Detecting genetic variants under selection using FST outlier analysis (OA) and environmental association analyses (EAAs) are popular approaches that provide insight into the genetic basis of local ...adaptation. Despite the frequent use of OA and EAA approaches and their increasing attractiveness for detecting signatures of selection, their application to field‐based empirical data have not been synthesized. Here, we review 66 empirical studies that use Single Nucleotide Polymorphisms (SNPs) in OA and EAA. We report trends and biases across biological systems, sequencing methods, approaches, parameters, environmental variables and their influence on detecting signatures of selection. We found striking variability in both the use and reporting of environmental data and statistical parameters. For example, linkage disequilibrium among SNPs and numbers of unique SNP associations identified with EAA were rarely reported. The proportion of putatively adaptive SNPs detected varied widely among studies, and decreased with the number of SNPs analysed. We found that genomic sampling effort had a greater impact than biological sampling effort on the proportion of identified SNPs under selection. OA identified a higher proportion of outliers when more individuals were sampled, but this was not the case for EAA. To facilitate repeatability, interpretation and synthesis of studies detecting selection, we recommend that future studies consistently report geographical coordinates, environmental data, model parameters, linkage disequilibrium, and measures of genetic structure. Identifying standards for how OA and EAA studies are designed and reported will aid future transparency and comparability of SNP‐based selection studies and help to progress landscape and evolutionary genomics.
Global climate is rapidly changing, and the ability for tree species to adapt is dependent on standing genomic variation; however, the distribution and abundance of functional and adaptive variants ...are poorly understood in natural systems. We test key hypotheses regarding the genetics of adaptive variation in a foundation tree: genomic variation is associated with climate, and genomic variation is more likely to be associated with temperature than precipitation or aridity. To test these hypotheses, we used 9,593 independent, genomic single‐nucleotide polymorphisms (SNPs) from 270 individuals sampled from Corymbia calophylla's entire distribution in south‐western Western Australia, spanning orthogonal temperature and precipitation gradients. Environmental association analyses returned 537 unique SNPs putatively adaptive to climate. We identified SNPs associated with climatic variation (i.e., temperature 458, precipitation 75 and aridity 78) across the landscape. Of these, 78 SNPs were nonsynonymous (NS), while 26 SNPs were found within gene regulatory regions. The NS and regulatory candidate SNPs associated with temperature explained more deviance (27.35%) than precipitation (5.93%) and aridity (4.77%), suggesting that temperature provides stronger adaptive signals than precipitation. Genes associated with adaptive variants include functions important in stress responses to temperature and precipitation. Patterns of allelic turnover of NS and regulatory SNPs show small patterns of change through climate space with the exception of an aldehyde dehydrogenase gene variant with 80% allelic turnover with temperature. Together, these findings provide evidence for the presence of adaptive variation to climate in a foundation species and provide critical information to guide adaptive management practices.
Climate change is testing the resilience of forests worldwide pushing physiological tolerance to climatic extremes. Plant functional traits have been shown to be adapted to climate and have evolved ...patterns of trait correlations (similar patterns of distribution) and coordinations (mechanistic trade‐off). We predicted that traits would differentiate between populations associated with climatic gradients, suggestive of adaptive variation, and correlated traits would adapt to future climate scenarios in similar ways.
We measured genetically determined trait variation and described patterns of correlation for seven traits: photochemical reflectance index (PRI), normalized difference vegetation index (NDVI), leaf size (LS), specific leaf area (SLA), δ13C (integrated water‐use efficiency, WUE), nitrogen concentration (NCONC), and wood density (WD). All measures were conducted in an experimental plantation on 960 trees sourced from 12 populations of a key forest canopy species in southwestern Australia.
Significant differences were found between populations for all traits. Narrow‐sense heritability was significant for five traits (0.15–0.21), indicating that natural selection can drive differentiation; however, SLA (0.08) and PRI (0.11) were not significantly heritable. Generalized additive models predicted trait values across the landscape for current and future climatic conditions (>90% variance). The percent change differed markedly among traits between current and future predictions (differing as little as 1.5% (δ13C) or as much as 30% (PRI)). Some trait correlations were predicted to break down in the future (SLA:NCONC, δ13C:PRI, and NCONC:WD).
Synthesis: Our results suggest that traits have contrasting genotypic patterns and will be subjected to different climate selection pressures, which may lower the working optimum for functional traits. Further, traits are independently associated with different climate factors, indicating that some trait correlations may be disrupted in the future. Genetic constraints and trait correlations may limit the ability for functional traits to adapt to climate change.
We tested whether functional traits of an important tree species in southwestern Australia were genetically determined and able to undergo selection. Our results suggest that some traits are heritable (Water Use Efficiency) while others are not (SLA), indicating that in the future, under different climates, selection will differentially effect traits. Therefore, it is likely that current trait combinations will change with climate.
Asexual seed reproduction, apomixis, is a relatively rare reproductive strategy in angiosperms. Its rarity is probably due to evolutionary constraints that require full and synchronous expression of ...all the steps that modify the ancestral sexual pathway. Therefore, the documentation of any new occurrence of apomixis, especially in taxonomic groups with no previous report, should be based on thorough and solid evidence. Here, we correct the report of suggested apomictic reproduction in two endemic hexaploid species of
Senecio
from Australia. Based on either excess or deficiency of expected heterozygosity across loci, over-representation of several multilocus genotypes, and segregation analysis assessed using microsatellite markers, it was suggested that apomixis together with selfing could explain the observed patterns of genetic variation in perennial
S. macrocarpus
and annual
S. squarrosus
. We used flow cytometric seed screening analyses to verify the mode of reproduction of several widespread multilocus genotypes that are considered to be apomictic. These analyses revealed that all seed progeny arose by the sexual pathway, as they exhibited a constant 3:2 endosperm to embryo ploidy ratio, typical of double fertilization of a reduced embryo sac by two reduced sperm cells. Therefore, both species reproduce sexually. We suggest that the unusual genetic patterns in both allopolyploids are caused by originally low variation in the parental species, which probably also reproduce by selfing, disomic inheritance and probably also the presence of null alleles. We call for a more careful and critical interpretation of the patterns obtained, taking into account all aspects related to apomictic reproduction.
Drought adaptation is critical to many tree species persisting under climate change, however our knowledge of the genetic basis for trees to adapt to drought is limited. This knowledge gap impedes ...our fundamental understanding of drought response and application to forest production and conservation. To improve our understanding of the genomic determinants, architecture, and trait constraints, we assembled a reference genome and detected ~ 6.5 M variants in 432 phenotyped individuals for the foundational tree Corymbia calophylla. We found 273 genomic variants determining traits with moderate heritability (h.sup.2.sub.SNP = 0.26-0.64). Significant variants were predominantly in gene regulatory elements distributed among several haplotype blocks across all chromosomes. Furthermore, traits were constrained by frequent epistatic and pleiotropic interactions. Our results on the genetic basis for drought traits in Corymbia calophylla have several implications for the ability to adapt to climate change: (1) drought related traits are controlled by complex genomic architectures with large haplotypes, epistatic, and pleiotropic interactions; (2) the most significant variants determining drought related traits occurred in regulatory regions; and (3) models incorporating epistatic interactions increase trait predictions. Our findings indicate that despite moderate heritability drought traits are likely constrained by complex genomic architecture potentially limiting trees response to climate change.
Summary
The frequency and severity of heatwave events are increasing, exposing species to conditions beyond their physiological limits. Species respond to heatwaves in different ways, however it ...remains unclear if plants have the adaptive capacity to successfully respond to hotter and more frequent heatwaves.
We exposed eight tree populations from two climate regions grown under cool and warm temperatures to repeated heatwave events of moderate (40°C) and extreme (46°C) severity to assess adaptive capacity to heatwaves.
Leaf damage and maximum quantum efficiency of photosystem II (Fv/Fm) were significantly impacted by heatwave severity and growth temperatures, respectively; populations from a warm‐origin avoided damage under moderate heatwaves compared to those from a cool‐origin, indicating a degree of local adaptation. We found that plasticity to heatwave severity and repeated heatwaves contributed to enhanced thermal tolerance and lower leaf temperatures, leading to greater thermal safety margins (thermal tolerance minus leaf temperature) in a second heatwave.
Notably, while we show that adaptation and physiological plasticity are important factors affecting plant adaptive capacity to thermal stress, plasticity of thermal tolerances and thermal safety margins provides the opportunity for trees to persist among fluctuating heatwave exposures.
Understanding local adaptation is critical for conservation management under rapidly changing environmental conditions. Local adaptation inferred from genotype‐environment associations may show ...different genomic patterns depending on the spatial scale of sampling, due to differences in the slope of environmental gradients and the level of gene flow. We compared signatures of local adaptation across the genome of mountain ash (Eucalyptus regnans) at two spatial scales: A species‐wide data set and a topographically‐complex subregional data set. We genotyped 367 individual trees at over 3700 single‐nucleotide polymorphisms (SNPs), quantified patterns of spatial genetic structure among populations, and used two analytical methods to identify loci associated with at least one of three environmental variables at each spatial scale. Together, the analyses identified 549 potentially adaptive SNPs at the subregion scale, and 435 SNPs at the range‐wide scale. A total of 39 genic or near‐genic SNPs, associated with 28 genes, were identified at both spatial scales, although no SNP was identified by both methods at both scales. We observed that nongenic regions had significantly higher homozygote excess than genic regions, possibly due to selective elimination of inbred genotypes during stand development. Our results suggest that strong environmental selection occurs in mountain ash, and that the identification of putatively adaptive loci can differ substantially depending on the spatial scale of analyses. We also highlight the importance of multiple adaptive genetic architectures for understanding patterns of local adaptation across large heterogenous landscapes, with comparison of putatively adaptive loci among spatial scales providing crucial insights into the process of adaptation.
Temperature and precipitation regimes are rapidly changing, resulting in forest dieback and extinction events, particularly in Mediterranean‐type climates (MTC). Forest management that enhance ...forests’ resilience is urgently required, however adaptation to climates in heterogeneous landscapes with multiple selection pressures is complex. For widespread trees in MTC we hypothesized that: patterns of local adaptation are associated with climate; precipitation is a stronger factor of adaptation than temperature; functionally related genes show similar signatures of adaptation; and adaptive variants are independently sorting across the landscape. We sampled 28 populations across the geographic distribution of Eucalyptus marginata (jarrah), in South‐west Western Australia, and obtained 13,534 independent single nucleotide polymorphic (SNP) markers across the genome. Three genotype‐association analyses that employ different ways of correcting population structure were used to identify putatively adapted SNPs associated with independent climate variables. While overall levels of population differentiation were low (FST = 0.04), environmental association analyses found a total of 2336 unique SNPs associated with temperature and precipitation variables, with 1440 SNPs annotated to genic regions. Considerable allelic turnover was identified for SNPs associated with temperature seasonality and mean precipitation of the warmest quarter, suggesting that both temperature and precipitation are important factors in adaptation. SNPs with similar gene functions had analogous allelic turnover along climate gradients, while SNPs among temperature and precipitation variables had uncorrelated patterns of adaptation. These contrasting patterns provide evidence that there may be standing genomic variation adapted to current climate gradients, providing the basis for adaptive management strategies to bolster forest resilience in the future.
The frequency and intensity of drought events are predicted to increase because of climate change, threatening biodiversity and terrestrial ecosystems in many parts of the world. Drought has already ...led to declines in functionally important tree species, which are documented in dieback events, shifts in species distributions, local extinctions, and compromised ecosystem function. Understanding whether tree species possess the capacity to adapt to future drought conditions is a major conservation challenge. In this study, we assess the capacity of a functionally important plant species from south-eastern Australia (
, Proteaceae) to adapt to water-limited environments. A water-manipulated common garden experiment was used to test for phenotypic plasticity and genetic adaptation in seedlings sourced from seven provenances of contrasting climate-origins (wet and dry). We found evidence of local adaptation relating to plant growth investment strategies with populations from drier climate-origins showing greater growth in well-watered conditions. The results also revealed that environment drives variation in physiological (stomatal conductance, predawn and midday water potential) and structural traits (wood density, leaf dry matter content). Finally, these results indicate that traits are coordinated to optimize conservation of water under water-limited conditions and that trait coordination (phenotypic integration) does not constrain phenotypic plasticity. Overall, this study provides evidence for adaptive capacity relating to drought conditions in
, and a basis for predicting the response to climate change in this functionally important plant species.
PDF
