Scholars@Duke

• Background
• 

  Education, Training, & Certifications

  • Ph.D., Yale University 1991
  • B.S., Yale University 1983
• 

  Duke Appointment History

  • Faculty Research Scholar of DuPRI's Center for Population Health & Aging, Center for Population Health & Aging, Duke Population Research Institute 2011
  • Associate Professor of Biology, Biology, Trinity College of Arts & Sciences 2001 - 2010
  • Assistant Professor of Biology, Biology, Trinity College of Arts & Sciences 2000 - 2001
  • Assistant Professor of Zoology, Biology, Trinity College of Arts & Sciences 1994 - 2000
• Research
• 

  Selected Grants

  • Genetics Training Grant awarded by National Institutes of Health 1979 - 2020
  • Collaborative Research: Connectivity in Western Atlantic Seep Populations: Oceanographic and Life-History Processes Underlying Genetic Structure awarded by  National Science Foundation 2010 - 2015
  • Collaborative Research: Assembling the Tree of Life-An Integrative Approach to Investigating Cnidarian Phylogeny awarded by  National Science Foundation 2005 - 2010
  • DISSERTATION RESEARCH: Novel Approaches to the Study of the Community Ecology of Tropical Trees awarded by  National Science Foundation 2006 - 2009
  • Deep arthropod phylogeny from 120 targeted nuclear coding-region sequences awarded by  National Science Foundation 2001 - 2007
  • Collaborative Research: Extreme discordance between allozyme and non-allozyme introgression in Baltic Mussels awarded by  National Science Foundation 2003 - 2006
  • DISSERTATION RESEARCH: A multi-locus study of genetic impact of rafting in North Atlantic amphipods. awarded by  National Science Foundation 2004 - 2006
  • RCN The North Atlantic Project: Historical Ecology of the Trans-Atlantic Biota awarded by  National Science Foundation 2002 - 2006
  • REU Supplement: PEET: Monographic Studies of the Hydractinioidea awarded by  National Science Foundation 1999 - 2005
  • PEET: Collaborative Research: Monographic Studies of the Hydractinioidea awarded by  National Science Foundation 1999 - 2003
  • Biogeographic History of Northern Hemisphere Coastal Fishes awarded by  National Science Foundation 2002 - 2003
  • Doctoral Dissertation: Comparative Phylogeography and Extinction-Recolonization Dynamics of the North Atlantic awarded by  National Science Foundation 1999 - 2001
  • Dissertation Enhancement: Testing the Independent Origin of Compound Eyes in Ostracoda (Crustacea): A Step Beyond ... 1999 - 2001
  • Utilization of Known Phylogenies for Assessing and Improving Reconstruction of the History of Life 1997 - 2000
  • Collaborative Research: Hermits, King, Convergence: Integrating Molecules and Morphology to Study the Phytogenetic Relationships of the Anomura awarded by  National Science Foundation 1997 - 2000
  • Collaborative Research: Hermits, Kings, and Convergence: Integrating Molecules and Morphology to Study the Phylogenetic Relationships of the Anomura awarded by  National Science Foundation 1997 - 2000
  • Documenting the Effect of the El Nino Southern Oscillation Event on a Broadly Dispersing.... awarded by  National Science Foundation 1998 - 1999
  • Utilization of Known Phylogenies for Assessing and Improving Reconstruction of the History of Life on Earth 1997 - 1999
  • Utilization of Known Phylogenies for Assessing & Improving Reconstruction of the History of Life 1997 - 1998
• Publications & Artistic Works
• 

  Selected Publications

  • Academic Articles

    • LaBella, A. L., C. L. Van Dover, D. Jollivet, and C. W. Cunningham. “Gene flow between Atlantic and Pacific Ocean basins in three lineages of deep-sea clams (Bivalvia: Vesicomyidae: Pliocardiinae) and subsequent limited gene flow within the Atlantic.” Deep Sea Research Part Ii: Topical Studies in Oceanography 137 (March 1, 2017): 307–17. https://doi.org/10.1016/j.dsr2.2016.08.013.
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    • Miglietta, Maria Pia, and Clifford W. Cunningham. “Evolution of life cycle, colony morphology, and host specificity in the family Hydractiniidae (Hydrozoa, Cnidaria).” Evolution; International Journal of Organic Evolution 66, no. 12 (December 2012): 3876–3901. https://doi.org/10.1111/j.1558-5646.2012.01717.x.
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    • Dexter, Kyle G., John W. Terborgh, and Clifford W. Cunningham. “Historical effects on beta diversity and community assembly in Amazonian trees.” Proceedings of the National Academy of Sciences of the United States of America 109, no. 20 (May 2012): 7787–92. https://doi.org/10.1073/pnas.1203523109.
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    • Thaler, Andrew D., Kevin Zelnio, William Saleu, Thomas F. Schultz, Jens Carlsson, Clifford Cunningham, Robert C. Vrijenhoek, and Cindy L. Van Dover. “The spatial scale of genetic subdivision in populations of Ifremeria nautilei, a hydrothermal-vent gastropod from the southwest Pacific.” Bmc Evolutionary Biology 11 (December 22, 2011): 372. https://doi.org/10.1186/1471-2148-11-372.
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    • Miglietta, Maria P., Leah McNally, and Clifford W. Cunningham. “Evolution of calcium-carbonate skeletons in the Hydractiniidae.” Integr Comp Biol 50, no. 3 (September 2010): 428–35. https://doi.org/10.1093/icb/icq102.
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    • Dexter, K. G., T. D. Pennington, and C. W. Cunningham. “Using DNA to assess errors in tropical tree identifications: How often are ecologists wrong and when does it matter?” Ecological Monographs 80, no. 2 (May 1, 2010): 267–86. https://doi.org/10.1890/09-0267.1.
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    • Regier, Jerome C., Jeffrey W. Shultz, Andreas Zwick, April Hussey, Bernard Ball, Regina Wetzer, Joel W. Martin, and Clifford W. Cunningham. “Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences.” Nature 463, no. 7284 (February 10, 2010): 1079–83. https://doi.org/10.1038/nature08742.
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    • Miglietta, M. P., P. Schuchert, and C. W. Cunningham. “Reconciling genealogical and morphological species in a worldwide study of the Family Hydractiniidae (Cnidaria, Hydrozoa).” Zoologica Scripta 38, no. 4 (July 1, 2009): 403–30. https://doi.org/10.1111/j.1463-6409.2008.00376.x.
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    • Regier, Jerome C., Jeffrey W. Shultz, Austen R. D. Ganley, April Hussey, Diane Shi, Bernard Ball, Andreas Zwick, et al. “Resolving arthropod phylogeny: exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence.” Systematic Biology 57, no. 6 (December 2008): 920–38. https://doi.org/10.1080/10635150802570791.
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    • Cunningham, Clifford W. “Lessons learned from coordinating research on the North Atlantic (CORONA).” Ecology 89, no. 11 Suppl (November 2008): S1–2. https://doi.org/10.1890/08-1533.1.
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    • Percy, Diana M., Adam M. Garver, Warren L. Wagner, Helen F. James, Clifford W. Cunningham, Scott E. Miller, and Robert C. Fleischer. “Progressive island colonization and ancient origin of Hawaiian Metrosideros (Myrtaceae).” Proceedings. Biological Sciences 275, no. 1642 (July 2008): 1479–90. https://doi.org/10.1098/rspb.2008.0191.
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    • Lindner, Alberto, Stephen D. Cairns, and Clifford W. Cunningham. “From offshore to onshore: multiple origins of shallow-water corals from deep-sea ancestors.” Plos One 3, no. 6 (June 18, 2008): e2429. https://doi.org/10.1371/journal.pone.0002429.
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    • Lindner, A., S. D. Cairns, and C. W. Cunningham. “Multiple origins of shallow-water corals from deep-sea ancestors.” Plos One 3, no. 6 (June 2008): e2429–33.
    • Bigg, Grant R., Clifford W. Cunningham, Geir Ottersen, Grant H. Pogson, Martin R. Wadley, and Phillip Williamson. “Ice-age survival of Atlantic cod: agreement between palaeoecology models and genetics.” Proceedings of the Royal Society B: Biological Sciences 275, no. 1631 (January 2008): 163–72. https://doi.org/10.1098/rspb.2007.1153.
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    • Cunningham, C. W. “How to use genetic data to distinguish between natural and human-mediated introduction of Littorina littorea to North America.” Biological Invasions 10, no. 1 (January 1, 2008): 1–6. https://doi.org/10.1007/s10530-007-9099-8.
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    • Riginos, Cynthia, and Clifford W. Cunningham. “Hybridization in postglacial marine habitats.” Molecular Ecology 16, no. 19 (October 2007): 3971–72. https://doi.org/10.1111/j.1365-294x.2007.03505.x.
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    • Hickerson, M. J., and C. W. Cunningham. “Nearshore fish (Pholis gunnellus) persists across the North Atlantic through multiple glacial episodes.” Molecular Ecology 15, no. 13 (November 2006): 4095–4107. https://doi.org/10.1111/j.1365-294x.2006.03085.x.
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    • Leebens-Mack, Jim, Todd Vision, Eric Brenner, John E. Bowers, Steven Cannon, Mark J. Clement, Clifford W. Cunningham, et al. “Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA).” Omics : A Journal of Integrative Biology 10, no. 2 (January 2006): 231–37. https://doi.org/10.1089/omi.2006.10.231.
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    • Emlen, Douglas J., Jennifer Marangelo, Bernard Ball, and Clifford W. Cunningham. “Diversity in the weapons of sexual selection: horn evolution in the beetle genus Onthophagus (Coleoptera: Scarabaeidae).” Evolution; International Journal of Organic Evolution 59, no. 5 (May 2005): 1060–84. https://doi.org/10.1111/j.0014-3820.2005.tb01044.x.
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    • Hickerson, Michael J., and Clifford W. Cunningham. “Contrasting quaternary histories in an ecologically divergent sister pair of low-dispersing intertidal fish (Xiphister) revealed by multilocus DNA analysis.” Evolution; International Journal of Organic Evolution 59, no. 2 (February 2005): 344–60. https://doi.org/10.1111/j.0014-3820.2005.tb00994.x.
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    • Riginos, C., and C. W. Cunningham. “Invited Review: Local adaptation and species segregation in two mussel (Mytilus edulis X Mytilus trossulus) hybrid zones.” Molecular Ecology 14, no. 2 (February 2005): 381–400.
    • Riginos, C., and C. W. Cunningham. “Local adaptation and species segregation in two mussel (Mytilus edulis x Mytilus trossulus) hybrid zones.” Molecular Ecology 14, no. 2 (February 2005): 381–400. https://doi.org/10.1111/j.1365-294x.2004.02379.x.
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    • Wares, John P., and Clifford W. Cunningham. “Diversification before the most recent glaciation in Balanus glandula.” The Biological Bulletin 208, no. 1 (February 2005): 60–68. https://doi.org/10.2307/3593101.
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    • Cunningham, C. “The right time for synthesis in evolutionary biology.” Bioscience 55, no. 2 (January 1, 2005): 99. https://doi.org/10.1641/0006-3568(2005)055[0099:TRTFSI]2.0.CO;2.
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    • Govindarajan, A. F., K. M. Halanych, and C. W. Cunningham. “Mitochondrial evolution and phylogeography in the hydrozoan Obelia geniculata (Cnidaria).” Marine Biology 146, no. 2 (January 1, 2005): 213–22. https://doi.org/10.1007/s00227-004-1434-3.
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    • Riginos, Cynthia, Michael J. Hickerson, Christine M. Henzler, and Clifford W. Cunningham. “Differential patterns of male and female mtDNA exchange across the Atlantic Ocean in the blue mussel, Mytilus edulis.” Evolution; International Journal of Organic Evolution 58, no. 11 (November 2004): 2438–51. https://doi.org/10.1111/j.0014-3820.2004.tb00873.x.
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    • Tudge, C. C., and C. W. Cunningham. “Molecular phylogeny of the mud lobsters and mud shrimps (Crustacea: Decapoda: Thalassinidea) using nuclear 18S rDNA and mitochondrial 16S rDNA.” Invertebrate Systematics 16, no. 6 (December 1, 2002): 839–47. https://doi.org/10.1071/IS02012.
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    • Young, A. M., C. Torres, J. E. Mack, and C. W. Cunningham. “Morphological and genetic evidence for vicariance and refugium in Atlantic and Gulf of Mexico populations of the hermit crab Pagurus longicarpus.” Marine Biology 140, no. 5 (December 1, 2002): 1059–66. https://doi.org/10.1007/s00227-002-0780-2.
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    • Wares, J. P., D. S. Goldwater, B. Y. Kong, and C. W. Cunningham. “Refuting a controversial case of a human-mediated marine species introduction.” Ecology Letters 5, no. 4 (August 10, 2002): 577–84. https://doi.org/10.1046/j.1461-0248.2002.00359.x.
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    • Hahn, Matthew W., Mark D. Rausher, and Clifford W. Cunningham. “Distinguishing between selection and population expansion in an experimental lineage of bacteriophage T7.” Genetics 161, no. 1 (May 2002): 11–20.
    • Buckley, Thomas R., and Clifford W. Cunningham. “The effects of nucleotide substitution model assumptions on estimates of nonparametric bootstrap support.” Molecular Biology and Evolution 19, no. 4 (April 2002): 394–405. https://doi.org/10.1093/oxfordjournals.molbev.a004094.
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    • Riginos, Cynthia, Kumar Sukhdeo, and Clifford W. Cunningham. “Evidence for selection at multiple allozyme loci across a mussel hybrid zone.” Molecular Biology and Evolution 19, no. 3 (March 2002): 347–51. https://doi.org/10.1093/oxfordjournals.molbev.a004088.
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    • Morrison, C. L., A. W. Harvey, S. Lavery, K. Tieu, Y. Huang, and C. W. Cunningham. “Mitochondrial gene rearrangements confirm the parallel evolution of the crab-like form.” Proceedings. Biological Sciences 269, no. 1489 (February 2002): 345–50. https://doi.org/10.1098/rspb.2001.1886.
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    • Oakley, Todd H., and Clifford W. Cunningham. “Molecular phylogenetic evidence for the independent evolutionary origin of an arthropod compound eye.” Proceedings of the National Academy of Sciences of the United States of America 99, no. 3 (February 2002): 1426–30. https://doi.org/10.1073/pnas.032483599.
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    • Hickerson, M. J., and C. W. Cunningham. “Erratum: Dramatic mitochondrial gene rearrangements in the hermit crab Pagurus longicarpus (Crustacea, Anomura) (Molecular Biology and Evolution (17) (639-644)).” Molecular Biology and Evolution 18, no. 12 (December 24, 2001): 2350.
    • Wares, J. P., and C. W. Cunningham. “Phylogeography and historical ecology of the North Atlantic intertidal.” Evolution; International Journal of Organic Evolution 55, no. 12 (December 2001): 2455–69. https://doi.org/10.1111/j.0014-3820.2001.tb00760.x.
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    • Wares, J. P., S. D. Gaines, and C. W. Cunningham. “A comparative study of asymmetric migration events across a marine biogeographic boundary.” Evolution; International Journal of Organic Evolution 55, no. 2 (February 2001): 295–306. https://doi.org/10.1111/j.0014-3820.2001.tb01294.x.
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    • Hickerson, M. J., and C. W. Cunningham. “Dramatic mitochondrial gene rearrangements in the hermit crab Pagurus longicarpus (Crustacea, anomura).” Molecular Biology and Evolution 17, no. 4 (April 2000): 639–44. https://doi.org/10.1093/oxfordjournals.molbev.a026342.
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    • Oakley, T. H., and C. W. Cunningham. “Independent contrasts succeed where ancestor reconstruction fails in a known bacteriophage phylogeny.” Evolution; International Journal of Organic Evolution 54, no. 2 (April 2000): 397–405. https://doi.org/10.1111/j.0014-3820.2000.tb00042.x.
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    • Kim, J., W. Kim, and C. W. Cunningham. “A new perspective on lower metazoan relationships from 18S rDNA sequences.” Molecular Biology and Evolution 16, no. 3 (March 1999): 423–27. https://doi.org/10.1093/oxfordjournals.molbev.a026124.
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    • Cunningham, C. W. “Some limitations of ancestral character-state reconstruction when testing evolutionary hypotheses.” Systematic Biology 48, no. 3 (January 1, 1999): 665–74. https://doi.org/10.1080/106351599260238.
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    • Stanger-Hall, K., and C. W. Cunningham. “Support for a monophyletic lemuriformes: overcoming incongruence between data partitions.” Molecular Biology and Evolution 15, no. 11 (November 1998): 1572–77. https://doi.org/10.1093/oxfordjournals.molbev.a025885.
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    • Cunningham, C. W., K. E. Omland, and T. H. Oakley. “Reconstructing ancestral character states: a critical reappraisal.” Trends in Ecology & Evolution 13, no. 9 (September 1998): 361–66. https://doi.org/10.1016/s0169-5347(98)01382-2.
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    • Cunningham, C. W., H. Zhu, and D. M. Hillis. “Best-fit maximum-likelihood models for phylogenetic inference: Empirical tests with known phylogenies.” Evolution 52, no. 4 (January 1, 1998): 978–87. https://doi.org/10.1111/j.1558-5646.1998.tb01827.x.
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    • Cunningham, C. W. “Is congruence between data partitions a reliable predictor of phylogenetic accuracy? Empirically testing an iterative procedure for choosing among phylogenetic methods.” Systematic Biology 46, no. 3 (September 1997): 464–78. https://doi.org/10.1093/sysbio/46.3.464.
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    • Cunningham, C. W. “Can three incongruence tests predict when data should be combined?” Molecular Biology and Evolution 14, no. 7 (July 1997): 733–40. https://doi.org/10.1093/oxfordjournals.molbev.a025813.
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    • Cunningham, C. W., K. Jeng, J. Husti, M. Badgett, I. J. Molineux, D. M. Hillis, and J. J. Bull. “Parallel molecular evolution of deletions and nonsense mutations in bacteriophage T7.” Molecular Biology and Evolution 14, no. 1 (January 1997): 113–16. https://doi.org/10.1093/oxfordjournals.molbev.a025697.
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    • Huelsenbeck, J. P., J. J. Bull, and C. W. Cunningham. “Combining data in phylogenetic analysis.” Trends in Ecology & Evolution 11, no. 4 (April 1996): 152–58. https://doi.org/10.1016/0169-5347(96)10006-9.
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    • Bridge, D., C. W. Cunningham, R. DeSalle, and L. W. Buss. “Class-level relationships in the phylum Cnidaria: molecular and morphological evidence.” Molecular Biology and Evolution 12, no. 4 (July 1995): 679–89. https://doi.org/10.1093/oxfordjournals.molbev.a040246.
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    • Hillis, D. M., J. P. Huelsenbeck, and C. W. Cunningham. “Application and accuracy of molecular phylogenies.” Science (New York, N.Y.) 264, no. 5159 (April 1994): 671–77. https://doi.org/10.1126/science.8171318.
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    • Huelsenbeck, J. P., D. L. Swofford, C. W. Cunningham, P. Bull, and P. J. Waddell. “Is character weighting a panacea for the problem of data heterogeneity in phylogenetic analysis?” Systematic Biology 43, no. 2 (January 1, 1994): 288–91. https://doi.org/10.1093/sysbio/43.2.288.
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    • Lessios, H. A., and C. W. Cunningham. “The evolution of gametic incompatibility in neotropical Echinometra: A reply to McClary.” Evolution 47, no. 6 (December 1, 1993): 1883–85.
    • Bull, J. J., C. W. Cunningham, I. J. Molineux, M. R. Badgett, and D. M. Hillis. “Experimental molecular evolution of bacteriophage-t7.” Evolution 47, no. 4 (August 1993): 993–1007.
    • Bull, J. J., J. P. Huelsenbeck, D. L. Swofford, C. W. Cunningham, and P. J. Waddell. “Partitioning and combining data in phylogenetic analysis.” Systematic Biology 42, no. 3 (January 1, 1993): 384–97. https://doi.org/10.1093/sysbio/42.3.384.
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    • Cunningham, C. W., and L. W. Buss. “Molecular evidence for multiple episodes of paedomorphosis in the family Hydractiniidae.” Biochemical Systematics and Ecology 21, no. 1 (January 1, 1993): 57–69. https://doi.org/10.1016/0305-1978(93)90009-G.
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    • Bridge, D., C. W. Cunningham, B. Schierwater, R. DeSalle, and L. W. Buss. “Class-level relationships in the phylum Cnidaria: evidence from mitochondrial genome structure.” Proceedings of the National Academy of Sciences of the United States of America 89, no. 18 (September 1992): 8750–53. https://doi.org/10.1073/pnas.89.18.8750.
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    • Cunningham, C. W., N. W. Blackstone, and L. W. Buss. “Evolution of king crabs from hermit crab ancestors.” Nature 355, no. 6360 (February 1992): 539–42. https://doi.org/10.1038/355539a0.
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    • Cunningham, C. W., L. W. Buss, and C. Anderson. “Molecular and geologic evidence of shared history between hermit crabs and the symbiotic genus Hydractinia.” Evolution 45, no. 6 (January 1, 1991): 1301–16. https://doi.org/10.1111/j.1558-5646.1991.tb02637.x.
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    • Lessios, H. A., and C. W. Cunningham. “Gametic incompatibility between species of the sea urchin Echinometra on the two sides of the Isthmus of Panama.” Evolution 44, no. 4 (January 1, 1990): 933–41.
    • Yund, P. O., C. W. Cunningham, and L. W. Buss. “Recruitment and postrecruitment interactions in a colonial hydroid.” Ecology 68, no. 4 (January 1, 1987): 971–82. https://doi.org/10.2307/1938368.
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    • Bertness, M. D., and C. Cunningham. “Crab shell-crushing predation and gastropod architectural defense.” Journal of Experimental Marine Biology and Ecology 50, no. 2–3 (March 16, 1981): 213–30. https://doi.org/10.1016/0022-0981(81)90051-4.
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• Teaching & Mentoring
• 

  Recent Courses

  • BIOLOGY 207: Organismal Evolution 2020
  • BIOLOGY 89S: First-Year Seminar 2019
  • ETHICS 89S: Special Topic: First-Year Seminar in Ethics 2019
  • BIOLOGY 293: Research Independent Study 2018
  • BIOLOGY 493: Research Independent Study 2018
• Scholarly, Clinical, & Service Activities
• 

  Presentations & Appearances

  • Three Lectures on Honorary Tour of Taiwan. February 16, 2014  2014
  • Three Lectures on Honorary Tour of Taiwan. December 31, 2013  2013
  • Life Tables and Senescence in 20 species of Frogs. October 8, 2013  2013
  • Dispersal and Equilibrium Theory in the Deep Sea and in Amazonian Trees Comparing Ecological and Genetic Estimates of Dispersal Between Amazonian Tree Communities. September 18, 2013  2013
  • Dispersal and Equilibrium Theory in the Deep Sea and in Amazonian Trees Comparing Ecological and Genetic Estimates of Dispersal Between Amazonian Tree Communities. November 28, 2011  2011
  • KeyNote Presentation:As the Ice Caps Melt – Seeking Biogeographic Generalities. November 23, 2011  2011
  • Dispersal and Equilibrium Theory in the Deep Sea and in Amazonian Trees Comparing Ecological and Genetic Estimates of Dispersal Between Amazonian Tree Communities. September 6, 2011  2011
  • After 10 years in the lab: a phylogenomic framework for arthropod comparative biology. October 21, 2010  2010
  • After 10 years in the lab: a phylogenomic framework for arthropod comparative biology. September 9, 2010  2010
  • As the ice caps melt: Using past phylogeography to predict the next trans-Arctic invasion. September 7, 2010  2010
  • Evolution of ontogeny in the Hydractiniidae: Losing jellyfish and committing to the colony stage. January 5, 2010  2010
  • Comparative methods and Phylogeography. September 23, 2009  2009
  • Comparative methods and the evolution of senescence. May 12, 2009  2009
  • Darwin Anniversary Seminar:From a hermit to a king: when and where did the hermit crab lose its shell?. February 20, 2009  2009
  • Comparing ecological and genetic estimates of dispersal between Amazonian tree communities.. November 10, 2008  2008
  • Community Assembly in the Northwest Atlantic and the Lesser Antilles. February 28, 2008  2008
  • Community Assembly in the Northwest Atlantic and the Lesser Antilles. February 8, 2008  2008
  • Community Assembly in the Northwest Atlantic and the Lesser Antilles. January 15, 2008  2008
• 

  Service to the Profession

  • Editor of Special Issue of Ecology. November 1, 2008  2008
  • Systematic Biology Panel : National Science Foundation (DEB). October 20, 2008  2008

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