Local adaptation to temperature and precipitation in naturally fragmented populations of Cephalotaxus oliveri, an endangered conifer endemic to China

Local adaptation in forest trees: genetic processes and relevance under climate change Forest trees will have to adapt to future climatic changes, a process that will comprise genetic changes as a key component. Owing to technological advances it is now possible to identify the signature of natural selection and local adaptation in the genome. Environmental association analyses aim at associating adaptive genetic patterns with environmental parameters describing the local habitat. On the basis of such studies – including own investigations using oak and beech in Switzerland –, we show that forest trees are genetically differentiated along various environmental gradients, especially temperature and precipitation. Numerous genes could be found that presumably play a role in the adaptation to such environmental factors. Based on these findings, one could identify trees or stands that are adapted to future local conditions, and respective seed material could be considered in silviculture. Because such approaches are still in their infancy and because genome-environment interactions are complex, management strategies should focus on the preservation of (adaptive) genetic diversity, natural regeneration, and connectivity among stands. This would set the basis for the local adaptation of forest stands to altered environmental conditions by natural processes.

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Climate adaptation shaped by subtle to moderate allele frequency shifts in loblolly pine

10.1101/635862 ◽

2019 ◽

Cited By ~ 1

Author(s):

Amanda R. De La Torre ◽

David B Neale

Keyword(s):

Allele Frequency ◽

Local Adaptation ◽

Loblolly Pine ◽

Climate Adaptation ◽

Geographic Location ◽

Woody Species ◽

Climatic Variables ◽

Whole Genome ◽

Temperature And Precipitation ◽

Genomic Regions

ABSTRACTUnderstanding the genomic basis of local adaptation is crucial to determine the potential of long-lived woody species to withstand changes in their natural environment. In the past, efforts to dissect the genomic architecture in gymnosperms species have been limited due to the absence of reference genomes. Recently, the genomes of some commercially important conifers, such as loblolly pine, have become available, allowing whole-genome studies of these species. In this study, we test for associations between 87k SNPs, obtained from whole-genome re-sequencing of loblolly pine individuals, and 270 environmental variables and combinations of them. We determine the geographic location of significant alleles and identify their genomic location using our newly constructed ultra-dense 26k SNP linkage map. We found that water availability is the main climatic variable shaping local adaptation of the species, and found 492 SNPs showing significant associations with climatic variables or combinations of them. Our results suggest that adaptation to climate in the species might have occurred by many changes in the allele frequency of alleles with moderate to small effect sizes, and by the smaller contribution of large effect alleles in genes related to moisture deficit, temperature and precipitation. Genomic regions of low recombination and high population differentiation harbored SNPs associated with principal components but not with individual climatic variables, suggesting climate adaptation might have evolved as a result of different selection pressures acting on groups of genes associated with an aspect of climate rather than on individual climatic variables.

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Climate warming weakens local adaptation

10.1101/2020.11.01.364349 ◽

2020 ◽

Author(s):

M. Bontrager ◽

C. D. Muir ◽

C. Mahony ◽

D. E. Gamble ◽

R. M. Germain ◽

...

Keyword(s):

Climate Change ◽

Local Adaptation ◽

Average Performance ◽

Temperature And Precipitation ◽

Quantitative Synthesis ◽

Effects Of Temperature ◽

Scientific Challenge ◽

Field Transplant ◽

Transplant Experiments ◽

Population Performance

AbstractAnthropogenic climate change is generating mismatches between the environmental conditions that populations historically experienced and those in which they reside. Understanding how climate change affects population performance is a critical scientific challenge. We combine a quantitative synthesis of field transplant experiments with a novel statistical approach based in evolutionary theory to quantify the effects of temperature and precipitation variability on population performance. We find that species’ average performance is affected by both temperature and precipitation, but populations show signs of local adaptation to temperature only. Contemporary responses to temperature are strongly shaped by the local climates under which populations evolved, resulting in performance declines when temperatures deviate from historic conditions. Adaptation to other local environmental factors is strong, but temperature deviations as small as 2°C erode the advantage that these non-climatic adaptations historically gave populations in their home sites.One sentence summaryClimate change is pulling the thermal rug out from under populations, reducing average performance and eroding their historical home-site advantage.

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Environmental Genome-Wide Association Reveals Climate Adaptation Is Shaped by Subtle to Moderate Allele Frequency Shifts in Loblolly Pine

Genome Biology and Evolution ◽

10.1093/gbe/evz220 ◽

2019 ◽

Vol 11 (10) ◽

pp. 2976-2989 ◽

Cited By ~ 4

Author(s):

Amanda R De La Torre ◽

Benjamin Wilhite ◽

David B Neale

Keyword(s):

Local Adaptation ◽

Loblolly Pine ◽

Environmental Variables ◽

Climate Adaptation ◽

Geographic Location ◽

Woody Species ◽

Whole Genome ◽

Temperature And Precipitation ◽

Whole Genome Resequencing ◽

Environmental Genome

Abstract Understanding the genomic basis of local adaptation is crucial to determine the potential of long-lived woody species to withstand changes in their natural environment. In the past, efforts to dissect the genomic architecture in gymnosperms species have been limited due to the absence of reference genomes. Recently, the genomes of some commercially important conifers, such as loblolly pine, have become available, allowing whole-genome studies of these species. In this study, we test for associations between 87k SNPs, obtained from whole-genome resequencing of loblolly pine individuals, and 270 environmental variables and combinations of them. We determine the geographic location of significant loci and identify their genomic location using our newly constructed ultradense 26k SNP linkage map. We found that water availability is the main climatic variable shaping local adaptation of the species, and found 821 SNPs showing significant associations with climatic variables or combinations of them based on the consistent results of three different genotype–environment association methods. Our results suggest that adaptation to climate in the species might have occurred by many changes in the frequency of alleles with moderate to small effect sizes, and by the smaller contribution of large effect alleles in genes related to moisture deficit, temperature and precipitation. Genomic regions of low recombination and high population differentiation harbored SNPs associated with groups of environmental variables, suggesting climate adaptation might have evolved as a result of different selection pressures acting on groups of genes associated with an aspect of climate rather than on individual environmental variables.

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Genetic differentiation, local adaptation and phenotypic plasticity in fragmented populations of a rare forest herb

PeerJ ◽

10.7717/peerj.4929 ◽

2018 ◽

Vol 6 ◽

pp. e4929 ◽

Cited By ~ 9

Author(s):

Rodolfo Gentili ◽

Aldo Solari ◽

Martin Diekmann ◽

Cecilia Duprè ◽

Gianna Serafina Monti ◽

...

Keyword(s):

Phenotypic Plasticity ◽

Genetic Differentiation ◽

Local Adaptation ◽

Size Range ◽

Population Decline ◽

Environmental Data ◽

Soil Parameters ◽

Phenotypic Traits ◽

Herbivorous Insect ◽

Fragmented Populations

BackgroundDue to habitat loss and fragmentation, numerous forest species are subject to severe population decline. Investigating variation in genetic diversity, phenotypic plasticity and local adaptation should be a prerequisite for implementing conservation actions. This study aimed to explore these aspects in ten fragmented populations ofPhysospermum cornubiensein view of translocation measures across its Italian range.MethodsFor each population we collected environmental data on landscape (habitat size, quality and fragmentation) and local conditions (slope, presence of alien species, incidence of the herbivorous insectMetcalfa pruinosaand soil parameters). We measured vegetative and reproductive traits in the field and analysed the genetic population structure using ISSR markers (STRUCTURE and AMOVA). We then estimated the neutral (FST) and quantitative (PST) genetic differentiation of populations.ResultsThe populations exhibited moderate phenotypic variation. Population size (range: 16–655 individuals), number of flowering adults (range: 3–420 individuals) and inflorescence size (range: 5.0–8.4 cm) were positively related to Mg soil content. Populations’ gene diversity was moderate (Nei-H = 0.071–0.1316); STRUCTURE analysis identified five different clusters and three main geographic groups: upper, lower, and Apennine/Western Po plain. Fragmentation did not have an influence on the local adaptation of populations, which for all measured traits showed PST < FST, indicating convergent selection.DiscussionThe variation of phenotypic traits across sites was attributed to plastic response rather than local adaptation. Plant translocation from suitable source populations to endangered ones should particularly take into account provenance according to identified genetic clusters and specific soil factors.

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