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George JP, Theroux-Rancourt G, Rungwattana K, Scheffknecht S, Momirovic N, Neuhauser L, Weißenbacher L, Watzinger A, Hietz P. Assessing adaptive and plastic responses in growth and functional traits in a 10-year-old common garden experiment with pedunculate oak ( Quercus robur L.) suggests that directional selection can drive climatic adaptation. Evol Appl 2020; 13:2422-2438. [PMID: 33005231 PMCID: PMC7513705 DOI: 10.1111/eva.13034] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 05/06/2020] [Accepted: 05/26/2020] [Indexed: 01/07/2023] Open
Abstract
Understanding how tree species will respond to a future climate requires reliable and quantitative estimates of intra-specific variation under current climate conditions. We studied three 10-year-old common garden experiments established across a rainfall and drought gradient planted with nearly 10,000 pedunculate oak (Quercus robur L.) trees from ten provenances with known family structure. We aimed at disentangling adaptive and plastic responses for growth (height and diameter at breast height) as well as for leaf and wood functional traits related to adaptation to dry environments. We used restricted maximum likelihood approaches to assess additive genetic variation expressed as narrow-sense heritability (h2), quantitative trait differentiation among provenances (QST), and genotype-by-environment interactions (GxE). We found strong and significant patterns of local adaptation in growth in all three common gardens, suggesting that transfer of seed material should not exceed a climatic distance of approximately 1°C under current climatic conditions, while transfer along precipitation gradients seems to be less stringent. Moreover, heritability reached 0.64 for tree height and 0.67 for dbh at the dry margin of the testing spectrum, suggesting significant additive genetic variation of potential use for future selection and tree breeding. GxE interactions in growth were significant and explained less phenotypic variation than origin of seed source (4% versus 10%). Functional trait variation among provenances was partly related to drought regimes at provenances origins but had moderate explanatory power for growth. We conclude that directional selection, either naturally or through breeding, is the most likely and feasible outcome for pedunculate oak to adapt to warmer and drier climate conditions in the future.
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Affiliation(s)
- Jan-Peter George
- Department of Forest Genetics Federal Research and Training Centre for Forests Natural Hazards and Landscape (BFW) Vienna Austria
- Present address: Tartu Observatory University of Tartu Tõravere Estonia
| | - Guillaume Theroux-Rancourt
- Institute of Botany University of Applied Life Sciences and Natural Resources Vienna (BOKU) Vienna Austria
| | - Kanin Rungwattana
- Institute of Botany University of Applied Life Sciences and Natural Resources Vienna (BOKU) Vienna Austria
- Present address: Department of Botany Faculty of Science Kasetsart University Bangkok Thailand
| | - Susanne Scheffknecht
- Institute of Botany University of Applied Life Sciences and Natural Resources Vienna (BOKU) Vienna Austria
| | - Nevena Momirovic
- Institute of Botany University of Applied Life Sciences and Natural Resources Vienna (BOKU) Vienna Austria
| | - Lea Neuhauser
- Institute of Botany University of Applied Life Sciences and Natural Resources Vienna (BOKU) Vienna Austria
| | - Lambert Weißenbacher
- Department of Forest Genetics Federal Research and Training Centre for Forests Natural Hazards and Landscape (BFW) Vienna Austria
| | - Andrea Watzinger
- Institute of Soil Research University of Applied Life Sciences and Natural Resources Vienna (BOKU) Vienna Austria
| | - Peter Hietz
- Institute of Botany University of Applied Life Sciences and Natural Resources Vienna (BOKU) Vienna Austria
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152
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Patsiou TS, Shestakova TA, Klein T, di Matteo G, Sbay H, Chambel MR, Zas R, Voltas J. Intraspecific responses to climate reveal nonintuitive warming impacts on a widespread thermophilic conifer. THE NEW PHYTOLOGIST 2020; 228:525-540. [PMID: 32402106 DOI: 10.1111/nph.16656] [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: 12/14/2019] [Accepted: 05/05/2020] [Indexed: 06/11/2023]
Abstract
Many ecologically important forest trees from dry areas have been insufficiently investigated for their ability to adapt to the challenges posed by climate change, which hampers the implementation of mitigation policies. We analyzed 14 common-garden experiments across the Mediterranean which studied the widespread thermophilic conifer Pinus halepensis and involved 157 populations categorized into five ecotypes. Ecotype-specific tree height responses to climate were applied to projected climate change (2071-2100 ad), to project potential growth patterns both locally and across the species' range. We found contrasting ecotypic sensitivities to annual precipitation but comparatively uniform responses to mean temperature, while evidence of local adaptation for tree height was limited to mesic ecotypes. We projected intriguing patterns of response range-wide, implying either height inhibition or stimulation of up to 75%, and deduced that the ecotype currently experiencing more favorable (wetter) conditions will show the largest inhibition. Extensive height reductions can be expected for coastal areas of France, Greece, Spain and northern Africa. Our findings underline the fact that intraspecific variations in sensitivity to precipitation must be considered when projecting tree height responses of dry forests to future climate. The ecotype-specific projected performances call for management activities to ensure forest resilience in the Mediterranean through, for example, tailored deployment strategies.
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Affiliation(s)
- Theofania S Patsiou
- Institute of Botany, University of Basel, Schönbeinstrasse 6, Basel, CH-4056, Switzerland
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, 3013, Switzerland
| | | | - Tamir Klein
- Department of Plant and Environmental sciences, Weizmann Institute of Science, 234 Herzl Street, Rehovot, 7610001, Israel
| | - Giovanni di Matteo
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment (CREA), via della Navicella 2-4, Rome, 00184, Italy
| | - Hassan Sbay
- Forest Research Centre (CRF), Av. Omar Ibn el Khattab. Agdal, Rabat, 110000, Morocco
| | | | - Rafael Zas
- Misión Biológica de Galicia, Consejo Superior de Investigaciones Científicas (MBG-CSIC), Apdo. 28, Salcedo, E-36080, Spain
| | - Jordi Voltas
- Joint Research Unit CTFC - AGROTECNIO, Av. Alcalde Rovira Roure 191, Lleida, E-25198, Spain
- Department of Crop and Forest Sciences, University of Lleida, Av. Alcalde Rovira Roure 191, Lleida, E-25198, Spain
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153
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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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154
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Du FK, Wang T, Wang Y, Ueno S, de Lafontaine G. Contrasted patterns of local adaptation to climate change across the range of an evergreen oak, Quercus aquifolioides. Evol Appl 2020; 13:2377-2391. [PMID: 33005228 PMCID: PMC7513717 DOI: 10.1111/eva.13030] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 05/02/2020] [Accepted: 05/09/2020] [Indexed: 12/27/2022] Open
Abstract
Long-lived tree species are genetically differentiated and locally adapted with respect to fitness-related traits, but the genetic basis of local adaptation remains largely unresolved. Recent advances in population genetics and landscape genomic analyses enable identification of putative adaptive loci and specific selective pressures acting on local adaptation. Here, we sampled 60 evergreen oak (Quercus aquifolioides) populations throughout the species' range and pool-sequenced 587 individuals at drought-stress candidate genes. We analyzed patterns of genetic diversity and differentiation for 381 single nucleotide polymorphisms (SNPs) from 65 candidate genes and eight microsatellites. Outlier loci were identified by genetic differentiation analysis and genome-environment associations. The response pattern of genetic variation to environmental gradient was assessed by linear isolation-by-distance/environment tests, redundancy analysis, and nonlinear methods. SNPs and microsatellites revealed two genetic lineages: Tibet and Hengduan Mountains-Western Sichuan Plateau (HDM-WSP), with reduced genetic diversity in Tibet lineage. More outlier loci were detected in HDM-WSP lineage than Tibet lineage. Among these, three SNPs in two genes responded to dry season precipitation in the HDM-WSP lineage but not in Tibet. By contrast, genetic variation in the Tibet lineage was related to geographic distance instead of the environment. Furthermore, risk of nonadaptedness (RONA) analyses suggested HDM-WSP lineage will have a better capacity to adapt in the predicted future climate compared with the Tibet lineage. We detected genetic imprints consistent with natural selection and molecular adaptation to drought on the Qinghai-Tibet Plateau (QTP) over a range of long-lived and widely distributed oak species in a changing environment. Our results suggest that different within-species adaptation processes occur in species occurring in heterogeneous environments.
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Affiliation(s)
- Fang K. Du
- School of Ecology and Nature ConservationBeijing Forestry UniversityBeijingChina
| | - Tianrui Wang
- School of Ecology and Nature ConservationBeijing Forestry UniversityBeijingChina
| | - Yuyao Wang
- School of Ecology and Nature ConservationBeijing Forestry UniversityBeijingChina
| | - Saneyoshi Ueno
- Department of Forest Molecular Genetics and BiotechnologyForestry and Forest Products Research InstituteForest Research and Management OrganizationTsukubaJapan
| | - Guillaume de Lafontaine
- Canada Research Chair in Integrative Biology of Northern FloraUniversité du Québec à RimouskiRimouskiQCCanada
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155
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Zhang X, Sun Y, Landis JB, Zhang J, Yang L, Lin N, Zhang H, Guo R, Li L, Zhang Y, Deng T, Sun H, Wang H. Genomic insights into adaptation to heterogeneous environments for the ancient relictual Circaeaster agrestis (Circaeasteraceae, Ranunculales). THE NEW PHYTOLOGIST 2020; 228:285-301. [PMID: 32426908 DOI: 10.1111/nph.16669] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/08/2020] [Indexed: 05/25/2023]
Abstract
Investigating the interaction between environmental heterogeneity and local adaptation is critical for understanding the evolutionary history of a species, providing the premise for studying the response of organisms to rapid climate change. However, for most species how exactly the spatial heterogeneity promotes population divergence and how genomic variations contribute to adaptive evolution remain poorly understood. We examine the contributions of geographical and environmental variables to population divergence of the relictual, alpine herb Circaeaster agrestis, as well as the genetic basis of local adaptation using RAD-seq and plastome data. We detected significant genetic structure with an extraordinary disequilibrium of genetic diversity among regions, and signals of isolation-by-distance along with isolation-by-resistance. The populations were estimated to begin diverging in the late Miocene, along with a possible ancestral distribution of the Hengduan Mountains and adjacent regions. Both environmental gradient and redundancy analyses revealed significant association between genetic variation and temperature variables. Genome-environment association analyses identified 16 putatively adaptive loci related mainly to biotic and abiotic stress resistance. Our genome-wide data provide new insights into the important role of environmental heterogeneity in shaping genetic structure, and access the footprints of local adaptation in an ancient relictual species, informing future conservation efforts.
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Affiliation(s)
- Xu Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanxia Sun
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Jacob B Landis
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, 92507, USA
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, 14850, USA
| | - Jianwen Zhang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Linsen Yang
- Hubei Key Laboratory of Shennongjia Golden Monkey Conservation Biology, Administration of Shennongjia National Park, Shennongjia, Hubei, 442400, China
| | - Nan Lin
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huajie Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Rui Guo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lijuan Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yonghong Zhang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Tao Deng
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Hengchang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
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156
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Ten Years of Provenance Trials and Application of Multivariate Random Forests Predicted the Most Preferable Seed Source for Silviculture of Abies sachalinensis in Hokkaido, Japan. FORESTS 2020. [DOI: 10.3390/f11101058] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Research highlights: Using 10-year tree height data obtained after planting from the range-wide provenance trials of Abies sachalinensis, we constructed multivariate random forests (MRF), a machine learning algorithm, with climatic variables. The constructed MRF enabled prediction of the optimum seed source to achieve good performance in terms of height growth at every planting site on a fine scale. Background and objectives: Because forest tree species are adapted to the local environment, local seeds are empirically considered as the best sources for planting. However, in some cases, local seed sources show lower performance in height growth than that showed by non-local seed sources. Tree improvement programs aim to identify seed sources for obtaining high-quality timber products by performing provenance trials. Materials and methods: Range-wide provenance trials for one of the most important silvicultural species, Abies sachalinensis, were established in 1980 at nine transplanting experimental sites. We constructed an MRF to estimate the responses of tree height at 10 years after planting at eight climatic variables at 1 km × 1 km resolution. The model was applied for prediction of tree height throughout Hokkaido Island. Results: Our model showed that four environmental variables were major factors affecting height growth—winter solar radiation, warmth index, maximum snow depth, and spring solar radiation. A tree height prediction map revealed that local seeds showed the best performance except in the southernmost region and several parts of northern regions. Moreover, the map of optimum seed provenance suggested that deployment of distant seed sources can outperform local sources in the southernmost and northern regions. Conclusions: We predicted that local seeds showed optimum growth, whereas non-local seeds had the potential to outperform local seeds in some regions. Several deployment options were proposed to improve tree growth.
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157
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Small-scale population divergence is driven by local larval environment in a temperate amphibian. Heredity (Edinb) 2020; 126:279-292. [PMID: 32958927 DOI: 10.1038/s41437-020-00371-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 09/06/2020] [Accepted: 09/08/2020] [Indexed: 02/07/2023] Open
Abstract
Genomic variation within and among populations is shaped by the interplay between natural selection and the effects of genetic drift and gene flow. Adaptive divergence can be found in small-scale natural systems even when population sizes are small, and the potential for gene flow is high, suggesting that local environments exert selection pressures strong enough to counteract the opposing effects of drift and gene flow. Here, we investigated genomic differentiation in nine moor frog (Rana arvalis) populations in a small-scale network of local wetlands using 16,707 ddRAD-seq SNPs, relating levels of differentiation with local environments, as well as with properties of the surrounding landscape. We characterized population structure and differentiation, and partitioned the effects of geographic distance, local larval environment, and landscape features on total genomic variation. We also conducted gene-environment association studies using univariate and multivariate approaches. We found small-scale population structure corresponding to 6-8 clusters. Local larval environment was the most influential component explaining 2.3% of the total genetic variation followed by landscape features (1.8%) and geographic distance (0.8%), indicative of isolation-by-environment, -by-landscape, and -by-distance, respectively. We identified 1000 potential candidate SNPs putatively under divergent selection mediated by the local larval environment. The candidate SNPs were involved in, among other biological functions, immune system function and development. Our results suggest that small-scale environmental differences can exert selection pressures strong enough to counteract homogenizing effects of gene flow and drift in this small-scale system, leading to observable population differentiation.
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158
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Brousseau L, Fine PVA, Dreyer E, Vendramin GG, Scotti I. Genomic and phenotypic divergence unveil microgeographic adaptation in the Amazonian hyperdominant tree Eperua falcata Aubl. (Fabaceae). Mol Ecol 2020; 30:1136-1154. [PMID: 32786115 DOI: 10.1111/mec.15595] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 06/19/2020] [Accepted: 07/31/2020] [Indexed: 01/04/2023]
Abstract
Plant populations can undergo very localized adaptation, allowing widely distributed populations to adapt to divergent habitats in spite of recurrent gene flow. Neotropical trees-whose large and undisturbed populations often span a variety of environmental conditions and local habitats-are particularly good models to study this process. Here, we explore patterns of adaptive divergence from large (i.e., regional) to small (i.e., microgeographic) spatial scales in the hyperdominant Amazonian tree Eperua falcata Aubl. (Fabaceae) under a replicated design involving two microhabitats (~300 m apart) in two study sites (~300 km apart). A three-year reciprocal transplant illustrates that, beyond strong maternal effects and phenotypic plasticity, genetically driven divergence in seedling growth and leaf traits was detected both between seedlings originating from different regions, and between seedlings from different microhabitats. In parallel, a complementary genome scan for selection was carried out through whole-genome sequencing of tree population pools. A set of 290 divergence outlier SNPs was detected at the regional scale (between study sites), while 185 SNPs located in the vicinity of 106 protein-coding genes were detected as replicated outliers between microhabitats within regions. Outlier-surrounding genomic regions are involved in a variety of physiological processes, including plant responses to stress (e.g., oxidative stress, hypoxia and metal toxicity) and biotic interactions. Together with evidence of microgeographic divergence in functional traits, the discovery of genomic candidates for microgeographic adaptive divergence represents a promising advance in our understanding of local adaptation, which probably operates across multiple spatial scales and underpins divergence and diversification in Neotropical trees.
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Affiliation(s)
- Louise Brousseau
- UMR EcoFoG, AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles, Kourou Cedex, France.,AMAP, Univ. Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, France
| | - Paul V A Fine
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Erwin Dreyer
- Université de Lorraine, AgroParisTech, INRAE, Silva, Nancy, France
| | - Giovanni G Vendramin
- Institute of Biosciences and BioResources (IBBR-CNR), National Research Council, Division of Florence, Sesto Fiorentino, Italy
| | - Ivan Scotti
- UR629 Ecologie des Forêts Méditerranéennes (URFM), INRAE, Avignon, France
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159
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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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160
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Anderson J, Song BH. Plant adaptation to climate change - Where are we? JOURNAL OF SYSTEMATICS AND EVOLUTION 2020; 58:533-545. [PMID: 33584833 PMCID: PMC7875155 DOI: 10.1111/jse.12649] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Climate change poses critical challenges for population persistence in natural communities, agriculture and environmental sustainability, and food security. In this review, we discuss recent progress in climatic adaptation in plants. We evaluate whether climate change exerts novel selection and disrupts local adaptation, whether gene flow can facilitate adaptive responses to climate change, and if adaptive phenotypic plasticity could sustain populations in the short term. Furthermore, we discuss how climate change influences species interactions. Through a more in-depth understanding of these eco-evolutionary dynamics, we will increase our capacity to predict the adaptive potential of plants under climate change. In addition, we review studies that dissect the genetic basis of plant adaptation to climate change. Finally, we highlight key research gaps, ranging from validating gene function, to elucidating molecular mechanisms, expanding research systems from model species to other natural species, testing the fitness consequences of alleles in natural environments, and designing multifactorial studies that more closely reflect the complex and interactive effects of multiple climate change factors. By leveraging interdisciplinary tools (e.g., cutting-edge omics toolkits, novel ecological strategies, newly-developed genome editing technology), researchers can more accurately predict the probability that species can persist through this rapid and intense period of environmental change, as well as cultivate crops to withstand climate change, and conserve biodiversity in natural systems.
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Affiliation(s)
- Jill Anderson
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
- Authors for correspondence. Bao-Hua Song. ; Jill Anderson.
| | - Bao-Hua Song
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
- Authors for correspondence. Bao-Hua Song. ; Jill Anderson.
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161
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DeSilva R, Dodd RS. Association of genetic and climatic variability in giant sequoia, Sequoiadendron giganteum, reveals signatures of local adaptation along moisture-related gradients. Ecol Evol 2020; 10:10619-10632. [PMID: 33072284 PMCID: PMC7548164 DOI: 10.1002/ece3.6716] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 07/28/2020] [Accepted: 08/05/2020] [Indexed: 11/12/2022] Open
Abstract
Uncovering the genetic basis of local adaptation is a major goal of evolutionary biology and conservation science alike. In an era of climate change, an understanding of how environmental factors shape adaptive diversity is crucial to predicting species response and directing management. Here, we investigate patterns of genomic variation in giant sequoia, an iconic and ecologically important tree species, using 1,364 bi-allelic single nucleotide polymorphisms (SNPs). We use an F ST outlier test and two genotype-environment association methods, latent factor mixed models (LFMMs) and redundancy analysis (RDA), to detect complex signatures of local adaptation. Results indicate 79 genomic regions of potential adaptive importance, with limited overlap between the detection methods. Of the 58 loci detected by LFMM, 51 showed strong correlations to a precipitation-driven composite variable and seven to a temperature-related variable. RDA revealed 24 outlier loci with association to climate variables, all of which showed strongest relationship to summer precipitation. Nine candidate loci were indicated by two methods. After correcting for geographic distance, RDA models using climate predictors accounted for 49% of the explained variance and showed significant correlations between SNPs and climatic factors. Here, we present evidence of local adaptation in giant sequoia along gradients of precipitation and provide a first step toward identifying genomic regions of adaptive significance. The results of this study will provide information to guide management strategies that seek to maximize adaptive potential in the face of climate change.
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Affiliation(s)
- Rainbow DeSilva
- Department of Environmental Science, Policy, and Management University of California at Berkeley Berkeley California USA
| | - Richard S Dodd
- Department of Environmental Science, Policy, and Management University of California at Berkeley Berkeley California USA
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162
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Napier JD, de Lafontaine G, Hu FS. Exploring genomic variation associated with drought stress in Picea mariana populations. Ecol Evol 2020; 10:9271-9282. [PMID: 32953060 PMCID: PMC7487243 DOI: 10.1002/ece3.6614] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 06/01/2020] [Accepted: 07/08/2020] [Indexed: 01/05/2023] Open
Abstract
Predicted increases in drought and heat stress will likely induce shifts in species bioclimatic envelopes. Genetic variants adapted to water limitation may prove pivotal for species response under scenarios of increasing drought. In this study, we aimed to explore this hypothesis by investigating genetic variation in 16 populations of black spruce (Picea mariana) in relation to climate variables in Alaska. A total of 520 single nucleotide polymorphisms (SNPs) were genotyped for 158 trees sampled from areas of contrasting climate regimes. We used multivariate and univariate genotype-by-environment approaches along with available gene annotations to investigate the relationship between climate and genetic variation among sampled populations. Nine SNPs were identified as having a significant association with climate, of which five were related to drought stress response. Outlier SNPs with respect to the overall environment were significantly overrepresented for several biological functions relevant for coping with variable hydric regimes, including osmotic stress response. This genomic imprint is consistent with local adaptation of black spruce to drought stress. These results suggest that natural selection acting on standing variation prompts local adaptation in forest stands facing water limitation. Improved understanding of possible adaptive responses could inform our projections about future forest dynamics and help prioritize populations that harbor valuable genetic diversity for conservation.
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Affiliation(s)
- Joseph D. Napier
- Department of Plant BiologyUniversity of IllinoisUrbanaILUSA
- Department of Integrative BiologyThe University of Texas at AustinAustinTXUSA
| | - Guillaume de Lafontaine
- Department of Plant BiologyUniversity of IllinoisUrbanaILUSA
- Canada Research Chair in Integrative Biology of Northern FloraUniversité du Québec à RimouskiRimouskiQCCanada
| | - Feng Sheng Hu
- Department of GeologyUniversity of IllinoisUrbanaILUSA
- Department of BiologyWashington UniversitySt. LouisMOUSA
- Department of Earth and Planetary SciencesWashington UniversitySt. LouisMOUSA
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163
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Genomics of Clinal Local Adaptation in Pinus sylvestris Under Continuous Environmental and Spatial Genetic Setting. G3-GENES GENOMES GENETICS 2020; 10:2683-2696. [PMID: 32546502 PMCID: PMC7407466 DOI: 10.1534/g3.120.401285] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Understanding the consequences of local adaptation at the genomic diversity is a central goal in evolutionary genetics of natural populations. In species with large continuous geographical distributions the phenotypic signal of local adaptation is frequently clear, but the genetic basis often remains elusive. We examined the patterns of genetic diversity in Pinus sylvestris, a keystone species in many Eurasian ecosystems with a huge distribution range and decades of forestry research showing that it is locally adapted to the vast range of environmental conditions. Making P. sylvestris an even more attractive subject of local adaptation study, population structure has been shown to be weak previously and in this study. However, little is known about the molecular genetic basis of adaptation, as the massive size of gymnosperm genomes has prevented large scale genomic surveys. We generated a both geographically and genomically extensive dataset using a targeted sequencing approach. By applying divergence-based and landscape genomics methods we identified several loci contributing to local adaptation, but only few with large allele frequency changes across latitude. We also discovered a very large (ca. 300 Mbp) putative inversion potentially under selection, which to our knowledge is the first such discovery in conifers. Our results call for more detailed analysis of structural variation in relation to genomic basis of local adaptation, emphasize the lack of large effect loci contributing to local adaptation in the coding regions and thus point out the need for more attention toward multi-locus analysis of polygenic adaptation.
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164
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Alvarez-Maldini C, Acevedo M, Dumroese RK, González M, Cartes E. Intraspecific Variation in Drought Response of Three Populations of Cryptocarya alba and Persea lingue, Two Native Species From Mediterranean Central Chile. FRONTIERS IN PLANT SCIENCE 2020; 11:1042. [PMID: 32765551 PMCID: PMC7378861 DOI: 10.3389/fpls.2020.01042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/24/2020] [Indexed: 05/24/2023]
Abstract
An increase in the severity of drought events on Mediterranean climates highlights the need of using plant material adapted to drought during restoration efforts. Thus, we investigated between-population morpho-physiological differences in Cryptocarya alba and Persea lingue, two native species from Mediterranean central Chile, for traits that could effectively discriminate population performance in response to water restriction (WR) testing. Three populations from each species were subjected to WR treatment and physiological, morphological, and growth parameters were assessed at the beginning and at the end of the experiment. In C. alba, the most xeric population displayed smaller plants with mesophyllous leaves and lower photosynthetic rates indicating a resource saving strategy. Moreover, the xeric population performed better during WR than the most mesic populations, exhibiting higher water use efficiency (iWUE) and maintenance of growth rates. All C. alba populations responded equally to WR in terms of morphology and biomass partitioning. In contrast, differences among P. lingue populations were subtle at the morpho-physiological level with no apparent relation to provenance environmental conditions, and no morphological traits were affected by WR. However, in response to WR application, the most mesic population was, as observed through reduction in relative growth rates, more affected than xeric populations. We attribute such discrete differences between P. lingue provenances to the lower distributional range of selected populations. Our results show that relative growth rates in both species, and iWUE only in C. alba, exhibited population specific responses upon WR imposition; these results correspond with the environmental conditions found at the origin of each populations. Both traits could further assist in the selection of populations for restoration according to their response to water stress.
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Affiliation(s)
- Carolina Alvarez-Maldini
- Institute of Agri-food, Animal and Environmental Sciences (ICA3), Universidad de O Higgins, San Fernando, Chile
| | - Manuel Acevedo
- Centro Tecnológico de la Planta Forestal, Instituto Forestal, San Pedro de la Paz, Chile
| | - R. Kasten Dumroese
- Rocky Mountain Research Station, US Department of Agriculture, Forest Service, Moscow, ID, United States
| | - Marta González
- Centro Tecnológico de la Planta Forestal, Instituto Forestal, San Pedro de la Paz, Chile
| | - Eduardo Cartes
- Centro Tecnológico de la Planta Forestal, Instituto Forestal, San Pedro de la Paz, Chile
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165
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Etterson JR, Cornett MW, White MA, Kavajecz LC. Assisted migration across fixed seed zones detects adaptation lags in two major North American tree species. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2020; 30:e02092. [PMID: 32058650 PMCID: PMC7534057 DOI: 10.1002/eap.2092] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 10/01/2019] [Accepted: 11/25/2019] [Indexed: 05/11/2023]
Abstract
Boreal forests are experiencing dramatic climate change, having warmed 1.0°-1.9°C over the last century. Yet forest regeneration practices are often still dictated by a fixed seed zone framework, in which seeds are both harvested from and planted into predefined areas. Our goal was to determine whether seedlings sourced from southern seed zones in Minnesota USA are already better adapted to northerly seed zones because of climate change. Bur oak (Quercus macrocarpa) and northern red oak (Quercus rubra) seedlings from two seed zones (i.e., tree ecotypes) were planted into 16 sites in two northern seed zones and measured for 3 yr. Our hypotheses were threefold: (1) tree species with more southern geographic distributions would thrive in northern forests where climate has already warmed substantially, (2) southern ecotypes of these species would have higher survival and growth than the northern ecotype in northern environments, and (3) natural selection would favor seedlings that expressed phenotypic and phenological traits characteristic of trees sourced from the more southern seed zone. For both species, survival was high (>93%), and southern ecotypes expressed traits consistent with our climate adaptation hypotheses. Ecotypic differences were especially evident for red oak; the southern ecotype had had higher survival, lower specific leaf area (SLA), faster height and diameter growth, and extended leaf phenology relative to the northern ecotype. Bur oak results were weaker, but the southern ecotype also had earlier budburst and lower SLA than the northern ecotype. Models based on the fixed seed zones failed to explain seedling performance as well as those with continuous predictors (e.g., climate and geographical position), suggesting that plant adaptations within current seed zone delineations do align with changing climate conditions. Adding support for this conclusion, natural selection favored traits expressed by the more southern tree ecotypes. Collectively, these results suggest that state seed sourcing guidelines should be reexamined to permit plantings across seed zones, a form of assisted migration. More extensive experiments (i.e., provenance trails) are necessary to make species-specific seed transfer guidelines that account for climate trends while also considering the precise geographic origin of seed sources.
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Affiliation(s)
- Julie R. Etterson
- Department of BiologyUniversity of Minnesota DuluthDuluthMinnesota55812USA
| | - Meredith W. Cornett
- The Nature Conservancy in Minnesota—North Dakota—South DakotaDuluthMinnesota55802USA
| | - Mark A. White
- The Nature Conservancy in Minnesota—North Dakota—South DakotaDuluthMinnesota55802USA
| | - Laura C. Kavajecz
- Department of BiologyUniversity of Minnesota DuluthDuluthMinnesota55812USA
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166
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Gauzere J, Klein EK, Brendel O, Davi H, Oddou-Muratorio S. Microgeographic adaptation and the effect of pollen flow on the adaptive potential of a temperate tree species. THE NEW PHYTOLOGIST 2020; 227:641-653. [PMID: 32167572 DOI: 10.1111/nph.16537] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/29/2020] [Indexed: 06/10/2023]
Abstract
In species with long-distance dispersal capacities and inhabiting a large ecological niche, local selection and gene flow are expected to be major evolutionary forces affecting the genetic adaptation of natural populations. Yet, in species such as trees, evidence of microgeographic adaptation and the quantitative assessment of the impact of gene flow on adaptive genetic variation are still limited. Here, we used extensive genetic and phenotypic data from European beech seedlings collected along an elevation gradient, and grown in a common garden, to study the signature of selection on the divergence of eleven potentially adaptive traits, and to assess the role of gene flow in resupplying adaptive genetic variation. We found a significant signal of adaptive differentiation among plots separated by < 1 km, with selection acting on growth and phenological traits. Consistent with theoretical expectations, our results suggest that pollen dispersal contributes to increase genetic diversity for these locally differentiated traits. Our results thus highlight that local selection is an important evolutionary force in natural tree populations and suggest that management interventions to facilitate movement of gametes along short ecological gradients would boost genetic diversity of individual tree populations, and enhance their adaptive potential to rapidly changing environments.
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Affiliation(s)
- Julie Gauzere
- INRAE, URFM, Avignon, 84000, France
- INRAE, BioSP, Avignon, 84000, France
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JT, UK
| | | | - Oliver Brendel
- Université de Lorraine, AgroParisTech, INRAE, UMR Silva, Nancy, 54000, France
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167
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Temunović M, Garnier-Géré P, Morić M, Franjić J, Ivanković M, Bogdan S, Hampe A. Candidate gene SNP variation in floodplain populations of pedunculate oak (Quercus robur L.) near the species' southern range margin: Weak differentiation yet distinct associations with water availability. Mol Ecol 2020; 29:2359-2378. [PMID: 32567080 DOI: 10.1111/mec.15492] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 05/03/2020] [Accepted: 05/18/2020] [Indexed: 01/03/2023]
Abstract
Populations residing near species' low-latitude range margins (LLMs) often occur in warmer and drier environments than those in the core range. Thus, their genetic composition could be shaped by climatic drivers that differ from those occurring at higher latitudes, resulting in potentially adaptive variants of conservation value. Such variants could facilitate the adaptation of populations from other portions of the geographical range to similar future conditions anticipated under ongoing climate change. However, very few studies have assessed standing genetic variation at potentially adaptive loci in natural LLM populations. We investigated standing genetic variation at single nucleotide polymorphisms (SNPs) located within 117 candidate genes and its links to putative climatic selection pressures across 19 pedunculate oak (Quercus robur L.) populations distributed along a regional climatic gradient near the species' southern range margin in southeastern Europe. These populations are restricted to floodplain forests along large lowland rivers, whose hydric regime is undergoing significant shifts under modern rapid climate change. The populations showed very weak geographical structure, suggesting extensive genetic connectivity and gene flow or shared ancestry. We identified eight (6.2%) positive FST -outlier loci, and genotype-environment association analyses revealed consistent associations between SNP allele frequencies and several climatic variables linked to water availability. A total of 61 associations involving 37 SNPs (28.5%) from 35 annotated genes provided important insights into putative functional mechanisms in our system. Our findings provide empirical support for the role of LLM populations as sources of potentially adaptive variation that could enhance species' resilience to climate change-related pressures.
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Affiliation(s)
- Martina Temunović
- Department of Forest Genetics, Dendrology and Botany, Faculty of Forestry, University of Zagreb, Zagreb, Croatia
| | | | - Maja Morić
- Department of Forest Genetics, Dendrology and Botany, Faculty of Forestry, University of Zagreb, Zagreb, Croatia
| | - Jozo Franjić
- Department of Forest Genetics, Dendrology and Botany, Faculty of Forestry, University of Zagreb, Zagreb, Croatia
| | | | - Saša Bogdan
- Department of Forest Genetics, Dendrology and Botany, Faculty of Forestry, University of Zagreb, Zagreb, Croatia
| | - Arndt Hampe
- INRAE, Univ. Bordeaux, BIOGECO, Cestas, France
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168
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Miryeganeh M. Synchronization of senescence and desynchronization of flowering in Arabidopsis thaliana. AOB PLANTS 2020; 12:plaa018. [PMID: 32577195 PMCID: PMC7299267 DOI: 10.1093/aobpla/plaa018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 05/04/2020] [Indexed: 06/11/2023]
Abstract
In a recent publication, we proposed that adjusting lifespan in order to synchronize senescence is important for timing of reproduction, and we quantified the synchrony of reproductive timing relative to germination timing. Here, in a second sequential seeding experiment (SSE), the germination timing of Arabidopsis thaliana accessions was manipulated and plants were then grown under two different temperature regimes. Life stage traits of plants in each temperature regime were analysed and it was evaluated whether the cohorts were grouped according to age and/or environmental conditions. While flowering-related traits showed desynchrony among cohorts, striking synchrony in the timing of senescence among cohorts for each group was found. A quantitative trait locus (QTL) analysis using a genotyped population of 'Cvi/Ler' recombinant inbred lines (RILs) was then conducted. Novel and known loci were assigned to flowering and senescence timing. However, senescence synchrony resulted in low variation in senescence time and weak QTL detection for flowering termination. Overlapping flowering and senescence genes with loci affecting either of those traits were found and suggest a potential interdependency of reproductive traits.
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Affiliation(s)
- Matin Miryeganeh
- Center for Ecological Research, Kyoto University, Hirano, Otsu, Japan
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169
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Solé-Medina A, Heer K, Opgenoorth L, Kaldewey P, Danusevicius D, Notivol E, Robledo-Arnuncio JJ, Ramírez-Valiente JA. Genetic variation in early fitness traits across European populations of silver birch ( Betula pendula). AOB PLANTS 2020; 12:plaa019. [PMID: 32665825 PMCID: PMC7320878 DOI: 10.1093/aobpla/plaa019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 05/18/2020] [Indexed: 05/11/2023]
Abstract
Given that the ecological niche of tree species is typically narrower for earlier life stages, intraspecific genetic variation at early fitness traits may greatly influence the adaptive response of tree populations to changing environmental conditions. In this study, we evaluated genetic variation in early fitness traits among 12 populations of Betula pendula from a wide latitudinal range in Europe (41-55°N). We first conducted a chamber experiment to test for population differences in germination and the effect of pre-chilling treatment on seed dormancy release. We then established three common gardens spread across the species latitudinal range in order to evaluate levels of quantitative genetic variation and genotype-by-environment interaction at different early life traits. Our results showed significant variation in chamber germination rates among populations (0-60 %), with southern populations exhibiting lower germination. Pre-chilling treatments did not generally improve germination success. Population seedling emergence rates in the field were correlated with chamber germination rates, though being an order of magnitude lower, with an average ranging from 0 to 1.3 % across gardens. Highly significant variation was found in field emergence rates among populations, and between seed-crop years within populations, but not among families within populations. Populations differed in seedling height, diameter, slenderness and budburst date, with significant among-family variation. Population latitude was positively associated with chamber germination rate and with seedling emergence rate in one of the central field sites. Overall, genetic, environmental and demographic factors seem to influence the observed high levels of variation in early fitness traits among B. pendula populations. Our results suggest limited regeneration capacity for the study species under drier conditions, but further field trials with sufficient replication over environments and seed crops will improve our understanding of its vulnerability to climate change.
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Affiliation(s)
- Aida Solé-Medina
- Department of Forest Ecology & Genetics, INIA-CIFOR, Madrid, Spain
- Escuela Internacional de Doctorado, Universidad Rey Juan Carlos, Móstoles, Spain
- Corresponding author’s e-mail address:
| | - Katrin Heer
- Conservation Biology, Philipps Universität Marburg, Marburg, Germany
| | - Lars Opgenoorth
- Department of Ecology, Philipps Universität Marburg, Marburg, Germany
- Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Phillip Kaldewey
- Conservation Biology, Philipps Universität Marburg, Marburg, Germany
| | - Darius Danusevicius
- Faculty of Forest Science and Ecology, Vytautas Magnus University, Akademija, Kaunas, Lithuania
| | - Eduardo Notivol
- Unidad de Recursos Forestales, CITA, Avda. Montañana 930, Zaragoza, Spain
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170
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González AV, Gómez-Silva V, Ramírez MJ, Fontúrbel FE. Meta-analysis of the differential effects of habitat fragmentation and degradation on plant genetic diversity. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2020; 34:711-720. [PMID: 31605401 DOI: 10.1111/cobi.13422] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 10/05/2019] [Accepted: 10/09/2019] [Indexed: 06/10/2023]
Abstract
Genetic diversity is a key factor for population survival and evolution. However, anthropogenic habitat disturbance can erode it, making populations more prone to extinction. Aiming to assess the global effects of habitat disturbance on plant genetic variation, we conducted a meta-analysis based on 92 case studies obtained from published literature. We compared the effects of habitat fragmentation and degradation on plant allelic richness and gene diversity (equivalent to expected heterozygosity) and tested whether such changes are sensitive to different life-forms, life spans, mating systems, and commonness. Anthropogenic disturbance had a negative effect on allelic richness, but not on gene diversity. Habitat fragmentation had a negative effect on genetic variation, whereas habitat degradation had no effect. When we examined the individual effects in fragmented habitats, allelic richness and gene diversity decreased, but this decrease was strongly dependent on certain plant traits. Specifically, common long-lived trees and self-incompatible species were more susceptible to allelic richness loss. Conversely, gene diversity decreased in common short-lived species (herbs) with self-compatible reproduction. In a wider geographical context, tropical plant communities were more sensitive to allelic richness loss, whereas temperate plant communities were more sensitive to gene diversity loss. Our synthesis showed complex responses to habitat disturbance among plant species. In many cases, the absence of effects could be the result of the time elapsed since the disturbance event or reproductive systems favoring self-pollination, but attention must be paid to those plant species that are more susceptible to losing genetic diversity, and appropriate conservation should be actions taken.
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Affiliation(s)
- Alejandra V González
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, 7800024, Santiago, Chile
| | - Valeria Gómez-Silva
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, 7800024, Santiago, Chile
| | - María José Ramírez
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, 7800024, Santiago, Chile
| | - Francisco E Fontúrbel
- Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Av. Universidad 330, Valparaíso, 2373223, Chile
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171
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Xie DF, Tan JB, Yu Y, Gui LJ, Su DM, Zhou SD, He XJ. Insights into phylogeny, age and evolution of Allium (Amaryllidaceae) based on the whole plastome sequences. ANNALS OF BOTANY 2020; 125:1039-1055. [PMID: 32239179 PMCID: PMC7262478 DOI: 10.1093/aob/mcaa024] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 04/01/2020] [Indexed: 05/22/2023]
Abstract
BACKGROUND AND AIMS The genus Allium L., one of the largest monocotyledonous genera and one that includes many economically important crops with nutritional and medicinal value, has been the focus of classification or phylogeny studies for centuries. Recent studies suggested that the genus can be divided into 15 subgenera and 72 sections, which were further classified into three evolutionary lineages. However, the phylogenetic relationships reconstructed by one or two loci showed weaker support, especially for the third evolutionary lineage, which might not show the species relationships very clearly and could hinder further adaptive and evolutionary study. METHODS In this study, a total of 39 complete chloroplast genomes of Allium (covering 12 Allium subgenera) were collected, and combining these with 125 species of plastomes from 19 other families of monocots, we reconstructed the phylogeny of the genus Allium, estimated the origin and divergence time of the three evolutionary lineages and investigated the adaptive evolution in this genus and related families. RESULTS Our phylogenetic analysis confirmed the monophyly and three evolutionary lineages of Allium, while new species relationships were detected within the third evolutionary lineage. The divergence time of the three evolutionary lineages was estimated to be in the early Eocene to the middle Miocene, and numerous positive selected genes (PSGs) and PSGs with high average Ka/Ks values were found in Allium species. CONCLUSIONS Our results detected a well-supported phylogenetic relationship of Allium. The PSGs and PSGs with high Ka/Ks values, as well as diversified morphologies, complicated chromosome characteristics and unique reproductive modes may play important roles in the adaptation and evolution of Allium species. This is the first study that conducted phylogenetic and evolutionary analyses on the genus Allium combined with the plastome and morphological and cytological data. We hope that this study can contribute to further analysis of Allium for other researchers.
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Affiliation(s)
- Deng-Feng Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Jin-Bo Tan
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Yan Yu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Lin-Jian Gui
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Dan-Mei Su
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People’s Republic of China
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172
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Van Nuland ME, Vincent JB, Ware IM, Mueller LO, Bayliss SLJ, Beals KK, Schweitzer JA, Bailey JK. Intraspecific trait variation across elevation predicts a widespread tree species' climate niche and range limits. Ecol Evol 2020; 10:3856-3867. [PMID: 32489616 PMCID: PMC7244802 DOI: 10.1002/ece3.5969] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 11/12/2019] [Accepted: 12/05/2019] [Indexed: 11/10/2022] Open
Abstract
Global change is widely altering environmental conditions which makes accurately predicting species range limits across natural landscapes critical for conservation and management decisions. If climate pressures along elevation gradients influence the distribution of phenotypic and genetic variation of plant functional traits, then such trait variation may be informative of the selective mechanisms and adaptations that help define climatic niche limits. Using extensive field surveys along 16 elevation transects and a large common garden experiment, we tested whether functional trait variation could predict the climatic niche of a widespread tree species (Populus angustifolia) with a double quantile regression approach. We show that intraspecific variation in plant size, growth, and leaf morphology corresponds with the species' total climate range and certain climatic limits related to temperature and moisture extremes. Moreover, we find evidence of genetic clines and phenotypic plasticity at environmental boundaries, which we use to create geographic predictions of trait variation and maximum values due to climatic constraints across the western US. Overall, our findings show the utility of double quantile regressions for connecting species distributions and climate gradients through trait-based mechanisms. We highlight how new approaches like ours that incorporate genetic variation in functional traits and their response to climate gradients will lead to a better understanding of plant distributions as well as identifying populations anticipated to be maladapted to future environments.
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Affiliation(s)
| | - John B. Vincent
- School of Environmental and Forest SciencesUniversity of WashingtonSeattleWAUSA
| | - Ian M. Ware
- Institute of Pacific Islands ForestryUSDA Forest ServicePacific Southwest Research StationHiloHIUSA
| | - Liam O. Mueller
- Department of Ecology and Evolutionary BiologyUniversity of TennesseeKnoxvilleTNUSA
| | | | - Kendall K. Beals
- Department of Ecology and Evolutionary BiologyUniversity of TennesseeKnoxvilleTNUSA
| | | | - Joseph K. Bailey
- Department of Ecology and Evolutionary BiologyUniversity of TennesseeKnoxvilleTNUSA
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173
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Leroy T, Louvet JM, Lalanne C, Le Provost G, Labadie K, Aury JM, Delzon S, Plomion C, Kremer A. Adaptive introgression as a driver of local adaptation to climate in European white oaks. THE NEW PHYTOLOGIST 2020; 226:1171-1182. [PMID: 31394003 PMCID: PMC7166132 DOI: 10.1111/nph.16095] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 07/31/2019] [Indexed: 05/10/2023]
Abstract
Latitudinal and elevational gradients provide valuable experimental settings for studies of the potential impact of global warming on forest tree species. The availability of long-term phenological surveys in common garden experiments for traits associated with climate, such as bud flushing for sessile oaks (Quercus petraea), provide an ideal opportunity to investigate this impact. We sequenced 18 sessile oak populations and used available sequencing data for three other closely related European white oak species (Quercus pyrenaica, Quercus pubescens, and Quercus robur) to explore the evolutionary processes responsible for shaping the genetic variation across latitudinal and elevational gradients in extant sessile oaks. We used phenotypic surveys in common garden experiments and climatic data for the population of origin to perform genome-wide scans for population differentiation and genotype-environment and genotype-phenotype associations. The inferred historical relationships between Q. petraea populations suggest that interspecific gene flow occurred between Q. robur and Q. petraea populations from cooler or wetter areas. A genome-wide scan of differentiation between Q. petraea populations identified single nucleotide polymorphisms (SNPs) displaying strong interspecific relative divergence between these two species. These SNPs followed genetic clines along climatic or phenotypic gradients, providing further support for the likely contribution of introgression to the adaptive divergence of Q. petraea populations. Overall, the results indicate that outliers and associated SNPs are Q. robur ancestry-informative. We discuss the results of this study in the framework of the postglacial colonization scenario, in which introgression and diversifying selection have been proposed as essential drivers of Q. petraea microevolution.
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Affiliation(s)
- Thibault Leroy
- BIOGECO, INRA, Université de Bordeaux, 69 Route d'Arcachon, 33612 Cestas, France
- ISEM, Univ. Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon, 34095 Montpellier, France
| | - Jean-Marc Louvet
- BIOGECO, INRA, Université de Bordeaux, 69 Route d'Arcachon, 33612 Cestas, France
| | - Céline Lalanne
- BIOGECO, INRA, Université de Bordeaux, 69 Route d'Arcachon, 33612 Cestas, France
| | - Grégoire Le Provost
- BIOGECO, INRA, Université de Bordeaux, 69 Route d'Arcachon, 33612 Cestas, France
| | - Karine Labadie
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Jean-Marc Aury
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Sylvain Delzon
- BIOGECO, INRA, Université de Bordeaux, 69 Route d'Arcachon, 33612 Cestas, France
| | - Christophe Plomion
- BIOGECO, INRA, Université de Bordeaux, 69 Route d'Arcachon, 33612 Cestas, France
| | - Antoine Kremer
- BIOGECO, INRA, Université de Bordeaux, 69 Route d'Arcachon, 33612 Cestas, France
- Corresponding author : Antoine Kremer, Phone number: +33(0)5 57 12 38 32,
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174
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Gerst KL, Crimmins TM, Posthumus EE, Rosemartin AH, Schwartz MD. How well do the spring indices predict phenological activity across plant species? INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2020; 64:889-901. [PMID: 32107635 DOI: 10.1007/s00484-020-01879-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 12/29/2019] [Accepted: 02/11/2020] [Indexed: 06/10/2023]
Abstract
The spring indices, models that represent the onset of spring season biological activity, were developed using a long-term observational record from the mid-to-late twentieth century of three species of lilacs and honeysuckles contributed by volunteer observers across the nation. The USA National Phenology Network (USA-NPN) produces and freely delivers maps of spring index onset dates at fine spatial scale for the USA. These maps are used widely in natural resource planning and management applications. The extent to which the models represent activity in a broad suite of plant species is not well documented. In this study, we used a rich record of observational plant phenology data (37,819 onset records) collected in recent years (1981-2017) to evaluate how well gridded maps of the spring index models predict leaf and flowering onset dates in (a) 19 species of ecologically important, broadly distributed deciduous trees and shrubs, and (b) the lilac and honeysuckle species used to construct the models. The extent to which the spring indices predicted vegetative and reproductive phenology varied by species and with latitude, with stronger relationships revealed for shrubs than trees and with the Bloom Index compared to the Leaf Index, and reduced concordance between the indices at higher latitudes. These results allow us to use the indices as indicators of when to expect activity across widely distributed species and can serve as a yardstick to assess how future changes in the timing of spring will impact a broad array of trees and shrubs across the USA.
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Affiliation(s)
- Katharine L Gerst
- USA National Phenology Network, National Coordinating Office, Tucson, AZ, USA.
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, USA.
| | - Theresa M Crimmins
- USA National Phenology Network, National Coordinating Office, Tucson, AZ, USA
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, USA
| | - Erin E Posthumus
- USA National Phenology Network, National Coordinating Office, Tucson, AZ, USA
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, USA
| | - Alyssa H Rosemartin
- USA National Phenology Network, National Coordinating Office, Tucson, AZ, USA
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, USA
| | - Mark D Schwartz
- Department of Geography, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
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175
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Analyses of Genetic Diversity, Differentiation and Geographic Origin of Natural Provenances and Land Races of Casuarina equisetifolia Based on EST-SSR Markers. FORESTS 2020. [DOI: 10.3390/f11040432] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Research Highlights: High variation of genetic diversity and differentiation among 27 seed sources within 14 natural provenances and 13 land race samples of Casuarina equisetifolia were found. High proportions of monoecious individuals may be present in some populations, as indicated by severe heterozytote deficiency and inbreeding found in many provenances and land races. The most probable origins of the land races were inferred according to the values of pairwise provenance differentiation and Nei’s genetic distances. Targeted introductions and testing of unrelated new accessions of C. equisetifolia from the Pacific and Philippines was proposed to identify Ralstonia-resistant genotypes. Background and Objectives: Casuarina equisetifolia was introduced to China a hundred years ago and has become a critically important tree species in coastal protection since the 1950s. Despite its importance, patterns of genetic variation, genetic relationships among natural provenances and probable origins of the land races remain unresolved. This has become a concern in China where Ralstonia solanacearum bacterial wilt has devastated plantations that are known to be from a narrow genetic base that urgently needs to be broadened. Materials and Methods: Fourteen natural provenances from Australia, Pacific islands and Southeast Asia, and 13 land race samples from parts of Asia and Africa outside the natural range were genotyped using 13 SSR (Simple Sequence Repeats) markers to characterize their allelic variation and genetic relationship. Results: Significant genetic diversity and differentiation among 27 seed sources within 14 provenances and 13 land race samples of C. equisetifolia was indicated. Significant heterozygote deficiency and inbreeding was indicated for a number of provenances, perhaps indicating a high proportion of monoecious parents in these populations. The most probable origins of the land races of the introduced countries were suggested according to the values of pairwise provenance differentiation (FST) and Nei’s genetic distances. Conclusions: We found significant genetic diversity and genetic differentiation among seed sources of C. equisetifolia. While individual land races do not appear to lack diversity, we were able to infer the origins of some, allowing targeted introductions of unrelated material to be made. In the case of the Chinese land race, targeting and testing new accessions from the Pacific and the Philippines may be a good strategy to identify Ralstonia-resistant genotypes.
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176
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Delpierre N, Soudani K, Berveiller D, Dufrêne E, Hmimina G, Vincent G. "Green pointillism": detecting the within-population variability of budburst in temperate deciduous trees with phenological cameras. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2020; 64:663-670. [PMID: 31912307 DOI: 10.1007/s00484-019-01855-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/09/2019] [Accepted: 12/21/2019] [Indexed: 06/10/2023]
Abstract
Phenological cameras have been used over a decade for identifying plant phenological markers (budburst, leaf senescence) and more generally the greenness dynamics of forest canopies. The analysis is usually carried out over the full camera field of view, with no particular analysis of the variability of phenological markers among trees. Here we show that images produced by phenological cameras can be used to quantify the within-population variability of budburst (WPVbb) in temperate deciduous forests. Using seven site-years of image analyses, we report a strong correlation (r2 = 0.97) between the WPVbb determined with a phenological camera and its quantification through ground observation. We show that WPVbb varies strongly (by a factor of 4) from year to year in a given population and that those variations are linked with temperature conditions during the budburst period, with colder springs associated to a higher differentiation of budburst (higher WPVbb) among trees. Deploying our approach at the continental scale, i.e., throughout phenological cameras networks, would improve the understanding of the spatial (across populations) and temporal (across years) variations of WPVbb, which have strong implications on forest functioning, tree fitness and phenological modelling.
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Affiliation(s)
- Nicolas Delpierre
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France.
| | - Kamel Soudani
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Daniel Berveiller
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Eric Dufrêne
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Gabriel Hmimina
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
- Center for Advanced Land Management Information Technologies, School of Natural Resources, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Gaëlle Vincent
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
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177
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De La Torre AR, Wilhite B, Neale DB. Environmental Genome-Wide Association Reveals Climate Adaptation Is Shaped by Subtle to Moderate Allele Frequency Shifts in Loblolly Pine. Genome Biol Evol 2020; 11:2976-2989. [PMID: 31599932 PMCID: PMC6821164 DOI: 10.1093/gbe/evz220] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2019] [Indexed: 01/21/2023] Open
Abstract
Understanding the genomic basis of local adaptation is crucial to determine the potential of long-lived woody species to withstand changes in their natural environment. In the past, efforts to dissect the genomic architecture in gymnosperms species have been limited due to the absence of reference genomes. Recently, the genomes of some commercially important conifers, such as loblolly pine, have become available, allowing whole-genome studies of these species. In this study, we test for associations between 87k SNPs, obtained from whole-genome resequencing of loblolly pine individuals, and 270 environmental variables and combinations of them. We determine the geographic location of significant loci and identify their genomic location using our newly constructed ultradense 26k SNP linkage map. We found that water availability is the main climatic variable shaping local adaptation of the species, and found 821 SNPs showing significant associations with climatic variables or combinations of them based on the consistent results of three different genotype–environment association methods. Our results suggest that adaptation to climate in the species might have occurred by many changes in the frequency of alleles with moderate to small effect sizes, and by the smaller contribution of large effect alleles in genes related to moisture deficit, temperature and precipitation. Genomic regions of low recombination and high population differentiation harbored SNPs associated with groups of environmental variables, suggesting climate adaptation might have evolved as a result of different selection pressures acting on groups of genes associated with an aspect of climate rather than on individual environmental variables.
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Affiliation(s)
| | | | - David B Neale
- Department of Plant Sciences, University of California-Davis
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178
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Blumstein M, Richardson A, Weston D, Zhang J, Muchero W, Hopkins R. A New Perspective on Ecological Prediction Reveals Limits to Climate Adaptation in a Temperate Tree Species. Curr Biol 2020; 30:1447-1453.e4. [PMID: 32220321 DOI: 10.1016/j.cub.2020.02.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/17/2019] [Accepted: 02/03/2020] [Indexed: 01/02/2023]
Abstract
Forests absorb a large fraction of anthropogenic CO2 emission, but their ability to continue to act as a sink under climate change depends in part on plant species undergoing rapid adaptation. Yet models of forest response to climate change currently ignore local adaptation as a response mechanism. Thus, considering the evolution of intraspecific trait variation is necessary for reliable, long-term species and climate projections. Here, we combine ecophysiology and predictive climate modeling with analyses of genomic variation to determine whether sugar and starch storage, energy reserves for trees under extreme conditions, have the heritable variation and genetic diversity necessary to evolve in response to climate change within populations of black cottonwood (Populus trichocarpa). Despite current patterns of local adaptation and extensive range-wide heritable variation in storage, we demonstrate that adaptive evolution in response to climate change will be limited by a lack of heritable variation within northern populations and by a need for extreme genetic changes in southern populations. Our method can help design more targeted species management interventions and highlights the power of using genomic tools in ecological prediction to scale from molecular to regional processes to determine the ability of a species to respond to future climates.
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Affiliation(s)
- Meghan Blumstein
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.
| | - Andrew Richardson
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011, USA; School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - David Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin Zhang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Robin Hopkins
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA; The Arnold Arboretum, 1300 Centre Street, Boston, MA 02130, USA
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179
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Yang T, Meng W, Guo B. Population Genomic Analysis of Two Endemic Schizothoracins Reveals Their Genetic Differences and Underlying Selection Associated with Altitude and Temperature. Animals (Basel) 2020; 10:ani10030447. [PMID: 32156058 PMCID: PMC7142781 DOI: 10.3390/ani10030447] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/02/2020] [Accepted: 03/03/2020] [Indexed: 01/18/2023] Open
Abstract
Simple Summary Diptychus maculates and Gymnodiptychus dybowskii are two rare aboriginal fishes in the Xinjiang Uygur Autonomous Region. In recent years, due to overfishing and habitat fragmentation caused by construction of water conservancy and hydropower projects, the fishery resources have decreased sharply. Understanding the genetic background is of great significance for resource protection. In this study, we revealed the similar trends of population genetic diversities in these two species collected from the Tarim River and the Yili River. In addition, outlier SNPs associated with temperature and altitude were detected in both of them, indicating that Schizothoracinae fishes represented by D. maculates and G. dybowskii were still under the selection pressure of plateau environments. Abstract Schizothoracins are a group of cyprinid fishes distributed throughout the Qinghai–Tibet Plateau, which can be classified in three grades: primitive, specialised and highly specialised according to adaptation ability to plateau environments. As the only specialised schizothoracins in Xinjiang, China, Diptychus maculates and Gymnodiptychus dybowskii are ideal materials for adaptive evolution research. Based on single-nucleotide polymorphism (SNP) loci detected by specific-locus amplified fragment (SLAF) technology, the genome-wide genetic diversities of these two species from nine sites in Xinjiang were evaluated. D.maculates in the Muzat River (BM) and G. dybowskii in the Kaidu River (LKG) presented the lowest genetic diversity levels, whereas D. maculates in the Kumarik River (BK) and G.dybowskii in the Kashi River (LK) were just the opposite. Cluster and principal component analysis demonstrated a distant genetic affinity between D. maculates in the Tashkurgan River (BT) and other populations. Outlier SNP loci were discovered both in D. maculates and G. dybowskii. The coalescent Bayenv and latent factor mixed model (LFMM) methods showed that a total of thirteen and eighteen SNPs in D. maculates were associated with altitude and temperature gradient, respectively. No intersection was revealed in G. dybowskii. The results indicated that D. maculates was subject to much greater divergent selection pressure. A strong signal of isolation-by-distance (IBD) was detected across D. maculates (Mantel test, rs = 0.65; p = 0.05), indicating an evident geographical isolation in the Tarim River. Isolation-by-environment (IBE) analysis implied that temperature and altitude selections were more intensive in D. maculates, with greater environmental variation resulting in weak gene flow.
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Affiliation(s)
- Tianyan Yang
- College of Fishery, Zhejiang Ocean University, Zhoushan 316022, China;
| | - Wei Meng
- Marine Fisheries Research Institute of Zhejiang, Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources of Zhejiang Province, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture, Zhoushan 316021, China
- Correspondence: (W.M.); (B.G.); Tel.: +86-580-229-9888 (W.M.); +86-10-6480-7978 (B.G.)
| | - Baocheng Guo
- Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (W.M.); (B.G.); Tel.: +86-580-229-9888 (W.M.); +86-10-6480-7978 (B.G.)
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180
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Hämälä T, Gorton AJ, Moeller DA, Tiffin P. Pleiotropy facilitates local adaptation to distant optima in common ragweed (Ambrosia artemisiifolia). PLoS Genet 2020; 16:e1008707. [PMID: 32210431 PMCID: PMC7135370 DOI: 10.1371/journal.pgen.1008707] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 04/06/2020] [Accepted: 03/05/2020] [Indexed: 12/23/2022] Open
Abstract
Pleiotropy, the control of multiple phenotypes by a single locus, is expected to slow the rate of adaptation by increasing the chance that beneficial alleles also have deleterious effects. However, a prediction arising from classical theory of quantitative trait evolution states that pleiotropic alleles may have a selective advantage when phenotypes are distant from their selective optima. We examine the role of pleiotropy in regulating adaptive differentiation among populations of common ragweed (Ambrosia artemisiifolia); a species that has recently expanded its North American range due to human-mediated habitat change. We employ a phenotype-free approach by using connectivity in gene networks as a proxy for pleiotropy. First, we identify loci bearing footprints of local adaptation, and then use genotype-expression mapping and co-expression networks to infer the connectivity of the genes. Our results indicate that the putatively adaptive loci are highly pleiotropic, as they are more likely than expected to affect the expression of other genes, and they reside in central positions within the gene networks. We propose that the conditionally advantageous alleles at these loci avoid the cost of pleiotropy by having large phenotypic effects that are beneficial when populations are far from their selective optima. We further use evolutionary simulations to show that these patterns are in agreement with a model where populations face novel selective pressures, as expected during a range expansion. Overall, our results suggest that highly connected genes may be targets of positive selection during environmental change, even though they likely experience strong purifying selection in stable selective environments.
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Affiliation(s)
- Tuomas Hämälä
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Amanda J. Gorton
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
| | - David A. Moeller
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, United States of America
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181
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Hämälä T, Guiltinan MJ, Marden JH, Maximova SN, dePamphilis CW, Tiffin P. Gene Expression Modularity Reveals Footprints of Polygenic Adaptation in Theobroma cacao. Mol Biol Evol 2020; 37:110-123. [PMID: 31501906 DOI: 10.1093/molbev/msz206] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Separating footprints of adaptation from demography is challenging. When selection has acted on a single locus with major effect, this issue can be alleviated through signatures left by selective sweeps. However, as adaptation is often driven by small allele frequency shifts at many loci, studies focusing on single genes are able to identify only a small portion of genomic variants responsible for adaptation. In face of this challenge, we utilize coexpression information to search for signals of polygenetic adaptation in Theobroma cacao, a tropical tree species that is the source of chocolate. Using transcriptomics and a weighted correlation network analysis, we group genes with similar expression patterns into functional modules. We then ask whether modules enriched for specific biological processes exhibit cumulative effects of differential selection in the form of high FST and dXY between populations. Indeed, modules putatively involved in protein modification, flowering, and water transport show signs of polygenic adaptation even though individual genes that are members of those groups do not bear strong signatures of selection. Modeling of demography, background selection, and the effects of genomic features reveal that these patterns are unlikely to arise by chance. We also find that specific modules are enriched for signals of strong or relaxed purifying selection, with one module bearing signs of adaptive differentiation and an excess of deleterious mutations. Our results provide insight into polygenic adaptation and contribute to understanding of population structure, demographic history, and genome evolution in T. cacao.
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Affiliation(s)
- Tuomas Hämälä
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN
| | - Mark J Guiltinan
- Department of Plant Sciences, The Pennsylvania State University, University Park, PA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA
| | - James H Marden
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA.,Department of Biology, The Pennsylvania State University, University Park, PA
| | - Siela N Maximova
- Department of Plant Sciences, The Pennsylvania State University, University Park, PA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA
| | - Claude W dePamphilis
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA.,Department of Biology, The Pennsylvania State University, University Park, PA
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN
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182
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Price N, Lopez L, Platts AE, Lasky JR. In the presence of population structure: From genomics to candidate genes underlying local adaptation. Ecol Evol 2020; 10:1889-1904. [PMID: 32128123 DOI: 10.1101/642306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 05/26/2023] Open
Abstract
Understanding the genomic signatures, genes, and traits underlying local adaptation of organisms to heterogeneous environments is of central importance to the field evolutionary biology. To identify loci underlying local adaptation, models that combine allelic and environmental variation while controlling for the effects of population structure have emerged as the method of choice. Despite being evaluated in simulation studies, there has not been a thorough investigation of empirical evidence supporting local adaptation across these alleles. To evaluate these methods, we use 875 Arabidopsis thaliana Eurasian accessions and two mixed models (GEMMA and LFMM) to identify candidate SNPs underlying local adaptation to climate. Subsequently, to assess evidence of local adaptation and function among significant SNPs, we examine allele frequency differentiation and recent selection across Eurasian populations, in addition to their distribution along quantitative trait loci (QTL) explaining fitness variation between Italy and Sweden populations and cis-regulatory/nonsynonymous sites showing significant selective constraint. Our results indicate that significant LFMM/GEMMA SNPs show low allele frequency differentiation and linkage disequilibrium across locally adapted Italy and Sweden populations, in addition to a poor association with fitness QTL peaks (highest logarithm of odds score). Furthermore, when examining derived allele frequencies across the Eurasian range, we find that these SNPs are enriched in low-frequency variants that show very large climatic differentiation but low levels of linkage disequilibrium. These results suggest that their enrichment along putative functional sites most likely represents deleterious variation that is independent of local adaptation. Among all the genomic signatures examined, only SNPs showing high absolute allele frequency differentiation (AFD) and linkage disequilibrium (LD) between Italy and Sweden populations showed a strong association with fitness QTL peaks and were enriched along selectively constrained cis-regulatory/nonsynonymous sites. Using these SNPs, we find strong evidence linking flowering time, freezing tolerance, and the abscisic-acid pathway to local adaptation.
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Affiliation(s)
- Nicholas Price
- Department of Bioagricultural Sciences & Pest Management Colorado State University Fort Collins CO USA
- Department of Biological Sciences University of Cyprus Nicosia Cyprus
| | - Lua Lopez
- Department of Biology Binghamton University (State University of New York) Binghamton NY USA
| | - Adrian E Platts
- Simons Center for Quantitative Biology Cold Spring Harbor Laboratory Cold Spring Harbor NY USA
- Department of Biology Center for Genomics and Systems Biology New York University New York NY USA
| | - Jesse R Lasky
- Department of Biology Pennsylvania State University University Park PA USA
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183
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Price N, Lopez L, Platts AE, Lasky JR. In the presence of population structure: From genomics to candidate genes underlying local adaptation. Ecol Evol 2020; 10:1889-1904. [PMID: 32128123 PMCID: PMC7042746 DOI: 10.1002/ece3.6002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 12/25/2022] Open
Abstract
Understanding the genomic signatures, genes, and traits underlying local adaptation of organisms to heterogeneous environments is of central importance to the field evolutionary biology. To identify loci underlying local adaptation, models that combine allelic and environmental variation while controlling for the effects of population structure have emerged as the method of choice. Despite being evaluated in simulation studies, there has not been a thorough investigation of empirical evidence supporting local adaptation across these alleles. To evaluate these methods, we use 875 Arabidopsis thaliana Eurasian accessions and two mixed models (GEMMA and LFMM) to identify candidate SNPs underlying local adaptation to climate. Subsequently, to assess evidence of local adaptation and function among significant SNPs, we examine allele frequency differentiation and recent selection across Eurasian populations, in addition to their distribution along quantitative trait loci (QTL) explaining fitness variation between Italy and Sweden populations and cis-regulatory/nonsynonymous sites showing significant selective constraint. Our results indicate that significant LFMM/GEMMA SNPs show low allele frequency differentiation and linkage disequilibrium across locally adapted Italy and Sweden populations, in addition to a poor association with fitness QTL peaks (highest logarithm of odds score). Furthermore, when examining derived allele frequencies across the Eurasian range, we find that these SNPs are enriched in low-frequency variants that show very large climatic differentiation but low levels of linkage disequilibrium. These results suggest that their enrichment along putative functional sites most likely represents deleterious variation that is independent of local adaptation. Among all the genomic signatures examined, only SNPs showing high absolute allele frequency differentiation (AFD) and linkage disequilibrium (LD) between Italy and Sweden populations showed a strong association with fitness QTL peaks and were enriched along selectively constrained cis-regulatory/nonsynonymous sites. Using these SNPs, we find strong evidence linking flowering time, freezing tolerance, and the abscisic-acid pathway to local adaptation.
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Affiliation(s)
- Nicholas Price
- Department of Bioagricultural Sciences & Pest ManagementColorado State UniversityFort CollinsCOUSA
- Department of Biological SciencesUniversity of CyprusNicosiaCyprus
| | - Lua Lopez
- Department of BiologyBinghamton University (State University of New York)BinghamtonNYUSA
| | - Adrian E. Platts
- Simons Center for Quantitative BiologyCold Spring Harbor LaboratoryCold Spring HarborNYUSA
- Department of BiologyCenter for Genomics and Systems BiologyNew York UniversityNew YorkNYUSA
| | - Jesse R. Lasky
- Department of BiologyPennsylvania State UniversityUniversity ParkPAUSA
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184
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Fréjaville T, Vizcaíno-Palomar N, Fady B, Kremer A, Benito Garzón M. Range margin populations show high climate adaptation lags in European trees. GLOBAL CHANGE BIOLOGY 2020; 26:484-495. [PMID: 31642570 DOI: 10.1111/gcb.14881] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 08/09/2019] [Accepted: 09/30/2019] [Indexed: 06/10/2023]
Abstract
How populations of long-living species respond to climate change depends on phenotypic plasticity and local adaptation processes. Marginal populations are expected to have lags in adaptation (i.e. differences between the climatic optimum that maximizes population fitness and the local climate) because they receive pre-adapted alleles from core populations preventing them from reaching a local optimum in their climatically marginal habitat. Yet, whether adaptation lags in marginal populations are a common feature across phylogenetically and ecologically different species and how lags can change with climate change remain unexplored. To test for range-wide patterns of phenotypic variation and adaptation lags of populations to climate, we (a) built model ensembles of tree height accounting for the climate of population origin and the climate of the site for 706 populations monitored in 97 common garden experiments covering the range of six European forest tree species; (b) estimated populations' adaptation lags as the differences between the climatic optimum that maximizes tree height and the climate of the origin of each population; (c) identified adaptation lag patterns for populations coming from the warm/dry and cold/wet margins and from the distribution core of each species range. We found that (a) phenotypic variation is driven by either temperature or precipitation; (b) adaptation lags are consistently higher in climatic margin populations (cold/warm, dry/wet) than in core populations; (c) predictions for future warmer climates suggest adaptation lags would decrease in cold margin populations, slightly increasing tree height, while adaptation lags would increase in core and warm margin populations, sharply decreasing tree height. Our results suggest that warm margin populations are the most vulnerable to climate change, but understanding how these populations can cope with future climates depend on whether other fitness-related traits could show similar adaptation lag patterns.
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Affiliation(s)
| | | | - Bruno Fady
- INRA, UR629, Ecologie des Forêts Méditerranéennes (URFM), Avignon, France
| | - Antoine Kremer
- BIOGECO (UMR 1202), INRA, University of Bordeaux, Cestas, France
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185
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Salmela MJ, Velmala SM, Pennanen T. Seedling traits from root to shoot exhibit genetic diversity and distinct responses to environmental heterogeneity within a tree population. OIKOS 2020. [DOI: 10.1111/oik.06797] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matti J. Salmela
- Natural Resources Inst. Finland (Luke) Latokartanonkaari 9 FI‐00790 Helsinki Finland
| | - Sannakajsa M. Velmala
- Natural Resources Inst. Finland (Luke) Latokartanonkaari 9 FI‐00790 Helsinki Finland
| | - Taina Pennanen
- Natural Resources Inst. Finland (Luke) Latokartanonkaari 9 FI‐00790 Helsinki Finland
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186
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Young DJN, Blush TD, Landram M, Wright JW, Latimer AM, Safford HD. Assisted gene flow in the context of large‐scale forest management in California,
USA. Ecosphere 2020. [DOI: 10.1002/ecs2.3001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Affiliation(s)
- Derek J. N. Young
- Department of Plant Sciences University of California Davis California 95616 USA
| | - Thomas D. Blush
- Pacific Southwest Region USDA Forest Service Vallejo California 94592 USA
| | - Michael Landram
- Pacific Southwest Region USDA Forest Service Vallejo California 94592 USA
| | - Jessica W. Wright
- Pacific Southwest Research Station USDA Forest Service Davis California 95618 USA
| | - Andrew M. Latimer
- Department of Plant Sciences University of California Davis California 95616 USA
| | - Hugh D. Safford
- Pacific Southwest Region USDA Forest Service Vallejo California 94592 USA
- Department of Environmental Science and Policy University of California Davis California95616USA
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187
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Santini F, Climent JM, Voltas J. Phenotypic integration and life history strategies among populations of Pinus halepensis: an insight through structural equation modelling. ANNALS OF BOTANY 2020; 124:1161-1172. [PMID: 31115443 PMCID: PMC6943711 DOI: 10.1093/aob/mcz088] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 05/20/2019] [Indexed: 05/26/2023]
Abstract
BACKGROUND AND AIMS Understanding inter-population variation in the allocation of resources to specific anatomical compartments and physiological processes is crucial to disentangle adaptive patterns in forest species. This work aims to evaluate phenotypic integration and trade-offs among functional traits as determinants of life history strategies in populations of a circum-Mediterranean pine that dwells in environments where water and other resources are in limited supply. METHODS Adult individuals of 51 populations of Pinus halepensis grown in a common garden were characterized for 11 phenotypic traits, including direct and indirect measures of water uptake at different depths, leaf area, stomatal conductance, chlorophyll content, non-structural carbohydrates, stem diameter and tree height, age at first reproduction and cone production. The population differentiation in these traits was tested through analysis of variance (ANOVA). The resulting populations' means were carried forward to a structural equation model evaluating phenotypic integration between six latent variables (summer water uptake depth, summer transpiration, spring photosynthetic capacity, growth, reserve accumulation and reproduction). KEY RESULTS Water uptake depth and transpiration covaried negatively among populations, as the likely result of a common selective pressure for drought resistance, while spring photosynthetic capacity was lower in populations originating from dry areas. Transpiration positively influenced growth, while growth was negatively related to reproduction and reserves among populations. Water uptake depth negatively influenced reproduction. CONCLUSIONS The observed patterns indicate a differentiation in life cycle features between fast-growing and slow-growing populations, with the latter investing significantly more in reproduction and reserves. We speculate that such contrasting strategies result from different arrays of life history traits underlying the very different ecological conditions that the Aleppo pine must face across its distribution range. These comprise, principally, drought as the main stressor and fire as the main ecological disturbance of the Mediterranean basin.
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Affiliation(s)
- Filippo Santini
- Joint Research Unit CTFC – AGROTECNIO, Lleida, Spain
- Department of Crop and Forest Sciences, University of Lleida, Lleida, Spain
| | - José M Climent
- INIA-CIFOR, Department of Ecology and Forest Genetics, Madrid, Spain
| | - Jordi Voltas
- Joint Research Unit CTFC – AGROTECNIO, Lleida, Spain
- Department of Crop and Forest Sciences, University of Lleida, Lleida, Spain
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188
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Mayol M, Riba M, Cavers S, Grivet D, Vincenot L, Cattonaro F, Vendramin GG, González‐Martínez SC. A multiscale approach to detect selection in nonmodel tree species: Widespread adaptation despite population decline in Taxus baccata L. Evol Appl 2020; 13:143-160. [PMID: 31892949 PMCID: PMC6935595 DOI: 10.1111/eva.12838] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 06/18/2019] [Accepted: 06/24/2019] [Indexed: 01/03/2023] Open
Abstract
Detecting the molecular basis of local adaptation and identifying selective drivers is still challenging in nonmodel species. The use of purely population genetic approaches is limited by some characteristics of genetic systems, such as pleiotropy and polygenic control, and parallel evidence from phenotypic-based experimental comparisons is required. In long-lived organisms, the detection of selective pressures might also be precluded by evolutionary lag times in response to the environment. Here, we used the English yew to showcase an example of a multiscale integrative approach in a nonmodel species with limited plant and genomic resources. We combined information from two independent sources, phenotypes in a common environment and genomic data in natural populations, to investigate the signature of selection. Growth differences among populations in a common environment, and phenological patterns of both shoot elongation and male strobili maturation, were associated with climate clines, providing evidence for local adaptation and guiding us in the selection of populations for genomic analyses. We used information on over 25,000 SNPs from c. 1,200 genes to infer the demographic history and to test for molecular signatures of selection at different levels: SNP, gene, and biological pathway. Our results confirmed an overall demographic history of population decline, but we also found evidence for putative local adaptation at the molecular level. We identified or confirmed several candidate genes for positive and negative selection in forest trees, including the pseudo-response regulator 7 (PRR7), an essential component of the circadian clock in plants. In addition, we successfully tested an approach to detect polygenic adaptation in biological pathways, allowing us to identify the flavonoid biosynthesis pathway as a candidate stress-response pathway that deserves further attention in other plants. Finally, our study contributes to the emerging view that explaining contemporary standing genetic variation requires considering adaptation to past climates, especially for long-lived trees.
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Affiliation(s)
| | - Miquel Riba
- CREAFCerdanyola del VallèsSpain
- Univ. Autònoma BarcelonaCerdanyola del VallèsSpain
| | | | - Delphine Grivet
- Department of Forest Ecology and Genetics, Forest Research CentreINIA‐CIFORMadridSpain
- Sustainable Forest Management Research Institute, INIA‐University of ValladolidMadridSpain
| | | | | | - Giovanni G. Vendramin
- Institute of Biosciences and Bioresources, Division of FlorenceNational Research CouncilSesto FiorentinoItaly
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189
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Pyhäjärvi T, Kujala ST, Savolainen O. 275 years of forestry meets genomics in Pinus sylvestris. Evol Appl 2020; 13:11-30. [PMID: 31988655 PMCID: PMC6966708 DOI: 10.1111/eva.12809] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 04/05/2019] [Accepted: 04/24/2019] [Indexed: 12/12/2022] Open
Abstract
Pinus sylvestris has a long history of basic and applied research that is relevant for both forestry and evolutionary studies. Its patterns of adaptive variation and role in forest economic and ecological systems have been studied extensively for nearly 275 years, detailed demography for a 100 years and mating system more than 50 years. However, its reference genome sequence is not yet available and genomic studies have been lagging compared to, for example, Pinus taeda and Picea abies, two other economically important conifers. Despite the lack of reference genome, many modern genomic methods are applicable for a more detailed look at its biological characteristics. For example, RNA-seq has revealed a complex transcriptional landscape and targeted DNA sequencing displays an excess of rare variants and geographically homogenously distributed molecular genetic diversity. Current DNA and RNA resources can be used as a reference for gene expression studies, SNP discovery, and further targeted sequencing. In the future, specific consequences of the large genome size, such as functional effects of regulatory open chromatin regions and transposable elements, should be investigated more carefully. For forest breeding and long-term management purposes, genomic data can help in assessing the genetic basis of inbreeding depression and the application of genomic tools for genomic prediction and relatedness estimates. Given the challenges of breeding (long generation time, no easy vegetative propagation) and the economic importance, application of genomic tools has a potential to have a considerable impact. Here, we explore how genomic characteristics of P. sylvestris, such as rare alleles and the low extent of linkage disequilibrium, impact the applicability and power of the tools.
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Affiliation(s)
- Tanja Pyhäjärvi
- Department of Ecology and GeneticsUniversity of OuluOuluFinland
- Biocenter OuluUniversity of OuluOuluFinland
| | | | - Outi Savolainen
- Department of Ecology and GeneticsUniversity of OuluOuluFinland
- Biocenter OuluUniversity of OuluOuluFinland
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190
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Isabel N, Holliday JA, Aitken SN. Forest genomics: Advancing climate adaptation, forest health, productivity, and conservation. Evol Appl 2020; 13:3-10. [PMID: 31892941 PMCID: PMC6935596 DOI: 10.1111/eva.12902] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/09/2019] [Accepted: 12/09/2019] [Indexed: 12/17/2022] Open
Abstract
Forest ecosystems provide important ecological services and resources, from habitat for biodiversity to the production of environmentally friendly products, and play a key role in the global carbon cycle. Humanity is counting on forests to sequester and store a substantial portion of the anthropogenic carbon dioxide produced globally. However, the unprecedented rate of climate change, deforestation, and accidental importation of invasive insects and diseases are threatening the health and productivity of forests, and their capacity to provide these services. Knowledge of genetic diversity, local adaptation, and genetic control of key traits is required to predict the adaptive capacity of tree populations, inform forest management and conservation decisions, and improve breeding for productive trees that will withstand the challenges of the 21st century. Genomic approaches have well accelerated the generation of knowledge of the genetic and evolutionary underpinnings of nonmodel tree species, and advanced their applications to address these challenges. This special issue of Evolutionary Applications features 14 papers that demonstrate the value of a wide range of genomic approaches that can be used to better understand the biology of forest trees, including species that are widespread and managed for timber production, and others that are threatened or endangered, or serve important ecological roles. We highlight some of the major advances, ranging from understanding the evolution of genomes since the period when gymnosperms separated from angiosperms 300 million years ago to using genomic selection to accelerate breeding for tree health and productivity. We also discuss some of the challenges and future directions for applying genomic tools to address long-standing questions about forest trees.
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Affiliation(s)
- Nathalie Isabel
- Laurentian Forestry CentreCanadian Forest ServiceNatural Resources CanadaQuébecCanada
- Canada Research Chair in Forest GenomicsCentre for Forest Research and Institute for Systems and Integrative BiologyUniversité LavalQuébecCanada
| | - Jason A. Holliday
- Department of Forest Resources and Environmental ConservationVirginia TechBlacksburgVAUSA
| | - Sally N. Aitken
- Centre for Forest Conservation Genetics and Department of Forest and Conservation SciencesUniversity of British ColumbiaVancouverCanada
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191
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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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192
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Peterson ML, Angert AL, Kay KM. Experimental migration upward in elevation is associated with strong selection on life history traits. Ecol Evol 2020; 10:612-625. [PMID: 32015830 PMCID: PMC6988539 DOI: 10.1002/ece3.5710] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 08/10/2019] [Accepted: 09/05/2019] [Indexed: 12/26/2022] Open
Abstract
One of the strongest biological impacts of climate change has been the movement of species poleward and upward in elevation. Yet, what is not clear is the extent to which the spatial distribution of locally adapted lineages and ecologically important traits may also shift with continued climate change. Here, we take advantage of a transplant experiment mimicking up-slope seed dispersal for a suite of ecologically diverse populations of yellow monkeyflower (Mimulus guttatus sensu lato) into a high-elevation common garden during an extreme drought period in the Sierra Nevada mountains, California, USA. We use a demographic approach to quantify fitness and test for selection on life history traits in local versus lower-elevation populations and in normal versus drought years to test the potential for up-slope migration and phenotypic selection to alter the distribution of key life history traits in montane environments. We find that lower-elevation populations tend to outperform local populations, confirming the potential for up-slope migration. Although selection generally favored some local montane traits, including larger flowers and larger stem size at flowering, drought conditions tended to select for earlier flowering typical of lower-elevation genotypes. Taken together, this suggests that monkeyflower lineages moving upward in elevation could experience selection for novel trait combinations, particularly under warmer and drier conditions that are predicted to occur with continued climate change.
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Affiliation(s)
- Megan L. Peterson
- Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzCalifornia
| | - Amy L. Angert
- Department of Botany and ZoologyUniversity of British ColumbiaVancouverBCCanada
| | - Kathleen M. Kay
- Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzCalifornia
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193
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Elfstrand M, Zhou L, Baison J, Olson Å, Lundén K, Karlsson B, Wu HX, Stenlid J, García‐Gil MR. Genotypic variation in Norway spruce correlates to fungal communities in vegetative buds. Mol Ecol 2020; 29:199-213. [PMID: 31755612 PMCID: PMC7003977 DOI: 10.1111/mec.15314] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 10/31/2019] [Accepted: 11/20/2019] [Indexed: 12/19/2022]
Abstract
The taxonomically diverse phyllosphere fungi inhabit leaves of plants. Thus, apart from the fungi's dispersal capacities and environmental factors, the assembly of the phyllosphere community associated with a given host plant depends on factors encoded by the host's genome. The host genetic factors and their influence on the assembly of phyllosphere communities under natural conditions are poorly understood, especially in trees. Recent work indicates that Norway spruce (Picea abies) vegetative buds harbour active fungal communities, but these are hitherto largely uncharacterized. This study combines internal transcribed spacer sequencing of the fungal communities associated with dormant vegetative buds with a genome-wide association study (GWAS) in 478 unrelated Norway spruce trees. The aim was to detect host loci associated with variation in the fungal communities across the population, and to identify loci correlating with the presence of specific, latent, pathogens. The fungal communities were dominated by known Norway spruce phyllosphere endophytes and pathogens. We identified six quantitative trait loci (QTLs) associated with the relative abundance of the dominating taxa (i.e., top 1% most abundant taxa). Three additional QTLs associated with colonization by the spruce needle cast pathogen Lirula macrospora or the cherry spruce rust (Thekopsora areolata) in asymptomatic tissues were detected. The identification of the nine QTLs shows that the genetic variation in Norway spruce influences the fungal community in dormant buds and that mechanisms underlying the assembly of the communities and the colonization of latent pathogens in trees may be uncovered by combining molecular identification of fungi with GWAS.
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Affiliation(s)
- Malin Elfstrand
- Uppsala BiocentreDepartment of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
| | - Linghua Zhou
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeåSweden
| | - John Baison
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeåSweden
| | - Åke Olson
- Uppsala BiocentreDepartment of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
| | - Karl Lundén
- Uppsala BiocentreDepartment of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
| | | | - Harry X. Wu
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeåSweden
| | - Jan Stenlid
- Uppsala BiocentreDepartment of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
| | - M. Rosario García‐Gil
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeåSweden
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194
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Cruz MV, Mori GM, Signori-Müller C, da Silva CC, Oh DH, Dassanayake M, Zucchi MI, Oliveira RS, de Souza AP. Local adaptation of a dominant coastal tree to freshwater availability and solar radiation suggested by genomic and ecophysiological approaches. Sci Rep 2019; 9:19936. [PMID: 31882752 PMCID: PMC6934818 DOI: 10.1038/s41598-019-56469-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 12/07/2019] [Indexed: 12/21/2022] Open
Abstract
Local adaptation is often a product of environmental variations in geographical space and has implications for biodiversity conservation. We investigated the role of latitudinal heterogeneity in climate on the organization of genetic and phenotypic variation in the dominant coastal tree Avicennia schaueriana. In a common garden experiment, samples from an equatorial region, with pronounced seasonality in precipitation, accumulated less biomass, and showed lower stomatal conductance and transpiration, narrower xylem vessels, smaller leaves and higher reflectance of long wavelengths by the stem epidermis than samples from a subtropical region, with seasonality in temperature and no dry season. Transcriptomic differences identified between trees sampled under field conditions at equatorial and subtropical sites, were enriched in functional categories such as responses to temperature, solar radiation, water deficit, photosynthesis and cell wall biosynthesis. Remarkably, the diversity based on genome-wide SNPs revealed a north-south genetic structure and signatures of selection were identified for loci associated with photosynthesis, anthocyanin accumulation and the responses to osmotic and hypoxia stresses. Our results suggest the existence of divergence in key resource-use characteristics, likely driven by seasonality in water deficit and solar radiation. These findings provide a basis for conservation plans and for predicting coastal plants responses to climate change.
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Affiliation(s)
- Mariana Vargas Cruz
- Department of Plant Biology, Institute of Biology, University of Campinas (Unicamp), Campinas, SP, 13083-863, Brazil
- Center for Molecular Biology and Genetic Engineering, University of Campinas (Unicamp), Campinas, SP, 13083-875, Brazil
| | - Gustavo Maruyama Mori
- Institute of Biosciences, São Paulo State University (Unesp), São Vicente, SP, 11330-900, Brazil
| | - Caroline Signori-Müller
- Department of Plant Biology, Institute of Biology, University of Campinas (Unicamp), Campinas, SP, 13083-863, Brazil
| | - Carla Cristina da Silva
- Center for Molecular Biology and Genetic Engineering, University of Campinas (Unicamp), Campinas, SP, 13083-875, Brazil
| | - Dong-Ha Oh
- Department of Biological Sciences, Louisiana State University (LSU), Louisiana, LA, 70803, United States
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University (LSU), Louisiana, LA, 70803, United States
| | | | - Rafael Silva Oliveira
- Department of Plant Biology, Institute of Biology, University of Campinas (Unicamp), Campinas, SP, 13083-863, Brazil
| | - Anete Pereira de Souza
- Department of Plant Biology, Institute of Biology, University of Campinas (Unicamp), Campinas, SP, 13083-863, Brazil.
- Center for Molecular Biology and Genetic Engineering, University of Campinas (Unicamp), Campinas, SP, 13083-875, Brazil.
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195
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Berzaghi F, Wright IJ, Kramer K, Oddou-Muratorio S, Bohn FJ, Reyer CPO, Sabaté S, Sanders TGM, Hartig F. Towards a New Generation of Trait-Flexible Vegetation Models. Trends Ecol Evol 2019; 35:191-205. [PMID: 31882280 DOI: 10.1016/j.tree.2019.11.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/15/2019] [Accepted: 11/25/2019] [Indexed: 12/17/2022]
Abstract
Plant trait variability, emerging from eco-evolutionary dynamics that range from alleles to macroecological scales, is one of the most elusive, but possibly most consequential, aspects of biodiversity. Plasticity, epigenetics, and genetic diversity are major determinants of how plants will respond to climate change, yet these processes are rarely represented in current vegetation models. Here, we provide an overview of the challenges associated with understanding the causes and consequences of plant trait variability, and review current developments to include plasticity and evolutionary mechanisms in vegetation models. We also present a roadmap of research priorities to develop a next generation of vegetation models with flexible traits. Including trait variability in vegetation models is necessary to better represent biosphere responses to global change.
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Affiliation(s)
- Fabio Berzaghi
- Laboratory for Sciences of Climate and Environment (LSCE) - UMR CEA/CNRS/UVSQ, Gif-sur-Yvette 91191, France; Department of Biological Sciences, Macquarie University, Sydney, NSW 2022, Australia; Dipartimento per la Innovazione nei sistemi Biologici, Agroalimentari e Forestali, University of Tuscia, Viterbo 01100, Italy.
| | - Ian J Wright
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2022, Australia
| | - Koen Kramer
- Wageningen University and Research, Droevendaalse steeg 4, 6700AA Wageningen, The Netherlands
| | | | - Friedrich J Bohn
- Karlsruhe Institute of Technology, Institute for Meteorology and Climate Research, Atmospheric Environmental Research (IMK-IFU), Kreuzeckbahnstrasse 19, Garmisch-Partenkirchen 82467, Germany; Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, Leipzig 04318, Germany
| | - Christopher P O Reyer
- Potsdam Institute for Climate Impact Research (PIK), Member of the Leibniz Association, PO Box 60 12 03, D-14412 Potsdam, Germany
| | - Santiago Sabaté
- Department of Evolutionary Biology, Ecology, and Environmental Sciences, University of Barcelona (UB), Barcelona 08028, Spain; CREAF (Center for Ecological Research and Forestry Applications), Cerdanyola del Vallès 08193, Spain
| | - Tanja G M Sanders
- Thuenen Institut of Forest Ecosystems, Alfred-Moeller-Str. 1, Haus 41/42, 16225 Eberswalde, Germany
| | - Florian Hartig
- Theoretical Ecology, Faculty of Biology and Preclinical Medicine, University of Regensburg, Universitätsstraße 3, 93053, Regensburg, Germany
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196
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Ismail SA, Kokko H. An analysis of mating biases in trees. Mol Ecol 2019; 29:184-198. [PMID: 31755136 PMCID: PMC7003921 DOI: 10.1111/mec.15312] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 11/01/2019] [Accepted: 11/20/2019] [Indexed: 11/29/2022]
Abstract
Assortative mating is a deviation from random mating based on phenotypic similarity. As it is much better studied in animals than in plants, we investigate for trees whether kinship of realized mating pairs deviates from what is expected from the set of potential mates and use this information to infer mating biases that may result from kin recognition and/or assortative mating. Our analysis covers 20 species of trees for which microsatellite data is available for adult populations (potential mates) as well as seed arrays. We test whether mean relatedness of observed mating pairs deviates from null expectations that only take pollen dispersal distances into account (estimated from the same data set). This allows the identification of elevated as well as reduced kinship among realized mating pairs, indicative of positive and negative assortative mating, respectively. The test is also able to distinguish elevated biparental inbreeding that occurs solely as a result of related pairs growing closer to each other from further assortativeness. Assortative mating in trees appears potentially common but not ubiquitous: nine data sets show mating bias with elevated inbreeding, nine do not deviate significantly from the null expectation, and two show mating bias with reduced inbreeding. While our data sets lack direct information on phenology, our investigation of the phenological literature for each species identifies flowering phenology as a potential driver of positive assortative mating (leading to elevated inbreeding) in trees. Since active kin recognition provides an alternative hypothesis for these patterns, we encourage further investigations on the processes and traits that influence mating patterns in trees.
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Affiliation(s)
- Sascha A Ismail
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Hanna Kokko
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
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197
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Søndreli KL, Kanaskie A, Keriö S, LeBoldus JM. Variation in Susceptibility of Tanoak to the NA1 and EU1 Lineages of Phytophthora ramorum, the Cause of Sudden Oak Death. PLANT DISEASE 2019; 103:3154-3160. [PMID: 31560616 DOI: 10.1094/pdis-04-19-0831-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Phytophthora ramorum, the cause of sudden oak death (SOD), kills tanoak (Notholithocarpus densiflorus) trees in southwestern Oregon and California. Two lineages of P. ramorum are now found in wildland forests of Oregon (NA1 and EU1). In addition to the management of SOD in forest ecosystems, disease resistance could be used as a way to mitigate the impact of P. ramorum. The objectives of this study were to (i) characterize the variability in resistance of N. densiflorus among families using lesion length; (ii) determine whether lineage, isolate, family, or their interactions significantly affect variation in lesion length; and (iii) determine whether there are differences among isolates and among families in terms of lesion length. The parameters isolate nested within lineage (isolate[lineage]) and family × isolate(lineage) interaction explained the majority of the variation in lesion length. There was no significant difference between the NA1 and EU1 lineages in terms of mean lesion length; however, there were differences among the six isolates. Lesions on seedlings collected from surviving trees at infested sites were smaller, on average, than lesions of seedlings collected from trees at noninfested sites (P = 0.0064). The results indicate that there is potential to establish a breeding program for tanoak resistance to SOD and that several isolates of P. ramorum should be used in an artificial inoculation assay.
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Affiliation(s)
- Kelsey L Søndreli
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331-2902
| | - Alan Kanaskie
- Oregon Department of Forestry, Private Forests Program, Forest Health Section, Salem, OR 97310
| | - Susanna Keriö
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331-2902
| | - Jared M LeBoldus
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331-2902
- Department of Forest Engineering, Resources, and Management, Oregon State University, Corvallis, OR 97331-5704
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198
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Naoe S, Tayasu I, Sakai Y, Masaki T, Kobayashi K, Nakajima A, Sato Y, Yamazaki K, Kiyokawa H, Koike S. Downhill seed dispersal by temperate mammals: a potential threat to plant escape from global warming. Sci Rep 2019; 9:14932. [PMID: 31624326 PMCID: PMC6797773 DOI: 10.1038/s41598-019-51376-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 09/13/2019] [Indexed: 01/08/2023] Open
Abstract
Vertical seed dispersal, i.e. seed dispersal towards a higher or lower altitude, is considered a critical process for plant escape from climate change. However, studies exploring vertical seed dispersal are scarce, and thus, its direction, frequency, and mechanisms are little known. In the temperate zone, evaluating vertical seed dispersal of animal-dispersed plants fruiting in autumn and/or winter is essential considering the dominance of such plants in temperate forests. We hypothesized that their seeds are dispersed towards lower altitudes because of the downhill movement of frugivorous animals following the autumn-to-winter phenology of their food plants which proceeds from the mountain tops to the foot in the temperate zone. We evaluated the vertical seed dispersal of the autumn-fruiting wild kiwi, Actinidia arguta, which is dispersed by temperate mammals. We collected dispersed seeds from mammal faeces in the Kanto Mountains of central Japan and estimated the distance of vertical seed dispersal using the oxygen isotope ratios of the dispersed seeds. We found the intensive downhill seed dispersal of wild kiwi by all seed dispersers, except the raccoon dog (bear: mean −393.1 m; marten: −245.3 m; macaque: −98.5 m; and raccoon dog: +4.5 m). Mammals with larger home ranges dispersed seeds longer towards the foot of the mountains. Furthermore, we found that seeds produced at higher altitudes were dispersed a greater distance towards the foot of the mountains. Altitudinal gradients in autumn-to-winter plant phenology and other mountain characteristics, i.e. larger surface areas and more attractive human crops at lower altitudes compared to higher altitudes, were considered drivers of downhill seed dispersal via animal movement. Strong downhill seed dispersal by mammals suggests that populations of autumn-to-winter fruiting plants dispersed by animals may not be able to sufficiently escape from current global warming in the temperate zone.
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Affiliation(s)
- Shoji Naoe
- Forestry and Forest Products Research Institute, Matsunosato 1, Tsukuba, Ibaraki, 305-8687, Japan. .,Tohoku Research Center, Forestry and Forest Products Research Institute, 92-25 Nabeyashiki, Shimokuriyagawa, Morioka, Iwate, 020-0123, Japan.
| | - Ichiro Tayasu
- Research Institute for Humanity and Nature, 457-4 Motoyama, Kamigamo, Kita-ku, Kyoto, 603-8047, Japan.,Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, Shiga, 520-2113, Japan
| | - Yoichiro Sakai
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, Shiga, 520-2113, Japan.,Lake Biwa Environmental Research Institute, 5-34 Yanagasaki, Ohtsu, Shiga, 520-0022, Japan
| | - Takashi Masaki
- Forestry and Forest Products Research Institute, Matsunosato 1, Tsukuba, Ibaraki, 305-8687, Japan
| | - Kazuki Kobayashi
- College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, 252-8510, Japan
| | - Akiko Nakajima
- College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, 252-8510, Japan
| | - Yoshikazu Sato
- College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, 252-8510, Japan.,Rakuno Gakuen University, 582 Bunkyodai-Midorimachi, Ebetsu, Hokkaido, 069-8501, Japan
| | - Koji Yamazaki
- Ibaraki Nature Museum, 700 Ohsaki, Bando, Ibaraki, 306-0622, Japan.,Department of Forest Science, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Hiroki Kiyokawa
- Laboratory of Biodiversity Science, School of Agriculture and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Shinsuke Koike
- Tokyo University of Agriculture and Technology, 3-5-8 Saiwai, Fuchu, Tokyo, 183-8509, Japan
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199
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Looking for Local Adaptation: Convergent Microevolution in Aleppo Pine ( Pinus halepensis). Genes (Basel) 2019; 10:genes10090673. [PMID: 31487909 PMCID: PMC6771008 DOI: 10.3390/genes10090673] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 08/29/2019] [Accepted: 09/03/2019] [Indexed: 01/15/2023] Open
Abstract
Finding outlier loci underlying local adaptation is challenging and is best approached by suitable sampling design and rigorous method selection. In this study, we aimed to detect outlier loci (single nucleotide polymorphisms, SNPs) at the local scale by using Aleppo pine (Pinus halepensis), a drought resistant conifer that has colonized many habitats in the Mediterranean Basin, as the model species. We used a nested sampling approach that considered replicated altitudinal gradients for three contrasting sites. We genotyped samples at 294 SNPs located in genomic regions selected to maximize outlier detection. We then applied three different statistical methodologies-Two Bayesian outlier methods and one latent factor principal component method-To identify outlier loci. No SNP was an outlier for all three methods, while eight SNPs were detected by at least two methods and 17 were detected only by one method. From the intersection of outlier SNPs, only one presented an allelic frequency pattern associated with the elevational gradient across the three sites. In a context of multiple populations under similar selective pressures, our results underline the need for careful examination of outliers detected in genomic scans before considering them as candidates for convergent adaptation.
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200
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Moncalvillo B, Méndez M, Iriondo JM. Ecotypic differentiation reveals seed colour-related alkaloid content in a crop wild relative. PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21:942-950. [PMID: 30980687 DOI: 10.1111/plb.12996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 04/09/2019] [Indexed: 05/12/2023]
Abstract
Crop wild relatives can be a useful source of genotypes that maximise crop survival and yield in specific habitats. Lupinus angustifolius is an annual forb with crop varieties derived from a narrow genetic basis but that are cultivated worldwide. Its seeds have high nutritional value, but they naturally contain alkaloids with anti-nutritive factors. The study of its wild populations can be useful to find genotypes that contribute to higher climate resilience and greater yield under stressing environmental conditions. Using a common garden, we evaluated ecotypic differentiation in four natural populations from two contrasting latitudes in terms of plant biomass, seed mass and number, alkaloid content in seeds for the three main alkaloids present in the plant and seed colour, including its possible influence on post-dispersal predation. Correlations among traits were also assessed. We found differences among populations for all traits except final biomass. Northern populations had lighter seeds and a tendency to yield more seeds when they produced white seeds, compared to southern populations and variegated seeds. Regardless of latitude, populations showed differences in alkaloid concentration, with all three alkaloids found generally in high or low concentrations in each population. Proportion of white seed morphs varied in each population. Seed colour did not influence predator preference. In addition, white seed colour was related to a low alkaloid content. Our results evidence the existence of natural ecotypic differentiation in L. angustifolius not only due to latitudinal range, but also to local environmental factors. White seed coat colour could be used as a visual clue for identification of low-alkaloid genotypes, a priority trait in L. angustifolius breeding programmes.
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Affiliation(s)
- B Moncalvillo
- Biodiversity and Conservation Unit, Department Biology, Geology, Physics and Inorganic Chemistry, ESCET, URJC, Móstoles, Madrid, Spain
| | - M Méndez
- Biodiversity and Conservation Unit, Department Biology, Geology, Physics and Inorganic Chemistry, ESCET, URJC, Móstoles, Madrid, Spain
| | - J M Iriondo
- Biodiversity and Conservation Unit, Department Biology, Geology, Physics and Inorganic Chemistry, ESCET, URJC, Móstoles, Madrid, Spain
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