Evolutionary genomics of rapid adaptation in worldwide fly populations

University of Virginia

P.I. Dr. Alan O. Bergland

Rapid evolution is ubiquitous in nature and allows adaptation to occur in few generations. Yet, we still lack a rigorous understanding of the circumstances and mechanisms governing this process. Fruit flies (Drosophila melanogaster) living in temperate regions experience strong fluctuations in the strength and direction of selection due to seasonality and evolve rapidly to track the changing fitness landscape. Consequentially, seasonally adaptive tracking represents a natural laboratory in which to understand whether rapid evolution is a repeatable and predictable process. In my current project I use the largest genomic datasets for natural propulations of Drosophila, DEST (,  to investigate the patterns of adaptive variation and demography  in natural of D. melanogaster flies exposed to seasonally varying selection. This work seeks ot provide insights to about the consequences of rapid evolution in natural populations as a result of anthropogenic climate change, agricultural practices. Moreover, the issue of rapid adaptation taps into a fundamental corollary in evolutionary biology: the idea that evolution is a slow process governed by random genetic drift, where adaptive events are rare outliers. Accordingly, my research will provide insights of whether rapid evolution undermines or synergizes with the current zeitgeist of population genetics.

Papers from this Project:

[ 1]“Drosophila Evolution over Space and Time (DEST) - A New Population Genomics Resource”
Martin Kapun, Joaquin C. B. Nunez, María Bogaerts-Márquez, Jesús Murga-Moreno, Margot Paris, Joseph Outten, Marta Coronado-Zamora, et al. bioRxiv 2021.02.01.428994; doi:

Figure 7.png

The core samples of the DEST database reveal worldwide structure

Population structure patterns in Europe show a peculiar East-West divide. What drives this signal?

8/2015 – 8/2020:

Ecological and evolutionary genomics of the northern acorn barnacle across ocean basins

Brown University

P.I. Dr. David Rand

The northern acorn barnacle (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 barnacles as models for ecological genomics in order to gain greater understanding of the genome-by-environment interactions involved in adaptations to highly heterogeneous environments.

This project in the media

Barnacles offer genetic clues on how organisms adapt to changing environments

By Phoebe Hall, Assistant Director of BioMedical Communications, Division of Biology and Medicine

Support for this Project:

“Ontogenetically mediated selection in response to environmental heterogeneity in the acorn barnacle (Semibalanus balanoides)”, Doctoral Dissertation Enhancement Grant (DDEG), Brown University, Dept. of Ecology and Evolutionary Biology. US $10,000; 2/1/2019 - 2/1/2020. Lead PI(s) JCB Nunez and DM Rand


“Evolutionary Genomics of the Northern Acorn Barnacle (Semibalanus balanoides)”, Graduate Research Fellowship (GRFP). National Science Foundation (NSF), US $138,000; 05/1/2015 - 05/1/2020. Lead PI(s) JCB Nunez


“Parallel evolution in the intertidal: investigating genetic responses to zonation", Graduate Research Opportunities Worldwide (GROW). A joint grant from the U.S. National Science Foundation (NSF), and the Swedish Research Council (Vetenskapsrådet), US $5,000 and SE kr 26,000. 7/2019 – 10/2019. Lead PI(s) JCB Nunez, DM Rand, K Johannesson and A Blomberg. 

“Tidally-zonated polymorphisms in the northern acorn barnacle in the North Atlantic: parallel evolution or ancient polymorphism?” KVA fund for internationalization and scientific renewal at the Sven Lovén Centre.The Royal Swedish Academy of Sciences(KVA), SE kr 64,100; 12/21/2018 - 12/1/2019. Lead PI(s) JCB Nunez and K Johannesson 

"NSF IGERT: Reverse Ecology: Computational Integration of Genomes, Organisms, and Environments." NSF training grant from DGE 0966060 to P.I Dr. David Rand (JCB Nunez supported under IGERT fellowship 2015-2017)


Barnacle zonation. Winter 2017


Characterizing thermal stress variation in the intertidal (Nunez et al 2020 PNAS)


Predicting protein structure differences of a key metabolic gene (Mpi) in the intertidal (Nunez et al 2020 PNAS)

Papers from this Project:

[1.] Joaquin C B Nunez, Stephen Rong, Alejandro Damian-Serrano, John T Burley, Rebecca G Elyanow, David A Ferranti, Kimberly B Neil, Henrik Glenner, Magnus Alm Rosenblad, Anders Blomberg, Kerstin Johannesson, David M Rand, Ecological load and balancing selection in circumboreal barnacles, Molecular Biology and Evolution, , msaa227,

[2.] Joaquin C. B. Nunez, Patrick A. Flight, Kimberly B. Neil, Stephen Rong, Leif A. Eriksson, David A. Ferranti, Magnus Alm Rosenblad, Anders Blomberg, and David M. Rand (2020) Footprints of natural selection at the mannose-6-phosphate isomerase locus in barnacles

PNAS first published February 25, 2020

[3.] 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:

NSF Highlights

6/2013 – 6/2015:

Mitochondrial genomics of Fundulus heteroclitus 

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.

Support for this Project:

“Evolutionary Genomics of the Mitochondrial Genome in Fundulus”, Small Undergraduate Research Grant Experience (SURGE). Rosenstiel School of Marine and Atmospheric Science, Amount: US $1500; 1/20/2015 - 5/1/2015. Lead PI(s) JCB Nunez 


“Searching for signatures of natural selection in the mitochondrial genome in Fundulus heteroclitus”, Small Undergraduate Research Grant Experience (SURGE). Rosenstiel School of Marine and Atmospheric Science, Amount: US $1500; 1/20/2014 - 5/1/2014. Lead PI(s) JCB Nunez 

Papers from this Project:

[1.] 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.

[2.] 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


As one of our findings, we observed an enrichment of non-synonymous mutations on the mtDNAs of fish living in the most polluted area of the New Bedford estuary, MA (Nunez et al 2018 RSOS)


M. Oleksiak and me  (2015)

1/2014 – 7/2014:

Population 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.

Support for this Project:

Department of Marine Biology and Ecology, University of Miami - RSMAS, Undergraduate program in Marine Biology

Papers from this project:

[1.] 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.


Population structure in south florida mollies (Nunez et al 2015)

 D. Crawford (background) and me collecting sailfin mollies. Pic by T. Seale 2014