Emily B. Josephs

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

This study examines introgressive hybridization in introduced urban Capsella bursa-pastoris, finding evidence of diploid C. rubella introgression contributing to genetic diversity.

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

This study examines how two Arabidopsis thaliana populations from different climates respond to heat and drought, finding conserved plasticity in drought response despite population-specific strategies.

The Euler Characteristic Transform Enables Classification of Complex Plant Shapes and Prediction of Leaf Venation from Blade Geometry

This paper introduces the Euler Characteristic Transform (ECT) for classifying plant shapes and predicting leaf venation from blade geometry using deep learning.

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

This study shows that high urban heat limits fruit morphology and reproduction in Capsella bursa-pastoris but not growth or survival.

Procrustean pseudo-landmark methods in Python to measure massive quantities of leaf shape data

The paper introduces a Python-based method using pseudo-landmarks and Procrustes analysis to compare leaf shapes across species and development, showing shape transitions and genetic correlations.

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

The paper compares machine learning models and summary statistics for inferring fixation times of hard sweeps and finds no significant improvement from machine learning.

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

SWIF-TE identifies novel transposable element insertions from short read data with high efficiency and precision.

Evaluating the Roles of Drift and Selection in Trait Loss along an Elevational Gradient

The paper investigates the roles of genetic drift and selection in the loss of short stamens in Arabidopsis thaliana along an elevational gradient and identifies different genetic loci associated with this trait variation.

Structural variants contribute to phenotypic variation in maize

The paper identifies structural variants in maize using whole genome alignment and short-read sequencing, linking them to life history traits and genotype-by-environment interactions.

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

This study uses geometric morphometric modeling to show that Capsella bursa-pastoris leaf shape variation is strongly linked to temperature, with no change in variation over 100 years.

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

The paper investigates Lewontin's paradox by comparing k-mer-based and SNP-based genetic diversity metrics across 112 plant species, finding that k-mer diversity scales more strongly with population size.

Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris

This study investigates the early stages of diploidization in Capsella bursa-pastoris, finding that gene loss is not rapid but rather associated with reduced selection efficacy due to demographic and genomic factors.