We study how duplicated genes diverge in function following duplication events, a process known as paralog subfunctionalization. Our work spans both genome-wide duplications, such as whole nuclear genome duplication, and gene-level processes including tandem duplication. By integrating comparative genomics, phylogenetic analyses, and functional data, we examine how ancestral functions are partitioned among paralogs, shaping molecular interactions, regulatory networks, and evolutionary innovation.

We investigate duplication of rpoB, the gene encoding the β-subunit of RNA polymerase, in acid-fast bacteria and its potential consequences for antibiotic resistance. Because rpoB is the primary target of rifampin, gene duplication may provide a mechanism for buffering essential transcriptional function while permitting sequence divergence, altered dosage, or functional partitioning. Using comparative genomics and evolutionary analyses, we examine how rpoB duplication may facilitate persistence and adaptive responses to rifampin exposure in pathogenic and environmental mycobacteria.

We investigate how biodiversity evolves in extreme environments. In a recent study, we used dense nuclear genomic sampling to reconstruct the first robust phylogeny of Lake Baikal sculpins, one of the world’s most remarkable adaptive radiations. We found that pelagic, bathybenthic, and lotic ecomorphologies evolved multiple times, each with striking shifts in body form and life history. Our results highlight depth and habitat as key drivers of diversification, while underscoring urgent conservation concerns.

Lentic waters of the Gulf-Atlantic Coastal Plain (GACP) include some of the most acidic environments found in subtropical latitudes. Fishes of this ecoregion have adapted to life in hyperthermal, hypoxic, and hyperacidic conditions, and natural selection may have influenced the physiology of independent lineages in a similar fashion. We are examining the evolution of the Electron Transport Chain to assess the functional consequences of extraordinary mtDNA variation observed in certain lentic fishes of the GACP.

In collaboration with academic and agency partners, we examine how energy budgets shape adaptation in extreme environments. Our work on cave-adapted sculpins, amblyopsid cavefishes, and nemacheilid loaches shows repeated evolutionary changes to the electron transport chain, reflecting metabolic adjustments to life in darkness and nutrient scarcity. These shifts parallel reductions in costly traits like vision and pigmentation, highlighting trade-offs that optimize survival underground. By integrating genomics and physiology, we are uncovering how natural selection rewires cellular energetics during extreme ecological transitions.

We investigate feral fish populations derived from the ornamental aquaculture trade to understand the long-term evolutionary consequences of domestication and release. Many of these populations retain advertent phenotypes (traits deliberately selected during domestication) at frequencies far higher than expected following establishment in the wild, with some persisting for more than three decades. By integrating field surveys, phylogenomics, and functional analyses, we examine why these domestication-associated traits are maintained, testing whether they reflect relaxed selection, genetic constraint, pleiotropy, or unanticipated adaptive value in novel environments.