233 Morrill Hall
Department of Animal Biology
University of Illinois at Urbana-Champaign
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
- How does the functional genome grow via the acquisition of genes and conserved
- How do some genomes excise non-coding DNA while others accumulate huge amounts
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
Julian Catchen, Principal Investigator
Shane Campbell-Staton, Postdoctoral Research Associate
Nicolas Rochette, Postdoctoral Research Associate
A. Amores, J. Catchen, W. Warren, R. Walter, M. Schartl, and J. Postlethwait. A RAD-tag genetic
map for the platyfish (Xiphophorus maculatus) reveals mechanisms of karyotype evolution among teleost
fish. Genetics, 197(2):625–641, 2014.
A. Rodríguez-Marí, C. Cañestro, R. BreMiller, J. Catchen, Y. Yan, and J. Postlethwait.
Retinoic Acid metabolic genes, meiosis, and gonadal sex differentiation in zebrafish.
PLoS One, 8(9):e73951, 2013.
G. Zhang, S. Hoersch, A. Amsterdam, C. Whittaker, E. Beert, J. Catchen, S. Farrington, J. Postlethwait,
E. Legius, N. Hopkins, and J. Lees. Comparative Oncogenomic Analysis of Copy Number Alterations in
Human and Zebrafish Tumors Enables Cancer Driver Discovery. PLoS Genetics,
C. Merz, J. Catchen, V. Hanson-Smith, K. Emerson, W. Bradshaw, and C. Holzapfel. Replicate
Phylogenies and Post-Glacial Range Expansion of the Pitcher-Plant Mosquito, Wyeomyia smithii,
in North America. PLoS One, 8(9):e72262, 2013.
J. Catchen, P. Hohenlohe, S. Bassham, A. Amores, and W. Cresko. Stacks: an analysis tool set for
population genomics. Molecular Ecology. 2013.
J. Catchen, S. Bassham, T. Wilson, M. Currey, C. O’Brien, Q. Yeates, and W. Cresko.
The population structure and recent colonization history of Oregon threespine stickleback determined
using restriction-site associated DNA-sequencing. Molecular Ecology. 2013.
M. Schartl, R. Walter, Y. Shen, T. Garcia, J. Catchen, A. Amores, I. Braasch, D. Chalopin, J. Volff,
K. Lesch, A. Bisazza, P. Minx, L. Hillier, R. Wilson, S. Fuerstenberg, J. Boore, S. Searle,
J. Postlethwait, and W. Warren. The genome of the platyfish, Xiphophorus maculatus, provides
insights into evolutionary adaptation and several complex traits. Nature
Genetics. 45:567-572, 2013.
J. Catchen, A. Amores, P. Hohenlohe, W. Cresko, and J. Postlethwait. Stacks: building and genotyping
loci de novo from short-read sequences. G3: Genes, Genomes, Genetics, 1:171-182, 2011.
A. Amores, J. Catchen, A. Ferrara, Q. Fontenot and J. Postlethwait. Genome evolution and meiotic maps
by massively parallel DNA sequencing: Spotted gar, an outgroup for the teleost genome duplication.
Genetics, 188:799-808, 2011.
J. Davey, P. Hohenlohe, P. Etter, J. Boone, J. Catchen and M. Blaxter. Genome-wide genetic
marker discovery and genotyping using next-generation sequencing.
Nature Reviews Genetics, 12:499-510. 2011.
- Y. Shen, J. Catchen, T. Garcia, A. Amores, I. Beldortha, J. Wagnera, Z. Zhang, J. Postlethwait, W. Warren,
M. Schartl, R. Walter. Identification of transcriptome SNPs between Xiphophorus lines and species for assessing
allele specific gene expression within F1 interspecies hybrids Comparative Biochemistry and Physiology
Part C: Toxicology & Pharmacology. In Press. 2011.
- T. Garcia, Y. Shen, J. Catchen, A. Amores, M. Schartl, J. Postlethwait, R. Walter. Effects of short
read quality and quantity on a de novo vertebrate transcriptome assembly.
Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology. In Press. 2011.
- P. Hohenlohe, S. Amish, J. Catchen, F. Allendorf, G. Luikart. RAD sequencing identifies
thousands of SNPs for assessing hybridization between rainbow trout and westslope cutthroat trout.
Molecular Ecology Resources, 11: 117-122. 2011.
- K. Emerson, C. Merz, J. Catchen, P. Hohenlohe, W. Cresko, W. Bradshaw, C. Holzapfel. Resolving
postglacial phylogeography using high-throughput sequencing. Proceedings of the National Academy of
Science, 107(37):16196-200, 2010.
- B. Eames, A. Singer, G. Smith, Z. Wood, J. Catchen, Y.-L. Yan, X. He, J. Polizzi, A. Rodríguez-Marí,
T. Linbo, D. Raible, J. Postlethwait. Uxs1 is required for proper morphogenesis and histogenesis of the
craniofacial skeleton. Developmental Biology, 341(2):400-15, 2010.
- C. Sullivan, J. Charette, J. Catchen, C. Lage, G. Giasson, J. Postlethwait, P. Millard, and C. Kim.
The gene history of zebrafish tlr4a and tlr4b is predictive of divergent
functions. The Journal of Immunology, 183(9):5896-5908 2009.
- J. Catchen. Automated Methods to Infer Ancient Homology and Synteny. Diss.
University of Oregon, 2009.
- J. Catchen, J. Conery, and J. Postlethwait. Automated identification of
conserved synteny after whole genome duplication. Genome Research,
- R. Jovelin, Y. Yan, X. He, J. Catchen, A. Amores, H. Yokoi, C. Canestro,
J. Postlethwait. Evolution of developmental regulation in the vertebrate FgfD
subfamily. Journal of Experimental Zoology Part B: Molecular and
Developmental Evolution, 314B(1):33-56, 2009.
- C. Canestro, J. Catchen, A. Rodríguez-Marí, H. Yokoi, and J. Postlethwait.
Consequences of lineage-specific gene loss gene loss on functional
evolution of surviving ohnologs in vertebrate genomes: ALDH1A and retinoic acid
signaling. PLoS Genetics, 5(5):e1000496, 2009.
- H. Yokoi, Y. Yan, M. Miller, R. BreMiller, J. Catchen, E. Johnson, and J. Postlethwait.
Expression profiling of zebrafish sox9 mutants
reveals that Sox9 is required for retinal differentiation.
Developmental Biology. 329(1):1-15, 2009.
- J. Bridgham, J. Brown, A. Rodríguez-Marí, J. Catchen, J. Thornton. Evolution of a new
function by degenerative mutation in cephalochordate steroid
receptors. PLoS Genetics 4(9):e1000191, 2008.
- J. Catchen, J. Conery, and J. Postlethwait.
Inferring Ancestral Gene Order.
Methods in Molecular Biology. 452: 365-383, 2008.
- J. Conery, J. Catchen, and M. Lynch.
Rule-based workflow management for bioinformatics.
VLDB Journal 14(3): 318-329, 2005.
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.
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.