Andrew Whitehead Google Scholar Profile
Ghalambor, C.K., E.S. Gross, E.D. Grosholtz, K.M. Jeffries, J.L. Largier, S.D. McCormick, T. Sommer, J.P. Velotta, and A. Whitehead (2021). Ecological Effects of Climate-Driven Salinity Variation in the San Francisco Estuary: Can We Anticipate and Manage the Coming Changes? San Francisco Estuary & Watershed Science. 19(2): Article 3. PDF.
Dong, Y., T.S. Blanchard, A. Noll, P. Vasquez, J. Schmitz, S.P. Kelly, P.A. Wright, and A. Whitehead (2021). Genomic and physiological mechanisms underlying skin plasticity during water to air transition in an amphibious fish. Journal of Experimental Biology. 224: jeb235515. PDF.
Komoroske, L.M., K.M. Jeffries, A. Whitehead, J. Roach, M. Britton, R.E. Connon, C. Verhille, S.M. Brander, and N.A. Fangue (2021). Transcriptional flexibility during thermal challenge corresponds with expanded thermal tolerance in an invasive compared to native fish. Evolutionary Applications. 14: 931-949. PDF.
Trego, M.L., C.A. Brown, B. Dubansky, C.D. Hess, F. Galvez, and A. Whitehead (2021). Transcriptome profiling in conservation physiology and ecotoxicology: mechanistic insights into organism-environment interactions to both test and generate hypotheses. In, Eds. Madliger, C., S. Cooke, C. Franklin, and O. Love, Conservation physiology: integrating physiology into animal conservation and management. Oxford University Press.
Swezey, D.S., S.E. Boles, K.M. Aquilino, H.K. Stott, D. Bush, A. Whitehead, L. Rogers-Bennett, T.M. Hill, and E. Sanford (2020). Evolved differences in energy metabolism and growth dictate the impacts of ocean acidification on abalone aquaculture. Proceedings of the National Academy of Sciences of the United States of America. 117 (42): 26513-26519. PDF.
Johnson, L.K., R. Sahasrabudhe, J.A. Gill, J.L. Roach, L. Froenicke, C.T. Brown, and A. Whitehead (2020). Draft genome assemblies using sequencing reads from Oxford Nanopore Technology and Illumina platforms for four species of North American killifish from the Fundulus genus. GigaScience. 9(6): giaa067. PDF.
Crawford, D.L., P.M. Schulte, A. Whitehead, and M.F. Oleksiak (2020). Evolutionary physiology and genomics in the highly adaptable killifish (Fundulus heteroclitus). Comprehensive Physiology. 10: 637-671. PDF.
Connon, R.E., S. Hasenbein, S.M. Brander, H.C. Poynton, E.B. Holland, D. Schlenk, J.L. Orlando, M.L. Hladik, T.K. Collier, N.L. Scholz, J.P. Incardona, N.D. Denslow, A. Hamdoun, S. Nicklisch, N. Garcia-Reyero, E.J. Perkins, E.P. Gallagher, X. Deng, D. Wang, S. Fong, R.S. Breuer, M. Hajibabei, J.B. Brown, J.K. Colbourne, T.M. Young, G. Cherr, A. Whitehead, and A. Todgham (2019). Review and recommendations for effect-based evaluations of contaminants in the San Francisco Bay-Delta. San Francisco Estuary and Watershed Science. 17(4). PDF.
McKenzie, J.L., D.J. Chung, T.M. Healy, R.S. Brennan, H.J. Bryant, A. Whitehead, and P.M. Schulte (2019). Mitochondrial ecophysiology: assessing the evolutionary forces that shape mitochondrial variation. Integrative and Comparative Biology. 59: 925-937. PDF.
Miller, J.T., N.M. Reid, D.L. Nacci, and A. Whitehead (2019). Developing a high-quality linkage map for the Atlantic killifish Fundulus heteroclitus. G3 Genes Genomes Genetics. 9: 2851-2862. PDF, Supplemental Materials.
Trego, M.L., A. Whitehead, N.M. Kellar, M. Lauf, and R.L. Lewison (2019). Tracking transcriptomic responses to endogenous and exogenous variation in cetaceans in the Southern California Bight. Conservation Physiology. 7: coz018. PDF.
Oziolor, E.M., N.M. Reid, S. Yair, K.M. Lee, S. Guberman VerPloeg, P.C. Bruns, J.R. Shaw, A. Whitehead*, and C.W. Matson* (2019). Adaptive introgression enables evolutionary rescue from extreme environmental pollution. Science. 364: 455-457. PDF, PDF+SOM.
- UC Davis Press Release, Perspective in Science, Research Highlight in Nature Reviews Genetics, NIEHS Paper of the Month, NIEHS Paper of the Year, Gizmodo, The Scientist, New Scientist, CNS, Earth.com, Forbes,
- Science PODCAST (the killifish story starts at 17:50)
- Video recording (the first 14 minutes is a narration of the main text, and the remainder is a detailed description of main text figures)
Trego, M.L., E. Hoh, A. Whitehead, N.M. Kellar, M. Lauf, D.O. Datuin, and R.L. Lewison (2019). Contaminant exposure linked to cellular and endocrine biomarkers in southern California bottlenose dolphins. Environmental Science and Technology. 53: 3811-3822. PDF.
Masonbrink, R., C. Purcell, S. Boles, A. Whitehead, J. Hyde, A. Seetharam, and A. Severin (2019). An annotated genome for Haliotis rufescens (red abalone) and resequenced green, pink, pinto, black and white abalone species. Genome Biology & Evolution. 11: 431-438. PDF.
Blanchard, T.S., A. Whitehead, Y.W. Dong, and P.A. Wright (2019). Phenotypic flexibility in respiratory traits is associated with improved aerial respiration in an amphibious fish out of water. Journal of Experimental Biology. 222: jeb186486. PDF.
- “Inside JEB” highlight
Rivkin, R.L., J.S. Santangelo, M. Alberti, M.F.J. Aronson, C.W. de Keyzer, S.E. Diamond, M.-J. Fortin, L.J. Frazee, A.J. Gorton, A.P. Hendry, Y. Liu, J.B. Losos, J.S. MacIvor, R.A. Martin, M. McDonnell, L.S. Miles, J. Munshi-South, R. Ness, A.E.M. Newman, M.R. Stothar, P. Theodorou, K.A. Thompson, B.C. Verrelli, A. Whitehead, K.M. Winchell, and M.T.J. Johnson (2019). A roadmap for urban evolutionary ecology. Evolutionary Applications. 12: 384-398. PDF.
Brennan, R.S., T.M. Healy, H.J. Bryant, M.V. La, P.M. Schulte, and A. Whitehead (2018). Integrative population and physiological genomics reveals mechanisms of adaptation in killifish. Molecular Biology & Evolution. 35: 2639-2653. PDF.
Trego, M.L., E. Hoh, N.M. Kellar, S. Meszaros, M. Robbins, N.G. Dodder, A. Whitehead, and R.L. Lewison (2018). Comprehensive screening links halogenated organic compounds with testosterone levels in male Delphinus delphis from the Southern California Bight. Environmental Science and Technology, 52: 3101-3109. PDF.
Rodgers, R., J.L. Roach, N.M. Reid, A. Whitehead, and D.D. Duvernell (2018). Phylogenomic analysis of Fundulidae (Teleostei: Cyprinodotiformes) using RNA-sequencing data. Molecular Phylogenetics and Evolution. 120: 150-157. PDF.
Thompson, L.R., et al., (41 authors), and The Earth Microbiome Consortium* (2017). A communal catalogue reveals Earth’s multiscale microbial diversity. Nature, 551: 457-463. (* Whitehead is a member of The Earth Microbiome Consortium, and contributed 1,000 samples and analyses to this project)
Holland, E., J.V. Goldstone, I.N. Pessah, A. Whitehead, N.M. Reid, S.I. Karchner, M.E. Hahn, D.E. Nacci, B.W. Clark, and J.J. Stegeman (2017). Ryanodine receptor and FK506 binding protein 1 in the Atlantic killifish (Fundulus heteroclitus): A phylogenetic and population-based comparison. Aquatic Toxicology, 192: 105-117. PDF.
Whitehead, A., B.W. Clark, N.M. Reid, M.E. Hahn, and D. Nacci (2017). When evolution is the solution to pollution: Key principles, and lessons from rapid repeated adaptation of killifish (Fundulus heteroclitus) populations. Evolutionary Applications, 10: 762-783. PDF.
- one of the journal’s Top 20 most downloaded recent papers (2016-2018)
Reid, N.M., C.E. Jackson, D. Gilbert, P. Minx, M.J. Montague, T.H. Hampton, L.W. Helfrich, B.L. King, D. Nacci, N. Aluru, S.I. Karchner, J.K. Colbourne, M.E. Hahn, J.R. Shaw, M.F. Oleksiak, D.L. Crawford, W.C. Warren, and A. Whitehead (2017). The Atlantic killifish (Fundulus heteroclitus) genome and the landscape of genome variation within a population. Genome Biology & Evolution, 9(3): 659-676. PDF.
Reid, N.M., D.A. Proestou, B.W. Clark, W.C. Warren, J.K. Colbourne, J.R. Shaw, S.I. Karchner, D.L. Crawford, M.F. Oleksiak, M.E. Hahn, D. Nacci, and A. Whitehead (2016). The genomic landscape of rapid repeated evolutionary adaptation to toxic pollution in wild fish. Science, 354(6317), 1305-1308. Full text (including full access to main article and supplement).
- UCD press release, Perspective in Science, The Atlantic, New York Times, Washington Post, National Geographic, New Scientist, CNBC, Independent (UK), National Science Foundation, AAAS podcast, F1000.
- Video recording (the first 17 minutes is a narration of the main text, and the remainder is a detailed description of main text figures)
López-Duarte, P.C., F.J. Fodrie, O.P. Jensen, A. Whitehead, F. Galvez, B. Dubansky, and K.W. Able (2016). Is exposure to Macondo oil reflected in the otolith chemistry of marsh-resident fish? PLoS One, 11(9): e0162699. PDF.
Reid, N.M., and A. Whitehead (2016). Functional genomics to assess biological responses to marine pollution at physiological and evolutionary timescales: toward a vision of predictive ecotoxicology. Briefings in Functional Genomics, 15(5), 2016, 358–364. PDF.
Brennan, R.S., R. Hwang, M. Tse, N.A. Fangue, and A. Whitehead (2016). Local adaptation to osmotic environment in killifish, Fundulus heteroclitus, is supported by divergence in swimming performance but not by differences in excess post-exercise oxygen consumption or aerobic scope. Comparative Biochemistry and Physiology, Part A, 196: 11-19. PDF.
Brennan, R.S., F. Galvez, and A. Whitehead (2015). Reciprocal osmotic challenges reveal mechanisms of divergence in phenotypic plasticity in the killifish Fundulus heteroclitus. Journal of Experimental Biology, 218: 1212-1222. PDF.
Shaw, J.R., T.H. Hampton, B.L. King, A. Whitehead, F. Galvez, R.H. Gross, R.N. Keith, E. Notch, D. Jung, S.P. Glaholt, C.Y. Chen, J.K. Colbourne, and B.A. Stanton (2014). Natural selection canalizes expression variation of environmentally induced plasticity-enabling genes. Molecular Biology & Evolution, 31(11): 3002-3015. PDF.
Pilcher, W., S. Miles, S. Tang, G. Mayer, and A. Whitehead (2014). Genomic and genotoxic responses to controlled weathered-oil exposures confirm and extend field studies on impacts of the Deepwater Horizon oil spill on native killifish. PLoS One, 9(9): e106351. PDF. Supporting information.
Fodrie, F.J., K.W. Able, F. Galvez, K.L. Heck, O.P. Jensen, P.C. López-Duarte, C.W. Martin, R.E. Turner, and A. Whitehead (2014). Integrating organismal and population responses of estuarine fishes in Macondo Spill Research. BioScience, 64: 778-788. PDF.
Dubansky, B., A. Whitehead, J.T. Miller, C.D. Rice, and F. Galvez (2014). Response to comment on “Multi-tissue molecular, genomic, and developmental effects of the Deepwater Horizon oil spill on resident Gulf killifish (Fundulus grandis)”. Environmental Science and Technology, 48: 7679-7680. PubMed. PDF.
Kozak, G., R. Brennan, E. Berdan, R. Fuller, and A. Whitehead (2014). Functional and population genomic divergence within and between two species of killifish adapted to different osmotic niches. Evolution, 68: 63-80. PubMed. PDF.
Whitehead, A. (2014). Evolutionary Genomics of Environmental Pollution. In, Ecological Genomics: Ecology and the Evolution of Genes and Genomes (Christian Landry and Nadia Aubin-Horth, editors). Springer, Dordrecht, The Netherlands.
McCulloch, E., A. Whitehead, S.J. Tello, C. Rolón-Mendoza, M. Maldonado-Rodríguez, and R. Stevens (2013). Fragmentation of Atlantic forest has not affected gene flow of a widespread seed-dispersing bat. Molecular Ecology, 22: 4619-4633. PubMed. PDF.
- highlighted by a “Perspectives” article in Molecular Ecology.
Dubansky, B., A. Whitehead, J.T. Miller, C.D. Rice, and F. Galvez (2013). Multi-tissue molecular, genomic, and developmental effects of the Deepwater Horizon oil spill on resident Gulf killifish (Fundulus grandis). Environmental Science & Technology, 47: 5074-5082. PubMed. PDF.
Miller, H.D., B.W. Clark, D.E. Hinton, A. Whitehead, S. Martin, K.W. Kwok, and S.W. Kullman (2012). Anchoring ethinylestradiol induced gene expression changes with testicular morphology and reproductive function in the medaka. PLoS One, 7(12): e52479. PubMed; PDF
Whitehead, A., B. Dubansky, C. Bodinier, T. Garcia, S. Miles, C. Pilley, V. Raghunathan, J. Roach, N. Walker, R.B. Walter, C.D. Rice, and F. Galvez (2012). Genomic and physiological footprint of the Deepwater Horizon oil spill on resident marsh fishes. PNAS, 109(50): 20298-20302; PubMed; PDF
- NSF Press Release, highlighted in the NSF – 2013 budget request to congress
- results presented by Senator Bill Nelson on the floor of the U.S. Senate
Whitehead, A., B. Dubansky, C. Bodinier, T. Garcia, S. Miles, C. Pilley, V. Raghunathan, J. Roach, N. Walker, R.B. Walter, C.D. Rice, and F. Galvez (2012). Reply to Jenkins et al.: Evidence for contaminating oil exposure is closely linked in space and time to biological effects. PNAS, 109(12): E679-E679. PubMed. PDF
Garcia, T.I., Y. Shen, D. Crawford, M.F. Oleksiak, A. Whitehead, and R.B. Walter (2012). RNA-Seq reveals complex genetic response to Deepwater Horizon oil release in Fundulus grandis. BMC Genomics, 13: 474. PubMed; PDF
Whitehead, A., J.L. Roach, S. Zhang, and F. Galvez (2012). Salinity- and population-dependent genome regulatory response during osmotic acclimation in the killifish (Fundulus heteroclitus) gill. Journal of Experimental Biology, 215: 1293-1305. PubMed; PDF
Whitehead, A., W. Pilcher, D. Champlin, and D. Nacci (2012). Common mechanism underlies repeated evolution of extreme pollution tolerance. Proceedings of the Royal Society B, 279(1728): 427-433. PubMed; PDF
Flight, P.A., D. Nacci, D. Champlin, A. Whitehead, and D.M. Rand (2011). The effects of mitochondrial genotype on hypoxic survival and gene expression in a hybrid population of the killifish, Fundulus heteroclitus. Molecular Ecology, 20: 4503-4520. PubMed; PDF
Whitehead, A., F. Galvez, S. Zhang, L.M. Williams, and M.F. Oleksiak (2011). Functional genomics of physiological plasticity and local adaptation in killifish. Journal of Heredity, 102(5): 499-511. PubMed; PDF
Whitehead, A., J. Roach, S. Zhang, and F. Galvez (2011). Genomic mechanisms of evolved physiological plasticity in killifish distributed along an environmental salinity gradient. PNAS, 108(15): 6193-6198. PubMed; PDF, PDF-suppl
- highlighted by an “In This Issue” article in PNAS
- highlighted by a “Highlights in the Literature” article in Physiology
Jackson, SA, M. Bagley, A. Whitehead, D.A. Roberts, D. Duvernell, D. Nacci, and R.-L. Wang (2010). Isolation and characterization of novel microsatellite loci for Atlantic coastal killifish (Fundulus heteroclitus) from an expressed sequence tag (EST) library and cross-species amplification. Molecular Ecology Resources, 10(6): 1098-1105. PubMed; PDF
Whitehead, A., D. Triant, D. Champlin, and D. Nacci (2010). Comparative transcriptomics implicates mechanisms of evolved pollution tolerance in a killifish population. Molecular Ecology, 19: 5186-5203. PubMed; PDF
- highlighted by a “News & Views” article in Molecular Ecology.
Kullman, S.W., C.J. Mattingly, J.N. Meyer, and A. Whitehead (2010). Perspectives on Informatics in Toxicology. In, A Textbook of Modern Toxicology, 4th edition (Ernest Hodgson, editor). John Wiley and Sons, Hoboken NJ.
Cheviron, Z.A., A. Whitehead, and R.T. Brumfield (2008). Transcriptomic variation and plasticity in rufous-collared sparrows (Zonotrichia capensis) along an altitudinal gradient. Molecular Ecology, 17: 4556-4569. PubMed; PDF
- highlighted by the Faculty of 1000.
Duvernell, D, J. Lindmeier, K. Faust, and A. Whitehead (2008). Relative influences of historical and contemporary forces shaping the distribution of genetic variation in the Atlantic killifish Fundulus heteroclitus. Molecular Ecology, 17: 1344-1360. PubMed; PDF
Burnett, K, and 25 authors including A. Whitehead (2007). Fundulus as the premier teleost model in environmental biology: Opportunities for new insights using genomics. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 2: 257-286. PubMed; PDF
- highlighted by the Faculty of 1000.
Whitehead, A, S.L. Anderson, A.B. Ramirez, and B.W. Wilson (2005). Cholinesterases in aquatic biomonitoring: Assay optimization and species-specific characterization for a California native fish. Ecotoxicology 14: 597-606. PubMed; PDF
Paschall, J., M.F. Oleksiak, J. VanWye, J.L. Roach, A. Whitehead, K.J. Kolell, and D.L. Crawford (2004). FunnyBase: A systems level functional annotation of Fundulus ESTs for the analysis of gene expression. BMC Genomics 5:96. PubMed; PDF
Whitehead, A., K. Kuivila, J.L. Orlando, S.Kotelevtsev, and S.L. Anderson (2004). Genotoxicity in native fish associated with agricultural runoff events. Environmental Toxicology and Chemistry. 23(12): 2868–2877. PubMed; PDF
Whitehead, A., S.L. Anderson, K.M. Kuivila, J.L. Roach, and B. May (2003). Genetic variation among interconnected populations of Catostomus occidentalis: Implications for distinguishing impacts of contaminants from biogeographical structuring. Molecular Ecology 12: 2817-2833. PubMed; PDF