Association of genetic and climatic variability in giant sequoia, <i>Sequoiadendron giganteum</i>, reveals signatures of local adaptation along moisture‐related gradients

DeSilva, Rainbow; Dodd, Richard S.

doi:10.1002/ece3.6716

Cited by 9 publications

(11 citation statements)

References 89 publications

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“…The PCA analysis showed consistent results to fastStructure, identifying eight genetic clusters in giant sequoia and three clusters in coast redwood (Supplementary Figure S1). These results were consistent with previous studies in the species using more individuals but fewer molecular markers [46,48].…”

Section: Population Structuresupporting

confidence: 93%

“…All data were based on the averages for years 1962-1990 and included seasonal and annual variables. Environmental variables were selected based on previous ecological and physiological studies in the species [48,51]. Correlations among all geographic (latitude, longitude, and elevation) and environmental variables were tested in R v3.6.1.…”

Section: Genome-wide Environmental Association (Gea)mentioning

confidence: 99%

“…Both coast redwood and giant sequoia are currently listed as endangered species by the International Union for Conservation of Nature (IUCN) Red List of Threatened Species [45]. Despite their unique ecological and economic importance, the genomics of local adaptation in coast redwood and giant sequoia are insufficiently studied [38,40,[46][47][48][49][50]. The objectives of this research were to dissect the genomic basis of local adaptation to climate in natural populations of giant sequoia and coast redwood by (i) locating genomic regions showing signals of natural selection that might provide information about the mode of adaptation, (ii) identifying the main environmental variables driving adaptation in the species, and (iii) understanding the main biological functions of genes associated with environmental variation.…”

Section: Introductionmentioning

confidence: 99%

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Selective Sweeps and Polygenic Adaptation Drive Local Adaptation along Moisture and Temperature Gradients in Natural Populations of Coast Redwood and Giant Sequoia

Torre

Sekhwal

Neale

2021

Genes

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Dissecting the genomic basis of local adaptation is a major goal in evolutionary biology and conservation science. Rapid changes in the climate pose significant challenges to the survival of natural populations, and the genomic basis of long-generation plant species is still poorly understood. Here, we investigated genome-wide climate adaptation in giant sequoia and coast redwood, two iconic and ecologically important tree species. We used a combination of univariate and multivariate genotype–environment association methods and a selective sweep analysis using non-overlapping sliding windows. We identified genomic regions of potential adaptive importance, showing strong associations to moisture variables and mean annual temperature. Our results found a complex architecture of climate adaptation in the species, with genomic regions showing signatures of selective sweeps, polygenic adaptation, or a combination of both, suggesting recent or ongoing climate adaptation along moisture and temperature gradients in giant sequoia and coast redwood. The results of this study provide a first step toward identifying genomic regions of adaptive significance in the species and will provide information to guide management and conservation strategies that seek to maximize adaptive potential in the face of climate change.

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Section: Population Structuresupporting

confidence: 93%

Section: Genome-wide Environmental Association (Gea)mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Selective Sweeps and Polygenic Adaptation Drive Local Adaptation along Moisture and Temperature Gradients in Natural Populations of Coast Redwood and Giant Sequoia

Torre

Sekhwal

Neale

2021

Genes

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“…There was little overlap between methods (nine loci common to both methods, Figure ), a phenomenon commonly reported in other studies (e.g. DeSilva & Dodd, 2020; de Villemereuil et al, 2014). In examining environmental associations with outlier loci, LFMM detected 12 SNPs related to longitude and 22 SNPs related to genetic structure defined by the three clusters identified by fastSTRUCTURE (Figure 2).…”

Section: Resultssupporting

confidence: 53%

Impact of roadside burning on genetic diversity in a high‐biomass invasive grass

Firn

Buckley

et al. 2022

Evolutionary Applications

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The invasive grass–fire cycle is a widely documented feedback phenomenon in which invasive grasses increase vegetation flammability and fire frequency, resulting in further invasion and compounded effects on fire regimes. Few studies have examined the role of short‐term adaptation in driving the invasive grass–fire cycle, despite invasive species often thriving after introduction to new environments. We used a replicated (nine locations), paired sampling design (burn vs unburnt sites) to test the hypothesis that roadside burning increases genetic diversity and thus adaptive potential in the invasive, high‐biomass grass Cenchrus ciliaris. Between four and five samples per site (n = 93) were genotyped using the DArTseq platform, and we filtered the data to produce panels of 15,965 neutral and 5030 non‐neutral single nucleotide polymorphism (SNP) markers. Using fastSTRUCTURE, we detected three distinct genetic clusters with extremely high FST values among them (0.94–0.97) suggesting three different cultivars. We found high rates of asexual reproduction, possibly related to clonality or apomixis common in this species. At three locations, burnt and unburnt sites were genetically different, but genetic structure was not consistently related to fire management across the study region. Burning was associated with high genetic diversity and sexual reproduction in one genetic cluster, but with low genetic diversity and clonality in another. Individual SNPs were associated with longitude and genetic clustering, but not with recent fire management. Overall, we found limited evidence that roadside burning consistently increased genetic diversity and adaptive potential in C. ciliaris; evolutionary and breeding history more strongly shaped genetic structure. Roadside burning could therefore continue to be used for managing biomass in this species, with continued monitoring. Our study provides a framework for detecting fire‐related changes on a genetic level–a process that could be used as an early warning system to detect the invasive grass–fire cycle in future.

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“…Climatic conditions also appear to affect giant sequoia trees' health as hotter droughts were reportedly linked to foliage dieback [40]. Recently, the genetic basis of local adaptation of giant sequoias to summer precipitations was unveiled and revealed variability in genomic regions correlated to precipitations and temperature [41]. This would explain the observed behaviour and sensibility to pathogens of giant sequoias in climate change.…”

Section: Discussionmentioning

confidence: 99%

Neofusicoccum parvum, A New Agent of Sequoia Canker and Dieback Identified in Geneva, Switzerland

Haenzi

Cochard

Chablais

et al. 2021

Forests

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Fungi were isolated in pure cultures from decaying giant sequoias in Geneva (Switzerland). Isolates were genetically identified by ITS rDNA sequencing. Young giant sequoia trees were artificially infected with a pure culture of Botryosphaeria parva. Henle-Koch’s Postulates demonstrated that Botryosphaeria parva was pathogenic to Sequoiadendron giganteum. When analysing the microorganisms associated to canker and dieback symptoms in a giant sequoias (Sequoiadendron giganteum) in Geneva, the fungus Neofusicoccum parvum (Pennycook & Samuels) Crous, Slippers & A.J.L. Phillips, teleomorph Botryosphaeria parva (Pennycook & Samuels) Crous, Slippers & A.J.L. Phillips, was isolated, whereas such symptoms are commonly associated to Fusicoccum aesculi (teleomorph Botryosphaeria dothidea). These two fungal species belong to the same genus Botryosphaeria of the Botryosphaeriaceae family. Because Neofusicoccum parvum was causing cankers and diebacks in other woody species around the world, we extended the analysis to other trees displaying sequoia dieback symptoms in order to evaluate the involvement of Neofusicoccum parvum in such increasing symptoms in sequoias in Geneva. Dried twigs, trunk, and branch cankers from diseased trees were sampled on several distinct sites. From all samples, isolated fungi in pure cultures showed a phenotype typical of Botryosphaeriaceae species. Isolates were then genetically identified at the species level. Subsequently Neofusicoccum parvum was inoculated to young giant sequoia trees, re-isolated in pure culture from provoked symptoms, and re-identified to fulfil Henle-Koch’s postulates. The identification confirmed that Neofusicoccum parvum was present on all sites, while Fusicoccum aesculi was retrieved only once alone. The inoculation of Neofusicoccum parvum isolates on young sequoias demonstrated for the first time that this fungus was able to develop cankers in Sequoiadendron gigantean. Neofusicoccum parvum could, therefore, be the major cause for dying of giant sequoias in the Geneva Lake area.

show abstract

Association of genetic and climatic variability in giant sequoia, Sequoiadendron giganteum, reveals signatures of local adaptation along moisture‐related gradients

Cited by 9 publications

References 89 publications

Selective Sweeps and Polygenic Adaptation Drive Local Adaptation along Moisture and Temperature Gradients in Natural Populations of Coast Redwood and Giant Sequoia

Selective Sweeps and Polygenic Adaptation Drive Local Adaptation along Moisture and Temperature Gradients in Natural Populations of Coast Redwood and Giant Sequoia

Impact of roadside burning on genetic diversity in a high‐biomass invasive grass

Neofusicoccum parvum, A New Agent of Sequoia Canker and Dieback Identified in Geneva, Switzerland

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