Biology subjects

Josephs, E. B.

Publications and source records attributed to Josephs, E. B..

11 recordsLinked to original sources

bioRxiv2026

Introgression across ploidies contributes to genetic diversity in introduced urban Capsella bursa-pastoris

Successful establishment of a species in a new range is a useful way to understand the impact of demography and selection on the evolution of globally distributed species. In particular, introductions influence genetic diversity and population structure in the introduced range in unpredictable ways. Additionally, introgressive hybridization is often associated with successful establishment in new ranges. In this study, we explore the impact of introgressive hybridization on the polyploid Capsella bursa-pastoris in the New York City metropolitan area. We find Capsella bursa-pastoris in the New York City metropolitan area likely originated from multiple introductions from northern Eurasia, and that populations across the New York City metropolitan area are generally panmictic. As with Capsella bursa-pastoris in Eurasia, we discover evidence of introgression from the diploid Capsella rubella in this population. By evaluating ancestry in regions across the genome, we find introgressed regions are rich in gene content and contribute to genetic diversity in this population. These results suggest that introgressive hybridization before introductions may buffer species from the negative effects of population bottlenecks and allow for successful establishment. SignificanceGene flow between groups of different ploidies is known to occur in natural systems, but has been understudied in evolutionary genetics until recently. In this study, we show that an introduced population of the allotetraploid Capsella bursa-pastoris contains introgressed material from the diploid C. rubella. The introgressed regions of the genome have a high degree of diversity suggesting that introgression from C. rubella to C. bursa-pastoris may have contributed to the overall high degree of diversity in the species. Understanding the evolutionary impact of gene flow between ploidies is an important step to identifying what makes some polyploid lineages successful.

plant biology↗

bioRxiv2026

Heat alters fruit morphology and severely limits reproduction but not growth in a widespread urban weed.

O_LIRationale: Plants in urban environments often experience heat stress and responses to heat stress often include vegetative and reproductive traits like rosette width and fruit morphology. However, our understanding of natural variation in vegetative and reproductive traits in urban environments is severely limited. C_LIO_LIMethods: We grew an urban weed, Capsella bursa-pastoris, in common garden environments that simulate an urban heat gradient to determine how heat affected growth, survival and reproduction. Additionally, we used geometric morphometric techniques alongside deterministic techniques to quantify variation in C. bursa-pastoris fruit shape and investigated the predictive relationship between fruit shape and seed production. C_LIO_LIKey results: We found that temperatures above 30C act as an environmental constraint on both C. bursa-pastoris fruit shape and reproduction, resulting in malformed fruits and no seed production. However, leaf number and plant survival were unaffected by high urban heat. C_LIO_LIMain conclusions: While plants may grow and survive in the high urban heat, heat could still limit population persistence. C_LI

plant biology↗

bioRxiv2026

Summary statistics and approximate bayesian computation are comparable to convolutional neural networks for inferring times to fixation

Detecting signatures of positive selection in genomes is a common application of population genetics and one of the most influential models for this task is the hard selective sweep where a de novo mutation rapidly fixes. Many statistics have been developed to detect hard sweeps, often attempting to summarize signatures left behind in the site frequency, spectrum, linkage disequilibrium, and haplotype frequency. However, potentially undiscovered signals could still exist. We attempted to test whether any undiscovered signatures of hard sweeps exist by comparing machine learning models, which can learn signatures from raw data without any prior knowledge, to known summary statistics for inferring the time to fixation (tf) of a hard sweep in a background of variable sweep ages (ta). Across approximately 200,000 simulations encompassing 5 different demographic scenarios of single panmictic populations, machine learning models trained directly on raw genotype data failed to better predict tf than methods based purely on common summary statistics. This suggests few undiscovered signals remain in single timepoint, single population genotype data that can better disentangle tf and ta of hard sweeps.

evolutionary biology↗

bioRxiv2026

Differentiation for drought strategy but conserved plasticity to heat and drought in locally adapted populations of Arabidopsis thaliana

Background and AimsAdaptive plasticity may be crucial for plants to survive rapid environmental changes long enough for evolutionary adaptation to occur. Heat and drought are both abiotic stresses projected to increase globally and their individual impact on plant growth and function is well-characterized. However, to understand potential responses to climate change, we must manipulate multiple stressors simultaneously. MethodsWe measured heat- and drought-related traits as well as fitness in two locally adapted populations of Arabidopsis thaliana from Rod[a]sen, Sweden and Castelnuovo di Porto, Italy. We used chamber common gardens that simulate the current fall and spring climate in Sweden and a hotter and drier climate to identify population differentiation for trait means, trait plasticity, and fitness. Key ResultsPopulation differentiation in both treatments suggests that the Swedish population avoids drought by investing in stress-tolerant leaves while the Italian population escapes drought by flowering early. Despite these differences, there is little evidence for genetic differentiation of plasticity; when experiencing heat and drought, both populations shift their traits in the direction expected to avoid drought. Further, both populations have greatly decreased fitness in heat and drought. ConclusionsThese results highlight that locally adapted populations with genetic differentiation for traits within a single environment can respond to the same stressors with plasticity in the same direction. Further, the combination of heat and drought will be extremely damaging to plant populations. Lay SummaryPlant populations respond to environmental stress in different ways, and their response can determine their survival. We found that plant populations that have evolved different drought responses in their native environments still have the same drought response in an experimental hot and dry environment. Both populations also make many fewer fruits, indicating they may decline in future climates.

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↗

bioRxiv2024

Previously unmeasured genetic diversity explains part of Lewontin's paradox in a k-mer-based meta-analysis of 112 plant species

At the molecular level, most evolution is expected to be neutral. A key prediction of this expectation is that the level of genetic diversity in a population should scale with population size. However, as was noted by Richard Lewontin in 1974 and reaffirmed by later studies, the slope of the population size-diversity relationship in nature is much weaker than expected under neutral theory. We hypothesize that one contributor to this paradox is that current methods relying on single nucleotide polymorphisms (SNPs) called from aligning short reads to a reference genome underestimate levels of genetic diversity in many species. To test this idea, we calculated nucleotide diversity ({pi}) and k-mer-based metrics of genetic diversity across 112 plant species, amounting to over 205 terabases of DNA sequencing data from 27,488 individual plants. We then compared how these different metrics correlated with proxies of population size that account for both range size and population density variation across species. We found that our population size proxies scaled anywhere from about 3 to over 20 times faster with k-mer diversity than nucleotide diversity after adjusting for evolutionary history, mating system, life cycle habit, cultivation status, and invasiveness. The relationship between k-mer diversity and population size proxies also remains significant after correcting for genome size, whereas the analogous relationship for nucleotide diversity does not. These results suggest that variation not captured by common SNP-based analyses explains part of Lewontins paradox in plants. Lay SummaryEven after many revolutions in our ability to sequence and understand DNA, many important biological questions remain unsolved. One such problem is Lewontins paradox, named after Richard Lewontin who first described it in 1974. The core of the paradox is a simple idea: species with more individuals should be more genetically diverse. The reasoning is that more individuals means more replication of DNA, and thus more opportunities for mutation to create new variation. However, species that differ massively in population size often have similar diversity levels. Lewontins paradox has several potential, previously investigated mechanisms but what if one contributor is simply that our measurements of genetic diversity are off? Most studies estimate diversity by comparing sample genomes to a standard reference genome. While this approach is useful, it is impossible to measure variation in DNA that is not represented in the reference - a phenomenon known as reference bias. We estimate metrics of diversity that are free of reference-bias and re-investigate Lewontins paradox in plants. Overall, we find that reference-free diversity metrics scale more with population size, compared to the reference-biased approach. While it is unlikely that reference-bias fully explains Lewontins paradox, our analyses suggest that reference-bias plays an important role.

evolutionary biology↗

bioRxiv2024

Herbarium specimens reveal links between Capsella bursa-pastoris leaf shape and climate

O_LIStudies into the evolution and development of leaf shape have connected variation in plant form, function, and fitness. For species with consistent leaf margin features, patterns in leaf architecture are related to both biotic and abiotic factors. However, for species with inconsistent leaf margin features, quantifying leaf shape variation and the effects of environmental factors on leaf shape has proven challenging. C_LIO_LITo investigate leaf shape variation in species with inconsistent shapes, we analyzed approxi-mately 500 digitized Capsella bursa-pastoris specimens collected throughout the continental U.S. over a 100-year period with geometric morphometric modeling and deterministic techniques. We generated a morphospace of C. bursa-pastoris leaf shapes and modeled leaf shape as a function of environment and time. C_LIO_LIOur results suggest C. bursa-pastoris leaf shape variation is strongly associated with temperature over the C. bursa-pastoris growing season, with lobing decreasing as temperature increases. While we expected to see changes in variation over time, our results show that level of leaf shape variation is consistent over the 100-year period. C_LIO_LIOur findings showed that species with inconsistent leaf shape variation can be quantified using geometric morphometric modeling techniques and that temperature is the main environmental factor influencing leaf shape variation. C_LI

plant biology↗

bioRxiv2020

Local adaptation contributes to gene expression divergence in maize

Gene expression links genotypes to phenotypes, so identifying genes whose expression is shaped by selection will be important for understanding the traits and processes underlying local adaptation. However, detecting local adaptation for gene expression will require distinguishing between divergence due to selection and divergence due to genetic drift. Here, we adapt a QST -FST framework to detect local adaptation for transcriptome-wide gene expression levels in a population of diverse maize genotypes. We compare the number and types of selected genes across a wide range of maize populations and tissues, as well as selection on cold-response genes, drought-response genes, and coexpression clusters. We identify a number of genes whose expression levels are consistent with local adaptation and show that genes involved in stress-response show enrichment for selection. Due to its history of intense selective breeding and domestication, maize evolution has long been of interest to researchers, and our study provides insight into the genes and processes important for in local adaptation of maize.

evolutionary biology↗

bioRxiv2019

Common genetic variants shape broad patterns of within-population variation in gene expression.

Understanding the persistence of genetic variation within populations has long been a goal of evolutionary biology. One promising route towards achieving this goal is using population genetic approaches to describe how selection acts on the loci associated with trait variation. Gene expression provides a model trait for addressing the challenge of the maintenance of variation because it can be measured genome-wide without information about how gene expression affects traits. Previous work has shown that loci affecting the expression of nearby genes (local or cis-eQTLs) are under negative selection, but we lack a clear understanding of the selective forces acting on variants that affect the expression of genes in trans. Here, we identify loci that affect gene expression in trans using genomic and transcriptomic data from one population of the obligately outcrossing plant, Capsella grandiflora. The allele frequencies of trans-eQTLs are consistent with stronger negative selection acting on trans-eQTLs than cis-eQTLs, and even more strongly on trans-eQTLs associated with the expression of multiple genes. However, despite this general pattern, we still observe the presence of a trans-eQTL at intermediate frequency that affects the expression of a large number of genes in the same coexpression module. Overall, our work highlights the different selective pressures shaping variation in cis- and trans- gene regulation.

evolutionary biology↗

bioRxiv2018

Detecting adaptive differentiation in structured populations with genomic data and common gardens

Adaptation in quantitative traits often occurs through subtle shifts in allele frequencies at many loci, a process called polygenic adaptation. While a number of methods have been developed to detect polygenic adaptation in human populations, we lack clear strategies for doing so in many other systems. In particular, there is an opportunity to develop new methods that leverage datasets with genomic data and common garden trait measurements to systematically detect the quantitative traits important for adaptation. Here, we develop methods that do just this, using principal components of the relatedness matrix to detect excess divergence consistent with polygenic adaptation and using a conditional test to control for confounding effects due to population structure. We apply these methods to inbred maize lines from the USDA germplasm pool and maize landraces from Europe. Ultimately, these methods can be applied to additional domesticated and wild species to give us a broader picture of the specific traits that contribute to adaptation and the overall importance of polygenic adaptation in shaping quantitative trait variation.

evolutionary biology↗

bioRxiv2018

Transposable elements are important contributors to standing variation in gene expression in Capsella grandiflora

Transposable elements (TEs) make up a significant portion of eukaryotic genomes, and thus are important drivers of genome evolution. However, the evolutionary forces controlling TE copy number and the extent to which TEs affect phenotypic variation on a genome-wide scale are still unclear. We characterised TE insertion polymorphism and its effects on gene expression in 124 whole genome sequences from a single population of Capsella grandiflora. The frequency of insertions was negatively correlated with distance to genes, as well as density of conserved non-coding elements, suggesting that the negative effects of TEs on gene regulation are important in limiting their abundance. Rare TE variants strongly influence gene expression variation, predominantly through downregulation. In contrast, rare single nucleotide polymorphisms (SNPs) contribute equally to up- and down-regulation, but have a weaker effect. Taken together, these results imply that TEs are a significant contributor to gene expression variation and can be more likely than rare SNPs to cause extreme changes in gene expression.\n\nAuthor SummaryTransposable elements (TEs), mobile DNA elements with the ability to excise from the genome and reinsert in new locations, are important components of genomic diversity. Due to their abundance and mobility, TEs play an influential role in genomic evolution, often deleterious. Here we show that TEs in a population of the plant Capsella grandiflora are most deleterious when they insert in genic and regulatory regions. We find that TEs indeed are associated with unusual levels of gene expression, predominantly decreased expression.\n\nFurthermore, this effect is stronger than the association of single nucleotide polymorphisms with gene expression variation, highlighting the importance of TE contribution to the maintenance of expression variation.

evolutionary biology↗