J.J. Emerson

Assistant Professor, Ecology & Evolutionary Biology
School of Biological Sciences

B.A., Rice University, 2000, Ecology & Evolutionary Biology

B.A., Rice University, 2000, Biochemistry

Ph.D., University of Chicago, 2006, Ecology & Evolution

Phone: (949) 824-9527
Email: jje@uci.edu

University of California, Irvine
5230 McGaugh Hall
Mail Code: 2525
Irvine, CA 92697
Research Interests
population genetics, population genomics, molecular evolution, genomics, evolutionary genetics, evolution, natural variation, allele specific expression, copy number variation, sex chromosomes, sex chromosome evolution, bioinformatics
Academic Distinctions
Life Science Research Foundation Fellowship finalist (2011) 50 finalists were chosen out of 880 applicants
Academia Sinica Distinguished Postdoctoral Researcher Fellowship (2007-2008)
National Science Foundation Doctoral Dissertation Improvement Grant (2004)
National Science Foundation Graduate Research Fellowship Award (2001)
Huxley Award for Excellence, Dept. of Ecology & Evolution, Rice U.
National Science Foundation Graduate Research Fellowship Honorable Mention (2000)
Magna Cum Laude, Rice University (2000)
Genome Research Institute, Academia Sinica, Taipei, Taiwan with Wen-Hsiung Li

Integrative Biology, UC Berkeley, with Doris Bachtrog
Research Abstract
I'm J.J. Emerson. My long-term research goals center around understanding the dynamics of genome evolution. In particular I am interested in understanding the origin of genetic novelties and gene regulatory variation as well as the influence of natural selection and genetic drift on the evolution of genomic structural changes. My previous research has focused on three areas:

  1. the importance of genomic context in the evolution of eukaryotic (and especially mammalian) sex chromosomes;

  2. using polymorphism data to measure the evolutionary forces that act upon copy number changes (duplications and deletions) that occur in model systems like Drosophila melanagaster and Saccharomyces cerevisiae;

  3. collecting genome-wide expression data for intraspecific polymorphism and interspecific divergence in order to make inferences about the action of natural selection on expression evolution in S. cerevsisiae and related species.

I am currently focusing my energy on Drosophila population genomics. I am also involved in various theoretical projects, including heuristic models of phenotypic adaptation.
Vicoso B.*, Emerson J.J.*, Zektser Y., Mahajan S., Bachtrog D. Comparative Sex Chromosome Genomics in Snakes: Differentiation, Evolutionary Strata, and Lack of Global Dosage Compensation. PLoS Biol 2013;11(8): e1001643.
Schaefke B.*, Emerson J.J.*, 3 others, Li WH. Inheritance of gene expression level and selective constraints on trans- and cis-regulatory changes in yeast. Mol. Biol. Evol. 2013 Jun 22. (Epub ahead of print)
Pool J.E., Corbett-Detig R.B., Sugino R.P., Stevens K.A., Cardeno C.M., Crepeau M.W., Duchen P., Emerson J.J., Saelao P., Begun D.J., Langley C.H. Population Genomics of sub-saharan Drosophila melanogaster: African diversity and non-African admixture. PLoS Genet. 2012;8(12): e1003080.
Cardoso-Moreira M., Emerson J.J., Clark A.G., Long M. Drosophila duplication hotspots are associated with late- replicating regions of the genome. PLoS Genet. 2011 Nov;7(11): e1002340.
Nikaido M., Sasaki T., Emerson J.J., 6 others, Li W.-?H., Okada N. Genetically distinct coelacanth population off the northern Tanzanian coast. Proc. Natl. Acad. Sci. U.S.A. 2011 Nov 1;108(44): 18009-?13.
Emerson J.J.*, Hsieh L.-C.,* Sung H.-M.*, Wang T.-Y.*, 4 others, Li W.-H. Natural selection on cis and trans regulation in yeasts. Genome Research 2010 Jun;20(6): 826-36. Epub 2010 May 5.
Emerson J.J., Li W.-H. The genetic basis of evolutionary change in gene expression levels. Phil. Trans. R. Soc. B. 2010 Aug 27;365(1552): 2581-90.
Emerson J.J.*, Cardoso-Moreira M.*, Borevitz J.O., Long M. Natural selection shapes genome-wide patterns of copy- number polymorphism in Drosophila melanogaster. Science. 2008 Jun 20;320(5883): 1629-31. Epub 2008 Jun 5.
Fan Chuanzhu, Emerson J.J., Manyuan Long, M. The origin of new genes. Evolutionary Genomics and Proteomics, Mark Pagel & Andrew Pomiankowski (eds.). 2007. Sinauer Associates, Inc., Sunderland, Massachusetts, USA. pp27-44.
Chen Y.*, Emerson J.J.*, Martin T.M.* Codon volatility does not detect selection. Nature. 2005 Jan 20;433:E6-7.
Cowan A.T., Bowman G.R., Edwards K.F., Emerson J.J., Turkewitz A.P. Genetics, genomic, and functional analysis of the granule lattics proteins in Tetrahymena secertory granules. Mol. Biol. Cell. 2005 Sept;17(9): 4046-60.
International Chicken Genome Sequencing Consortium. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 2004 Dec 09;432:695-716.
Emerson J.J.*, Kaessmann H.*, Betrán E., Long M. Extensive gene traffic on the mammalian X chromosome. Science. 2004 Jan 23;303(5657): 537-40.
Betrán E., Emerson J.J., Kaessmann H., Long M. Sex Chromosomes and Male Functions: Where Do New Genes Go? Cell Cycle. 2004 Jul 5.
Wang W., Thornton K., Emerson J.J., Long M. Nucleotide variation and recombination along the fourth chromosome in Drosophila simulans. Genetics. 2004 Apr;166(4): 1783-94.
Strassmann J.E., Queller D.C., Emerson J.J., Stagi M., Cervo R., Turillazzi S. Comparing the costs and benefits of grouping with non-relatives in the social amoeba Dictyostelium discoideum (Amoebazoa) and the social wasp Polistes dominulus (Hymenoptera vespidae). Redia, LXXXVII, 2004: 145-148.
Bergelson J., Dwyer G., Emerson J.J. Models and data on plant-enemy coevolution. Annu. Rev. Genet. 2001;35:469-99.
Professional Society
Society for Molecular Biology & Evolution
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