2025​

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​Footprints of worldwide adaptation in structured populations of D. melanogaster through the expanded DEST 2.0 genomic resource​

Joaquin C. B. Nunez, Marta Coronado-Zamora, Mathieu Gautier, Martin Kapun, Sonja Steindl, Lino Ometto, Katja M Hoedjes, Julia Beets, R Axel W Wiberg, Giovanni R Mazzeo, David J Bass, et al.

Molecular Biology and Evolution. doi: https://doi.org/10.1093/molbev/msaf132 

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Microbiome composition shapes temperature tolerance in a Hawaiian picture-winged Drosophila
Donald K Price, Kristian West, Michelle Cevallos-Zea, Sara Cahan, Emily K. Longman, Joaquin C. B. Nunez, Joanne Yew, Matthew J Mederios

Journal of Experimental Biology. doi: https://doi.org/10.1242/jeb.250973

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Precursors of Sea Star Wasting: Immune and Microbial Disruption During Initial Disease Outbreak in Southeast Alaska

​McCracken A., Roger A., Saratkar C., Brusch S., Sularz S., Nunez J.C.B.,  Pespeni M. (2025). bioRxiv (PrePrint) doi: https://doi.org/10.1101/2025.07.05.662347

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Geographic Divergence in Population Genomics and Shell Morphology Reveal History of Glacial Refugia in a Coastal Dogwhelk
EK Longman, JCB Nunez, E Sanford, M Pespeni
(2025). bioRxiv, (PrePrint); doi: https://doi.org/10.1101/2025.07.22.66445

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Early life-stage thermal resilience is determined by climate-linked regulatory variation
JCB Nunez, S Tangwancharoen, KM Finnegan, LA Proud, BL Lockwood
(2025). bioRxiv, (PrePrint); doi: https://doi.org/10.1101/2025.07.07.663603

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2024​

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Trans-Specific Polymorphisms Between Cryptic Daphnia Species Affect Fitness and Behavior
Connor S. Murray, Madison Karram, David J. Bass, Madison Doceti, Dörthe Becker, Joaquin C. B. Nunez, Aakrosh Ratan, Alan O. Bergland (2024)
Molecular Ecology, DOI: https://doi.org/10.1111/mec.17632

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A cosmopolitan inversion facilitates seasonal adaptation in overwintering Drosophila

Joaquin C. B. Nunez, Benedict A Lenhart, Alyssa Bangerter, Connor S Murray, Giovanni R Mazzeo, Yang Yu, Taylor L Nystrom, Courtney Tern, Priscilla A Erickson, Alan O Bergland (2024)

Genetics; iyad207, https://doi.org/10.1093/genetics/iyad207 

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2023

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Parasite manipulation of host phenotypes inferred from transcriptional analyses in a trematode-amphipod system.

David M. Rand,  Joaquin C. B. Nunez,  Shawn Williams,  Stephen Rong,  John T. Burley,  Kimberly B. Neil,  Adam N. Spierer,  Wilson McKerrow,  David S. Johnson,  Yevgeniy Raynes,  Thomas J. Fayton,  Nicholas Skvir,  David A. Ferranti,  Maya Greenhill Zeff,  Amanda Lyons,  Naima Okami,  David M. Morgan,  Kealohanuiopuna Kinney,  Bianca R. P. Brown,  Anne E. Giblin,  Zoe G. Cardon (2023).

Molecular Ecology, DOI: https://doi.org/10.1111/mec.17093

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2022

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Polygenic variation in sexual investment across an ephemerality gradient in Daphnia pulex

Karen Barnard-Kubow, Dörthe Becker, Connor S. Murray, Robert Porter, Grace Gutierrez, Priscilla Erickson, Joaquin C. B. Nunez, Erin Voss, Kushal Suryamohan, Aakrosh Ratan, Andrew Beckerman, Alan O. Bergland (2022).
Molecular Biology and Evolution, msac121, https://doi.org/10.1093/molbev/msac121 [link]

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2021

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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.  (2021).

Molecular Biology and Evolution, msab259, https://doi.org/10.1093/molbev/msab259 [link]

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From tides to nucleotides: genomic signatures of adaptation to environmental heterogeneity in barnacles.

Nunez JCB, Rong S., Ferranti DAU, Damian-Serrano A., Neil K.B., Glenner H., Elyanow R.G., Brown. BRP, Rosenblad MA, Blomberg A., Johannesson K., and Rand DM. (2021).

Molecular Ecology, DOI:10.1111/mec.15949 [link]

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2020

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Characterizing the cirri and gut microbiomes of the intertidal barnacle Semibalanus balanoides.

Brown, B.R.P., Nunez, J.C.B. & Rand, D.M. (2020).

anim microbiome 2, 41. https://doi.org/10.1186/s42523-020-00058-0 [PDF] [link]

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Ecological load and balancing selection in circumboreal barnacles

Nunez JCB, Rong S, Damian-Serrano A, Burley JT, Elyanow RG, Ferranti DA U, Neil KB, Glenner H, Rosenblad MA, Blomberg A, Johannesson K, Rand DM. (2020) 

Molecular Biology and Evolution, msaa227, DOI: https://doi.org/10.1093/molbev/msaa227 [PDF]

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Footprints of natural selection at the mannose-6-phosphate isomerase locus in barnacles [PDF]

Nunez JCB, Flight PA, Neil KB, Rong S, Eriksson LA, Ferranti DA, Rosenblad MA, Blomberg A, and Rand DM. (2020). 

Proceedings of the National Academy of Sciences; Feb;117(10).  DOI: https://doi.org/10.1073/pnas.1918232117

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2018

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Population Genomics and Biogeography of the Northern Acorn Barnacle (Semibalanus balanoides) Using Pooled Sequencing Approaches. [link]

[Book Chapter available in Springer's Website]

Nunez J.C.B., Elyanow R.G., Ferranti D.A., Rand D.M. (2018)

In: Oleksiak M., Rajora O. (eds) Population Genomics: Marine Organisms.

Population Genomics. Springer, Cham

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Stable genetic structure and connectivity in pollution-adapted and nearby pollution-sensitive populations of Fundulus heteroclitus. [PDF]

Joaquin C. B. Nunez, Leann M. Biancani , Patrick A. Flight , Diane E. Nacci , David M. Rand , Douglas L. Crawford  and Marjorie F. Oleksiak

Published:09 May 2018. https://doi.org/10.1098/rsos.171532

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2016

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A Cost-Effective Approach to Sequence Hundreds of Complete Mitochondrial Genomes. [PDF]

Joaquin C. B. Nunez, Marjorie F. Oleksiak 

Published: August 9, 2016. https://doi.org/10.1371/journal.pone.0160958

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2015

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Population Genomics of the Euryhaline Teleost Poecilia latipinna. [PDF]

J. C. B. Nunez, T. P. Seale , M. A. Fraser , T. L. Burton , T. N. Fortson , D. Hoover, J. Travis, M. F. Oleksiak, D. L. Crawford 

Published: September 3, 2015. https://doi.org/10.1371/journal.pone.0137077