Sam Yeaman

A simulation-based method for genotype-environment association analysis

This paper introduces SimGEA, a simulation-based method for genotype-environment association analysis that controls false discovery rates while maintaining statistical power.

A conundrum of pleiotropy: GWAS-derived pleiotropy is weakly negatively associated with co-expression network centrality in Arabidopsis thaliana

The Genomic Architecture of Local Adaptation in Two Connected Populations of Three-Spined Stickleback.

This study examines how recombination and structural variants contribute to local adaptation in three-spined sticklebacks, finding population-specific recombination shifts and associations between structural variants, reduced recombination, and genomic differentiation.

Replicated hybrid zones reveal genomic patterns of local adaptation and introgression in spruce

The paper compares genomic patterns of adaptation and introgression in two replicated hybrid zones of spruce, finding similar differentiation and directional introgression despite different environmental gradients.

Polygenic and redundant architectures of climate-adaptive traits may complicate genomic predictions of maladaptation

The paper investigates the genetic architecture of climate-adaptive traits in Douglas-fir, finding polygenic and redundant patterns that complicate genomic predictions of maladaptation to future climates.

Maintenance of polymorphism in spatially heterogeneous environments

The paper develops a theoretical method to analyze complex spatially heterogeneous population models and shows that high environmental spatial autocorrelation promotes the maintenance of locally adaptive alleles.

Genetic architecture underlying response to the fungal pathogen Dothistroma septosporum in lodgepole pine, jack pine, and their hybrids

This study identifies genetic factors underlying resistance to Dothistroma septosporum in lodgepole pine, jack pine, and their hybrids using genome-wide association analysis.

Repeated global adaptation across plant species

This study identifies gene families involved in repeated global adaptation across 17 plant species, showing reduced pleiotropy and increased gene duplication compared to local adaptation.

The persistence of locally adapted polymorphisms under mutation swamping

This paper develops a mathematical model to analyze how mutation swamping affects genetic architecture under varying mutation rates and selection pressures, finding a threshold mutation rate range of 10^-3 to 10^-2.

Impacts of pleiotropy and migration on repeated genetic adaptation

This study uses simulations to show that migration increases repeated genetic adaptation despite pleiotropy, suggesting repeatability is more common in local adaptation than global adaptation.

Genomic signatures of selection associated with benzimidazole drug treatments in Haemonchus contortus field populations

This study identifies genomic signatures of benzimidazole drug resistance in Haemonchus contortus using field populations with defined treatment histories, showing the isotype-1 β-tubulin gene as the primary resistance locus.

Haploid, diploid, and pooled exome capture recapitulate features of biology and paralogy in two non-model tree species

The paper uses pool-seq and exome capture to identify SNPs in two conifer species, showing high correlation between pooled and individual sequencing with improved accuracy using haploid tissue.

Partial genome assembly of the medicinal plant Ephedra sinica.

The paper reports a partial genome assembly of Ephedra sinica using Illumina short-read sequencing at low coverage.

rearrvisr: an R package to detect, classify, and visualize genome rearrangements

rearrvisr detects, classifies, and visualizes genome rearrangements by projecting them onto a reference genome, achieving high precision and recall on simulated data.

A Novel Post Hoc Method For Detecting Index Switching Finds No Evidence For Increased Switching On The Illumina HiSeq X

The paper tests for index switching in Illumina HiSeq sequencing data and finds no evidence of increased switching on HiSeq X.