N. L. Clark

Overlapping enhancer activity robustly regulates rax expression during ocular development in zebrafish

This study identifies five novel ocular enhancers in zebrafish that regulate rax expression during eye development and shows their robustness to perturbations.

HyphAeon: Attention on Evolution Across Deep Time Transforms Comparative Genomics

HyphAeon is a transformer model that accelerates detection of episodic diversifying selection in mammalian genomes and enables new analytical capabilities beyond traditional dN/dS methods.

Sperm competition intensity shapes divergence in both sperm morphology and reproductive genes across murine rodents

This study examines how sperm competition intensity influences sperm morphology and reproductive gene evolution across murine rodents, finding that smaller testes correlate with faster molecular evolution due to relaxed selection.

Evolutionary Rate Covariation is a reliable predictor of co-functional interactions but not necessarily physical interactions

This study investigates whether evolutionary rate covariation (ERC) signals reflect physical interactions or other factors, finding weak evidence for physical coevolution and suggesting selective pressures may drive the signal.

Reduction of Paraoxonase expression followed by inactivation across independent semiaquatic mammals suggests stepwise path to pseudogenization

The paper shows that reduced expression and inactivation of the Pon1 gene in aquatic/semiaquatic mammals precedes pseudogenization, suggesting a stepwise loss of function linked to environmental adaptation.

Highly Dynamic Gene Family Evolution Suggests Changing Roles for PON Genes Within Metazoa

The paper investigates the dynamic evolution of the PON gene family across metazoa, identifying multiple expansion and loss events in different lineages and suggesting environmental factors like pathogen infection and oxidative stress as drivers.

A cautionary tale on proper use of branch-site models to detect convergent positive selection

The paper warns against misinterpreting branch-site models in comparative genomics, showing how failing to distinguish phylogeny-wide from branch-specific positive selection leads to false inferences and proposes a 'drop-out' test to address this issue.

Robust methods for detecting convergent shifts in evolutionary rates

The paper improves a method for detecting convergent evolutionary rate shifts by addressing statistical limitations through data transformation and weighted regression.

RERconverge: an R package for associating evolutionary rates with convergent traits

RERconverge associates evolutionary rates with convergent traits across phylogenies, supporting binary and continuous traits with visualization and enrichment tools.