2009. Neigel, J. Population Genetics and Biogeography of the Gulf of Mexico. In: Felder, D.F. and Camp, C.K. Gulf of Mexico – Its Origins, Waters, and Biota: Biota. Texas A&M University Press, College Station, Texas. in press.

2008. Mahon, B.C and J.E. Neigel. Utility of arginine kinase for resolution of phylogenetic relationships among brachyuran genera and families. Molecular Phylogenetics and Evolution. 48:718-727.

2007. Neigel, J., A. Domingo, and J. Stake. DNA barcoding as a tool for coral reef conservation. Coral Reefs  26: 487-499.

2007. Neigel, J.E. and B. C. Mahon. Molecular Approaches In Crustacean Evolutionary Ecology. In Ecology and Evolution of Social Behavior: Crustaceans as Model Systems. J. Emmett Duffy and Martin Thiel, editors. Oxford University Press.

2006. Dukes, J.P., R. Deaville, D. Gottelli, J.E. Neigel, M.W. Bruford and W.C. Jordan. Isolation and characterization of main olfactory and vomeronasal receptor gene families from the Atlantic Salmon (Salmo salar). Gene 371: 257-267

2005. Bilodeau, A.L, Felder, D.L and J.E. Neigel. Population structure at two geographic scales in the burrowing crustacean Callichirus islagrande (Decapoda, Thalassinidea): Historical and contemporary barriers to planktonic dispersal. Evolution (10): 59: 2125-2138. 

2005. Bilodeau, A.L, Felder, D.L and J.E. Neigel. Multiple paternity in the thalassinidean ghost shrimp, Callichirus islagrande. Marine Biology 146: 381-385.  

2004. Neigel, J. and P. Leberg. A prototype database for surveys of animal mitochondrial DNA variation. Journal of Heredity 95:85-88.  

2003. Neigel, J. E. Species-area relationships and marine conservation. Ecological Applications 13(1): S138-S145.

2003. Carr, M. H., J. E. Neigel, J. A. Estes, S. Andelman, R. R. Warner and J. L. Largier (2003). Comparing marine and terrestrial ecosystems: Implications for the design of coastal marine reserves. Ecological Applications 13(1): S90-S107.

2002. Hellberg, M.E., Burton, R.S., Neigel,J.E.and S. R. Palumbi. Genetic assessment of connectivity among marine populations. Bulletin of Marine Science 70:273-290 Suppl. S.

2002. Thorrold, S.R., Jones, G.P., Hellberg, M.E., Burton, R.S., Swearer, S.E., Neigel, J.E., Morgan, S.G. and R. R. Warner. Quantifying larval retention and connectivity in marine populations with artificial and natural markers. Bulletin of Marine Science 70:291-308 Suppl S.

2002. Mathews LM, Schubart CD, Neigel JE, and Felder DL. Genetic, ecological, and behavioural divergence between two sibling snapping shrimp species (Crustacea : Decapoda : Alpheus). Molecular Ecology 11:1427-1437.

2002 Neigel, J.E. Is F_ST obsolete? Conservation Genetics 3:167-173.

2000. Schubart, C.D., Neigel, J.E. and D.L. Felder. Molecular phylogeny of mud crabs (Brachyura: Panopeidae) from the northwestern Atlantic and the role of morphological stasis and convergence. Marine Biology 137:11-18.

2000. Spencer, C.C., Neigel, J.E. and P.L. Leberg. Evaluation of the Usefulness of Microsatellite DNA for Detecting Demographic Bottlenecks. Molecular Ecology 9:1517-1528.

2000. Schubart, C.D., Neigel, J.E. and D.L. Felder. Use of the mitochondrial 16S rRNA gene for phylogenetic and population studies of Crustacea. Crustacean Issues 12: 817-830.

1999. Leberg, P.L, and J.E. Neigel. Enhancing the retrievability of population genetic survey data: An assessment of animal mtDNA studies. Evolution 53:1961-1965.

1999. MaKinster JG, Roberts JE, Felder DL, Chlan CA, Boudreaux M, and J.E. Neigel. PCR amplification of a middle repetitive element detects larval stone crabs (Crustacea: Decapoda: Menippidae) in estuarine plankton samples. Marine Ecology Progress Series 188:161-168.

1999. Bilodeau A.L., Lankford W., Kim T., Felder D.L. and J.E. Neigel. An Ultrasensitive Method for Detection of Single Crab Larvae (Sesarma reticulatum) by PCR Amplification of a Highly Repetitive DNA Sequence. Molecular Ecology 8:683-684.

1999. Spencer, C.C., Chlan, C. A., Neigel, J.E., Scribner, K.T., Wooten, M.C. and P.L. Leberg. Polymorphic microsatellite markers in the Western Mosquitofish, Gambusia affinis. Molecular Ecology 8:157-158.

1998. Schneider-Broussard, R. Felder, D.L., C.A. Chlan and J.E. Neigel. Tests of phylogeographic models with nuclear and mitochondrial dna sequence variation in the stone crabs, Menippe adina and M. mercenaria. Evolution 52:1671-1678.

1997. Neigel, J.E. A comparison of alternative strategies for estimating dispersal and gene flow from genetic markers. Annual Reviews of Ecology and Systematics, 28: 105-128.

1997. Neigel, J.E. Population Genetics And Demography Of Marine Species. pp 274-292 in R.Ormond (ed.) Marine Biodiversity, Cambridge University Press, Cambridge, U.K.

1997. Schneider-Broussard, R. and J.E. Neigel. A large subunit mitochondrial ribosomal DNA sequence translocated to the nuclear genomes of two stone crabs. Molecular Biology and Evolution 14:156-165.

1996. Neigel, J.E. Estimation of Effective Population Size and Migration Parameters from Genetic Data. in T.Smith and R.Wayne (eds.) Molecular Conservation Genetics. Oxford University Press. 

1996. Jordan, W.C., M.W. Courtney, and J.E. Neigel. Low levels of intraspecific genetic variation at a rapidly evolving chloroplast DNA locus in duckweeds (Lemnaceae). American Journal of Botany 83:430-439

1994. Neigel, J.E. Alternative Approaches to the Detection of Genetic Structure in Marine Populations. CalCOFI Reports 35:82-89.

1993. Wong, S., T.H. Morales, J.E. Neigel and D.A. Campbell. Transcriptional linkage of the genes for calmodulin, an EF-Hand protein and ubiquitin-EP52 in Trypanosoma brucei. Molecular and Cell Biology 13:207-216.

1993. Neigel, J.E. and J.C. Avise. Application of a non-equilibrium model to geographic variation in animal mitochondrial DNA distributions. Genetics 135:1209-1220.

1992. Neigel, J.E. Proposal to establish a molecular population genetics database. Evolution 46:860.

1991. Sullivan, V.L. and J.E. Neigel and B. Maio. Bias in inheritance of chloroplast DNA and mechanisms of hybridization between wind- and insect- pollinated Eupatorium (ASTERACEAE). American Journal of Botany, 78:695-705.

1991. Neigel, J.E., D.L. Felder, C.A. Chlan and R. LaPorte. Cloning and screening of DNA hybridization probes for genetic studies in stone crabs (Decapoda: Xanthidae: Menippe). Journal of Crustacean Biology 11(4):496-505.

1991. Neigel, J.E., R.M. Ball and J.C. Avise. Estimation of single generation migration distances from geographic variation in animal mitochondrial DNA. Evolution 45:423-432.

1990. Ball, R.M., J.E. Neigel and J.C. Avise. Gene genealogies within the organismal pedigrees of random mating populations. Evolution 44:360-370.

1988. Neigel, J.E. Recognition of Self or Nonself? Theoretical Implications and an Empirical Test. in J. Clegg (ed.) The Mechanisms, Ecology and Evolution of Historecognition in Marine Invertebrates. Plenum, New York.

1987. Avise, J.C, J. Arnold, R. M. Ball, E. Bermingham, T. Lamb, J. E. Neigel, C. A. Reeb, and N. Saunders. Intraspecific phylogeography:  The mitochondrial DNA bridge between population genetics and systematics. Annual Review of Ecology and Systematics 18:489-522.

1986. Neigel, J.E. and J.C. Avise. Phylogenetic relationships of mitochondrial DNA under various demographic models of  speciation. in S. Karlin and E. Nevo (eds.) Evolutionary Processes and Theory. Academic Press, New York.

1985. Neigel, J.E. and J.C. Avise. The precision of histocompatibility responses in clonal recognition in  tropical marine sponges. Evolution 39:724-732.

1985. Neigel, J.E. Graft compatibility and clonal identity in invertebrates. Science 229:487-489.

1984. Neigel, J.E. and J.C. Avise. On a coral reef, it's a hard knock life. Natural History 93:58-65.

1984. Neigel, J.E. and G.P. Schmahl. Phenotypic variation within histocompatibility-defined clones of marine sponges. Science 224:413-415.

1984. Avise, J.C., J.E. Neigel and J. Arnold. Demographic influences on mitochondrial DNA lineage survivorship in animal populations. Journal of Molecular Evolution 20:99-105.

1983. Neigel, J.E. and J.C. Avise. Clonal diversity and population structure in a reef-building coral, Acropora cervicornis: Self-recognition analysis and demographic interpretation. Evolution 37:437-453.

1983. Neigel, J.E. and J.C. Avise. Histocompatibility bioassays of population structure in marine sponges:  Clonal structure in Verongia longissima and Iotrochota birotulata. Journal of Heredity 74:134-140.

1981. Woodley, J.D. (with 19 others). Hurricane Allen's impact on Jamaican coral reefs. Science 214: 749-755.

1981. Porter, J.W., J.D. Woodley, G.J. Smith, J.E. Neigel, J.F. Battey, and D.G. Dallmeyer. Population trends among Jamaican reef corals. Nature 294: 249-250.