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Zacharias M, Pampuch T, Dauphin B, Opgenoorth L, Roland C, Schnittler M, Wilmking M, Bog M, Heer K. Genetic basis of growth reaction to drought stress differs in contrasting high-latitude treeline ecotones of a widespread conifer. Mol Ecol 2022; 31:5165-5181. [PMID: 35951000 DOI: 10.1111/mec.16648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/29/2022] [Accepted: 08/08/2022] [Indexed: 12/15/2022]
Abstract
Climate change is increasing the frequency and intensity of drought events in many boreal forests. Trees are sessile organisms with a long generation time, which makes them vulnerable to fast climate change and hinders fast adaptations. Therefore, it is important to know how forests cope with drought stress and to explore the genetic basis of these reactions. We investigated three natural populations of white spruce (Picea glauca) in Alaska, located at one drought-limited and two cold-limited treelines with a paired plot design of one forest and one treeline plot. We obtained individual increment cores from 458 trees and climate data to assess dendrophenotypes, in particular the growth reaction to drought stress. To explore the genetic basis of these dendrophenotypes, we genotyped the individual trees at 3000 single nucleotide polymorphisms in candidate genes and performed genotype-phenotype association analysis using linear mixed models and Bayesian sparse linear mixed models. Growth reaction to drought stress differed in contrasting treeline populations. Therefore, the populations are likely to be unevenly affected by climate change. We identified 40 genes associated with dendrophenotypic traits that differed among the treeline populations. Most genes were identified in the drought-limited site, indicating comparatively strong selection pressure of drought-tolerant phenotypes. Contrasting patterns of drought-associated genes among sampled sites and in comparison to Canadian populations in a previous study suggest that drought adaptation acts on a local scale. Our results highlight genes that are associated with wood traits which in turn are critical for the establishment and persistence of future forests under climate change.
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Affiliation(s)
- Melanie Zacharias
- Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
| | - Timo Pampuch
- Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
| | | | - Lars Opgenoorth
- Plant Ecology and Geobotany, Philipps Universität Marburg, Marburg, Germany
| | - Carl Roland
- Denali National Park and Preserve, Fairbanks, Alaska, USA
| | - Martin Schnittler
- Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
| | - Martin Wilmking
- Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
| | - Manuela Bog
- Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
| | - Katrin Heer
- Forest Genetics, Faculty of Environment and Natural Resources, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
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Zacharias M, Pampuch T, Heer K, Avanzi C, Würth DG, Trouillier M, Bog M, Wilmking M, Schnittler M. Population structure and the influence of microenvironment and genetic similarity on individual growth at Alaskan white spruce treelines. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 798:149267. [PMID: 34332391 DOI: 10.1016/j.scitotenv.2021.149267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
Knowledge on the adaptation of trees to rapid environmental changes is essential to preserve forests and their ecosystem services under climate change. Treeline populations are particularly suitable for studying adaptation processes in trees, as environmental stress together with reduced gene flow can enhance local adaptation. We investigated white spruce (Picea glauca) populations in Alaska on one moisture-limited and two cold-limited treeline sites with a paired plot design of one forest and one treeline population each, resulting in six plots. Additionally, one forest plot in the middle of the distribution range complements the study design. We combined spatial, climatic and dendrochronological data with neutral genetic marker of 2203 trees to investigate population genetic structure and drivers of tree growth. We used several individual-based approaches including random slope mixed-effects models to test the influence of genetic similarity and microenvironment on growth performance. A high degree of genetic diversity was found within each of the seven plots associated with high rates of gene flow. We discovered a low genetic differentiation between the three sites which was better explained by geographic distances than by environmental differences, indicating genetic drift as the main driver of population differentiation. Our findings indicated that microenvironmental features had an overall larger influence on growth performances than genetic similarity among individuals. The effects of climate on growth differed between sites but were smaller than the effect of tree size. Overall, our results suggest that the high genetic diversity of white spruce may result in a wider range of phenotypes which enhances the efficiency of selection when the species is facing rapid climatic changes. In addition, the large intra-individual variability in growth responses may indicate the high phenotypic plasticity of white spruce which can buffer short-term environmental changes and, thus, allow enduring the present changing climate conditions.
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Affiliation(s)
- Melanie Zacharias
- Institute of Botany und Landscape Ecology, University of Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany.
| | - Timo Pampuch
- Institute of Botany und Landscape Ecology, University of Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany.
| | - Katrin Heer
- Conservation Biology, University of Marburg, Karl-von-Frisch-Strasse 8, 35043 Marburg, Germany.
| | - Camilla Avanzi
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy.
| | - David G Würth
- Institute of Botany und Landscape Ecology, University of Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany
| | - Mario Trouillier
- Institute of Botany und Landscape Ecology, University of Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany.
| | - Manuela Bog
- Institute of Botany und Landscape Ecology, University of Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany.
| | - Martin Wilmking
- Institute of Botany und Landscape Ecology, University of Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany.
| | - Martin Schnittler
- Institute of Botany und Landscape Ecology, University of Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany.
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Resente G, Gillert A, Trouillier M, Anadon-Rosell A, Peters RL, von Arx G, von Lukas U, Wilmking M. Mask, Train, Repeat! Artificial Intelligence for Quantitative Wood Anatomy. FRONTIERS IN PLANT SCIENCE 2021; 12:767400. [PMID: 34804101 PMCID: PMC8601631 DOI: 10.3389/fpls.2021.767400] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/15/2021] [Indexed: 06/13/2023]
Abstract
The recent developments in artificial intelligence have the potential to facilitate new research methods in ecology. Especially Deep Convolutional Neural Networks (DCNNs) have been shown to outperform other approaches in automatic image analyses. Here we apply a DCNN to facilitate quantitative wood anatomical (QWA) analyses, where the main challenges reside in the detection of a high number of cells, in the intrinsic variability of wood anatomical features, and in the sample quality. To properly classify and interpret features within the images, DCNNs need to undergo a training stage. We performed the training with images from transversal wood anatomical sections, together with manually created optimal outputs of the target cell areas. The target species included an example for the most common wood anatomical structures: four conifer species; a diffuse-porous species, black alder (Alnus glutinosa L.); a diffuse to semi-diffuse-porous species, European beech (Fagus sylvatica L.); and a ring-porous species, sessile oak (Quercus petraea Liebl.). The DCNN was created in Python with Pytorch, and relies on a Mask-RCNN architecture. The developed algorithm detects and segments cells, and provides information on the measurement accuracy. To evaluate the performance of this tool we compared our Mask-RCNN outputs with U-Net, a model architecture employed in a similar study, and with ROXAS, a program based on traditional image analysis techniques. First, we evaluated how many target cells were correctly recognized. Next, we assessed the cell measurement accuracy by evaluating the number of pixels that were correctly assigned to each target cell. Overall, the "learning process" defining artificial intelligence plays a key role in overcoming the issues that are usually manually solved in QWA analyses. Mask-RCNN is the model that better detects which are the features characterizing a target cell when these issues occur. In general, U-Net did not attain the other algorithms' performance, while ROXAS performed best for conifers, and Mask-RCNN showed the highest accuracy in detecting target cells and segmenting lumen areas of angiosperms. Our research demonstrates that future software tools for QWA analyses would greatly benefit from using DCNNs, saving time during the analysis phase, and providing a flexible approach that allows model retraining.
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Affiliation(s)
- Giulia Resente
- Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany
| | - Alexander Gillert
- Fraunhofer-Institut für Graphische Datenverarbeitung IGD, Rostock, Germany
| | - Mario Trouillier
- Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany
| | - Alba Anadon-Rosell
- Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany
- CREAF, Campus de Bellaterra (UAB), Cerdanyola del Vallès, Spain
| | - Richard L. Peters
- Department of Environment, Faculty of Bioscience Engineering, Ghent, Belgium
- Swiss Federal Institute for Forest, Snow and Landscape Research, Birmensdorf, Switzerland
| | - Georg von Arx
- Swiss Federal Institute for Forest, Snow and Landscape Research, Birmensdorf, Switzerland
- Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
| | - Uwe von Lukas
- Fraunhofer-Institut für Graphische Datenverarbeitung IGD, Rostock, Germany
- Institute for Visual and Analytic Computing, University of Rostock, Rostock, Germany
| | - Martin Wilmking
- Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany
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Griffin KL, Schmiege SC, Bruner SG, Boelman NT, Vierling LA, Eitel JUH. High Leaf Respiration Rates May Limit the Success of White Spruce Saplings Growing in the Kampfzone at the Arctic Treeline. FRONTIERS IN PLANT SCIENCE 2021; 12:746464. [PMID: 34790212 PMCID: PMC8591130 DOI: 10.3389/fpls.2021.746464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/01/2021] [Indexed: 06/13/2023]
Abstract
Arctic Treeline is the transition from the boreal forest to the treeless tundra and may be determined by growing season temperatures. The physiological mechanisms involved in determining the relationship between the physical and biological environment and the location of treeline are not fully understood. In Northern Alaska, we studied the relationship between temperature and leaf respiration in 36 white spruce (Picea glauca) trees, sampling both the upper and lower canopy, to test two research hypotheses. The first hypothesis is that upper canopy leaves, which are more directly coupled to the atmosphere, will experience more challenging environmental conditions and thus have higher respiration rates to facilitate metabolic function. The second hypothesis is that saplings [stems that are 5-10cm DBH (diameter at breast height)] will have higher respiration rates than trees (stems ≥10cm DBH) since saplings represent the transition from seedlings growing in the more favorable aerodynamic boundary layer, to trees which are fully coupled to the atmosphere but of sufficient size to persist. Respiration did not change with canopy position, however respiration at 25°C was 42% higher in saplings compared to trees (3.43±0.19 vs. 2.41±0.14μmolm-2 s-1). Furthermore, there were significant differences in the temperature response of respiration, and seedlings reached their maximum respiration rates at 59°C, more than two degrees higher than trees. Our results demonstrate that the respiratory characteristics of white spruce saplings at treeline impose a significant carbon cost that may contribute to their lack of perseverance beyond treeline. In the absence of thermal acclimation, the rate of leaf respiration could increase by 57% by the end of the century, posing further challenges to the ecology of this massive ecotone.
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Affiliation(s)
- Kevin L. Griffin
- Department of Earth and Environmental Sciences, Columbia University, Palisades, NY, United States
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, United States
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, United States
| | - Stephanie C. Schmiege
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, United States
- New York Botanical Garden, Bronx, NY, United States
| | - Sarah G. Bruner
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, United States
| | - Natalie T. Boelman
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, United States
| | - Lee A. Vierling
- Department of Natural Resources and Society, College of Natural Resources, University of Idaho, Moscow, ID, United States
| | - Jan U. H. Eitel
- Department of Natural Resources and Society, College of Natural Resources, University of Idaho, Moscow, ID, United States
- McCall Outdoor Science School, College of Natural Resources, University of Idaho, McCall, ID, United States
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Pampuch T, Anadon-Rosell A, Trouillier M, Lange J, Wilmking M. Direct and Indirect Effects of Environmental Limitations on White Spruce Xylem Anatomy at Treeline. FRONTIERS IN PLANT SCIENCE 2021; 12:748055. [PMID: 34759941 PMCID: PMC8573320 DOI: 10.3389/fpls.2021.748055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/04/2021] [Indexed: 06/13/2023]
Abstract
Treeline ecosystems are of great scientific interest to study the effects of limiting environmental conditions on tree growth. However, tree growth is multidimensional, with complex interactions between height and radial growth. In this study, we aimed to disentangle effects of height and climate on xylem anatomy of white spruce [Picea glauca (Moench) Voss] at three treeline sites in Alaska; i.e., one warm and drought-limited, and two cold, temperature-limited. To analyze general growth differences between trees from different sites, we used data on annual ring width, diameter at breast height (DBH), and tree height. A representative subset of the samples was used to investigate xylem anatomical traits. We then used linear mixed-effects models to estimate the effects of height and climatic variables on our study traits. Our study showed that xylem anatomical traits in white spruce can be directly and indirectly controlled by environmental conditions: hydraulic-related traits seem to be mainly influenced by tree height, especially in the earlywood. Thus, they are indirectly driven by environmental conditions, through the environment's effects on tree height. Traits related to mechanical support show a direct response to environmental conditions, mainly temperature, especially in the latewood. These results highlight the importance of assessing tree growth in a multidimensional way by considering both direct and indirect effects of environmental forcing to better understand the complexity of tree growth responses to the environment.
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Affiliation(s)
- Timo Pampuch
- Institute of Botany and Landscape Ecology, University Greifswald, Greifswald, Germany
| | - Alba Anadon-Rosell
- Institute of Botany and Landscape Ecology, University Greifswald, Greifswald, Germany
- CREAF – Centre for Research on Ecology and Forestry Applications, Barcelona, Spain
| | - Mario Trouillier
- Institute of Botany and Landscape Ecology, University Greifswald, Greifswald, Germany
| | - Jelena Lange
- Institute of Botany and Landscape Ecology, University Greifswald, Greifswald, Germany
- Department of Physical Geography and Geoecology, Charles University in Prague, Prague, Czechia
| | - Martin Wilmking
- Institute of Botany and Landscape Ecology, University Greifswald, Greifswald, Germany
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