Biology subjects

Josephs, E.

Publications and source records attributed to Josephs, E..

6 recordsLinked to original sources

bioRxiv2025

SWIF-TE: identifying novel transposable element insertions from short read data

Transposable element (TE) insertion polymorphisms (TIPs) are TEs not in the same location between individuals. TIPs have contributed to genomic and phenomic variation but have been historically difficult to study due to their repetitive nature. Here, we describe a fast and memory-efficient tool to identify novel TIPs from short read sequences. SWIF-TE was able to identify 1,438 insertions at a precision rate of 27% using 0.10 Gb of memory and 0.82 hours of runtime from 15x resequencing data of a non-reference maize inbred. SWIF-TE is a powerful tool for studying TE variation in species with TE-rich genomes.

bioinformatics↗

bioRxiv2022

Weaker selection on genes with treatment-specific expression may limit plasticity evolution in Arabidopsis thaliana

Differential gene expression between environments often underlies phenotypic plasticity. However, environment-specific expression patterns are hypothesized to relax selection on genes, and thus limit plasticity evolution. We collated over 27 terabases of RNA-sequencing data on Arabidopsis thaliana from over 300 peer-reviewed studies and 200 treatment conditions to investigate this hypothesis. Consistent with relaxed selection, genes with more treatment-specific expression have higher levels of nucleotide diversity and divergence at nonsynonymous sites but lack stronger signals of positive selection. This result persisted even after controlling for expression level, gene length, GC content, the tissue specificity of expression, and technical variation between studies. Overall, our investigation supports the existence of a hypothesized trade-off between the environment specificity of a genes expression and the strength of selection on said gene in A. thaliana. Future studies should leverage multiple genome-scale datasets to tease apart the contributions of many variables in limiting plasticity evolution.

evolutionary biology↗

bioRxiv2022

Seasonal models reveal niche changes in Capsella bursa-pastoris

Researchers often use ecological niche models to predict where species might establish and persist under future or novel climate conditions. However, these predictive methods assume species have stable niches across time and space. Furthermore, ignoring the time of occurrence data can obscure important information about species reproduction and ultimately fitness. In this study, we generate full-year and monthly ecological niche models for Capsella bursa-pastoris to see if we can detect changes in the seasonal niche of the species after long-distance dispersal. We find full-year ecological niche models have low transferability across continents and there are continental differences in the climate conditions that influence the distribution of C. bursa-pastoris. Monthly models have greater predictive accuracy than full-year models in cooler seasons, but the inability of any model to predict summer occurrence in North America suggests a change in the seasonal niche from the native range to the non-native range. These results highlight the utility of ecological niche models at finer temporal scales in predicting species distributions and unmasking subtle patterns of evolution.

ecology↗

bioRxiv2022

Ramp-shaped neural tuning supports graded population-level representation of the object-to-scene continuum

We can easily perceive the spatial scale depicted in a picture, regardless of whether it is a small space (e.g., a close-up view of a chair) or a much larger space (e.g., an entire class room). How does the human visual system encode this continuous dimension? Here, we investigated the underlying neural coding of depicted spatial scale, by examining the voxel tuning and topographic organization of brain responses. We created naturalistic yet carefully-controlled stimuli by constructing virtual indoor environments, and rendered a series of snapshots to smoothly sample between a close-up view of the central object and far-scale view of the full environment (object-to-scene continuum). Human brain responses were measured to each position using functional magnetic resonance imaging. We did not find evidence for a smooth topographic mapping for the object-to-scene continuum on the cortex. Instead, we observed large swaths of cortex with opposing ramp-shaped profiles, with highest responses to one end of the object-to-scene continuum or the other, and a small region showing a weak tuning to intermediate scale views. Importantly, when we considered the multi-voxel patterns of the entire ventral occipito-temporal cortex, we found smooth and linear representation of the object-to-scene continuum. Thus, our results together suggest that depicted spatial scale is coded parametrically in large-scale population codes across the entire ventral occipito-temporal cortex.

neuroscience↗

bioRxiv2020

Adaptive and maladaptive expression plasticity underlying herbicide resistance in an agricultural weed.

Plastic phenotypic responses to environmental change are common, yet we lack a clear understanding of the fitness consequences of these plastic responses. Here, we use the evolution of herbicide resistance in the common morning glory (Ipomoea purpurea) as a model for understanding the relative importance of adaptive and maladaptive gene expression responses to herbicide. Specifically, we compare leaf gene expression changes caused by herbicide to the expression changes that evolve in response to artificial selection for herbicide resistance. We identify a number of genes that show plastic and evolved responses to herbicide and find that for the majority of genes with both plastic and evolved responses, plastic responses appear to be adaptive. We also find that selection for herbicide response increases gene expression plasticity. Overall, these results show the importance of adaptive plasticity for herbicide resistance in a common weed and that expression changes in response to strong environmental change can be adaptive. Impact statementPredicting whether and how organisms will adapt to environmental change is a crucial goal. However, this goal can be complicated because environmental change can alter traits, in a process called plasticity. The extent and fitness consequences of plasticity will have important effects on the adaptive process. In this study, we use adaptation to herbicide in the agricultural weed, the common morning glory, as a model for understanding the extent and fitness consequences of plasticity in gene expression. We find evidence that gene expression plasticity is adaptive in the presence of herbicide, suggesting that understanding plasticity is crucial for understanding how organisms adapt to new environments.

evolutionary biology↗

bioRxiv2020

Molecular Parallelism Underlies Convergent Highland Adaptation of Maize Landraces

Convergent phenotypic evolution provides some of the strongest evidence for adaptation. However, the extent to which recurrent phenotypic adaptation has arisen via parallelism at the molecular level remains unresolved, as does the evolutionary origin of alleles underlying such adaptation. Here, we investigate genetic mechanisms of convergent highland adaptation in maize landrace populations and evaluate the genetic sources of recurrently selected alleles. Population branch excess statistics reveal strong evidence of parallel adaptation at the level of individual SNPs, genes and pathways in four independent highland maize populations, even though most SNPs show unique patterns of local adaptation. The majority of selected SNPs originated via migration from a single population, most likely in the Mesoamerican highlands. Polygenic adaptation analyses of quantitative traits reveal that alleles affecting flowering time are significantly associated with elevation, indicating the flowering time pathway was targeted by highland adaptation. In addition, repeatedly selected genes were significantly enriched in the flowering time pathway, indicating their significance in adapting to highland conditions. Overall, our study system represents a promising model to study convergent evolution in plants with potential applications to crop adaptation across environmental gradients.

evolutionary biology↗