Research

The overall structure of the vertebrate eye and many genes essential to eye development are highly conserved across species. Yet species experience different visual environments and must respond to these differences within the constraints of eye development, often through changes in gene expression. Furthermore, many species experience changes in their visual environment across ontogeny, or as they develop from juvenile to adult stages, and it is unclear how these ontogenetic shifts in visual environment alter transcriptome-wide retina expression profiles. Salmonid fishes (salmon and trout) provide an ideal system for investigating gene expression evolution in the retina across ontogeny in response to different visual environments. Many salmonid species migrate between shallower and deeper water, and some species also have both migratory and non-migratory populations. For example, Oncorhynchus mykiss has two main forms: steelhead trout, which migrate to deeper water, and non-migratory rainbow trout, which stay in shallow streams and tributaries. Despite being the same species and developing in the same environment, their adult forms exist in very different visual environments, and therefore, are predicted to diverge in retinal gene expression in these later adult stages. I use functional genomics to investigate gene expression evolution in the trout retina across environments and life stages.

Vision is critical for foraging, avoiding predators, and finding mates in many species. Despite the importance of vision, visual acuity is highly variable across species, and the relative contributions of different selective pressures and developmental processes to this variation are still unclear. Many vertebrates have specialized high visual acuity regions in the retina, such as an area centralis (region of high retinal ganglion cell density), a horizontal streak (elongated region of high density stretching across the retina), or a fovea (physical indentation in the retina surrounded by a region of high density). Many have proposed hypotheses regarding the ecological drivers that select for these retinal specializations. For example, the fovea is thought to help with vision in complex three-dimensional environments or dim light environments. However, these hypotheses had not been tested using phylogenetic comparisons across multiple species. Additionally, vision is a complex sensory system that requires the successful integration of molecular, cellular, and morphological traits, which may impose constraints on each other. It is unclear how selective pressures on vision act at these different biological scales. I use phylogenetic comparative approaches to uncover the ecological selective pressures and functional constraints shaping the evolution of retinal specializations in both fish and mammals (Kopania and Clark 2025, Evolution Letters). See here for a summary of my mammal retina work on the Evolution Letters Editor's Blog.

Murine rodents comprise a rapid radiation of rats and mice from Europe, Africa, Asia, and Oceania. They exhibit remarkable diversity in reproductive traits and rapid evolution of genes involved in reproduction. This diversity and rapid evolution is thought to reflect variation in the intensity of sexual selection among species, but other forces such as developmental constraints may play an important role in patterns of reproductive evolution across species. I combine comparative genomics, transcriptomics, and phylogenetic comparative approaches across species spanning the murine radiation to understand the relationships among sexual selection pressures, phenotypic evolution, and the molecular evolution of reproduction in murine rodents (Kopania et al. 2025, Evolution).

Genes involved in sperm development (spermatogenesis) tend to evolve rapidly, but some aspects of spermatogenesis are highly conserved and essential for fertility. These contrasting patterns may result from varying intensities of different selection pressures across the developmental process of spermatogenesis. Rapid spermatogenesis evolution may also have important consequences for sex chromosome evolution and male hybrid sterility, an important reproductive barrier between incipient species. My work investigates the causes and consequences of rapid spermatogenesis evolution (Kopania et al. 2022, MBE; Kopania et al. 2022, Genetics).