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Candido-Ribeiro R, Aitken SN. Weak local adaptation to drought in seedlings of a widespread conifer. THE NEW PHYTOLOGIST 2024; 241:2395-2409. [PMID: 38247230 DOI: 10.1111/nph.19543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024]
Abstract
Tree seedlings from populations native to drier regions are often assumed to be more drought tolerant than those from wetter provenances. However, intraspecific variation in drought tolerance has not been well-characterized despite being critical for developing climate change mitigation and adaptation strategies, and for predicting the effects of drought on forests. We used a large-scale common garden drought-to-death experiment to assess range-wide variation in drought tolerance, measured by decline of photosynthetic efficiency, growth, and plastic responses to extreme summer drought in seedlings of 73 natural populations of the two main varieties of Douglas-fir (Pseudotsuga menziesii var. menziesii and var. glauca). Local adaptation to drought was weak in var. glauca and nearly absent in menziesii. Var. glauca showed higher tolerance to drought but slower growth than var. menziesii. Clinal variation in drought tolerance and growth species-wide was mainly associated with temperature rather than precipitation. A higher degree of plasticity for growth was observed in var. menziesii in response to extreme drought. Genetic variation for drought tolerance in seedlings within varieties is maintained primarily within populations. Selective breeding within populations may facilitate adaptation to drought more than assisted gene flow.
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Affiliation(s)
- Rafael Candido-Ribeiro
- Department of Forest and Conservation Sciences, Centre for Forest Conservation Genetics, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Sally N Aitken
- Department of Forest and Conservation Sciences, Centre for Forest Conservation Genetics, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
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2
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Wadgymar SM, DeMarche ML, Josephs EB, Sheth SN, Anderson JT. Local adaptation: Causal agents of selection and adaptive trait divergence. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2022; 53:87-111. [PMID: 37790997 PMCID: PMC10544833 DOI: 10.1146/annurev-ecolsys-012722-035231] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Divergent selection across the landscape can favor the evolution of local adaptation in populations experiencing contrasting conditions. Local adaptation is widely observed in a diversity of taxa, yet we have a surprisingly limited understanding of the mechanisms that give rise to it. For instance, few have experimentally confirmed the biotic and abiotic variables that promote local adaptation, and fewer yet have identified the phenotypic targets of selection that mediate local adaptation. Here, we highlight critical gaps in our understanding of the process of local adaptation and discuss insights emerging from in-depth investigations of the agents of selection that drive local adaptation, the phenotypes they target, and the genetic basis of these phenotypes. We review historical and contemporary methods for assessing local adaptation, explore whether local adaptation manifests differently across life history, and evaluate constraints on local adaptation.
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Affiliation(s)
| | - Megan L DeMarche
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Emily B Josephs
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, 48824, USA
| | - Seema N Sheth
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Jill T Anderson
- Department of Genetics and Odum School of Ecology, University of Georgia, Athens, GA, 30602
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3
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Yu Y, Aitken SN, Rieseberg LH, Wang T. Using landscape genomics to delineate seed and breeding zones for lodgepole pine. THE NEW PHYTOLOGIST 2022; 235:1653-1664. [PMID: 35569109 PMCID: PMC9545436 DOI: 10.1111/nph.18223] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 05/08/2022] [Indexed: 06/15/2023]
Abstract
Seed and breeding zones traditionally are delineated based on local adaptation of phenotypic traits associated with climate variables, an approach requiring long-term field experiments. In this study, we applied a landscape genomics approach to delineate seed and breeding zones for lodgepole pine. We used a gradient forest (GF) model to select environment-associated single nucleotide polymorphisms (SNPs) using three SNP datasets (full, neutral and candidate) and 20 climate variables for 1906 lodgepole pine (Pinus contorta) individuals in British Columbia and Alberta, Canada. The two GF models built with the full (28 954) and candidate (982) SNPs were compared. The GF models identified winter-related climate as major climatic factors driving genomic patterns of lodgepole pine's local adaptation. Based on the genomic gradients predicted by the full and candidate GF models, lodgepole pine distribution range in British Columbia and Alberta was delineated into six seed and breeding zones. Our approach is a novel and effective alternative to traditional common garden approaches for delineating seed and breeding zone, and could be applied to tree species lacking data from provenance trials or common garden experiments.
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Affiliation(s)
- Yue Yu
- Department of Forest Sciences, Centre for Forest Conservation GeneticsUniversity of British Columbia3041‐2424 Main MallVancouverBCV6T 1Z4Canada
| | - Sally N. Aitken
- Department of Forest Sciences, Centre for Forest Conservation GeneticsUniversity of British Columbia3041‐2424 Main MallVancouverBCV6T 1Z4Canada
| | - Loren H. Rieseberg
- Department of Botany and Biodiversity Research CentreUniversity of British Columbia6270 University BoulevardVancouverBCV6T 1Z4Canada
| | - Tongli Wang
- Department of Forest Sciences, Centre for Forest Conservation GeneticsUniversity of British Columbia3041‐2424 Main MallVancouverBCV6T 1Z4Canada
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4
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Leaf Economic and Hydraulic Traits Signal Disparate Climate Adaptation Patterns in Two Co-Occurring Woodland Eucalypts. PLANTS 2022; 11:plants11141846. [PMID: 35890479 PMCID: PMC9320154 DOI: 10.3390/plants11141846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/06/2022] [Accepted: 07/09/2022] [Indexed: 11/23/2022]
Abstract
With climate change impacting trees worldwide, enhancing adaptation capacity has become an important goal of provenance translocation strategies for forestry, ecological renovation, and biodiversity conservation. Given that not every species can be studied in detail, it is important to understand the extent to which climate adaptation patterns can be generalised across species, in terms of the selective agents and traits involved. We here compare patterns of genetic-based population (co)variation in leaf economic and hydraulic traits, climate–trait associations, and genomic differentiation of two widespread tree species (Eucalyptus pauciflora and E. ovata). We studied 2-year-old trees growing in a common-garden trial established with progeny from populations of both species, pair-sampled from 22 localities across their overlapping native distribution in Tasmania, Australia. Despite originating from the same climatic gradients, the species differed in their levels of population variance and trait covariance, patterns of population variation within each species were uncorrelated, and the species had different climate–trait associations. Further, the pattern of genomic differentiation among populations was uncorrelated between species, and population differentiation in leaf traits was mostly uncorrelated with genomic differentiation. We discuss hypotheses to explain this decoupling of patterns and propose that the choice of seed provenances for climate-based plantings needs to account for multiple dimensions of climate change unless species-specific information is available.
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5
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Climate Adaptation, Drought Susceptibility, and Genomic-Informed Predictions of Future Climate Refugia for the Australian Forest Tree Eucalyptus globulus. FORESTS 2022. [DOI: 10.3390/f13040575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Understanding the capacity of forest tree species to adapt to climate change is of increasing importance for managing forest genetic resources. Through a genomics approach, we modelled spatial variation in climate adaptation within the Australian temperate forest tree Eucalyptus globulus, identified putative climate drivers of this genomic variation, and predicted locations of future climate refugia and populations at-risk of future maladaptation. Using 812,158 SNPs across 130 individuals from 30 populations (i.e., localities) spanning the species’ natural range, a gradientForest algorithm found 1177 SNPs associated with locality variation in home-site climate (climate-SNPs), putatively linking them to climate adaptation. Very few climate-SNPs were associated with population-level variation in drought susceptibility, signalling the multi-faceted nature and complexity of climate adaptation. Redundancy analysis (RDA) showed 24% of the climate-SNP variation could be explained by annual precipitation, isothermality, and maximum temperature of the warmest month. Spatial predictions of the RDA climate vectors associated with climate-SNPs allowed mapping of genomically informed climate selective surfaces across the species’ range under contemporary and projected future climates. These surfaces suggest over 50% of the current distribution of E. globulus will be outside the modelled adaptive range by 2070 and at risk of climate maladaptation. Such surfaces present a new integrated approach for natural resource managers to capture adaptive genetic variation and plan translocations in the face of climate change.
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6
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Non-Native Forest Tree Species in Europe: The Question of Seed Origin in Afforestation. FORESTS 2022. [DOI: 10.3390/f13020273] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Non-native forest tree species have been introduced in Europe since the 16th century, but only in the second half of the 20th century the significance of the seed source origin for their economic use was recognized, resulting in the establishment of numerous provenance trials at a national, regional, European and International level, as those led by IUFRO. Breeding programs have also been launched in the continent for the most economically important species. Aim of this work is the formulation of provenance recommendations for planting of five non-native tree species in Europe (Douglas fir, grand fir, Sitka spruce, lodgepole pine and black locust), based on the information obtained from twenty countries, in the frame of the EU FP-1403 NNEXT Cost Action. The survey revealed that official and non-official national recommendations, based on provenance research results, have been elaborated and followed at a different level and extend for the above five species, but only for Douglas fir recommendations exist in almost all the participating to the survey countries. The compilation of provenance recommendations across Europe for each species is presented in the current work. Besides the recommended introduced seed sources, European seed sources are also preferred for planting, due to ease of access and high availability of forest reproductive material. European breeding programs yielding genetic material of high productivity and quality constitute currently the seed source of choice for several species and countries. Consolidation of trial data obtained across countries will allow the joint analysis that is urgently needed to draw solid conclusions, and will facilitate the development of ‘Universal-Response-Functions’ for the species of interest, rendering possible the identification of the genetic material suitable for global change. New provenance trial series that will test seed sources from the entire climatic range of the species, established in sites falling within and outside the environmental envelopes of their natural ranges, are urgently needed to pinpoint and understand the species-specific climate constraints, as well as to correlate functional traits to the seed origin and the environmental conditions of the test sites, so that the selection of suitable forest reproductive material of non-native tree species in the face of climate change can be feasible.
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7
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Paril JF, Balding DJ, Fournier-Level A. Optimizing sampling design and sequencing strategy for the genomic analysis of quantitative traits in natural populations. Mol Ecol Resour 2021; 22:137-152. [PMID: 34192415 DOI: 10.1111/1755-0998.13458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 05/02/2021] [Accepted: 06/25/2021] [Indexed: 11/27/2022]
Abstract
Mapping the genes underlying ecologically relevant traits in natural populations is fundamental to develop a molecular understanding of species adaptation. Current sequencing technologies enable the characterization of a species' genetic diversity across the landscape or even over its whole range. The relevant capture of the genetic diversity across the landscape is critical for a successful genetic mapping of traits and there are no clear guidelines on how to achieve an optimal sampling and which sequencing strategy to implement. Here we determine, through simulation, the sampling scheme that maximizes the power to map the genetic basis of a complex trait in an outbreeding species across an idealized landscape and draw genomic predictions for the trait, comparing individual and pool sequencing strategies. Our results show that quantitative trait locus detection power and prediction accuracy are higher when more populations over the landscape are sampled and this is more cost-effectively done with pool sequencing than with individual sequencing. Additionally, we recommend sampling populations from areas of high genetic diversity. As progress in sequencing enables the integration of trait-based functional ecology into landscape genomics studies, these findings will guide study designs allowing direct measures of genetic effects in natural populations across the environment.
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Affiliation(s)
- Jefferson F Paril
- School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia
| | - David J Balding
- School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia.,Melbourne Integrative Genomics, The University of Melbourne, Parkville, Victoria, Australia.,School of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria, Australia
| | - Alexandre Fournier-Level
- School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia.,Melbourne Integrative Genomics, The University of Melbourne, Parkville, Victoria, Australia
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8
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Silica Particles Trigger the Exopolysaccharide Production of Harsh Environment Isolates of Growth-Promoting Rhizobacteria and Increase Their Ability to Enhance Wheat Biomass in Drought-Stressed Soils. Int J Mol Sci 2021; 22:ijms22126201. [PMID: 34201354 PMCID: PMC8229586 DOI: 10.3390/ijms22126201] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/25/2021] [Accepted: 05/27/2021] [Indexed: 01/16/2023] Open
Abstract
In coming decades, drought is expected to expand globally owing to increased evaporation and reduced rainfall. Understanding, predicting, and controlling crop plants’ rhizosphere has the potential to manipulate its responses to environmental stress. Our plant growth-promoting rhizobacteria (PGPR) are isolated from a natural laboratory, ‘The Evolution Canyon’, Israel, (EC), from the wild progenitors of cereals, where they have been co-habituating with their hosts for long periods of time. The study revealed that commercial TM50 silica particles (SN) triggered the PGPR production of exopolysaccharides (EPS) containing D-glucuronate (D-GA). The increased EPS content increased the PGPR water-holding capacity (WHC) and osmotic pressure of the biofilm matrix, which led to enhanced plant biomass in drought-stressed growth environments. Light- and cryo-electron- microscopic studies showed that, in the presence of silica (SN) particles, bacterial morphology is changed, indicating that SNs are associated with significant reprogramming in bacteria. The findings encourage the development of large-scale methods for isolate formulation with natural silicas that ensure higher WHC and hyperosmolarity under field conditions. Osmotic pressure involvement of holobiont cohabitation is also discussed.
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9
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Girardin MP, Isabel N, Guo XJ, Lamothe M, Duchesne I, Lenz P. Annual aboveground carbon uptake enhancements from assisted gene flow in boreal black spruce forests are not long-lasting. Nat Commun 2021; 12:1169. [PMID: 33608515 PMCID: PMC7895975 DOI: 10.1038/s41467-021-21222-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/12/2021] [Indexed: 01/31/2023] Open
Abstract
Assisted gene flow between populations has been proposed as an adaptive forest management strategy that could contribute to the sequestration of carbon. Here we provide an assessment of the mitigation potential of assisted gene flow in 46 populations of the widespread boreal conifer Picea mariana, grown in two 42-year-old common garden experiments and established in contrasting Canadian boreal regions. We use a dendroecological approach taking into account phylogeographic structure to retrospectively analyse population phenotypic variability in annual aboveground net primary productivity (NPP). We compare population NPP phenotypes to detect signals of adaptive variation and/or the presence of phenotypic clines across tree lifespans, and assess genotype-by-environment interactions by evaluating climate and NPP relationships. Our results show a positive effect of assisted gene flow for a period of approximately 15 years following planting, after which there was little to no effect. Although not long lasting, well-informed assisted gene flow could accelerate the transition from carbon source to carbon sink after disturbance.
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Affiliation(s)
- Martin P. Girardin
- grid.146611.50000 0001 0775 5922Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC Canada ,grid.38678.320000 0001 2181 0211Centre d’étude de la forêt, Université du Québec à Montréal, Montréal, QC Canada
| | - Nathalie Isabel
- grid.146611.50000 0001 0775 5922Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC Canada ,grid.23856.3a0000 0004 1936 8390Canada Research Chair in Forest Genomics, Faculté de Foresterie, de Géographie et de Géomatique, Université Laval, Québec, QC Canada
| | - Xiao Jing Guo
- grid.146611.50000 0001 0775 5922Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC Canada
| | - Manuel Lamothe
- grid.146611.50000 0001 0775 5922Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC Canada
| | - Isabelle Duchesne
- grid.202033.00000 0001 2295 5236Natural Resources Canada, Canadian Wood Fibre Centre, Québec, QC Canada
| | - Patrick Lenz
- grid.23856.3a0000 0004 1936 8390Canada Research Chair in Forest Genomics, Faculté de Foresterie, de Géographie et de Géomatique, Université Laval, Québec, QC Canada ,grid.202033.00000 0001 2295 5236Natural Resources Canada, Canadian Wood Fibre Centre, Québec, QC Canada
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10
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Bisbing SM, Urza AK, Buma BJ, Cooper DJ, Matocq M, Angert AL. Can long‐lived species keep pace with climate change? Evidence of local persistence potential in a widespread conifer. DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13191] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Sarah M. Bisbing
- Department of Natural Resources & Environmental Science Program in Ecology, Evolution, & Conservation Biology University of Nevada ‐ Reno Reno NV USA
| | - Alexandra K. Urza
- Department of Natural Resources & Environmental Science Program in Ecology, Evolution, & Conservation Biology University of Nevada ‐ Reno Reno NV USA
- Rocky Mountain Research Station USDA Forest Service Reno NV USA
| | - Brian J. Buma
- Department of Integrative Biology University of Colorado Denver CO USA
| | - David J. Cooper
- Department of Forest and Rangeland Stewardship & Graduate Degree Program in Ecology Colorado State University Fort Collins CO USA
| | - Marjorie Matocq
- Department of Natural Resources & Environmental Science Program in Ecology, Evolution, & Conservation Biology University of Nevada ‐ Reno Reno NV USA
| | - Amy L. Angert
- Departments of Botany and Zoology University of British Columbia Vancouver BC Canada
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11
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Csilléry K, Buchmann N, Fady B. Adaptation to drought is coupled with slow growth, but independent from phenology in marginal silver fir ( Abies alba Mill.) populations. Evol Appl 2020; 13:2357-2376. [PMID: 33042220 PMCID: PMC7539328 DOI: 10.1111/eva.13029] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 05/01/2020] [Accepted: 05/05/2020] [Indexed: 12/20/2022] Open
Abstract
Drought is one of the most important selection pressures for forest trees in the context of climate change. Yet, the different evolutionary mechanisms, and their environmental drivers, by which certain populations become more drought tolerant than others is still little understood. We studied adaptation to drought in 16 silver fir (Abies alba Mill.) populations from the French Mediterranean Alps by combining observations on seedlings from a greenhouse experiment (N = 8,199) and on adult tress in situ (N = 315). In the greenhouse, we followed half-sib families for four growing seasons for growth and phenology traits, and tested their water stress response in a "drought until death" experiment. Adult trees in the field were assessed for δ 13C, a proxy for water use efficiency, and genotyped at 357 SNP loci. SNP data was used to generate a null expectation for seedling trait divergence between populations in order to detect the signature of selection, and 31 environmental variables were used to identify the selective environment. We found that seedlings originating from populations with low soil water capacity grew more slowly, attained a smaller stature, and resisted water stress for a longer period of time in the greenhouse. Additionally, adult trees of these populations exhibited a higher water use efficiency as evidenced by their δ 13C. These results suggest a correlated evolution of the growth-drought tolerance trait complex. Population divergence in bud break phenology was adaptive only in the second growing season, and evolved independently from the growth-drought tolerance trait complex. Adaptive divergence in bud break phenology was principally driven by the inter- and intra-annual variation in temperature at the geographic origin of the population. Our results illustrate the different evolutionary strategies used by populations to cope with drought stress at the range limits across a highly heterogeneous landscape, and can be used to inform assisted migration programs.
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Affiliation(s)
- Katalin Csilléry
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZürichZürichSwitzerland
- Biodiversity & Conservation BiologySwiss Federal Research Institute WSLBirmensdorfSwitzerland
| | - Nina Buchmann
- Institute of Agricultural SciencesETH ZürichZürichSwitzerland
| | - Bruno Fady
- INRAEcology of Mediterranean Forests (URFM)UR629AvignonFrance
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12
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Fréchette E, Chang CYY, Ensminger I. Variation in the phenology of photosynthesis among eastern white pine provenances in response to warming. GLOBAL CHANGE BIOLOGY 2020; 26:5217-5234. [PMID: 32396692 DOI: 10.1111/gcb.15150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 04/01/2020] [Indexed: 06/11/2023]
Abstract
In higher-latitude trees, temperature and photoperiod control the beginning and end of the photosynthetically active season. Elevated temperature (ET) has advanced spring warming and delayed autumn cooling while photoperiod remains unchanged. We assessed the effects of warming on the length of the photosynthetically active season of three provenances of Pinus strobus L. seedlings from different latitudes, and evaluated the accuracy of the photochemical reflectance index (PRI) and the chlorophyll/carotenoid index (CCI) for tracking the predicted variation in spring and autumn phenology of photosynthesis among provenances. Seedlings from northern, local and southern P. strobus provenances were planted in a temperature-free-air-controlled enhancement (T-FACE) experiment and exposed to ET (+1.5/3°C; day/night). Over 18 months, we assessed photosynthetic phenology by measuring chlorophyll fluorescence, gas exchange, leaf spectral reflectance and pigment content. During autumn, all seedlings regardless of provenance followed the same sequence of phenological events with the initial downregulation of photosynthesis, followed by the modulation of non-photochemical quenching and associated adjustments of zeaxanthin pool sizes. However, the timing of autumn downregulation differed between provenances, with delayed onset in the southern provenance (SP) and earlier onset in the northern relative to the local provenance, indicating that photoperiod at the provenance origin is a dominant factor controlling autumn phenology. Experimental warming further delayed the downregulation of photosynthesis during autumn in the SP. A provenance effect during spring was also observed but was generally not significant. The vegetation indices PRI and CCI were both effective at tracking the seasonal variations of energy partitioning in needles and the differences of carotenoid pigments indicative of the stress status of needles. These results demonstrate that PRI and CCI can be useful tools for monitoring conifer phenology and for the remote monitoring of the length of the photosynthetically active season of conifers in a changing climate.
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Affiliation(s)
- Emmanuelle Fréchette
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Christine Yao-Yun Chang
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Ingo Ensminger
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
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13
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Hargreaves AL, Germain RM, Bontrager M, Persi J, Angert AL. Local Adaptation to Biotic Interactions: A Meta-analysis across Latitudes. Am Nat 2020; 195:395-411. [PMID: 32097037 DOI: 10.1086/707323] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Adaptation to local conditions can increase species' geographic distributions and rates of diversification, but which components of the environment commonly drive local adaptation-particularly the importance of biotic interactions-is unclear. Biotic interactions should drive local adaptation when they impose consistent divergent selection; if this is common, we expect transplant experiments to detect more frequent and stronger local adaptation when biotic interactions are left intact. We tested this hypothesis using a meta-analysis of transplant experiments from >125 studies (mostly of plants). Overall, local adaptation was common, and biotic interactions affected fitness. Nevertheless, local adaptation was neither more common nor stronger when biotic interactions were left intact, either between experimental treatments within studies (control vs. biotic interactions experimentally manipulated) or between studies that used natural versus biotically altered transplant environments. However, the effect of ameliorating negative interactions varied with latitude, suggesting that interactions may promote local adaptation more often in tropical than in temperate ecosystems, although few tropical studies were available to test this. Our results suggest that biotic interactions often fail to drive local adaptation even though they strongly affect fitness, perhaps because temperate biotic environments are unpredictable at the spatiotemporal scales required for local adaptation.
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14
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Mahony CR, MacLachlan IR, Lind BM, Yoder JB, Wang T, Aitken SN. Evaluating genomic data for management of local adaptation in a changing climate: A lodgepole pine case study. Evol Appl 2020; 13:116-131. [PMID: 31892947 PMCID: PMC6935591 DOI: 10.1111/eva.12871] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 06/29/2019] [Accepted: 07/24/2019] [Indexed: 01/03/2023] Open
Abstract
We evaluate genomic data, relative to phenotypic and climatic data, as a basis for assisted gene flow and genetic conservation. Using a seedling common garden trial of 281 lodgepole pine (Pinus contorta) populations from across western Canada, we compare genomic data to phenotypic and climatic data to assess their effectiveness in characterizing the climatic drivers and spatial scale of local adaptation in this species. We find that phenotype-associated loci are equivalent or slightly superior to climate data for describing local adaptation in seedling traits, but that climate data are superior to genomic data that have not been selected for phenotypic associations. We also find agreement between the climate variables associated with genomic variation and with 20-year heights from a long-term provenance trial, suggesting that genomic data may be a viable option for identifying climatic drivers of local adaptation where phenotypic data are unavailable. Genetic clines associated with the experimental traits occur at broad spatial scales, suggesting that standing variation of adaptive alleles for this and similar species does not require management at scales finer than those indicated by phenotypic data. This study demonstrates that genomic data are most useful when paired with phenotypic data, but can also fill some of the traditional roles of phenotypic data in management of species for which phenotypic trials are not feasible.
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Affiliation(s)
- Colin R. Mahony
- Centre for Forest Conservation Genetics and Department of Forest and Conservation SciencesUniversity of British ColumbiaVancouverBCCanada
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
| | - Ian R. MacLachlan
- Centre for Forest Conservation Genetics and Department of Forest and Conservation SciencesUniversity of British ColumbiaVancouverBCCanada
| | - Brandon M. Lind
- Centre for Forest Conservation Genetics and Department of Forest and Conservation SciencesUniversity of British ColumbiaVancouverBCCanada
| | - Jeremy B. Yoder
- Centre for Forest Conservation Genetics and Department of Forest and Conservation SciencesUniversity of British ColumbiaVancouverBCCanada
- Department of BiologyCalifornia State University NorthridgeNorthridgeCAUSA
| | - Tongli Wang
- Centre for Forest Conservation Genetics and Department of Forest and Conservation SciencesUniversity of British ColumbiaVancouverBCCanada
| | - Sally N. Aitken
- Centre for Forest Conservation Genetics and Department of Forest and Conservation SciencesUniversity of British ColumbiaVancouverBCCanada
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15
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Isaac-Renton M, Montwé D, Hamann A, Spiecker H, Cherubini P, Treydte K. Northern forest tree populations are physiologically maladapted to drought. Nat Commun 2018; 9:5254. [PMID: 30531998 PMCID: PMC6288165 DOI: 10.1038/s41467-018-07701-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 11/14/2018] [Indexed: 11/08/2022] Open
Abstract
Northern forests at the leading edge of their distributions may not show increased primary productivity under climate warming, being limited by climatic extremes such as drought. Looking beyond tree growth to underlying physiological mechanisms is fundamental for accurate predictions of forest responses to climate warming and drought stress. Within a 32-year genetic field trial, we analyze relative contributions of xylem plasticity and inferred stomatal response to drought tolerance in regional populations of a widespread conifer. Genetic adaptation leads to varying responses under drought. Trailing-edge tree populations produce fewer tracheids with thicker cell walls, characteristic of drought-tolerance. Stomatal response explains the moderate drought tolerance of tree populations in central areas of the species range. Growth loss of the northern population is linked to low stomatal responsiveness combined with the production of tracheids with thinner cell walls. Forests of the western boreal may therefore lack physiological adaptations necessary to tolerate drier conditions.
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Affiliation(s)
- Miriam Isaac-Renton
- Department of Renewable Resources, University of Alberta, Edmonton, AB, T6G 2H1, Canada.
| | - David Montwé
- Department of Renewable Resources, University of Alberta, Edmonton, AB, T6G 2H1, Canada
| | - Andreas Hamann
- Department of Renewable Resources, University of Alberta, Edmonton, AB, T6G 2H1, Canada
| | - Heinrich Spiecker
- Chair of Forest Growth and Dendroecology, Albert-Ludwigs-Universität-Freiburg, Tennenbacherstrasse 4, 79106, Freiburg, Germany
| | - Paolo Cherubini
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
| | - Kerstin Treydte
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
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16
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Lotterhos KE, Yeaman S, Degner J, Aitken S, Hodgins KA. Modularity of genes involved in local adaptation to climate despite physical linkage. Genome Biol 2018; 19:157. [PMID: 30290843 PMCID: PMC6173883 DOI: 10.1186/s13059-018-1545-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 09/18/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Linkage among genes experiencing different selection pressures can make natural selection less efficient. Theory predicts that when local adaptation is driven by complex and non-covarying stresses, increased linkage is favored for alleles with similar pleiotropic effects, with increased recombination favored among alleles with contrasting pleiotropic effects. Here, we introduce a framework to test these predictions with a co-association network analysis, which clusters loci based on differing associations. We use this framework to study the genetic architecture of local adaptation to climate in lodgepole pine, Pinus contorta, based on associations with environments. RESULTS We identify many clusters of candidate genes and SNPs associated with distinct environments, including aspects of aridity and freezing, and discover low recombination rates among some candidate genes in different clusters. Only a few genes contain SNPs with effects on more than one distinct aspect of climate. There is limited correspondence between co-association networks and gene regulatory networks. We further show how associations with environmental principal components can lead to misinterpretation. Finally, simulations illustrate both benefits and caveats of co-association networks. CONCLUSIONS Our results support the prediction that different selection pressures favor the evolution of distinct groups of genes, each associating with a different aspect of climate. But our results went against the prediction that loci experiencing different sources of selection would have high recombination among them. These results give new insight into evolutionary debates about the extent of modularity, pleiotropy, and linkage in the evolution of genetic architectures.
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Affiliation(s)
- Katie E Lotterhos
- Department of Marine and Environmental Sciences, Northeastern Marine Science Center, 430 Nahant Rd, Nahant, MA, 01908, USA.
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N1N4, Canada
| | - Jon Degner
- Department of Forest and Conservation Sciences, Faculty of Forestry, Vancouver, BC, V6T 1Z4, Canada
| | - Sally Aitken
- Department of Forest and Conservation Sciences, Faculty of Forestry, Vancouver, BC, V6T 1Z4, Canada
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Wellington Rd, Clayton, Melbourne, VIC, 3800, Australia
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17
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Wos G, Willi Y. Genetic differentiation in life history traits and thermal stress performance across a heterogeneous dune landscape in Arabidopsis lyrata. ANNALS OF BOTANY 2018; 122:473-484. [PMID: 29846507 PMCID: PMC6110339 DOI: 10.1093/aob/mcy090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/30/2018] [Indexed: 06/08/2023]
Abstract
Background and Aims Over very short spatial scales, the habitat of a species can differ in multiple abiotic and biotic factors. These factors may impose natural selection on several traits and can cause genetic differentiation within a population. We studied multivariate genetic differentiation in a plant species of a sand dune landscape by linking environmental variation with differences in genotypic trait values and gene expression levels to find traits and candidate genes of microgeographical adaptation. Methods Maternal seed families of Arabidopsis lyrata were collected in Saugatuck Dunes State Park, Michigan, USA, and environmental parameters were recorded at each collection site. Offspring plants were raised in climate chambers and exposed to one of three temperature treatments: regular occurrence of frost, heat, or constant control conditions. Several traits were assessed: plant growth, time to flowering, and frost and heat resistance. Key Results The strongest trait-environment association was between a fast switch to sexual reproduction and weaker growth under frost, and growing in the open, away from trees. The second strongest association was between the trait combination of small plant size and early flowering under control conditions combined with large size under frost, and the combination of environmental conditions of growing close to trees, at low vegetation cover, on dune bottoms. Gene expression analysis by RNA-seq revealed candidate genes involved in multivariate trait differentiation. Conclusions The results support the hypothesis that in natural populations, many environmental factors impose selection, and that they affect multiple traits, with the relative direction of trait change being complex. The results highlight that heterogeneity in the selection environment over small spatial scales is a main driver of the maintenance of adaptive genetic variation within populations.
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Affiliation(s)
- Guillaume Wos
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
- Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- Department of Botany, Charles University, Prague, Czech Republic
| | - Yvonne Willi
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
- Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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18
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Park A, Talbot C. Information Underload: Ecological Complexity, Incomplete Knowledge, and Data Deficits Create Challenges for the Assisted Migration of Forest Trees. Bioscience 2018. [DOI: 10.1093/biosci/biy001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Andrew Park
- Department of Biology at the University of Winnipeg, in Manitoba, Canada
| | - Carolyn Talbot
- Technology and Public Policy at the University of Winnipeg
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19
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Sebastian‐Azcona J, Hacke UG, Hamann A. Adaptations of white spruce to climate: strong intraspecific differences in cold hardiness linked to survival. Ecol Evol 2018; 8:1758-1768. [PMID: 29435250 PMCID: PMC5792524 DOI: 10.1002/ece3.3796] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/14/2017] [Accepted: 12/11/2017] [Indexed: 02/02/2023] Open
Abstract
Understanding local adaptation of tree populations to climate allows the development of assisted migration guidelines as a tool for forest managers to address climate change. Here, we study the relationship among climate, a wide range of physiological traits, and field performance of selected white spruce provenances originating from throughout the species range. Tree height, survival, cold hardiness, hydraulic, and wood anatomical traits were measured in a 32-year-old common garden trial, located in the center of the species range. Provenance performance included all combinations of high versus low survival and growth, with the most prevalent population differentiation for adaptive traits observed in cold hardiness. Cold hardiness showed a strong association with survival and was associated with cold winter temperatures at the site of seed origin. Tree height was mostly explained by the length of the growing season at the origin of the seed source. Although population differentiation was generally weak in wood anatomical and hydraulic traits, within-population variation was substantial in some traits, and a boundary analysis revealed that efficient water transport was associated with vulnerable xylem and low wood density, indicating that an optimal combination of high water transport efficiency and high cavitation resistance is not possible. Our results suggest that assisted migration prescriptions may be advantageous under warming climate, but pronounced trade-offs between survival and cold hardiness require a careful consideration of the distances of these transfers.
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Affiliation(s)
| | - Uwe G Hacke
- Department of Renewable ResourcesUniversity of AlbertaEdmontonABCanada
| | - Andreas Hamann
- Department of Renewable ResourcesUniversity of AlbertaEdmontonABCanada
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20
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Conte GL, Hodgins KA, Yeaman S, Degner JC, Aitken SN, Rieseberg LH, Whitlock MC. Bioinformatically predicted deleterious mutations reveal complementation in the interior spruce hybrid complex. BMC Genomics 2017; 18:970. [PMID: 29246191 PMCID: PMC5731209 DOI: 10.1186/s12864-017-4344-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 11/21/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Mutation load is expected to be reduced in hybrids via complementation of deleterious alleles. While local adaptation of hybrids confounds phenotypic tests for reduced mutation load, it may be possible to assess variation in load by analyzing the distribution of putatively deleterious alleles. Here, we use this approach in the interior spruce (Picea glauca x P. engelmannii) hybrid complex, a group likely to suffer from high mutation load and in which hybrids exhibit local adaptation to intermediate conditions. We used PROVEAN to bioinformatically predict whether non-synonymous alleles are deleterious, based on conservation of the position and abnormality of the amino acid change. RESULTS As expected, we found that predicted deleterious alleles were at lower average allele frequencies than alleles not predicted to be deleterious. We were unable to detect a phenotypic effect on juvenile growth rate of the many rare alleles predicted to be deleterious. Both the proportion of alleles predicted to be deleterious and the proportion of loci homozygous for predicted deleterious alleles were higher in P. engelmannii (Engelmann spruce) than in P. glauca (white spruce), due to higher diversity and frequencies of rare alleles in Engelmann. Relative to parental species, the proportion of alleles predicted to be deleterious was intermediate in hybrids, and the proportion of loci homozygous for predicted deleterious alleles was lowest. CONCLUSION Given that most deleterious alleles are recessive, this suggests that mutation load is reduced in hybrids due to complementation of deleterious alleles. This effect may enhance the fitness of hybrids.
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Affiliation(s)
- Gina L Conte
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada. .,Department of Botany, University of British Columbia, 3200-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada.
| | - Kathryn A Hodgins
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada.,Present Address: School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, 3800, Australia
| | - Sam Yeaman
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada.,Present Address: Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, AB, T2N 1N4, Canada
| | - Jon C Degner
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Sally N Aitken
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Loren H Rieseberg
- Department of Botany, University of British Columbia, 3200-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
| | - Michael C Whitlock
- Department of Zoology, University of British Columbia, 4200-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
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21
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MacLachlan IR, Yeaman S, Aitken SN. Growth gains from selective breeding in a spruce hybrid zone do not compromise local adaptation to climate. Evol Appl 2017; 11:166-181. [PMID: 29387153 PMCID: PMC5775489 DOI: 10.1111/eva.12525] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/20/2017] [Indexed: 01/16/2023] Open
Abstract
Hybrid zones contain extensive standing genetic variation that facilitates rapid responses to selection. The Picea glauca × Picea engelmannii hybrid zone in western Canada is the focus of tree breeding programs that annually produce ~90 million reforestation seedlings. Understanding the direct and indirect effects of selective breeding on adaptive variation is necessary to implement assisted gene flow (AGF) polices in Alberta and British Columbia that match these seedlings with future climates. We decomposed relationships among hybrid ancestry, adaptive traits, and climate to understand the implications of selective breeding for climate adaptations and AGF strategies. The effects of selection on associations among hybrid index estimated from ~6,500 SNPs, adaptive traits, and provenance climates were assessed for ~2,400 common garden seedlings. Hybrid index differences between natural and selected seedlings within breeding zones were small in Alberta (average +2%), but larger and more variable in BC (average −7%, range −24% to +1%), slightly favoring P. glauca ancestry. The average height growth gain of selected seedlings over natural seedlings within breeding zones was 36% (range 12%–86%). Clines in growth with temperature‐related variables were strong, but differed little between selected and natural populations. Seedling hybrid index and growth trait associations with evapotranspiration‐related climate variables were stronger in selected than in natural seedlings, indicating possible preadaptation to drier future climates. Associations among cold hardiness, hybrid ancestry, and cold‐related climate variables dominated signals of local adaptation and were preserved in breeding populations. Strong hybrid ancestry–phenotype–climate associations suggest that AGF will be necessary to match interior spruce breeding populations with shifting future climates. The absence of antagonistic selection responses among traits and maintenance of cold adaptation in selected seedlings suggests breeding populations can be safely redeployed using AGF prescriptions similar to those of natural populations.
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Affiliation(s)
- Ian R MacLachlan
- Department of Forest and Conservation Sciences Faculty of Forestry University of British Columbia Vancouver BC Canada
| | - Sam Yeaman
- Department of Biological Sciences University of Calgary Calgary AB Canada
| | - Sally N Aitken
- Department of Forest and Conservation Sciences Faculty of Forestry University of British Columbia Vancouver BC Canada
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22
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Copenhaver‐Parry PE, Shuman BN, Tinker DB. Toward an improved conceptual understanding of North American tree species distributions. Ecosphere 2017. [DOI: 10.1002/ecs2.1853] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Affiliation(s)
| | - Bryan N. Shuman
- Program in Ecology and Department of Geology & Geophysics University of Wyoming 1000 E. University Avenue Laramie Wyoming 82071 USA
| | - Daniel B. Tinker
- Program in Ecology and Department of Botany University of Wyoming 1000 E. University Avenue Laramie Wyoming 82071 USA
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23
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Yeaman S, Hodgins KA, Lotterhos KE, Suren H, Nadeau S, Degner JC, Nurkowski KA, Smets P, Wang T, Gray LK, Liepe KJ, Hamann A, Holliday JA, Whitlock MC, Rieseberg LH, Aitken SN. Convergent local adaptation to climate in distantly related conifers. Science 2016; 353:1431-1433. [DOI: 10.1126/science.aaf7812] [Citation(s) in RCA: 215] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 08/11/2016] [Indexed: 01/18/2023]
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