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Brady MV, Farrer EC. The soil microbiome affects patterns of local adaptation in an alpine plant under moisture stress. AMERICAN JOURNAL OF BOTANY 2024; 111:e16304. [PMID: 38517213 DOI: 10.1002/ajb2.16304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 03/23/2024]
Abstract
PREMISE The soil microbiome plays a role in plant trait expression and fitness, and plants may be locally adapted or maladapted to their soil microbiota. However, few studies of local adaptation in plants have incorporated a microbial treatment separate from manipulations of the abiotic environment, so our understanding of microbes in plant adaptation is limited. METHODS Here we tested microbial effects on local adaptation in four paired populations of an abundant alpine plant from two community types, dry and moist meadow. In a 5-month greenhouse experiment, we manipulated source population, soil moisture, and soil microbiome and measured plant survival and biomass to assess treatment effects. RESULTS Dry meadow populations had higher biomass than moist meadow populations at low moisture, demonstrating evidence of local adaptation to soil moisture in the absence of microbes. In the presence of microbes, dry meadow populations had greater survival than moist meadow populations when grown with dry meadow microbes regardless of moisture. Moist meadow populations showed no signs of adaptation or maladaptation. CONCLUSIONS Our research highlights the importance of microbial mutualists in local adaptation, particularly in dry environments with higher abiotic stress. Plant populations from environments with greater abiotic stress exhibit different patterns of adaptation when grown with soil microbes versus without, while plant populations from less abiotically stressful environments do not. Improving our understanding of the role microbes play in plant adaptation will require further studies incorporating microbial manipulations.
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Affiliation(s)
- Monica V Brady
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, 70118, LA, USA
| | - Emily C Farrer
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, 70118, LA, USA
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Alatalo JM, Dai J, Pandey R, Erfanian MB, Ahmed T, Bai Y, Molau U, Jägerbrand AK. Impact of ambient temperature, precipitation and seven years of experimental warming and nutrient addition on fruit production in an alpine heath and meadow community. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 836:155450. [PMID: 35490820 DOI: 10.1016/j.scitotenv.2022.155450] [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: 12/21/2021] [Revised: 04/10/2022] [Accepted: 04/18/2022] [Indexed: 06/14/2023]
Abstract
Alpine and polar regions are predicted to be among the most vulnerable to changes in temperature, precipitation, and nutrient availability. We carried out a seven-year factorial experiment with warming and nutrient addition in two alpine vegetation communities. We analyzed the relationship between fruit production and monthly mean, maximum, and min temperatures during the fall of the pre-fruiting year, the fruiting summer, and the whole fruit production period, and measured the effects of precipitation and growing and thawing degree days (GDD & TDD) on fruit production. Nutrient addition (heath: 27.88 ± 3.19 fold change at the end of the experiment; meadow: 18.02 ± 4.07) and combined nutrient addition and warming (heath: 20.63 ± 29.34 fold change at the end of the experiment; meadow: 18.21 ± 16.28) increased total fruit production and fruit production of graminoids. Fruit production of evergreen and deciduous shrubs fluctuated among the treatments and years in both the heath and meadow. Pre-maximum temperatures had a negative effect on fruit production in both communities, while current year maximum temperatures had a positive impact on fruit production in the meadow. Pre-minimum, pre-mean, current mean, total minimum, and total mean temperatures were all positively correlated with fruit production in the meadow. The current year and total precipitation had a negative effect on the fruit production of deciduous shrubs in the heath. GDD had a positive effect on fruit production in both communities, while TDD only impacted fruit production in the meadow. Increased nutrient availability increased fruit production over time in the high alpine plant communities, while experimental warming had either no effect or a negative effect. Deciduous shrubs were the most sensitive to climate parameters in both communities, and the meadow was more sensitive than the heath. The difference in importance of TDD for fruit production may be due to differences in snow cover in the two communities.
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Affiliation(s)
- Juha M Alatalo
- Environmental Science Center, Qatar University, PO Box 2713, Doha, Qatar.
| | - Junhu Dai
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographical Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Rajiv Pandey
- Division of Forestry Statistics, Indian Council of Forestry Research and Education, Dehradun, India
| | - Mohammad Bagher Erfanian
- Quantitative Plant Ecology and Biodiversity Research Lab, Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Talaat Ahmed
- Environmental Science Center, Qatar University, PO Box 2713, Doha, Qatar
| | - Yang Bai
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
| | - Ulf Molau
- Department of Plant and Environmental Sciences, University of Gothenburg, PO Box 461, SE-405 30 Gothenburg, Sweden
| | - Annika K Jägerbrand
- Department of Environmental and Biosciences, School of Business, Innovation and Sustainability, Halmstad University, P.O. Box 823, SE-301 18 Halmstad, Sweden
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Keeler AM, Rafferty NE. Legume germination is delayed in dry soils and in sterile soils devoid of microbial mutualists: Species-specific implications for upward range expansions. Ecol Evol 2022; 12:e9186. [PMID: 36016820 PMCID: PMC9398887 DOI: 10.1002/ece3.9186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/27/2022] [Accepted: 07/15/2022] [Indexed: 11/14/2022] Open
Abstract
Climate change is affecting species and their mutualists and can lead to the weakening or loss of important interspecific interactions. Through independent shifts in partner phenology and distribution, climatic stress can separate mutualists temporally or spatially, leading to alterations in partner functional traits and fitness. Here, we explored the effects of the loss of microbial mutualists on legume germination success and phenology. In particular, we assessed the effects of mutualism loss via soil sterilization, increased drought, and introduction to novel soils found beyond the current distributions of two focal legume species in subalpine environments. Through common garden experiments in controlled environments, we found evidence that soil sterilization (and consequent microbial absence) and dry soils caused species-specific phenological delays of 2-5 weeks in germination, likely as a result of interaction loss between legumes and specialized germination-promoting soil microbes, such as mutualistic rhizobia. Delays in germination caused by a mismatch between legumes and beneficial microbes could negatively affect legume fitness through increased plant-plant competition later in the season. Additionally, we found evidence of the presence of beneficial microbes beyond the current elevational range of one of our focal legumes, which may allow for expansion of the leading edge, although harsh abiotic factors in the alpine may hinder this. Alterations in the strength of soil microbe-legume mutualisms may lead to reduced fitness and altered demography for both soil microbes and legumes.
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Affiliation(s)
- Andrea M. Keeler
- Department of Evolution, Ecology, and Organismal BiologyUniversity of California, RiversideRiversideCaliforniaUSA
- Rocky Mountain Biological LaboratoryCrested ButteColoradoUSA
| | - Nicole E. Rafferty
- Department of Evolution, Ecology, and Organismal BiologyUniversity of California, RiversideRiversideCaliforniaUSA
- Rocky Mountain Biological LaboratoryCrested ButteColoradoUSA
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Magos Brehm J, Gaisberger H, Kell S, Parra‐Quijano M, Thormann I, Dulloo ME, Maxted N. Planning complementary conservation of crop wild relative diversity in southern Africa. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
| | - Hannes Gaisberger
- The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT) Rome Italy
- Department of Geoinformatics Paris Lodron University of Salzburg Salzburg Austria
| | - Shelagh Kell
- School of Biosciences University of Birmingham Birmingham UK
| | - Mauricio Parra‐Quijano
- Facultad de Ciencias Agrarias Universidad Nacional de Colombia, Ciudad Universitaria Bogotá Colombia
| | - Imke Thormann
- The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT) Rome Italy
| | - Mohammad Ehsan Dulloo
- The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT) Rose‐Hill Mauritius
| | - Nigel Maxted
- School of Biosciences University of Birmingham Birmingham UK
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Topography of the Dolomites modulates range dynamics of narrow endemic plants under climate change. Sci Rep 2022; 12:1398. [PMID: 35082360 PMCID: PMC8792058 DOI: 10.1038/s41598-022-05440-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 01/11/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractClimate change is expected to threaten endemic plants in the Alps. In this context, the factors that may modulate species responses are rarely investigated at a local scale. We analyzed eight alpine narrow endemics of the Dolomites (southeastern Alps) under different predicted climate change scenarios at fine spatial resolutions. We tested possible differences in elevation, topographic heterogeneity and velocity of climate change among areas of gained, lost, or stable climatic habitat. The negative impact of climate change ranged from moderate to severe, depending on scenario and species. Generally, range loss occurred at the lowest elevations, while gained and stable areas were located at highest elevations. For six of the species, climate change velocity had higher values in stable and gained areas than in lost ones. Our findings support the role of topographic heterogeneity in maintaining climatic microrefugia, however, the peculiar topography of the Dolomites, characterized by high altitude plateaus, resulted in high climate change velocity in areas of projected future climatic suitability. Our study supports the usefulness of multiple predictors of spatio-temporal range dynamics for regional climate-adapted management and eventual assisted colonization planning to not overlook or overestimate the potential impact of climate change locally.
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Falcão JCF, Carvalheiro LG, Guevara R, Lira-Noriega A. The risk of invasion by angiosperms peaks at intermediate levels of human influence. Basic Appl Ecol 2021. [DOI: 10.1016/j.baae.2021.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Singh D, Chaudhary P, Taunk J, Singh CK, Singh D, Tomar RSS, Aski M, Konjengbam NS, Raje RS, Singh S, Sengar RS, Yadav RK, Pal M. Fab Advances in Fabaceae for Abiotic Stress Resilience: From 'Omics' to Artificial Intelligence. Int J Mol Sci 2021; 22:10535. [PMID: 34638885 PMCID: PMC8509049 DOI: 10.3390/ijms221910535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/17/2021] [Accepted: 09/23/2021] [Indexed: 11/16/2022] Open
Abstract
Legumes are a better source of proteins and are richer in diverse micronutrients over the nutritional profile of widely consumed cereals. However, when exposed to a diverse range of abiotic stresses, their overall productivity and quality are hugely impacted. Our limited understanding of genetic determinants and novel variants associated with the abiotic stress response in food legume crops restricts its amelioration. Therefore, it is imperative to understand different molecular approaches in food legume crops that can be utilized in crop improvement programs to minimize the economic loss. 'Omics'-based molecular breeding provides better opportunities over conventional breeding for diversifying the natural germplasm together with improving yield and quality parameters. Due to molecular advancements, the technique is now equipped with novel 'omics' approaches such as ionomics, epigenomics, fluxomics, RNomics, glycomics, glycoproteomics, phosphoproteomics, lipidomics, regulomics, and secretomics. Pan-omics-which utilizes the molecular bases of the stress response to identify genes (genomics), mRNAs (transcriptomics), proteins (proteomics), and biomolecules (metabolomics) associated with stress regulation-has been widely used for abiotic stress amelioration in food legume crops. Integration of pan-omics with novel omics approaches will fast-track legume breeding programs. Moreover, artificial intelligence (AI)-based algorithms can be utilized for simulating crop yield under changing environments, which can help in predicting the genetic gain beforehand. Application of machine learning (ML) in quantitative trait loci (QTL) mining will further help in determining the genetic determinants of abiotic stress tolerance in pulses.
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Affiliation(s)
- Dharmendra Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Priya Chaudhary
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Jyoti Taunk
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Chandan Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Deepti Singh
- Department of Botany, Meerut College, Meerut 250001, India
| | - Ram Sewak Singh Tomar
- College of Horticulture and Forestry, Rani Lakshmi Bai Central Agricultural University, Jhansi 284003, India
| | - Muraleedhar Aski
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Noren Singh Konjengbam
- College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University, Imphal 793103, India
| | - Ranjeet Sharan Raje
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Sanjay Singh
- ICAR- National Institute of Plant Biotechnology, LBS Centre, Pusa Campus, New Delhi 110012, India
| | - Rakesh Singh Sengar
- College of Biotechnology, Sardar Vallabh Bhai Patel Agricultural University, Meerut 250001, India
| | - Rajendra Kumar Yadav
- Department of Genetics and Plant Breeding, Chandra Shekhar Azad University of Agriculture and Technology, Kanpur 208002, India
| | - Madan Pal
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
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Guevara-Escudero M, Osorio AN, Cortés AJ. Integrative Pre-Breeding for Biotic Resistance in Forest Trees. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10102022. [PMID: 34685832 PMCID: PMC8541610 DOI: 10.3390/plants10102022] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 05/18/2023]
Abstract
Climate change is unleashing novel biotic antagonistic interactions for forest trees that may jeopardize populations' persistence. Therefore, this review article envisions highlighting major opportunities from ecological evolutionary genomics to assist the identification, conservation, and breeding of biotic resistance in forest tree species. Specifically, we first discuss how assessing the genomic architecture of biotic stress resistance enables us to recognize a more polygenic nature for a trait typically regarded Mendelian, an expectation from the Fisherian runaway pathogen-host concerted arms-race evolutionary model. Secondly, we outline innovative pipelines to capture and harness natural tree pre-adaptations to biotic stresses by merging tools from the ecology, phylo-geography, and omnigenetics fields within a predictive breeding platform. Promoting integrative ecological genomic studies promises a better understanding of antagonistic co-evolutionary interactions, as well as more efficient breeding utilization of resistant phenotypes.
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Affiliation(s)
- Melisa Guevara-Escudero
- Department de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Sede Medellín, Medellín 050034, Colombia; (M.G.-E.); (A.N.O.)
| | - Angy N. Osorio
- Department de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Sede Medellín, Medellín 050034, Colombia; (M.G.-E.); (A.N.O.)
| | - Andrés J. Cortés
- Department de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Sede Medellín, Medellín 050034, Colombia; (M.G.-E.); (A.N.O.)
- Main Address: Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, C.I. La Selva, Km 7 Vía Rionegro, Las Palmas, Rionegro 054048, Colombia
- Correspondence:
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9
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Hancock JT, Russell G. Downstream Signalling from Molecular Hydrogen. PLANTS (BASEL, SWITZERLAND) 2021; 10:367. [PMID: 33672953 PMCID: PMC7918658 DOI: 10.3390/plants10020367] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/09/2021] [Accepted: 02/09/2021] [Indexed: 12/23/2022]
Abstract
Molecular hydrogen (H2) is now considered part of the suite of small molecules that can control cellular activity. As such, H2 has been suggested to be used in the therapy of diseases in humans and in plant science to enhance the growth and productivity of plants. Treatments of plants may involve the creation of hydrogen-rich water (HRW), which can then be applied to the foliage or roots systems of the plants. However, the molecular action of H2 remains elusive. It has been suggested that the presence of H2 may act as an antioxidant or on the antioxidant capacity of cells, perhaps through the scavenging of hydroxyl radicals. H2 may act through influencing heme oxygenase activity or through the interaction with reactive nitrogen species. However, controversy exists around all the mechanisms suggested. Here, the downstream mechanisms in which H2 may be involved are critically reviewed, with a particular emphasis on the H2 mitigation of stress responses. Hopefully, this review will provide insight that may inform future research in this area.
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Affiliation(s)
- John T. Hancock
- Department of Applied Sciences, University of the West of England, Bristol BS16 1QY, UK;
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10
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Reyes-Herrera PH, Muñoz-Baena L, Velásquez-Zapata V, Patiño L, Delgado-Paz OA, Díaz-Diez CA, Navas-Arboleda AA, Cortés AJ. Inheritance of Rootstock Effects in Avocado ( Persea americana Mill.) cv. Hass. FRONTIERS IN PLANT SCIENCE 2020; 11:555071. [PMID: 33424874 PMCID: PMC7785968 DOI: 10.3389/fpls.2020.555071] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 11/17/2020] [Indexed: 05/16/2023]
Abstract
Grafting is typically utilized to merge adapted seedling rootstocks with highly productive clonal scions. This process implies the interaction of multiple genomes to produce a unique tree phenotype. However, the interconnection of both genotypes obscures individual contributions to phenotypic variation (rootstock-mediated heritability), hampering tree breeding. Therefore, our goal was to quantify the inheritance of seedling rootstock effects on scion traits using avocado (Persea americana Mill.) cv. Hass as a model fruit tree. We characterized 240 diverse rootstocks from 8 avocado cv. Hass orchards with similar management in three regions of the province of Antioquia, northwest Andes of Colombia, using 13 microsatellite markers simple sequence repeats (SSRs). Parallel to this, we recorded 20 phenotypic traits (including morphological, biomass/reproductive, and fruit yield and quality traits) in the scions for 3 years (2015-2017). Relatedness among rootstocks was inferred through the genetic markers and inputted in a "genetic prediction" model to calculate narrow-sense heritabilities (h 2) on scion traits. We used three different randomization tests to highlight traits with consistently significant heritability estimates. This strategy allowed us to capture five traits with significant heritability values that ranged from 0.33 to 0.45 and model fits (r) that oscillated between 0.58 and 0.73 across orchards. The results showed significance in the rootstock effects for four complex harvest and quality traits (i.e., total number of fruits, number of fruits with exportation quality, and number of fruits discarded because of low weight or thrips damage), whereas the only morphological trait that had a significant heritability value was overall trunk height (an emergent property of the rootstock-scion interaction). These findings suggest the inheritance of rootstock effects, beyond root phenotype, on a surprisingly wide spectrum of scion traits in "Hass" avocado. They also reinforce the utility of polymorphic SSRs for relatedness reconstruction and genetic prediction of complex traits. This research is, up to date, the most cohesive evidence of narrow-sense inheritance of rootstock effects in a tropical fruit tree crop. Ultimately, our work highlights the importance of considering the rootstock-scion interaction to broaden the genetic basis of fruit tree breeding programs while enhancing our understanding of the consequences of grafting.
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Affiliation(s)
- Paula H. Reyes-Herrera
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA)—CI Tibaitatá, Mosquera, Colombia
| | - Laura Muñoz-Baena
- Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - Valeria Velásquez-Zapata
- Department of Plant Pathology and Microbiology, Interdepartmental Bioinformatics and Computational Biology, Iowa State University, Ames, IA, United States
| | - Laura Patiño
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA)—CI La Selva, Rionegro, Colombia
| | - Oscar A. Delgado-Paz
- Facultad de Ingenierías, Universidad Católica de Oriente—UCO, Rionegro, Antioquia
| | - Cipriano A. Díaz-Diez
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA)—CI La Selva, Rionegro, Colombia
| | | | - Andrés J. Cortés
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA)—CI La Selva, Rionegro, Colombia
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Cruzan MB, Hendrickson EC. Landscape Genetics of Plants: Challenges and Opportunities. PLANT COMMUNICATIONS 2020; 1:100100. [PMID: 33367263 PMCID: PMC7748010 DOI: 10.1016/j.xplc.2020.100100] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/03/2020] [Accepted: 07/17/2020] [Indexed: 05/06/2023]
Abstract
Dispersal is one of the most important but least understood processes in plant ecology and evolutionary biology. Dispersal of seeds maintains and establishes populations, and pollen and seed dispersal are responsible for gene flow within and among populations. Traditional views of dispersal and gene flow assume models that are governed solely by geographic distance and do not account for variation in dispersal vector behavior in response to heterogenous landscapes. Landscape genetics integrates population genetics with Geographic Information Systems (GIS) to evaluate the effects of landscape features on gene flow patterns (effective dispersal). Surprisingly, relatively few landscape genetic studies have been conducted on plants. Plants present advantages because their populations are stationary, allowing more reliable estimates of the effects of landscape features on effective dispersal rates. On the other hand, plant dispersal is intrinsically complex because it depends on the habitat preferences of the plant and its pollen and seed dispersal vectors. We discuss strategies to assess the separate contributions of pollen and seed movement to effective dispersal and to delineate the effects of plant habitat quality from those of landscape features that affect vector behavior. Preliminary analyses of seed dispersal for three species indicate that isolation by landscape resistance is a better predictor of the rates and patterns of dispersal than geographic distance. Rates of effective dispersal are lower in areas of high plant habitat quality, which may be due to the effects of the shape of the dispersal kernel or to movement behaviors of biotic vectors. Landscape genetic studies in plants have the potential to provide novel insights into the process of gene flow among populations and to improve our understanding of the behavior of biotic and abiotic dispersal vectors in response to heterogeneous landscapes.
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Cortés AJ, Restrepo-Montoya M, Bedoya-Canas LE. Modern Strategies to Assess and Breed Forest Tree Adaptation to Changing Climate. FRONTIERS IN PLANT SCIENCE 2020; 11:583323. [PMID: 33193532 PMCID: PMC7609427 DOI: 10.3389/fpls.2020.583323] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/29/2020] [Indexed: 05/02/2023]
Abstract
Studying the genetics of adaptation to new environments in ecologically and industrially important tree species is currently a major research line in the fields of plant science and genetic improvement for tolerance to abiotic stress. Specifically, exploring the genomic basis of local adaptation is imperative for assessing the conditions under which trees will successfully adapt in situ to global climate change. However, this knowledge has scarcely been used in conservation and forest tree improvement because woody perennials face major research limitations such as their outcrossing reproductive systems, long juvenile phase, and huge genome sizes. Therefore, in this review we discuss predictive genomic approaches that promise increasing adaptive selection accuracy and shortening generation intervals. They may also assist the detection of novel allelic variants from tree germplasm, and disclose the genomic potential of adaptation to different environments. For instance, natural populations of tree species invite using tools from the population genomics field to study the signatures of local adaptation. Conventional genetic markers and whole genome sequencing both help identifying genes and markers that diverge between local populations more than expected under neutrality, and that exhibit unique signatures of diversity indicative of "selective sweeps." Ultimately, these efforts inform the conservation and breeding status capable of pivoting forest health, ecosystem services, and sustainable production. Key long-term perspectives include understanding how trees' phylogeographic history may affect the adaptive relevant genetic variation available for adaptation to environmental change. Encouraging "big data" approaches (machine learning-ML) capable of comprehensively merging heterogeneous genomic and ecological datasets is becoming imperative, too.
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Affiliation(s)
- Andrés J. Cortés
- Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, Rionegro, Colombia
- Departamento de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia – Sede Medellín, Medellín, Colombia
| | - Manuela Restrepo-Montoya
- Departamento de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia – Sede Medellín, Medellín, Colombia
| | - Larry E. Bedoya-Canas
- Departamento de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia – Sede Medellín, Medellín, Colombia
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Cortés AJ, López-Hernández F, Osorio-Rodriguez D. Predicting Thermal Adaptation by Looking Into Populations' Genomic Past. Front Genet 2020; 11:564515. [PMID: 33101385 PMCID: PMC7545011 DOI: 10.3389/fgene.2020.564515] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/24/2020] [Indexed: 12/18/2022] Open
Abstract
Molecular evolution offers an insightful theory to interpret the genomic consequences of thermal adaptation to previous events of climate change beyond range shifts. However, disentangling often mixed footprints of selective and demographic processes from those due to lineage sorting, recombination rate variation, and genomic constrains is not trivial. Therefore, here we condense current and historical population genomic tools to study thermal adaptation and outline key developments (genomic prediction, machine learning) that might assist their utilization for improving forecasts of populations' responses to thermal variation. We start by summarizing how recent thermal-driven selective and demographic responses can be inferred by coalescent methods and in turn how quantitative genetic theory offers suitable multi-trait predictions over a few generations via the breeder's equation. We later assume that enough generations have passed as to display genomic signatures of divergent selection to thermal variation and describe how these footprints can be reconstructed using genome-wide association and selection scans or, alternatively, may be used for forward prediction over multiple generations under an infinitesimal genomic prediction model. Finally, we move deeper in time to comprehend the genomic consequences of thermal shifts at an evolutionary time scale by relying on phylogeographic approaches that allow for reticulate evolution and ecological parapatric speciation, and end by envisioning the potential of modern machine learning techniques to better inform long-term predictions. We conclude that foreseeing future thermal adaptive responses requires bridging the multiple spatial scales of historical and predictive environmental change research under modern cohesive approaches such as genomic prediction and machine learning frameworks.
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Affiliation(s)
- Andrés J Cortés
- Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, C.I. La Selva, Rionegro, Colombia.,Departamento de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia - Sede Medellín, Medellín, Colombia
| | - Felipe López-Hernández
- Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, C.I. La Selva, Rionegro, Colombia
| | - Daniela Osorio-Rodriguez
- Division of Geological and Planetary Sciences, California Institute of Technology (Caltech), Pasadena, CA, United States
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Valencia JB, Mesa J, León JG, Madriñán S, Cortés AJ. Climate Vulnerability Assessment of the Espeletia Complex on Páramo Sky Islands in the Northern Andes. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.565708] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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15
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Russell G, Zulfiqar F, Hancock JT. Hydrogenases and the Role of Molecular Hydrogen in Plants. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1136. [PMID: 32887396 PMCID: PMC7569912 DOI: 10.3390/plants9091136] [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] [Received: 07/30/2020] [Revised: 08/27/2020] [Accepted: 08/31/2020] [Indexed: 12/17/2022]
Abstract
Molecular hydrogen (H2) has been suggested to be a beneficial treatment for a range of species, from humans to plants. Hydrogenases catalyze the reversible oxidation of H2, and are found in many organisms, including plants. One of the cellular effects of H2 is the selective removal of reactive oxygen species (ROS) and reactive nitrogen species (RNS), specifically hydroxyl radicals and peroxynitrite. Therefore, the function of hydrogenases and the action of H2 needs to be reviewed in the context of the signalling roles of a range of redox active compounds. Enzymes can be controlled by the covalent modification of thiol groups, and although motifs targeted by nitric oxide (NO) can be predicted in hydrogenases sequences it is likely that the metal prosthetic groups are the target of inhibition. Here, a selection of hydrogenases, and the possibility of their control by molecules involved in redox signalling are investigated using a bioinformatics approach. Methods of treating plants with H2 along with the role of H2 in plants is also briefly reviewed. It is clear that studies report significant effects of H2 on plants, improving growth and stress responses, and therefore future work needs to focus on the molecular mechanisms involved.
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Affiliation(s)
- Grace Russell
- Department of Applied Sciences, University of the West of England, Bristol BS 16 1QY, UK;
| | - Faisal Zulfiqar
- Institute of Horticultural Sciences, Faculty of Agriculture, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan;
| | - John T. Hancock
- Department of Applied Sciences, University of the West of England, Bristol BS 16 1QY, UK;
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16
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Sakaguchi S, Nagano AJ, Yasugi M, Kudoh H, Ishikawa N, Ito M. Genetic consequences of being a dwarf: do evolutionary changes in life-history traits influence gene flow patterns in populations of the world's smallest goldenrod? ANNALS OF BOTANY 2020; 126:163-177. [PMID: 32249287 PMCID: PMC7304467 DOI: 10.1093/aob/mcaa062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 04/03/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND AND AIMS Contrasting life-history traits can evolve through generations of dwarf plant ecotypes, yet such phenotypic changes often involve decreased plant size and reproductive allocation, which can configure seed dispersal patterns and, subsequently, population demography. Therefore, evolutionary transitions to dwarfism can represent good study systems to test the roles of life-history traits in population demography by comparing genetic structure between related but phenotypically divergent ecotypes. METHODS In this study, we examined an ecotypic taxon pair of the world's smallest goldenrod (stem height 2.6 cm) in alpine habitats and its closely related lowland taxon (30-40 cm) found on Yakushima Island, Japan. Genetic variation in chloroplast DNA sequences, nuclear microsatellites and genome-wide single-nucleotide polymorphisms were used to investigate 197 samples from 16 populations, to infer the population genetic demography and compare local genetic structure of the ecotypes. KEY RESULTS We found a pronounced level of genetic differentiation among alpine dwarf populations, which were much less geographically isolated than their lowland counterparts. In particular, several neighbouring dwarf populations (located ~500 m apart) harboured completely different sets of chloroplast haplotypes and nuclear genetic clusters. Demographic modelling revealed that the dwarf populations have not exchanged genes at significant levels after population divergence. CONCLUSIONS These lines of evidence suggest that substantial effects of genetic drift have operated on these dwarf populations. The low-growing stature and reduced fecundity (only 3.1 heads per plant) of the dwarf plants may have reduced gene flow and rare long-distance seed dispersal among habitat patches, although the effects of life-history traits require further evaluation using ecological approaches.
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Affiliation(s)
- Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto, Japan
| | | | - Masaki Yasugi
- National Institute for Basic Biology, Myodaiji, Okazaki, Aichi, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
| | - Naoko Ishikawa
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Motomi Ito
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
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17
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Bueno de Mesquita CP, Sartwell SA, Schmidt SK, Suding KN. Growing-season length and soil microbes influence the performance of a generalist bunchgrass beyond its current range. Ecology 2020; 101:e03095. [PMID: 32380574 DOI: 10.1002/ecy.3095] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 07/14/2019] [Accepted: 04/03/2020] [Indexed: 11/10/2022]
Abstract
As organisms shift their geographic distributions in response to climate change, biotic interactions have emerged as an important factor driving the rate and success of range expansions. Plant-microbe interactions are an understudied but potentially important factor governing plant range shifts. We studied the distribution and function of microbes present in high-elevation unvegetated soils, areas that plants are colonizing as climate warms, snow melts earlier, and the summer growing season lengthens. Using a manipulative snowpack and microbial inoculation transplant experiment, we tested the hypothesis that growing-season length and microbial community composition interact to control plant elevational range shifts. We predicted that a lengthening growing season combined with dispersal to patches of soils with more mutualistic microbes and fewer pathogenic microbes would facilitate plant survival and growth in previously unvegetated areas. We identified negative effects on survival of the common alpine bunchgrass Deschampsia cespitosa in both short and long growing seasons, suggesting an optimal growing-season length for plant survival in this system that balances time for growth with soil moisture levels. Importantly, growing-season length and microbes interacted to affect plant survival and growth, such that microbial community composition increased in importance in suboptimal growing-season lengths. Further, plants grown with microbes from unvegetated soils grew as well or better than plants grown with microbes from vegetated soils. These results suggest that the rate and spatial extent of plant colonization of unvegetated soils in mountainous areas experiencing climate change could depend on both growing-season length and soil microbial community composition, with microbes potentially playing more important roles as growing seasons lengthen.
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Affiliation(s)
- Clifton P Bueno de Mesquita
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309-0334, USA.,Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado, 80309-0450, USA
| | - Samuel A Sartwell
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309-0334, USA.,Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado, 80309-0450, USA
| | - Steven K Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309-0334, USA
| | - Katharine N Suding
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309-0334, USA.,Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado, 80309-0450, USA
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18
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Hao L, Zhang G, Lu D, Hu J, Jia H. Analysis of the genetic diversity and population structure of Salix psammophila based on phenotypic traits and simple sequence repeat markers. PeerJ 2019; 7:e6419. [PMID: 30805247 PMCID: PMC6383557 DOI: 10.7717/peerj.6419] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 01/04/2019] [Indexed: 01/03/2023] Open
Abstract
Salix psammophila (desert willow) is a shrub endemic to the Kubuqi Desert and the Mu Us Desert, China, that plays an important role in maintaining local ecosystems and can be used as a biomass feedstock for biofuels and bioenergy. However, the lack of information on phenotypic traits and molecular markers for this species limits the study of genetic diversity and population structure. In this study, nine phenotypic traits were analyzed to assess the morphological diversity and variation. The mean coefficient of variation of 17 populations ranged from 18.35% (branch angle (BA)) to 38.52% (leaf area (LA)). Unweighted pair-group method with arithmetic mean analysis of nine phenotypic traits of S. psammophila showed the same results, with the 17 populations clustering into five groups. We selected 491 genets of the 17 populations to analyze genetic diversity and population structure based on simple sequence repeat (SSR) markers. Analysis of molecular variance (AMOVA) revealed that most of the genetic variance (95%) was within populations, whereas only a small portion (5%) was among populations. Moreover, using the animal model with SSR-based relatedness estimated of S. psammophila, we found relatively moderate heritability values for phenotypic traits, suggesting that most of trait variation were caused by environmental or developmental variation. Principal coordinate and phylogenetic analyses based on SSR data revealed that populations P1, P2, P9, P16, and P17 were separated from the others. The results showed that the marginal populations located in the northeastern and southwestern had lower genetic diversity, which may be related to the direction of wind. These results provide a theoretical basis for germplasm management and genetic improvement of desert willow.
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Affiliation(s)
- Lei Hao
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, China.,Inner Mongolia University of Finance and Economics, Hohhot, China
| | - Guosheng Zhang
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, China
| | - Dongye Lu
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, China
| | - Jianjun Hu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Huixia Jia
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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19
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Niu Y, Yang S, Zhou J, Chu B, Ma S, Zhu H, Hua L. Vegetation distribution along mountain environmental gradient predicts shifts in plant community response to climate change in alpine meadow on the Tibetan Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 650:505-514. [PMID: 30205341 DOI: 10.1016/j.scitotenv.2018.08.390] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 08/27/2018] [Accepted: 08/27/2018] [Indexed: 06/08/2023]
Abstract
Plants are particularly sensitive to climate change in alpine ecosystem of the Tibetan Plateau. The various mountain micro-climates provide a natural gradient for space-for-time substitution research that plant responses to climate change. In this study, we surveyed the plant community in term of species composition, diversity and biomass across 189 sites on a hill of the Tibetan Plateau and analysed the individual and integrated effects of soil temperature and moisture on the plant community. The results showed that, at the quadrat scale, there were decrease in richness of 1.08 species for every 1 °C increase in soil temperature and 3.56 species for every 10% decrease in soil moisture. The integrated effects of increasing soil temperature and decreasing moisture are expected to lead to a rapid decrease in species richness. Biomass had no significant correlation with soil temperature but significantly decreased with soil moisture decreasing (p < 0.01). Biomass would decrease when soil moisture was below 20%, no matter how the change of soil temperature. We also found that gramineae and perennial forbs were sensitive to climate change. With soil temperature increased, the proportion of gramineae increased, whereas the proportion of perennial forbs decreased. The integrated effects of soil temperature increasing and moisture decreasing caused a shift from sedge-controlled to gramineae-controlled communities in alpine meadow. This study not only enhances our understanding of mountain plant community dynamics under climate change, but also predicts the shift of vegetation response to climate change on high-elevation alpine meadow.
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Affiliation(s)
- Yujie Niu
- College of Grassland Science, Gansu Agricultural University/Key Laboratory of Grassland Ecosystem of the Ministry of Education, Lanzhou 730070, China
| | - Siwei Yang
- College of Grassland Science, Gansu Agricultural University/Key Laboratory of Grassland Ecosystem of the Ministry of Education, Lanzhou 730070, China
| | - Jianwei Zhou
- College of Grassland Science, Gansu Agricultural University/Key Laboratory of Grassland Ecosystem of the Ministry of Education, Lanzhou 730070, China
| | - Bin Chu
- College of Grassland Science, Gansu Agricultural University/Key Laboratory of Grassland Ecosystem of the Ministry of Education, Lanzhou 730070, China
| | - Sujie Ma
- College of Grassland Science, Gansu Agricultural University/Key Laboratory of Grassland Ecosystem of the Ministry of Education, Lanzhou 730070, China
| | - Huimin Zhu
- College of Grassland Science, Gansu Agricultural University/Key Laboratory of Grassland Ecosystem of the Ministry of Education, Lanzhou 730070, China
| | - Limin Hua
- College of Grassland Science, Gansu Agricultural University/Key Laboratory of Grassland Ecosystem of the Ministry of Education, Lanzhou 730070, China.
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Cortés AJ, Skeen P, Blair MW, Chacón-Sánchez MI. Does the Genomic Landscape of Species Divergence in Phaseolus Beans Coerce Parallel Signatures of Adaptation and Domestication? FRONTIERS IN PLANT SCIENCE 2018; 9:1816. [PMID: 30619396 PMCID: PMC6306030 DOI: 10.3389/fpls.2018.01816] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 11/22/2018] [Indexed: 05/10/2023]
Abstract
Exploring the genomic architecture of species and populations divergence aids understanding how lineages evolve and adapt, and ultimately can show the repeatability of evolutionary processes. Yet, the genomic signatures associated with divergence are still relatively unexplored, leading to a knowledge gap on whether species divergence ultimately differs in its genetic architecture from divergence at other spatial scales (i.e., populations, ecotypes). Our goal in this research was to determine whether genomic islands of speciation are more prone to harbor within-species differentiation due to genomic features, suppressed recombination, smaller effective population size or increased drift, across repeated hierarchically nested levels of divergence. We used two species of Phaseolus beans with strong genepool and population sub-structure produced by multiple independent domestications each especially in Andean and Mesoamerican / Middle American geographies. We genotyped 22,531 GBS-derived SNP markers in 209 individuals of wild and cultivated Phaseolus vulgaris and Phaseolus lunatus. We identified six regions for species-associated divergence. Out of these divergence peaks, 21% were recovered in the four within-species between-genepool comparisons and in the five within-genepool wild-cultivated comparisons (some of the latter did retrieve genuine signatures of the well described multiple domestication syndromes). However, genomic regions with overall high relative differentiation (measured by FST) coincided with regions of low SNP density and regions of elevated delta divergence between-genepools (ΔDiv), independent of the scale of divergence. The divergence in chromosome Pv10 further coincided with a between-species pericentric inversion. These convergences suggest that shared variants are being recurrently fixed at replicated regions of the genome, and in a similar manner across different hierarchically nested levels of divergence, likely as result of genomic features that make certain regions more prone to accumulate islands of speciation and within-species divergence. In summary, neighboring signatures of speciation, adaptation and domestication in Phaseolus beans are influenced by ubiquitous genomic constrains, which may continue to fortuitously shape genomic differentiation at various others scales of divergence.
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Affiliation(s)
- Andrés J. Cortés
- Corporación Colombiana de Investigación Agropecuaria (Agrosavia) – Centro de Investigación La Selva, Rionegro, Colombia
- Universidad Nacional de Colombia – Sede Medellín, Facultad de Ciencias Agrarias – Departamento de Ciencias
Forestales, Medellín, Colombia
| | - Paola Skeen
- Universidad Nacional de Colombia – Bogotá, Facultad de Ciencias Agrarias – Departamento de Agronomía, Bogotá, Colombia
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Matthew W. Blair
- Department of Agricultural and Environmental Science, Tennessee State University, Nashville, TN, United States
| | - María I. Chacón-Sánchez
- Universidad Nacional de Colombia – Bogotá, Facultad de Ciencias Agrarias – Departamento de Agronomía, Bogotá, Colombia
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21
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Cortés AJ, Garzón LN, Valencia JB, Madriñán S. On the Causes of Rapid Diversification in the Páramos: Isolation by Ecology and Genomic Divergence in Espeletia. FRONTIERS IN PLANT SCIENCE 2018; 9:1700. [PMID: 30581444 PMCID: PMC6294130 DOI: 10.3389/fpls.2018.01700] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 11/01/2018] [Indexed: 05/10/2023]
Abstract
How diversity arises and what is the relative role of allopatric and ecological divergence are among the most persistent questions in evolution and ecology. Here, we assessed whether ecological divergence has enhanced the diversification of the Neotropical alpine plant complex Espeletia, also known as frailejones. This genus has one of the highest diversification rates ever reported and is distributed in the world's fastest evolving biodiversity hotspot, the Páramo (Neotropical alpine grasslands at elevations of c. 2800-4700 m). Our goal was to determine whether ecology plays a role in divergence within the Espeletia complex by quantifying genome-wide patterns of ecological divergence. We characterized 162 samples of the three most common and contrasting ecotypes (distinct morphotypes occupying particular habitats) co-occurring in six localities in the northern Andes using Genotyping by Sequencing. Contrasting ecotypes were caulescent cloud forest populations, caulescent populations from wind-sheltered and well-irrigated depressions and acaulescent populations from wind-exposed drier slopes. We found high polymorphism with a total of 1,273 single nucleotide polymorphisms (SNPs) that defined the relationships among nine genetic clusters. We quantified allelic associations of these markers with localities and habitats using 18 different general and mixed-effects statistical models that accounted for phylogenetic distance. Despite that these models always yielded more SNPs associated with the localities, markers associated with the habitat types were recovered too. We found strong evidence for isolation-by-distance (IBD) across populations despite rampant gene flow, as expected for plant groups with limited seed dispersal. Contrasts between populations of different habitat types showed that an isolation-by-environment (IBE) trend emerged and masked the IBD signal. Maximum likelihood estimation of the number of migrants per generation (Nem) among ecotypes confirmed the IBE pattern. This result illustrates the importance of mountains' environmental variation at a local scale in generating rapid morphological radiations and maintaining multiple adaptations in a fast-evolving ecosystem like the Páramo.
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Affiliation(s)
- Andrés J. Cortés
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Luz N. Garzón
- Escuela de Biología, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Jhon B. Valencia
- Facultad de Ingeniera y Administracin, Universidad Nacional de Colombia - Sede Palmira, Palmira, Colombia
| | - Santiago Madriñán
- Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
- Jardín Botánico de Cartagena “Guillermo Piñeres”, Turbaco, Colombia
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22
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Plant–plant interactions could limit recruitment and range expansion of tall shrubs into alpine and Arctic tundra. Polar Biol 2018. [DOI: 10.1007/s00300-018-2355-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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23
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Cortés AJ, Blair MW. Genotyping by Sequencing and Genome-Environment Associations in Wild Common Bean Predict Widespread Divergent Adaptation to Drought. FRONTIERS IN PLANT SCIENCE 2018; 9:128. [PMID: 29515597 PMCID: PMC5826387 DOI: 10.3389/fpls.2018.00128] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 01/23/2018] [Indexed: 05/18/2023]
Abstract
Drought will reduce global crop production by >10% in 2050 substantially worsening global malnutrition. Breeding for resistance to drought will require accessing crop genetic diversity found in the wild accessions from the driest high stress ecosystems. Genome-environment associations (GEA) in crop wild relatives reveal natural adaptation, and therefore can be used to identify adaptive variation. We explored this approach in the food crop Phaseolus vulgaris L., characterizing 86 geo-referenced wild accessions using genotyping by sequencing (GBS) to discover single nucleotide polymorphisms (SNPs). The wild beans represented Mesoamerica, Guatemala, Colombia, Ecuador/Northern Peru and Andean groupings. We found high polymorphism with a total of 22,845 SNPs across the 86 accessions that confirmed genetic relationships for the groups. As a second objective, we quantified allelic associations with a bioclimatic-based drought index using 10 different statistical models that accounted for population structure. Based on the optimum model, 115 SNPs in 90 regions, widespread in all 11 common bean chromosomes, were associated with the bioclimatic-based drought index. A gene coding for an ankyrin repeat-containing protein and a phototropic-responsive NPH3 gene were identified as potential candidates. Genomic windows of 1 Mb containing associated SNPs had more positive Tajima's D scores than windows without associated markers. This indicates that adaptation to drought, as estimated by bioclimatic variables, has been under natural divergent selection, suggesting that drought tolerance may be favorable under dry conditions but harmful in humid conditions. Our work exemplifies that genomic signatures of adaptation are useful for germplasm characterization, potentially enhancing future marker-assisted selection and crop improvement.
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Affiliation(s)
- Andrés J. Cortés
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Matthew W. Blair
- Department of Agricultural and Environmental Science, Tennessee State University, Nashville, TN, United States
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24
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Van Nuland ME, Bailey JK, Schweitzer JA. Divergent plant–soil feedbacks could alter future elevation ranges and ecosystem dynamics. Nat Ecol Evol 2017; 1:150. [DOI: 10.1038/s41559-017-0150] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 03/22/2017] [Indexed: 11/09/2022]
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Gramlich S, Hörandl E. Fitness of natural willow hybrids in a pioneer mosaic hybrid zone. Ecol Evol 2016; 6:7645-7655. [PMID: 30128118 PMCID: PMC6093150 DOI: 10.1002/ece3.2470] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 08/10/2016] [Accepted: 08/24/2016] [Indexed: 01/20/2023] Open
Abstract
Hybrid fitness is an important parameter to predict the evolutionary consequences of a hybridization event and to characterize hybrid zones. We studied fitness parameters of F1 and later-generation hybrids between the lowland species Salix purpurea and the alpine S. helvetica that have recently emerged during colonization of an alpine glacier forefield. Fruit production (number of capsules per catkin and fruit set) did not differ between hybrids and parents, but the number of seeds per capsule of F1 hybrids was slightly lower than that of later-generation hybrids and of the parents. Germination rates and seedling growth were tested on three substrates (pH 4.5, 7.0, and 8.0). Germination rates of seeds collected from F1 hybrids were lower on acid and neutral substrates, but equal at pH 8.0 compared to all other groups, while the seeds from later-generation hybrids performed as well as the parents on all three substrates. In seedling growth, the colonizer S. purpurea performed better than all other taxa on all three substrates, while hybrids resembled the subalpine species S. helvetica. Results suggest that endogenous selection acts against F1 hybrids, but favors fitter genotypes in later-generation hybrids. Exogenous selection via soil pH appears to be weak during seedling establishment. The pioneer vegetation on the glacier forefield may offer sufficient niche space for hybrid seedlings. Owing to the relatively high fitness of the hybrids and the scattered distribution of hybrids and parental individuals on the glacier forefield, this hybrid zone can be assigned to a mosaic model, probably facilitating gene flow and introgression between the parental species. As establishment of the hybrid zone appears to be linked to a colonization process, we propose to call it a pioneer mosaic hybrid zone.
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Affiliation(s)
- Susanne Gramlich
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium)Georg August University GöttingenGöttingenGermany
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium)Georg August University GöttingenGöttingenGermany
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Sedlacek J, Cortés AJ, Wheeler J, Bossdorf O, Hoch G, Klápště J, Lexer C, Rixen C, Wipf S, Karrenberg S, van Kleunen M. Evolutionary potential in the Alpine: trait heritabilities and performance variation of the dwarf willow Salix herbacea from different elevations and microhabitats. Ecol Evol 2016; 6:3940-52. [PMID: 27516856 PMCID: PMC4972222 DOI: 10.1002/ece3.2171] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 04/04/2016] [Accepted: 04/04/2016] [Indexed: 01/18/2023] Open
Abstract
Alpine ecosystems are seriously threatened by climate change. One of the key mechanisms by which plants can adapt to changing environmental conditions is through evolutionary change. However, we still know little about the evolutionary potential in wild populations of long-lived alpine plants. Here, we investigated heritabilities of phenological traits, leaf size, and performance traits in natural populations of the long-lived alpine dwarf shrub Salix herbacea using relatedness estimates inferred from SSR (Simple Sequence Repeat) markers. Salix herbacea occurs in early- and late-snowmelt microhabitats (ridges and snowbeds), and we assessed how performance consequences of phenological traits and leaf size differ between these microhabitats in order to infer potential for evolutionary responses. Salix herbacea showed low, but significant, heritabilities of leaf size, clonal and sexual reproduction, and moderate heritabilities of phenological traits. In both microhabitats, we found that larger leaves, longer intervals between snowmelt and leaf expansion, and longer GDD (growing-degree days) until leaf expansion resulted in a stronger increase in the number of stems (clonal reproduction). In snowbeds, clonal reproduction increased with a shorter GDD until flowering, while the opposite was found on ridges. Furthermore, the proportion of flowering stems increased with GDD until flowering in both microhabitats. Our results suggest that the presence of significant heritable variation in morphology and phenology might help S. herbacea to adapt to changing environmental conditions. However, it remains to be seen if the rate of such an evolutionary response can keep pace with the rapid rate of climate change.
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Affiliation(s)
- Janosch Sedlacek
- EcologyDepartment of BiologyUniversity of KonstanzUniversitätsstraße 1078457KonstanzGermany
| | - Andrés J. Cortés
- Department of Ecology and GeneticsUppsala UniversityNorbyvägen 18 D75236UppsalaSweden
- Present address: Department of Plant BiologySwedish Agricultural UniversityUndervisningsplan 7E75007UppsalaSweden
| | - Julia Wheeler
- WSL Institute for Snow and Avalanche Research SLFFlüelastrasse 117260DavosSwitzerland
- Institute of BotanyUniversity of BaselSchönbeinstrasse 64056BaselSwitzerland
- Present address: Department of Environmental ConservationUniversity of MassachusettsAmherstMassachusetts01003
| | - Oliver Bossdorf
- Plant Evolutionary EcologyInstitute of Evolution and EcologyAuf der Morgenstelle 5University of Tübingen72076TübingenGermany
| | - Guenter Hoch
- Institute of BotanyUniversity of BaselSchönbeinstrasse 64056BaselSwitzerland
| | - Jaroslav Klápště
- Department of Forest and Conservation SciencesFaculty of ForestryUniversity of British Columbia2424 Main MallVancouverBritish ColumbiaV6T 1Z4Canada
- Department of Genetics and Physiology of Forest TreesFaculty of Forestry and Wood SciencesCzech University of Life Sciences in PragueKamýcká 129165 21Prague 6Czech Republic
- Present address: Scion (New Zealand Forest Research Institute Ltd.)49 Sala StreetWhakarewarewa3046RotoruaNew Zealand
| | - Christian Lexer
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14A‐1030ViennaAustria
| | - Christian Rixen
- WSL Institute for Snow and Avalanche Research SLFFlüelastrasse 117260DavosSwitzerland
| | - Sonja Wipf
- WSL Institute for Snow and Avalanche Research SLFFlüelastrasse 117260DavosSwitzerland
| | - Sophie Karrenberg
- Department of Ecology and GeneticsUppsala UniversityNorbyvägen 18 D75236UppsalaSweden
| | - Mark van Kleunen
- EcologyDepartment of BiologyUniversity of KonstanzUniversitätsstraße 1078457KonstanzGermany
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Evolution in situ: hybrid origin and establishment of willows (Salix L.) on alpine glacier forefields. Heredity (Edinb) 2016; 116:531-41. [PMID: 26980342 PMCID: PMC4868266 DOI: 10.1038/hdy.2016.14] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 01/18/2016] [Accepted: 01/25/2016] [Indexed: 11/21/2022] Open
Abstract
Little attention has been paid to the evolutionary consequences of the colonizing dynamics and succession processes following glacier retreat. Here we studied hybrid populations that have recently formed and established on glacier forefields of the European Alps owing to secondary contact of a lowland colonizer with a subalpine species. We analyzed the composition of two hybrid populations between Salix purpurea and Salix helvetica with nine microsatellite markers by using Bayesian methods (structure and NewHybrids), and simulations. We also studied niche differentiation between the hybrids and the parental species based on indicator values, soil pH and water retention potential measurements. Allelic structure of hybrids confirms the assumed parentage and in situ origin of the crosses on two independent sites within the last decades. Both hybrid populations comprised F1 and later generation hybrids (F2 and backcrosses), confirming hybrid fertility. The parental species showed significant differences in niche characteristics for temperature, soil pH, nutrients and moisture. Remarkably, the hybrids exhibited a higher tolerance to cold temperatures, nutrient-poor and acidic soils than either parent. Our results show that willow hybrids originated after glacier retreat and have established persistent populations within a few decades. One factor contributing to hybrid establishment in sympatry with their parents is their ability to occupy more extreme niches than either parental species within a mosaic-like pattern of microhabitats on the forefield. Introgression and/or transgressive segregation may have resulted in novel genotypes that are able to expand the ecological spectrum of either parent.
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Münzbergová Z, Šurinová M. The importance of species phylogenetic relationships and species traits for the intensity of plant-soil feedback. Ecosphere 2015. [DOI: 10.1890/es15-00206.1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Little CJ, Wheeler JA, Sedlacek J, Cortés AJ, Rixen C. Small-scale drivers: the importance of nutrient availability and snowmelt timing on performance of the alpine shrub Salix herbacea. Oecologia 2015; 180:1015-24. [PMID: 26235963 DOI: 10.1007/s00442-015-3394-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 07/07/2015] [Indexed: 10/23/2022]
Abstract
Alpine plant communities are predicted to face range shifts and possibly extinctions with climate change. Fine-scale environmental variation such as nutrient availability or snowmelt timing may contribute to the ability of plant species to persist locally; however, variation in nutrient availability in alpine landscapes is largely unmeasured. On three mountains around Davos, Switzerland, we deployed Plant Root Simulator probes around 58 Salix herbacea plants along an elevational and microhabitat gradient to measure nutrient availability during the first 5 weeks of the summer growing season, and used in situ temperature loggers and observational data to determine date of spring snowmelt. We also visited the plants weekly to assess performance, as measured by stem number, fruiting, and herbivory damage. We found a wide snowmelt gradient which determined growing season length, as well as variations of an order of magnitude or more in the accumulation of 12 nutrients between different microhabitats. Higher nutrient availability had negative effects on most shrub performance metrics, for instance decreasing stem number and the proportion of stems producing fruits. High nutrient availability was associated with increased herbivory damage in early-melting microhabitats, but among late-emerging plants this pattern was reversed. We demonstrate that nutrient availability is highly variable in alpine settings, and that it strongly influences performance in an alpine dwarf shrub, sometimes modifying the response of shrubs to snowmelt timing. As the climate warms and human-induced nitrogen deposition continues in the Alps, these factors may contribute to patterns of local plants persistence.
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Affiliation(s)
- Chelsea J Little
- WSL Institute for Snow and Avalanche Research SLF, 7260, Davos, Switzerland. .,Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, 8600, Dübendorf, Switzerland.
| | - Julia A Wheeler
- WSL Institute for Snow and Avalanche Research SLF, 7260, Davos, Switzerland.,Institute of Botany, University of Basel, 4056, Basel, Switzerland
| | - Janosch Sedlacek
- Department of Biology, University of Konstanz, 78457, Constance, Germany
| | - Andrés J Cortés
- Department of Ecology and Genetics, Uppsala University, 75236, Uppsala, Sweden
| | - Christian Rixen
- WSL Institute for Snow and Avalanche Research SLF, 7260, Davos, Switzerland
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Wheeler J, Schnider F, Sedlacek J, Cortés A, Wipf S, Hoch G, Rixen C. With a little help from my friends: Community facilitation increases performance in the dwarf shrub Salix herbacea. Basic Appl Ecol 2015. [DOI: 10.1016/j.baae.2015.02.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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31
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Sedlacek J, Wheeler JA, Cortés AJ, Bossdorf O, Hoch G, Lexer C, Wipf S, Karrenberg S, van Kleunen M, Rixen C. The Response of the Alpine Dwarf Shrub Salix herbacea to Altered Snowmelt Timing: Lessons from a Multi-Site Transplant Experiment. PLoS One 2015; 10:e0122395. [PMID: 25893438 PMCID: PMC4403918 DOI: 10.1371/journal.pone.0122395] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 02/20/2015] [Indexed: 11/20/2022] Open
Abstract
Climate change is altering spring snowmelt patterns in alpine and arctic ecosystems, and these changes may alter plant phenology, growth and reproduction. To predict how alpine plants respond to shifts in snowmelt timing, we need to understand trait plasticity, its effects on growth and reproduction, and the degree to which plants experience a home-site advantage. We tested how the common, long-lived dwarf shrub Salix herbacea responded to changing spring snowmelt time by reciprocally transplanting turfs of S. herbacea between early-exposure ridge and late-exposure snowbed microhabitats. After the transplant, we monitored phenological, morphological and fitness traits, as well as leaf damage, during two growing seasons. Salix herbacea leafed out earlier, but had a longer development time and produced smaller leaves on ridges relative to snowbeds. Longer phenological development times and smaller leaves were associated with reduced sexual reproduction on ridges. On snowbeds, larger leaves and intermediate development times were associated with increased clonal reproduction. Clonal and sexual reproduction showed no response to altered snowmelt time. We found no home-site advantage in terms of sexual and clonal reproduction. Leaf damage probability depended on snowmelt and thus exposure period, but had no short-term effect on fitness traits. We conclude that the studied populations of S. herbacea can respond to shifts in snowmelt by plastic changes in phenology and leaf size, while maintaining levels of clonal and sexual reproduction. The lack of a home-site advantage suggests that S. herbacea may not be adapted to different microhabitats. The studied populations are thus unlikely to react to climate change by rapid adaptation, but their responses will also not be constrained by small-scale local adaptation. In the short term, snowbed plants may persist due to high stem densities. However, in the long term, reduction in leaf size and flowering, a longer phenological development time and increased exposure to damage may decrease overall performance of S. herbacea under earlier snowmelt.
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Affiliation(s)
- Janosch Sedlacek
- Ecology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Julia A. Wheeler
- WSL Institute for Snow and Avalanche Research SLF, 7260, Davos, Switzerland
- Institute of Botany, University of Basel, 4056, Basel, Switzerland
| | - Andrés J. Cortés
- Department of Ecology and Genetics, Uppsala University, 75236, Uppsala, Sweden
| | - Oliver Bossdorf
- Plant Evolutionary Ecology, Institute of Evolution and Ecology, University of Tübingen, 72076, Tübingen, Germany
| | - Guenter Hoch
- Institute of Botany, University of Basel, 4056, Basel, Switzerland
| | - Christian Lexer
- Unit of Ecology and Evolution, Department of Biology, University of Fribourg, 1700, Fribourg, Switzerland
| | - Sonja Wipf
- WSL Institute for Snow and Avalanche Research SLF, 7260, Davos, Switzerland
| | - Sophie Karrenberg
- Department of Ecology and Genetics, Uppsala University, 75236, Uppsala, Sweden
| | - Mark van Kleunen
- Ecology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Christian Rixen
- WSL Institute for Snow and Avalanche Research SLF, 7260, Davos, Switzerland
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