Publications

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

EB Josephs, ML Van Etten, A Harkess, A Platts, RS Baucom

Evolution Letters (2021)

In collaboration with Gina Baucom’s lab at the University of Michigan, we investigated the potential for gene expression responses to herbicide to be adaptive. We used gene expression data from plants that had been grown with and without herbicide, along with expression data from artificial selection experiments for herbicide resistance to show that expression responses are often likely beneficial

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The evolutionary forces shaping cis- and trans-regulation of gene expression in a population of outcrossing plants

EB Josephs, YW Lee, CW Wood, DJ Schoen, SI Wright, and JR Stinchcombe

MBE (2020)

We detected loci that affect the expression of nearby genes (cis-eQTLs) and of far away genes (trans-eQTLs) and compared their allele frequencies and other signatures of selection to show that negative selection acts more strongly on trans-eQTLs than cis-eQTLs. We also developed a method using coexpression networks to identify loci that affected the expression of large modules of genes with correlated expression

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

EB Josephs, JJ Berg, J Ross-Ibarra, G Coop

Genetics (2019)

We developed a method to detect local adaptation in diverse samples that have been genotyped and phenotyped in common garden. Specifically, we look for excess trait differentiation along the principal components of relatedness beyond an expectation based on neutral genetic drift. We then applied these methods to detect adaptation in domesticated maize.

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The relationship between selection, network connectivity, and regulatory variation within a population of Capsella grandiflora

EB Josephs, SI Wright, JR Stinchcombe, DJ Schoen

Genome Biology and Evolution (2017)

We used leaf expression data to construct coexpression networks that describe the correlation in expression between genes. Connectivity in these networks was associated with both the strength of negative selection on gene sequence and the presence of local regulatory variants (‘eQTLs’)

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What can genome-wide association studies tell us about the evolutionary forces maintaining genetic variation for quantitative traits?

EB Josephs, JR Stinchcombe, SI Wright

New Phytologist (2017)

A review of techniques and best practices for understanding the maintenance of genetic variation using population and quantitative genetics

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Association mapping reveals the role of purifying selection in the maintenance of genomic variation in gene expression

EB Josephs, YW Lee, JR Stinchcombe, SI Wright

PNAS (2015)

We identified genetic variants that control gene expression and showed that purifying (or negative) selection acts on these variants based on patterns of allele frequency and effect sizes.

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Evidence for widespread positive and negative selection in coding and conserved noncoding regions of Capsella grandiflora

RJ Williamson, EB Josephs, AE Platts, KM Hazzouri, A Haudry, M Blanchette, SI Wright.

Plos Genetics (2014)

We analyzed population genetic signatures of selection in Capsella and showed that selection is important in shaping genomic variation.

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