miller Plant Sciences Building, Athens, GA 30602 USA
- Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France
| | - John M. Burke
- Department of Plant Biology, University of Georgia, Miller Plant Sciences Building, Athens, GA 30602 USA
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78
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Galbiati F, Chiozzotto R, Locatelli F, Spada A, Genga A, Fornara F. Hd3a, RFT1 and Ehd1 integrate photoperiodic and drought stress signals to delay the floral transition in rice. PLANT, CELL & ENVIRONMENT 2016; 39:1982-93. [PMID: 27111837 DOI: 10.1111/pce.12760] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 04/10/2016] [Indexed: 05/20/2023]
Abstract
Plants show a high degree of developmental plasticity in response to external cues, including day length and environmental stress. Water scarcity in particular can interfere with photoperiodic flowering, resulting in the acceleration of the switch to reproductive growth in several species, a process called drought escape. However, other strategies are possible and drought stress can also delay flowering, albeit the underlying mechanisms have never been addressed at the molecular level. We investigated these interactions in rice, a short day species in which drought stress delays flowering. A protocol that allows the synchronization of drought with the floral transition was set up to profile the transcriptome of leaves subjected to stress under distinct photoperiods. We identified clusters of genes that responded to drought differently depending on day length. Exposure to drought stress under floral-inductive photoperiods strongly reduced transcription of EARLY HEADING DATE 1 (Ehd1), HEADING DATE 3a (Hd3a) and RICE FLOWERING LOCUS T 1 (RFT1), primary integrators of day length signals, providing a molecular connection between stress and the photoperiodic pathway. However, phenotypic and transcriptional analyses suggested that OsGIGANTEA (OsGI) does not integrate drought and photoperiodic signals as in Arabidopsis, highlighting molecular differences between long and short day model species.
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Affiliation(s)
- Francesca Galbiati
- Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milan, Italy
- Department of Agricultural and Environmental Sciences - Production, Territory, Agroenergy, University of Milan, Via Celoria 2, 20133, Milan, Italy
| | - Remo Chiozzotto
- Institute of Agricultural Biology and Biotechnology, National Research Council, Via Bassini 15, 20133, Milan, Italy
| | - Franca Locatelli
- Institute of Agricultural Biology and Biotechnology, National Research Council, Via Bassini 15, 20133, Milan, Italy
| | - Alberto Spada
- Department of Agricultural and Environmental Sciences - Production, Territory, Agroenergy, University of Milan, Via Celoria 2, 20133, Milan, Italy
| | - Annamaria Genga
- Institute of Agricultural Biology and Biotechnology, National Research Council, Via Bassini 15, 20133, Milan, Italy
| | - Fabio Fornara
- Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milan, Italy
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79
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Wood CW, Brodie ED. Evolutionary response when selection and genetic variation covary across environments. Ecol Lett 2016; 19:1189-200. [DOI: 10.1111/ele.12662] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 06/27/2016] [Accepted: 07/13/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Corlett W. Wood
- Mountain Lake Biological Station and Department of Biology University of Virginia Charlottesville VA22904 USA
| | - Edmund D. Brodie
- Mountain Lake Biological Station and Department of Biology University of Virginia Charlottesville VA22904 USA
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80
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Hendrick MF, Finseth FR, Mathiasson ME, Palmer KA, Broder EM, Breigenzer P, Fishman L. The genetics of extreme microgeographic adaptation: an integrated approach identifies a major gene underlying leaf trichome divergence in Yellowstone Mimulus guttatus. Mol Ecol 2016; 25:5647-5662. [PMID: 27393073 DOI: 10.1111/mec.13753] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 06/15/2016] [Accepted: 06/22/2016] [Indexed: 12/30/2022]
Abstract
Microgeographic adaptation provides a particularly interesting context for understanding the genetic basis of phenotypic divergence and may also present unique empirical challenges. In particular, plant adaptation to extreme soil mosaics may generate barriers to gene flow or shifts in mating system that confound simple genomic scans for adaptive loci. Here, we combine three approaches - quantitative trait locus (QTL) mapping of candidate intervals in controlled crosses, population resequencing (PoolSeq) and analyses of wild recombinant individuals - to investigate one trait associated with Mimulus guttatus (yellow monkeyflower) adaptation to geothermal soils in Yellowstone National Park. We mapped a major QTL causing dense leaf trichomes in thermally adapted plants to a <50-kb region of linkage Group 14 (Tr14) previously implicated in trichome divergence between independent M. guttatus populations. A PoolSeq scan of Tr14 region revealed a cluster of six genes, coincident with the inferred QTL peak, with high allele frequency differences sufficient to explain observed phenotypic differentiation. One of these, the R2R3 MYB transcription factor Migut.N02661, is a plausible functional candidate and was also strongly associated (r2 = 0.27) with trichome phenotype in analyses of wild-collected admixed individuals. Although functional analyses will be necessary to definitively link molecular variants in Tr14 with trichome divergence, our analyses are a major step in that direction. They point to a simple, and parallel, genetic basis for one axis of Mimulus guttatus adaptation to an extreme habitat, suggest a broadly conserved genetic basis for trichome variation across flowering plants and pave the way for further investigations of this challenging case of microgeographic incipient speciation.
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Affiliation(s)
- Margaret F Hendrick
- Division of Biological Sciences, University of Montana, 32 Campus Dr., Missoula, MT, 59812, USA.,Department of Earth and Environment, Boston University, 685 Commonwealth Ave., Boston, MA, 02215, USA
| | - Findley R Finseth
- Division of Biological Sciences, University of Montana, 32 Campus Dr., Missoula, MT, 59812, USA
| | - Minna E Mathiasson
- School of Biology and Ecology, University of Maine, 5751 Murray Hall, Orono, ME, 04469, USA
| | - Kristen A Palmer
- Department of Biology, Wheaton College, 26 E. Main St., Norton, MA, 02766, USA
| | - Emma M Broder
- Biology Department, Wesleyan University, 45 Wyllys Ave., Middletown, CT, 06259, USA
| | - Peter Breigenzer
- Division of Biological Sciences, University of Montana, 32 Campus Dr., Missoula, MT, 59812, USA
| | - Lila Fishman
- Division of Biological Sciences, University of Montana, 32 Campus Dr., Missoula, MT, 59812, USA
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81
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DeMarche ML, Kay KM, Angert AL. The scale of local adaptation in Mimulus guttatus: comparing life history races, ecotypes, and populations. THE NEW PHYTOLOGIST 2016; 211:345-356. [PMID: 27102088 DOI: 10.1111/nph.13971] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/16/2016] [Indexed: 06/05/2023]
Abstract
Fitness trade-offs between environments are central to the evolution of biodiversity. Although transplant studies often document fitness trade-offs consistent with local adaptation (LA), many have also found an advantage of foreign genotypes (foreign advantage (FA)). Understanding the mechanisms driving the magnitude and distribution of fitness variation requires comparative approaches that test the ecological scales at which these different patterns emerge. We used a common garden transplant experiment to compare the relative fitnesses of native vs foreign genotypes at three nested ecological scales within Mimulus guttatus: annual vs perennial life history races, perennial ecotypes across an elevational range, and populations within perennial elevational ecotypes. We integrated fitness across the life-cycle and decomposed LA vs FA into contributions from different fitness components. We found LA, measured as home-site advantage, between annual and perennial races and a trend towards LA among populations within montane habitats. Conversely, we found strong FA of low-elevation perennials in a montane environment. LA between life history races reflects the fitness advantages of adult survival and vegetative growth in a mesic environment. Within the perennial race, recent climate conditions or nonselective processes, such as dispersal limitation or mutational load, could explain FA of low-elevation perennials in a montane environment.
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Affiliation(s)
- Megan L DeMarche
- Ecology and Evolutionary Biology, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Kathleen M Kay
- Ecology and Evolutionary Biology, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Amy L Angert
- Departments of Botany and Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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82
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Leaf morphological and anatomical traits from tropical to temperate coniferous forests: Mechanisms and influencing factors. Sci Rep 2016; 6:19703. [PMID: 26796339 PMCID: PMC4726163 DOI: 10.1038/srep19703] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 12/16/2015] [Indexed: 01/09/2023] Open
Abstract
Leaf traits may reflect the adaptation mechanisms of plants to the environment. In this study, we investigated leaf morphological and anatomical traits in nine cold-temperate to tropical forests along a 4,200-km transect to test how they vary across latitudinal gradients. The results showed that leaf dry weight decreased (P < 0.05), while specific leaf area (SLA) increased (P < 0.05) with increasing latitude. Stomatal length and stomatal density did not change significantly, while stomatal pore area index increased (P < 0.05) with increasing latitude. The palisade-leaf mesophyll thickness ratio increased (P < 0.01), while the spongy-leaf mesophyll thickness ratio decreased, with increasing latitude (P < 0.01). Climate and leaf nutrients were the main factors that regulated leaf morphological and anatomical traits. Furthermore, we identified positive correlations between leaf area and leaf dry weight, leaf thickness and palisade mesophyll thickness, but negative correlations between stomatal length and stomatal density (all P < 0.01). The observed negative correlations represented the adaptive mechanisms of leaves through their morphological and anatomical traits. These findings provided new insights into the responses of leaf morphological and anatomical traits to climate changes and important parameters for future model optimization.
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83
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Bragg JG, Supple MA, Andrew RL, Borevitz JO. Genomic variation across landscapes: insights and applications. THE NEW PHYTOLOGIST 2015; 207:953-67. [PMID: 25904408 DOI: 10.1111/nph.13410] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Accepted: 03/09/2015] [Indexed: 05/22/2023]
Abstract
The distribution of genomic variation across landscapes can provide insights into the complex interactions between the environment and the genome that influence the distribution of species, and mediate phenotypic adaptation to local conditions. High throughput sequencing technologies now offer unprecedented power to explore these interactions, allowing powerful inferences about historical processes of colonization, gene flow and divergence, as well as the identification of loci that mediate local adaptation. These 'landscape genomic' approaches have been validated in model species and are now being applied to nonmodel organisms, including foundation species that have substantial effects on ecosystem processes. Here we review the growing field of landscape genomics from a very broad perspective. In particular, we describe the inferential power that is gained by taking a genome-wide view of genetic variation, strategies for study design to best capture adaptive variation, and how to apply this information to practical challenges, such as restoration.
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Affiliation(s)
- Jason G Bragg
- Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Canberra, ACT, 0200, Australia
| | - Megan A Supple
- Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Canberra, ACT, 0200, Australia
| | - Rose L Andrew
- Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Canberra, ACT, 0200, Australia
- School of Environmental and Rural Science, University of New England, Armidale, NSW, 2350, Australia
| | - Justin O Borevitz
- Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Canberra, ACT, 0200, Australia
- ARC Centre of Excellence in Plant Energy Biology, Australian National University, Canberra, ACT, 0200, Australia
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84
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Adrion JR, Hahn MW, Cooper BS. Revisiting classic clines in Drosophila melanogaster in the age of genomics. Trends Genet 2015; 31:434-44. [PMID: 26072452 PMCID: PMC4526433 DOI: 10.1016/j.tig.2015.05.006] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 05/11/2015] [Accepted: 05/12/2015] [Indexed: 12/16/2022]
Abstract
Adaptation to spatially varying environments has been studied for decades, but advances in sequencing technology are now enabling researchers to investigate the landscape of genetic variation underlying this adaptation genome wide. In this review we highlight some of the decades-long research on local adaptation in Drosophila melanogaster from well-studied clines in North America and Australia. We explore the evidence for parallel adaptation and identify commonalities in the genes responding to clinal selection across continents as well as discussing instances where patterns differ among clines. We also investigate recent studies utilizing whole-genome data to identify clines in D. melanogaster and several other systems. Although connecting segregating genomic variation to variation in phenotypes and fitness remains challenging, clinal genomics is poised to increase our understanding of local adaptation and the selective pressures that drive the extensive phenotypic diversity observed in nature.
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Affiliation(s)
- Jeffrey R Adrion
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN 47405, USA; School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
| | - Brandon S Cooper
- Center for Population Biology, University of California, Davis, CA 95616, USA; Department of Evolution and Ecology, University of California, Davis, CA 95616, USA.
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85
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Hübner S, Korol AB, Schmid KJ. RNA-Seq analysis identifies genes associated with differential reproductive success under drought-stress in accessions of wild barley Hordeum spontaneum. BMC PLANT BIOLOGY 2015; 15:134. [PMID: 26055625 PMCID: PMC4459662 DOI: 10.1186/s12870-015-0528-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Accepted: 05/20/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND The evolutionary basis of reproductive success in different environments is of major interest in the study of plant adaptation. Since the reproductive stage is particularly sensitive to drought, genes affecting reproductive success during this stage are key players in the evolution of adaptive mechanisms. We used an ecological genomics approach to investigate the reproductive response of drought-tolerant and sensitive wild barley accessions originating from different habitats in the Levant. RESULTS We sequenced mRNA extracted from spikelets at the flowering stage in drought-treated and control plants. The barley genome was used for a reference-guided assembly and differential expression analysis. Our approach enabled to detect biological processes affecting grain production under drought stress. We detected novel candidate genes and differentially expressed alleles associated with drought tolerance. Drought associated genes were shown to be more conserved than non-associated genes, and drought-tolerance genes were found to evolve more rapidly than other drought associated genes. CONCLUSIONS We show that reproductive success under drought stress is not a habitat-specific trait but a shared physiological adaptation that appeared to evolve recently in the evolutionary history of wild barley. Exploring the genomic basis of reproductive success under stress in crop wild progenitors is expected to have considerable ecological and economical applications.
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Affiliation(s)
- Sariel Hübner
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel 31905, Haifa, Israel.
- Current address: Department of Botany, University of British Columbia, Vancouver, Canada.
| | - Abraham B Korol
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel 31905, Haifa, Israel.
| | - Karl J Schmid
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, D-70593, Stuttgart, Germany.
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86
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Twyford AD, Streisfeld MA, Lowry DB, Friedman J. Genomic studies on the nature of species: adaptation and speciation inMimulus. Mol Ecol 2015; 24:2601-9. [DOI: 10.1111/mec.13190] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 03/25/2015] [Accepted: 03/27/2015] [Indexed: 12/27/2022]
Affiliation(s)
- Alex D. Twyford
- Ashworth Laboratories; Institute of Evolutionary Biology; The University of Edinburgh; Charlotte Auerbach Road Edinburgh EH9 3FL UK
- Department of Biology; Syracuse University; 107 College Place Syracuse NY 13244 USA
| | | | - David B. Lowry
- Plant Biology Laboratories; Department of Plant Biology; Michigan State University; 612 Wilson Road Room 166 East Lansing MI 48824 USA
| | - Jannice Friedman
- Department of Biology; Syracuse University; 107 College Place Syracuse NY 13244 USA
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87
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Kooyers NJ. The evolution of drought escape and avoidance in natural herbaceous populations. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 234:155-62. [PMID: 25804818 DOI: 10.1016/j.plantsci.2015.02.012] [Citation(s) in RCA: 180] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 02/04/2015] [Accepted: 02/19/2015] [Indexed: 05/03/2023]
Abstract
While the functional genetics and physiological mechanisms controlling drought resistance in crop plants have been intensely studied, less research has examined the genetic basis of adaptation to drought stress in natural populations. Drought resistance adaptations in nature reflect natural rather than human-mediated selection and may identify novel mechanisms for stress tolerance. Adaptations conferring drought resistance have historically been divided into alternative strategies including drought escape (rapid development to complete a life cycle before drought) and drought avoidance (reducing water loss to prevent dehydration). Recent studies in genetic model systems such as Arabidopsis, Mimulus, and Panicum have begun to elucidate the genes, expression profiles, and physiological changes responsible for ecologically important variation in drought resistance. Similar to most crop plants, variation in drought escape and avoidance is complex, underlain by many QTL of small effect, and pervasive gene by environment interactions. Recently identified major-effect alleles point to a significant role for genetic constraints in limiting the concurrent evolution of both drought escape and avoidance strategies, although these constraints are not universally found. This progress suggests that understanding the mechanistic basic and fitness consequences of gene by environment interactions will be critical for crop improvement and forecasting population persistence in unpredictable environments.
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Affiliation(s)
- Nicholas J Kooyers
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA.
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88
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Greenham K, Lou P, Remsen SE, Farid H, McClung CR. TRiP: Tracking Rhythms in Plants, an automated leaf movement analysis program for circadian period estimation. PLANT METHODS 2015; 11:33. [PMID: 26019715 PMCID: PMC4445800 DOI: 10.1186/s13007-015-0075-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 03/12/2015] [Indexed: 05/22/2023]
Abstract
BACKGROUND A well characterized output of the circadian clock in plants is the daily rhythmic movement of leaves. This process has been used extensively in Arabidopsis to estimate circadian period in natural accessions as well as mutants with known defects in circadian clock function. Current methods for estimating circadian period by leaf movement involve manual steps throughout the analysis and are often limited to analyzing one leaf or cotyledon at a time. RESULTS In this study, we describe the development of TRiP (Tracking Rhythms in Plants), a new method for estimating circadian period using a motion estimation algorithm that can be applied to whole plant images. To validate this new method, we apply TRiP to a Recombinant Inbred Line (RIL) population in Arabidopsis using our high-throughput imaging platform. We begin imaging at the cotyledon stage and image through the emergence of true leaves. TRiP successfully tracks the movement of cotyledons and leaves without the need to select individual leaves to be analyzed. CONCLUSIONS TRiP is a program for analyzing leaf movement by motion estimation that enables high-throughput analysis of large populations of plants. TRiP is also able to analyze plant species with diverse leaf morphologies. We have used TRiP to estimate period for 150 Arabidopsis RILs as well as 5 diverse plant species, highlighting the broad applicability of this new method.
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Affiliation(s)
- Kathleen Greenham
- />Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, 03755 USA
| | - Ping Lou
- />Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, 03755 USA
| | - Sara E Remsen
- />Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, 03755 USA
| | - Hany Farid
- />Department of Computer Science, Dartmouth College, 6211 Sudikoff Lab, Hanover, 03755 USA
| | - C Robertson McClung
- />Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, 03755 USA
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