catchenlab.life.illinois.eduCatchenLab

Research People Publications Software . Research People Publications Software 233 Morrill Hall Department of Animal Biology University of Illinois at Urbana-Champaign (217) 244-4298; Research How do genomes change over evolutionary time? Numerous questions fall under this rubric, such as: 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? How does the functional genome grow via the acquisition of genes and conserved non-coding elements? 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. Research Highlights People Julian Catchen , Principal Investigator Google Scholar ; Angel Rivera-Colón , Graduate Student Niraj Rayamajhi , Graduate Student Selected Publications 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 ] N. Rochette & J. Catchen. Deriving genotypes from RAD-seq short-read data using Stacks . Nature Protocols . 2017. [ 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 ] J. Paris, J. Stevens & J. Catchen. Lost in parameter space: a road map for Stacks . Methods in Ecology and Evolution 188:799–14. 2017. [ reprint ] J. Catchen, P. Hohenlohe, L. Bernatchez, W. Funk, K. Andrews & F. Allendorf. Unbroken: RADseq remains a powerful tool for understanding the genetics of adaptation in natural populations . Molecular Ecology Resources , 26:420–4. 2017. [ reprint ] S. Hoffberg, T. Kieran, J. Catchen, A. Devault, B. Faircloth, R. Mauricio & T.Glenn. RADcap: sequence capture of dual-digest RADseq libraries with identifiable duplicates and reduced missing data . Molecular Ecology Resources , 16(5):1264–1278. 2016. [ reprint ] C. Small, S. Bassham, J. Catchen, A. Amores, A. Fuiten, R. Brown & W. Cresko. The genome of the Gulf pipefish enables understanding of evolutionary innovations . Genome Biology , 17(1), 1–23. 2016. [ 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 F ST . 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. The Synteny Database is a system to identify regions of conserved synteny within teleost species and between teleosts and other outgroups such as mouse and human. Conserved synteny refers to the preservation of a gene neighborhood between two organisms, indicating an ancestral relationship between the two regions....