Daniel I. Bolnick

This study examines parallel evolution of nuclear OXPHOS genes in threespine stickleback across freshwater populations and identifies mitonuclear evolutionary coupling in specific functional modules.

The paper uses single-cell RNAseq and population genomic data to show that immune cell types have faster evolutionary divergence in their characteristic genes compared to non-immune cell types.

The paper shows host immune strategies affect parasite transmission timing and magnitude in a helminth parasite, with intermediate parasite burdens maximizing transmission potential.

The paper reared stickleback embryos from 27 lake populations in a lab to determine if trait-environment correlations reflect heritable evolution or plasticity, finding both heritable and plastic traits.

The paper investigates immune variation in threespine stickleback populations by analyzing fibrosis responses to parasites and environmental factors.

This paper investigates how pooling data from different biological populations affects gene co-expression network analysis and finds that it disrupts module structure and is undetectable by common metrics.

The paper creates a cell atlas and organoid model for threespine stickleback intestines, characterizing cell types and developing a functional experimental system.

This study examines metabolome variation in threespine stickleback across populations, showing both genetic and environmental influences on liver metabolites.

This study uses ddPCR and Bayesian path analysis to link land-use changes to parasite dynamics in freshwater ecosystems, finding a positive correlation between deforestation and copepod density.

This study assesses antimicrobial resistance in freshwater fish by integrating molecular measurements with geospatial modeling to identify environmental factors linked to AMR gene distribution.

The paper tests mating patterns in replicated secondary contact experiments and finds disassortative mating instead of expected assortative mating or reproductive isolation.

This study shows that gene network centrality influences parallel evolution and local adaptation in wild yeast by affecting which genes evolve in parallel or show adaptive fitness effects.

The paper examines gene regulation changes in threespine stickleback populations with varying resistance to a freshwater cestode, showing population-specific transcriptomic responses and the role of fibrosis in parasite defense.

This study tests the use of vivo-morpholino oligonucleotides for gene knockdown in threespine stickleback, showing successful knockdown of Spi1b but inconsistent effects for other genes.

This study introduces >12,000 threespine stickleback into nine lakes to test if environmental matching or intrinsic population traits predict introduction success, finding intrinsic traits are more important.

The paper tests macroevolutionary stability of transcriptomic responses to an immune challenge across 15 jawed fish species, finding inconsistent gene expression patterns despite conserved phenotypic responses.

This study shows that lake size influences how body mass relates to gut microbiota diversity in threespine stickleback fish, with intermediate-sized lakes showing the most diverse microbiota.

This study shows warming reshapes PFAS tissue concentrations and distribution, influencing fish energy-allocation trade-offs.

This study shows rapid genome-wide adaptive introgression in threespine stickleback following immigration, with beneficial alleles driving evolutionary change.

Hi-reComb estimates recombination maps from bulk gamete Hi-C data, showing accurate results in fish sperm and enabling structural variant analysis.

The paper develops a droplet digital PCR assay to detect and quantify rare helminth parasites in environmental samples, demonstrating its sensitivity and applicability across multiple helminth systems.

The paper tests if local adaptation of yeast affects community composition and performance, finding it shapes composition but not performance.

This study identifies population-level differences in the proteome of Schistocephalus solidus, including excretory/secretory proteins, suggesting potential adaptations to host genetic variation.

The paper investigates how winter environment affects immune gene expression and energy storage in wood frogs, finding constitutive immune upregulation in those from harsher ancestral winters.

This study tracks the eco-evolutionary dynamics of tapeworm infection and fibrosis immune response in marine stickleback over 50 years in a freshwater pond, showing increased immunity reduced infection rates.

The paper introduces snQTL, a network-based method to map QTLs affecting gene co-expression networks, demonstrating its effectiveness in stickleback data by uncovering missed candidate genes.

This study shows hybridization and gene flow alter gene co-expression networks by creating spurious correlations due to linkage disequilibrium and migration rates, not functional relationships.

The paper experimentally studies host-parasite dynamics in newly founded stickleback populations, finding destabilized infection rates and rapid eco-evolutionary responses.