General interests: Evolutionary genomics; genomics of thermal stress and ecological clines; molecular populations genetics

Dissertation topic: Ecological and evolutionary genomics of the northern acorn barnacle (Semibalanus balanoides)

Senior thesis topic: Population genetics using complete mitochondrial genomes from population of Fundulus heteroclitus distributed along a pollution cline


8/2015 – Present:

Integrative Graduate Education and Research Traineeship (IGERT): Reverse Ecology: Computational Integration of Genomes, Organisms, and Environments
Brown University
P.I. Dr. David Rand

S. balanoides has wide regional gene flow and strong patterns of selection in local habitats. Moreover, this organism is exposed to annual cycles of reproduction and settlement that may limit local adaptation in favor of adaptation to environmental heterogeneity. This project utilizes S. balanoides as a model for ecological genomics in order to gain greater understanding of the genome-by-environment interactions involved in adaptations to highly heterogeneous environments.

Field collections in Narragansett, RI, with Bianca Brown.


Papers from this Project:

Nunez J.C.B., Elyanow R.G., Ferranti D.A., Rand D.M. (2018) Population Genomics and Biogeography of the Northern Acorn Barnacle (Semibalanus balanoides) Using Pooled Sequencing Approaches. In Population Genomics: Marine Organisms. M. F. O. and O. P. Rajora, Springer, Cham. DOI:

6/2013 – 6/2015:

Population genomics using complete mitochondrial sequences from populations of Fundulus heteroclitus distributed along ecological clines
Rosenstiel School Of Marine And Atmospheric Science
P.I.s Dr. Marjorie Oleksiak and Dr. Douglas Crawford

We utilized next generation sequencing approaches to obtain several complete mitochondrial genomes from populations of Fundulus heteroclitus distributed along ecological clines, particularly a pollution cline and a thermal cline. Our goal is to utilize SNPs found in mitochondrial the genome to find correlations between mitochondrial haplotypes and ecological adaptation.


Papers from this Project:

Nunez JCB, Biancani LM, Flight PA, Nacci DE, Rand DM, Crawford DL, Oleksiak MF. 2018 Stable genetic structure and connectivity in pollution-adapted and nearby pollution-sensitive populations of Fundulus heteroclitus. Royal Society Open Science 5: 171532.

Nunez JCB, Oleksiak MF (2016) A Cost-Effective Approach to Sequence Hundreds of Complete Mitochondrial Genomes. PLoS ONE 11(8): e0160958. doi: 10.1371/journal.pone.0160958

1/2014 – 7/2014:

Conservation genetics of the euryhaline teleost Poecilia latipinna
Rosenstiel School Of Marine And Atmospheric Science.
P.I.s Dr. Marjorie Oleksiak and Dr. Douglas Crawford

We used a genotyping by sequencing (GBS) approach to examined hundreds of SNPs to determine the genetic diversity of Sailfin molly (Poecilia latipinna) among three geographically close mangrove salt marsh flats in the Florida Keys and compare this to populations in southern and northern Florida.

See the publication from this project:

Nunez, J. C. B., Seale, T. P., Fraser, M. A., Burton, T. L., Fortson, T. N., Hoover, D., Travis, J., Oleksiak, M. F., Crawford, D. L. (2015). “Population Genomics of the Euryhaline Teleost Poecilia latipinna.” PLoS ONE 10(9): e0137077.

From Nunez et al. 2015. doi:10.1371/journal.pone.0137077.g002

2/2012 – 7/2012:

Up scaling green fluorescent protein overproduction in E. coli using the bioflo110 bioreactor.
Miami Dade College. Biotechnology Research Learning Collaborative
P.I.s Prof. Juan Morata and Dr. Edwin Candelaria

I participated in this research project as an intern participating in the Biotechnology Research Learning Collaborative project. The goal of the project was to study optimization parameters for the overproduction of GFP in E. coli.