Biology subjects

Fenster, C. B.

Publications and source records attributed to Fenster, C. B..

9 recordsLinked to original sources

bioRxiv2023

Scaling the fitness effects of mutations with respect to differentially adapted Arabidopsis thaliana accessions under natural conditions

Mutations are the ultimate source of genetic variation for natural selection to act upon. A major question in evolutionary biology is the extent to which new mutations can generate genetic variation under natural conditions to permit adaptive evolution over ecological time scales. Here we collected fitness data for chemically induced (ethylmethane sulfonate, EMS) mutant lines descended from two Arabidopsis thaliana ecotypes that show differential adaptation to the local environment of our common garden plot. Using a novel nonparametric Bayesian statistical approach, we found that both ecotypes accumulated substantial proportions of beneficial mutations. The poorly adapted ecotype showed higher variance in the fitness effect of mutations than the well-adapted ecotype. Furthermore, we predict that it takes less than 4000 generations for the fitness space of the two ecotypes to overlap through mutation accumulation, and that a single founder, through mutation accumulation, is able to achieve the species-wide genetic variation in less than 10,000 generations. Our results provide evidence for relatively rapid local adaptation of Arabidopsis thaliana in natural conditions through new mutations, as well as the utility of nonparametric Bayesian method for modeling the distribution of fitness effects for field-collected data.

evolutionary biology↗

bioRxiv2022

Report of mutation biases mirroring selection in Arabidopsis thaliana unlikely to be entirely due to variant calling errors

It has recently been proposed that the uneven distribution of epigenomic features might facilitate reduced mutation rate in constrained regions of the Arabidopsis thaliana genome, even though previous work had shown that it would be difficult for reduced mutation rates to evolve on a gene-by-gene basis. A solution to Lynchs equations for the barrier imposed by genetic drift on the evolution of targeted hypomutation can, however, come from epigenomic features that are enriched in certain portions of the genome, for example, coding regions of essential genes, and which simultaneously affect mutation rate. Such theoretical considerations draw on what is known about DNA repair guided by epigenomic features. A recent publication challenged these conclusions, because several mutation data sets that support a lower mutation rate in constrained regions suffered from variant calling errors. Here we show that neither homopolymer errors nor elevated mutation rates at transposable elements are likely to entirely explain reported mutation rate biases. Observed mutation biases are also supported by a meta-analysis of several independent germline mutation data sets, with complementary experimental data providing a mechanistic basis for reduced mutation rate in genes and specifically in essential genes. Finally, models derived from the drift-barrier hypothesis demonstrate that mechanisms linking DNA repair to chromatin marks and other epigenomic features can evolve in response to second-order selection on emergent mutation biases.

evolutionary biology↗

bioRxiv2021

Pleiotropy is associated with fitness consequences of new mutations in mutation accumulation lines

Understanding the mechanisms by which mutations affect fitness and the distribution of mutational effects are central goals in evolutionary biology. Mutation accumulation (MA) lines have long been an important tool for understanding the effect of new mutations on fitness, phenotypic variation, and mutational parameters. However, there is a clear gap in predicting the effect of specific new mutations to their effects on fitness. Here, we complete gene ontology analysis and metabolomics experiments on Arabidopsis thaliana MA lines to determine how spontaneous mutations directly affect global metabolic output in lines that have measured fitness consequences. For these analyses, we compared three lines with relative fitness consistently higher than the unmutated progenitor and three lines with lower relative fitness as measured in four different field trials. In a gene ontology analysis, we find that the high fitness lines were significantly enriched in mutations in or near genes with transcription regulator activity. We also find that although they do not have an average difference in the number of mutations, low fitness lines have significantly more metabolic subpathways disrupted than high fitness lines. Taken together, these results suggest that the effect of a new mutation on fitness depends less on the specific metabolic pathways disrupted and more on the pleiotropic effects of those mutations, and that organisms can explore a considerable amount of physiological space with only a few mutations. Significance StatementAs the source of all genetic variation, new mutations are crucial for understanding how organisms adapt to their environment. However, the ways in which new mutations affect the range of metabolic reactions that occur in the cell is unknown. With a combination of gene functional analyses and measurement of the small molecules that drive cellular function and physiology, we find that mutations associated with high fitness are disproportionately found in or near proteins-coding genes that regulate the specific timing and location of gene expression and are less disruptive of cellular physiology.

evolutionary biology↗

bioRxiv2021

Use of botanical gardens as arks for conserving pollinators and plant-pollinator interactions: A case study from the US Northern Great Plains

Botanical gardens have contributed to plant conservation through the maintenance of both living and preserved plant specimens for decades. However, there is still a large gap in the literature with regards to understanding the potential conservation value botanical gardens could provide for local pollinators. We investigated how plant-pollinator community structure and diversity may differ between botanical gardens and native habitats by sampling and comparing between two environments: a restored native grassland patch within a local botanical garden and fifteen native, remnant temperate grassland sites in the Northern Great Plains. We found pollinator diversity within the restored native grassland patch was greater than 55% of total remnant temperate grassland transects throughout the entire flowering season, while plant diversity and network community metrics between the two environments remained similar throughout, except that remnant prairies have more links (higher connectance) with pollinators than the garden patch. Overall, our findings demonstrate the promising role restored native grassland patches in botanical gardens could play as reservoirs for local pollinator communities by supporting plant-pollinator interactions comparable to those found in native habitat remnants in the same region.

ecology↗

bioRxiv2021

Quantifying habitat and landscape effects on composition and structure of plant-pollinator networks in the US Northern Great Plains

Community structure contributes to ecosystem persistence and stability. To understand the mechanisms underlying pollination and community stability of natural areas in a human influenced landscape, a better understanding of the interaction patterns between plants and pollinators in disturbed landscapes is needed. The Northern Great Plains still retain extensive tracts of remnant temperate grassland habitat within a matrix of varying land-uses. We used a network-based approach to quantify how temperate grassland attributes and landscape heterogeneity influence plant-pollinator community structure in natural habitats. We also quantified pollinator diversity and floral diversity to assess the functional role of temperate grassland attributes and the surrounding landscape on the composition of the plant-pollinator communities in natural habitats. We found that the amount of local nectar sugar and increased proportions of certain land-uses contribute to pollinator diversity that in turn influences the structure of interactions between plants and pollinators. Understanding the factors contributing to plant-pollinator network structure can guide management decisions to support resilient plant-pollinator communities and conserve the stability of pollination services.

ecology↗

bioRxiv2021

Fine-scale Population Structure of North American Arabidopsis thaliana Reveals Multiple Sources of Introduction from Across Eurasia

Large-scale movement of organisms across their habitable range, or migration, is an important evolutionary process that can contribute to observed patterns of genetic diversity and our understanding of the adaptive spread of alleles. While human migrations have been studied in great detail with modern and ancient genomes, recent anthropogenic influence on reducing the biogeographical constraints on the migration of non-native species has presented opportunities in several study systems to ask the questions about how repeated introductions shape genetic diversity in the introduced range. We present here the most comprehensive view of population structure of North American Arabidopsis thaliana by studying a set of 500 (whole-genome sequenced) and over 2800 (RAD-seq genotyped) individuals in the context of global diversity represented by Afro-Eurasian genomes. We use haplotype-sharing, phylogenetic modeling and rare-allele sharing based methods to identify putative sources of introductions of extant N. American A. thaliana from the native range of Afro-Eurasia. We find evidence of admixture among the introduced lineages that has resulted in the increased haplotype diversity and reduced mutational load. Further, we also present signals of selection in the immune-system related genes that impart qualitative disease resistance to pathogens of bacterial and oomycete origins. Thus, multiple introductions to a non-native range can quickly increase adaptive potential of a colonizing species by increasing haplotypic diversity through admixture. The results presented here lay the foundation for further investigations into the functional significance of admixture.

evolutionary biology↗

bioRxiv2020

Quantitative genetic basis of floral design in a natural plant population

The amount of genetic variation of floral traits and the degree to which they are genetically correlated are important parameters for the study of plant evolution. Estimates of these parameters can reveal the effect of historical selection relative to neutral processes such as mutation and drift, and allow us to predict the short-term evolutionary trajectory of a population under various selective regimes. Here, we assess the heritability and genetic correlation of the floral design of a native N. American tetraploid plant, Silene stellata (Caryophyllaceae), in a natural population. Specifically, we use a linear mixed model to estimate the genetic parameters based on a genealogy reconstructed from highly variable molecular markers. Overall, we found significant heritabilities in five out of nine studied traits. The level of heritability was intermediate (0.027 - 0.441). Interestingly, the floral trait showing the highest level of genetic variation was previously shown to be under strong sexually conflicting selection, which may serve as a mechanism for maintaining the observed genetic variation. Additionally, we also found prevalent positive genetic correlations between floral traits. Our results suggest that S. stellata is capable of responding to phenotypic selection on its floral design, while the abundant positive genetic correlations could also constrain the evolutionary trajectories to certain directions. Furthermore, this study demonstrates the utility and feasibility of marker-based approaches for estimating genetic parameters in natural populations.

evolutionary biology↗

bioRxiv2020

Mutation bias shapes gene evolution in Arabidopsis thaliana

Classical evolutionary theory maintains that mutation rate variation between genes should be random with respect to fitness 1-4 and evolutionary optimization of genic mutation rates remains controversial 3,5. However, it has now become known that cytogenetic (DNA sequence + epigenomic) features influence local mutation probabilities 6, which is predicted by more recent theory to be a prerequisite for beneficial mutation rates between different classes of genes to readily evolve 7. To test this possibility, we used de novo mutations in Arabidopsis thaliana to create a high resolution predictive model of mutation rates as a function of cytogenetic features across the genome. As expected, mutation rates are significantly predicted by features such as GC content, histone modifications, and chromatin accessibility. Deeper analyses of predicted mutation rates reveal effects of introns and untranslated exon regions in distancing coding sequences from mutational hotspots at the start and end of transcribed regions in A. thaliana. Finally, predicted coding region mutation rates are significantly lower in genes where mutations are more likely to be deleterious, supported by numerous estimates of evolutionary and functional constraint. These findings contradict neutral expectations that mutation probabilities are independent of fitness consequences. Instead they are consistent with the evolution of lower mutation rates in functionally constrained loci due to cytogenetic features, with important implications for evolutionary biology8.

evolutionary biology↗

bioRxiv2018

Rapid evolution of spontaneous mutation increases genetic diversity facilitating plant population survival

Using a mechanistic eco-evolutionary trait-based neighborhood-model, we quantify the impact of mutations on spatial interactions to better understand the potential effect of niche evolution through mutations on the population dynamics of Arabidopsis thaliana. We use 100 twenty-fifth generation mutation accumulation (MA) lines (genotypes) derived from one founder genotype to study mutational effects on neighbor responses in a field experiment. We created individual-based maps (15,000 individuals), including phenotypic variation, to quantify mutational effects within genotypes versus between genotypes on reproduction and survival. At small-scale, survival is enhanced but reproduction is decreased when a genotype is surrounded by different genotypes. At large-scale, seed set is facilitated by different genotypes while the same genotype has either no effect or negative effects. Mutations may provide a mechanism for plants to quickly evolve niches and may drive competition, facilitation and selection with profound consequences for future population and community dynamics.

ecology↗