CatchenLab.

Research

How do genomes change over evolutionary time? Numerous questions fall under this rubric, such as:

1. Is the state of a genome in the present defined by an accumulation of large numbers of infinitesimally small substitutions, or, are there large, disruptive changes that, in short periods of time, can erect barriers to recombination and facilitate speciation?
2. How does the functional genome grow via the acquisition of genes and conserved non-coding elements?
3. How do some genomes excise non-coding DNA while others accumulate huge amounts of it?

These questions can be addressed at several different scales, from whole genome duplication over millions of years to structural variation within a species over thousands of years, to somatic evolution and cancer within an individual over a handful of years. The research strategy of the Catchen Lab is to apply novel algorithmic developments to the questions of genome evolution.

The lab's work is mostly focused on teleost fish. Teleosts represent the most species rich vertebrate clade and within the teleosts lie laboratory model organisms, such as zebrafish, and several fascinating natural evolutionary models, including the threespine stickleback. We have projects focused on a number of species, from Antarctic notothenioids, to stickleback, killifish, and several modern and ancient salmon species.

Research Highlights

People

	Jack Calvery, Graduate Student
	Julian Catchen, Principal Investigator Google Scholar; Mastodon; Blue Sky;
	Akane Hatsuda, Postdoctoral Research Associate
	Gio Madrigal, Graduate Student Google Scholar;
	Bushra Minhas, Graduate Student Google Scholar;
⇒ Former lab members

Selected Publications

• N. Rayamajhi, et al. The genome of the cryopelagic Antarctic bald notothen, Trematomus borchgrevinki. G3: Genes, Genomes, Genetics, 15(1):jkae267. 2025. [reprint]
• G. Madrigal, et al. Klumpy: A tool to evaluate the integrity of long-read genome assemblies and illusive sequence motifs. Molecular Ecology Resources, 25(1):e13982. 2024. [reprint]
• A. Rivera-Colón, et al. Genomics of Secondarily Temperate Adaptation in the Only Non-Antarctic Icefish. Molecular Biology and Evolution, 40(3):msad029. 2023. [reprint]
• B. Minhas, et al. Novel mitochondrial genome rearrangements including duplications and extensive heteroplasmy could underlie temperature adaptations in Antarctic notothenioid fishes. Scientific Reports, 13:6939. 2023. [reprint]
• N. Rochette, et al. On the causes, consequences, and avoidance of PCR duplicates: Towards a theory of library complexity. Molecular Ecology Resources, 23:1299–1318. 2023. [reprint]
• N. Rochette, A. Rivera-Colón, & J. Catchen. Stacks 2: Analytical methods for paired‐end sequencing improve RADseq‐based population genomics. Molecular Ecology, 28(21):4737-4754. 2019. [reprint]
• S. Bassham, J. Catchen, E. Lescak F. von Hippel & W. Cresko. Repeated Selection of Alternatively Adapted Haplotypes Creates Sweeping Genomic Remodeling in Stickleback. Genetics, 209, 921–939. 2018. [reprint]
• S. Campbell-Staton, Z. Cheviron, N. Rochette, J. Catchen, J. Losos & S. Edwards. Winter storms drive rapid phenotypic, regulatory, and genomic shifts in the green anole lizard. Science, 357(6350):495–498, 2017. [reprint]

Software

	Stacks is a parallelized software system that can assemble and genotype tens of thousands of restriction enzyme-based markers in thousands of individuals. Stacks can be used to develop ultra dense genetic maps, or it can be used to identify evolutionarily divergent segments of the genome using population genomic statistics such as π and FST.
	Klumpy is a tool designed to look for either missassembled regions in a long-read genome assembly or a set of query sequences in another set of sequences (e.g., finding genes of interest in a reference genome). Results can be visualized alongside other features (e.g., sequence gaps) for easier interpretation.
	RADinitio is a forward simulator for creating population-level RAD data sets, based on a given reference genome. This in silico RADseq library preparation and sequencing process, allows for the exploration of parameters including restriction enzyme selection, library insert size, PCR duplicate distribution, and sequencing coverage.
	Chromonomer is a program designed to integrate a genome assembly with a genetic map.