I am an evolutionary genomicist whose research sits at the interface of bioinformatics methods development, empirical evolutionary genomics, and theoretical population genetics. Using a variety of non-model systems, I study the genetic bases and the evolutionary mechanisms driving adaptation and differentiation, and link these empirical observations to evolutionary theory. See my Publications page for more examples.
I worked with Antarctic icefishes (family Channichthyidae) as a Ph.D. student at the University of Illinois Urbana-Champaign. With their antifreeze glycoproteins and loss of hemoglobin, this group displays extreme physiological specialization, which limits them to the chronically cold Antarctic environment. Despite this, a single icefish species (Champsocephalus esox) is found outside Antarctica, providing a unique case to study the evolution of adaptation away from a highly specialized ancestral state. I assembled the genome of this non-polar icefish (Rivera-Colón et al. 2023), which I then compared against genomes of closely related Antarctic species. I also quantified genetic diversity and selection in C. esox using population genomics approaches. I found evidence for the loss of antifreeze protein genes and selection on mitochondrial genes and molecular chaperones linked to this polar-to-temperate transition, providing insights into the mechanisms of adaptation to ecologically disparate environments.
In addition to my work on this non-polar icefish species, I have also worked on the genomes of other notothenioid fishes. These include Eleginops maclovinus, the non-polar sister species of the Antarctic notothenioid clade (Cheng et al. 2023), and the cryopelagic bald notothen Trematomus borchgrevinki (Rayamajhi et al. 2025). Also, using comparative analyses across the Antarctic notothenioid radiation, I collaborated in identifying a transposable element insertion as the possible culprit in the hemoglobin deletion seen in icefishes (Desvignes et al. 2025).
My postdoctoral work at the University of Oregon establishes the Pacific acorn barnacle (Balanus glandula) as a model to study evolution in large populations. The size of a population mediates evolutionary processes (e.g., the balance between drift and selection); yet empirical observations remain limited to small-to-moderate population scales. With densities exceeding 104 individuals per square meter across thousands of kilometers along the Pacific coastline, B. glandula is an ideal system to study evolution at large population sizes. I assembled the B. glandula genome and quantified genetic diversity in central Oregon barnacles (Rivera-Colón et al. 2026). I found extreme levels of genetic diversity (π > 5%), several times higher than that of other highly diverse model arthropods, e.g., Drosophila and Anopheles. Yet, I observed a nearly two-fold reduction of diversity in coding sequences, suggesting highly efficacious purifying selection. Additionally, I estimated selection regimes using McDonald-Kreitman tests. Protein-coding genes show an excess of non-synonymous substitutions, a hallmark of positive selection. In contrast, I find a strong depletion of sequences showing an excess of non-synonymous polymorphism. This finding, combined with our diversity estimates, reinforces the increase in the efficacy of purifying selection expected for large populations. This work presents one of the few empirical studies of genetic diversity in such large populations and allows for the testing of evolutionary theory at demographic extremes.
Expanding from our observations on the Oregon coast, I look at how these patterns of genetic diversity interact with spatial and environmental heterogeneity along the Pacific coast. While we have shown selection to be strong, the widespread nature of B. glandula and its ability for planktonic dispersal suggest a fascinating interplay between migration and selection. In agreement with previous work, I find a biogeographic break in central California. Populations south of this break show higher diversity and increased genome-wide differentiation than northern populations. I also identified a new genetic break off the Washington coast, separating populations in coastal Oregon and Washington from those ranging from the Puget Sound up to Alaska. In contrast to the break in California, differentiation across this Washington break is largely limited to a handful of loci in the B. glandula genome. The underlying causes of these patterns of population structure remain unknown and are a central subject of my future research.
My empirical work is complemented by the development of new bioinformatic methods that I use to analyze comparative and population genomics data.
During my Ph.D. at the University of Illinois, I worked on developing methods
for the analysis and simulation of Restriction-site Associated DNA sequencing
(RADseq) data.
I co-led the development of the Stacks 2
(Rochette et al. 2019),
RADinitio
(Rivera-Colón et al. 2021),
and decoratio
(Rochette et al. 2023)
software.
Additionally, I published several protocol papers describing the analysis and
troubleshooting of RADseq experiments, e.g.,
Rivera-Colón & Catchen (2022) and
Cerca et al. (2021).
As a postdoc at the University of Oregon, I worked on the development of
MKado, a tool for applying McDonald-Kreitman analyses of molecular
evolution
(Rivera-Colón et al. 2026).
I am also an author on the manuscript for pg_gpu
(Pope et al. 2026),
a software for the analysis of population genomics data using GPUs.