Biology subjects

Oakley, C. G.

Publications and source records attributed to Oakley, C. G..

7 recordsLinked to original sources

bioRxiv2026

Environment-dependent and often antagonistic effects of dominance and epistasis on heterosis in crosses between natural populations

Genetic drift in natural populations reduces the efficacy of selection, promoting the fixation of deleterious recessive alleles with consequences for maladaptation and population persistence. Heterosis, or increased F1 fitness relative to the parental mean, has been proposed as a tool for investigating the role of drift on genetic variation in fitness, but its genetic basis and environmental dependence remain unclear in natural populations. We used heterozygous near-isogenic lines (NILs) derived from a cross between locally adapted Arabidopsis thaliana ecotypes to assess how specific genomic regions influence heterosis. Cumulative fitness, estimated as fruits per seedling, was evaluated in a greenhouse and two simulated native environments. There was strong overall heterosis in the greenhouse and one simulated environment. Non-additive effects in heterozygous NILs were highly environment- and background-dependent, varying in magnitude and sign, and no NIL had consistent effects across environments. The relative fitness of heterozygous NILs was not correlated with gene number or genomic load in the introgressed regions. Small heterozygous regions often had large effects, indicating that complementation of mildly deleterious alleles alone does not fully explain heterosis. Evidence of epistasis was also observed, including outbreeding depression in some NILs, likely due to negative additive-by-dominance interactions. Summed effects of individual heterozygous genomic regions often exceeded the fitness increase of the F1 suggesting dominance-by-dominance epistasis, but the direction of these epistatic effects depended on both genetic background and environment. Our results demonstrate that F1 fitness reflects both positive dominance and different epistatic interactions that are environment- and background-dependent.

evolutionary biology↗

bioRxiv2025

Museum genomics reveals temporal genetic stasis and global genetic diversity in Arabidopsis thaliana

Global patterns of population genetic variation through time offer a window into evolutionary processes that maintain diversity. Over time, lineages may expand or contract their distribution, causing turnover in population genetic composition. At individual loci, migration, drift, and selection (among other processes) may affect allele frequencies. Museum specimens of widely distributed species offer a unique window into the genetics of understudied populations and changes over time. Here, we sequenced genomes of 130 herbarium specimens and 91 new field collections of Arabidopsis thaliana and combined these with published genomes. We sought a broader view of genomic diversity across the species, and to test if population genomic composition is changing through time. We documented extensive and previously uncharacterized diversity in a range of populations in Africa, populations that are under threat from anthropogenic climate change. Through time, we did not find dramatic changes in genomic composition of populations. Instead, we found a pattern of genetic change every 100 years of the same magnitude seen when comparing Eurasian populations that are 185 km apart, potentially due to a combination of drift and changing selection. We found only mixed signals of polygenic adaptation at phenology and physiology QTL. We did find that genes conserved across eudicots show altered levels of directional allele frequency change, potentially due to variable purifying and background selection. Our study highlights how museum specimens can reveal new dimensions of population diversity and show how wild populations are evolving in recent history.

evolutionary biology↗

bioRxiv2024

Heterosis in crosses between remnant populations of a rare prairie forb: implications for restoration genetics

PremiseCalls to adopt seed sourcing strategies in biological restoration that preserve local adaptation while maximizing genetic variation (e.g., regional admixture provenancing) are increasingly common. Heterosis, the increased fitness of progeny from between-relative to within-population crosses, could provide an added benefit under such strategies, but several open questions remain. MethodsWe quantified heterosis in crosses between three small remnant populations of the rare prairie forb Silene regia. We measured early fitness components (seed number per fruit, germination, and juvenile survival) in a greenhouse. Adult fitness components (survival and reproduction) were quantified over two flowering seasons in two different environments: a field experiment simulating the initial stages of a restoration, and a greenhouse. Our approach is unique in estimating heterosis in an environment most relevant to the early stages of a restoration and in comparing heterosis under field and controlled conditions. Key ResultsThe consequences of between-population crosses for cumulative fitness in the field were strongly positive in two of the populations (281% and 50% heterosis) and nearly neutral in a third. Heterosis was generally stronger when measured under field conditions, and stage specific patterns of heterosis varied among populations. ConclusionsRegional admixture provenancing in restorations should be beneficial for this species. We advocate for more research on heterosis in rare species, particularly in restorations. We also provide a cautionary note on how to calculate and report results for heterosis studies.

evolutionary biology↗

bioRxiv2024

The Roles of Drift and Selection on Short Stamen Loss in Arabidopsis thaliana along an Elevational Gradient in the Spanish Pyrenees

Traits that have lost function sometimes persist through evolutionary time. These traits may persist if there is not enough standing genetic variation for the trait to allow a response to selection, if selection against the trait is weak relative to drift, or if the trait has a residual function. To determine the evolutionary processes shaping whether nonfunctional traits are retained or lost, we investigated short stamens in 16 populations of Arabidopsis thaliana along an elevational cline in northeast Spain. We found a cline in short stamen number from retention of short stamens in high elevation populations to incomplete loss in low elevation populations. We did not find evidence that limited genetic variation constrains the loss of short stamens at high elevations, nor evidence for divergent selection on short stamens between high and low elevations. Finally, we identified loci associated with short stamens in northeast Spain that are different from loci associated with variation in short stamen number across latitudes from a previous study. Overall, we did not identify the evolutionary mechanisms contributing to an elevational cline in short stamen number but did identify different genetic loci underlying variation in short stamen along similar phenotypic clines. Teaser textThe evolutionary mechanisms underlying loss or retention of traits that have lost function are poorly understood. Short stamens in Arabidopsis thaliana provide a compelling system to investigate the roles of genetic drift and selection in trait loss across latitudinal and elevational clines. This study investigates how drift and selection shape short stamen loss in 16 populations of A. thaliana along an elevational gradient in Northeast Spain. An investigation of the loci underlying variation in short stamen number suggests variants in different genes may cause trait loss in similar phenotypic clines within a species.

evolutionary biology↗

bioRxiv2023

A large effect genetic trade-off is caused by a single mutation in CBF2

Identifying the genetic basis of local adaptation and fitness trade-offs across environments is a central goal of evolutionary biology. Cold acclimation is an adaptive plastic response for surviving seasonal freezing, and costs of acclimation may be a general mechanism for fitness trade-offs across environments in temperate zone species. Starting with locally adapted ecotypes of Arabidopsis thaliana from Italy and Sweden, we examined the fitness consequences of a naturally occurring functional polymorphism in CBF2. This gene encodes a transcription factor that is a major regulator of cold-acclimated freezing tolerance, and resides within a locus responsible for a genetic trade-off for long-term mean fitness. We estimated the consequences of alternate genotypes of CBF2 on 5-year mean fitness and fitness components at the native field sites by comparing near isogenic lines with alternate genotypes of CBF2 to their genetic background ecotypes. The effects of CBF2 were validated at the nucleotide level using gene edited lines in the native genetic backgrounds grown in simulated parental environments. The foreign CBF2 genotype in the local genetic background reduced long-term mean fitness in Sweden by more than 10%, primarily via effects on survival. In Italy, fitness was reduced by more than 20%, primarily via effects on fecundity. At both sites, the effects were temporally variable and much stronger in some years. The gene edited lines confirmed that CBF2 encodes the causal variant underlying this genetic trade-off. Additionally, we demonstrated a substantial fitness cost of cold acclimation, which has broad implications for potential maladaptive responses to climate change.

evolutionary biology↗

bioRxiv2023

Relative energetic economy of cleistogamous selfing in three populations of the perennial Ruellia humilis

Premise of researchWhat maintains mixed selfing and outcrossing is an enduring mystery in evolutionary biology. Cleistogamy, where individuals produce both potentially outcrossing chasmogamous and obligately selfing cleistogamous flowers, provides an ideal framework in which to study the evolutionary forces maintaining mixed-mating. Despite their promise for providing insight into mating system evolution, few studies of cleistogamous species have comprehensively investigated the relative costs and benefits of cleistogamous selfing. MethodologyWe quantified the necessary components to calculate the relative energetic cost of reproduction of the different flower types in three natural populations of the perennial Ruellia humilis Nutt (Acanthaceae). These components include flower dry mass, fertility (fruit set), and seed mass and number per fruit. We also measured pollen-ovule ratios for both flower types as another measure of relative energetic investment. We additionally tracked phenology of the two flower types and used the proportion of chasmogamous flowers to estimate maximum potential outcrossing rates. Pivotal ResultsWe found that the energetic cost of reproduction via cleistogamous flowers was about 4-10 times less than that of reproduction via chasmogamous flowers, and this energetic economy was from both reduced mass and increased fertility of cleistogamous flowers. Pollen ovule ratios in cleistogamous flowers were one third to one half those of chasmogamous flowers, providing additional support for their energetic economy. Maximum potential outcrossing rates in these populations based on chasmogamous flower production were between 43-61%, but chasmogamous flowers can autogamously self at rates of 33-75%. ConclusionsThe relative energetic economy of cleistogamous flowers suggest that progeny from chasmogamous flowers would have to have 4-10 times greater relative fitness to explain their evolutionary maintenance. These values are likely even greater considering the reduced investment in pollen production in cleistogamous flowers. Ongoing work will quantify potential advantages of chasmogamous flowers due to inbreeding depression and heterosis.

evolutionary biology↗

bioRxiv2019

Genetic and physiological mechanisms of freezing tolerance in locally adapted populations of a winter annual

Premise of the studyDespite myriad examples of local adaptation, the phenotypes and genetic variants underlying such adaptive differentiation are seldom known. Recent work on freezing tolerance and local adaptation in ecotypes of Arabidopsis thaliana from Sweden and Italy provides the essential foundation for uncovering the genotype-phenotype-fitness map for an adaptive response to a key environmental stress.\n\nMethodsHere we examine the consequences of a naturally occurring loss of function (LOF) mutation in an Italian allele of the gene that encodes the transcription factor CBF2, which underlies a major freezing tolerance locus. We used four lines with a Swedish genetic background, each containing a LOF CBF2 allele. Two lines had introgression segments containing of the Italian CBF2 allele, and two were created using CRISPR-Cas9. We used a growth chamber experiment to quantify freezing tolerance and gene expression both before and after cold acclimation.\n\nKey resultsFreezing tolerance was greater in the Swedish (72%) compared to the Italian (11%) ecotype, and all four experimental CBF2 LOF lines had reduced freezing tolerance compared to the Swedish ecotype. Differential expression analyses identified ten genes for which all CBF2 LOF lines and the IT ecotype showed similar patterns of reduced cold responsive expression compared to the SW ecotype.\n\nConclusionsWe identified ten genes that are at least partially regulated by CBF2 that may contribute to the differences in cold acclimated freezing tolerance between the Italian and Swedish ecotypes. These results provide novel insight into the molecular and physiological mechanisms connecting a naturally occurring sequence polymorphism to an adaptive response to freezing conditions.

evolutionary biology↗