Clifford W. Cunningham | Scholars@Duke

Clifford W. Cunningham
Professor in the Department of Biology

Current Appointments & Affiliations

Professor in the Department of Biology, Biology, Trinity College of Arts & Sciences 2010

Contact Information

227 Bio Sci Bldg, Durham, NC 27708
Box 90338, Biology Department, Durham, NC 27708-0338
cliff@duke.edu (919) 660-7356
http://www.biology.duke.edu/cunningham/

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 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 ... awarded by Division of International Programs 1999 - 2001
- Utilization of Known Phylogenies for Assessing and Improving Reconstruction of the History of Life awarded by National Aeronautics and Space Administration 1997 - 2000
- (97-0011) Collaborative Research: Hermits, Kings, and Convergence: Integrating Molecules and Morphology to Study the Phy awarded by National Science Foundation 1997 - 2000
- (97-0658) Collaborative Research: Hermits, King, Convergence: Integrating Molecules and Morphology to Study the Phytogen awarded by National Science Foundation 1997 - 2000
- (98-0526) 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 awarded by National Aeronautics and Space Administration 1997 - 1999
- (97-0604) Utilization of Known Phylogenies for Assessing & Improving Reconstruction of the History of Life awarded by National Aeronautics and Space Administration 1997 - 1998
Publications & Artistic Works
Selected Publications
- Journal Articles
  - LaBella, AL, Van Dover, CL, Jollivet, D, and Cunningham, CW. "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 2017): 307-317. Full Text
  - Dexter, KG, Terborgh, JW, and Cunningham, CW. "Historical effects on beta diversity and community assembly in Amazonian trees." Proc Natl Acad Sci U S A 109, no. 20 (May 15, 2012): 7787-7792. Full Text Link to Item
  - Miglietta, MP, and Cunningham, CW. "Evolution of life cycle, colony morphology, and host specificity in the family hydractiniidae (hydrozoa, cnidaria)." Evolution 66, no. 12 (2012): 3876-3901. Full Text
  - Thaler, AD, Zelnio, K, Saleu, W, Schultz, TF, Carlsson, J, Cunningham, C, Vrijenhoek, RC, and Van Dover, CL. "The spatial scale of genetic subdivision in populations of Ifremeria nautilei, a hydrothermal-vent gastropod from the southwest Pacific." BMC evolutionary biology 11 (January 2011): 372-. Full Text
  - Regier, JC, Shultz, JW, Zwick, A, Hussey, A, Ball, B, Wetzer, R, Martin, JW, and Cunningham, CW. "Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences." Nature 463, no. 7284 (February 10, 2010): 1079-1083. Full Text
  - Dexter, KG, Pennington, TD, and Cunningham, CW. "Using DNA to assess errors in tropical tree identifications: How often are ecologists wrong and when does it matter?." Ecological Monographs 80, no. 2 (2010): 267-286. Full Text
  - Miglietta, MP, McNally, L, and Cunningham, CW. "Evolution of calcium-carbonate skeletons in the hydractiniidae." Integrative and Comparative Biology 50, no. 3 (2010): 428-435. Full Text
  - Miglietta, MP, Schuchert, P, and Cunningham, CW. "Reconciling genealogical and morphological species in a worldwide study of the Family Hydractiniidae (Cnidaria, Hydrozoa)." Zoologica Scripta 38, no. 4 (2009): 403-430. Full Text
  - Regier, JC, Shultz, JW, Ganley, ARD, Hussey, A, Shi, D, Ball, B, Zwick, A, Stajich, JE, Cummings, MP, Martin, JW, and Cunningham, CW. "Resolving arthropod phylogeny: exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence." Systematic Biology 57, no. 6 (December 2008): 920-938. Full Text
  - Percy, DM, Garver, AM, Wagner, WL, James, HF, Cunningham, CW, Miller, SE, and Fleischer, RC. "Progressive island colonization and ancient origin of Hawaiian Metrosideros (Myrtaceae)." Proceedings. Biological Sciences 275, no. 1642 (July 2008): 1479-1490. Full Text
  - Lindner, A, Cairns, SD, and Cunningham, CW. "From offshore to onshore: multiple origins of shallow-water corals from deep-sea ancestors." Plos One 3, no. 6 (June 18, 2008): e2429-null. Full Text Open Access Copy
  - Lindner, A, Cairns, SD, and Cunningham, CW. "Multiple origins of shallow-water corals from deep-sea ancestors." PLOs ONE 3, no. 6 (June 2008): e2429-e2433. (Academic Article)
  - Bigg, GR, Cunningham, CW, Ottersen, G, Pogson, GH, Wadley, MR, and Williamson, P. "Ice-age survival of Atlantic cod: agreement between palaeoecology models and genetics." Proceedings. Biological Sciences 275, no. 1631 (January 2008): 163-172. Full Text
  - Cunningham, CW. "How to use genetic data to distinguish between natural and human-mediated introduction of Littorina littorea to North America." Biological Invasions 10, no. 1 (2008): 1-6. Full Text
  - Cunningham, CW. "Lessons learned from coordinating research on the North Atlantic (CORONA)." Ecology 89, no. 11 SUPPL. (2008): S1-. Full Text
  - Riginos, C, and Cunningham, CW. "Hybridization in postglacial marine habitats." Molecular Ecology 16, no. 19 (2007): 3971-3972. Full Text
  - Hickerson, MJ, and Cunningham, CW. "Nearshore fish (Pholis gunnellus) persists across the North Atlantic through multiple glacial episodes." Mol Ecol 15, no. 13 (November 2006): 4095-4107. Full Text Link to Item
  - Leebens-Mack, J, Vision, T, Brenner, E, Bowers, JE, Cannon, S, Clement, MJ, Cunningham, CW, dePamphilis, C, deSalle, R, Doyle, JJ, Eisen, JA, Gu, X, Harshman, J, Jansen, RK, Kellogg, EA, Koonin, EV, Mishler, BD, Philippe, H, Pires, JC, Qiu, Y-L, Rhee, SY, Sjölander, K, Soltis, DE, Soltis, PS, Stevenson, DW, Wall, K, Warnow, T, and Zmasek, C. "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): 231-237. (Review) Full Text
  - Emlen, DJ, Marangelo, J, Ball, B, and Cunningham, CW. "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): 1060-1084. Full Text
  - Hickerson, MJ, and Cunningham, CW. "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): 344-360. Full Text
  - Riginos, C, and Cunningham, CW. "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. (Academic Article)
  - Riginos, C, and Cunningham, CW. "Local adaptation and species segregation in two mussel (Mytilus edulis x Mytilus trossulus) hybrid zones." Molecular Ecology 14, no. 2 (February 2005): 381-400. (Review) Full Text
  - Wares, JP, and Cunningham, CW. "Diversification before the most recent glaciation in Balanus glandula." The Biological Bulletin 208, no. 1 (February 2005): 60-68. Full Text
  - Cunningham, C. "The right time for synthesis in evolutionary biology." BioScience 55, no. 2 (2005): 99--.
  - Govindarajan, AF, Halanych, KM, and Cunningham, CW. "Mitochondrial evolution and phylogeography in the hydrozoan Obelia geniculata (Cnidaria)." Marine Biology 146, no. 2 (2005): 213-222. Full Text
  - Riginos, C, Hickerson, MJ, Henzler, CM, and Cunningham, CW. "Differential patterns of male and female mtDNA exchange across the Atlantic Ocean in the blue mussel, Mytilus edulis." Evolution 58, no. 11 (November 2004): 2438-2451. Link to Item
  - Hahn, MW, Rausher, MD, and Cunningham, CW. "Distinguishing between selection and population expansion in an experimental lineage of bacteriophage T7." Genetics 161, no. 1 (May 2002): 11-20.
  - Buckley, TR, and Cunningham, CW. "The effects of nucleotide substitution model assumptions on estimates of nonparametric bootstrap support." Molecular Biology and Evolution 19, no. 4 (April 2002): 394-405. Full Text
  - Riginos, C, Sukhdeo, K, and Cunningham, CW. "Evidence for selection at multiple allozyme loci across a mussel hybrid zone." Molecular Biology and Evolution 19, no. 3 (March 2002): 347-351. (Letter) Full Text
  - Oakley, TH, and Cunningham, CW. "Molecular phylogenetic evidence for the independent evolutionary origin of an arthropod compound eye." Proc Natl Acad Sci U S A 99, no. 3 (February 5, 2002): 1426-1430. Full Text Link to Item
  - Morrison, CL, Harvey, AW, Lavery, S, Tieu, K, Huang, Y, and Cunningham, CW. "Mitochondrial gene rearrangements confirm the parallel evolution of the crab-like form." Proceedings. Biological Sciences 269, no. 1489 (February 2002): 345-350. Full Text
  - Tudge, CC, and Cunningham, CW. "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 (2002): 839-847. Full Text
  - Wares, JP, Goldwater, DS, Kong, BY, and Cunningham, CW. "Refuting a controversial case of a human-mediated marine species introduction." Ecology Letters 5, no. 4 (2002): 577-584. Full Text
  - Young, AM, Torres, C, Mack, JE, and Cunningham, CW. "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 (2002): 1059-1066. Full Text
  - Wares, JP, and Cunningham, CW. "Phylogeography and historical ecology of the North Atlantic intertidal." Evolution 55, no. 12 (December 2001): 2455-2469. Link to Item
  - Wares, JP, Gaines, SD, and Cunningham, CW. "A comparative study of asymmetric migration events across a marine biogeographic boundary." Evolution 55, no. 2 (February 2001): 295-306. Link to Item
  - Hickerson, MJ, and Cunningham, CW. "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 (2001): 2350--.
  - Hickerson, MJ, and Cunningham, CW. "Dramatic mitochondrial gene rearrangements in the hermit crab Pagurus longicarpus (Crustacea, anomura)." Molecular Biology and Evolution 17, no. 4 (April 2000): 639-644. Full Text
  - Oakley, TH, and Cunningham, CW. "Independent contrasts succeed where ancestor reconstruction fails in a known bacteriophage phylogeny." Evolution 54, no. 2 (April 2000): 397-405. Link to Item
  - Cunningham, CW. "Some limitations of ancestral character-state reconstruction when testing evolutionary hypotheses." Systematic Biology 48, no. 3 (1999): 665-674.
  - Kim, J, Kim, W, and Cunningham, CW. "A new perspective on lower metazoan relationships from 18S rDNA sequences [2]." Molecular Biology and Evolution 16, no. 3 (1999): 423-427.
  - Cunningham, CW, Omland, KE, and Oakley, TH. "Reconstructing ancestral character states: a critical reappraisal." Trends Ecol Evol 13, no. 9 (September 1, 1998): 361-366. Link to Item
  - Cunningham, CW, Zhu, H, and Hillis, DM. "Best-fit maximum-likelihood models for phylogenetic inference: Empirical tests with known phylogenies." Evolution 52, no. 4 (1998): 978-987.
  - Stanger-Hall, K, and Cunningham, CW. "Support for a monophyletic Lemuriformes: Overcoming incongruence between data partitions [3]." Molecular Biology and Evolution 15, no. 11 (1998): 1572-1577.
  - Cunningham, CW. "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): 464-478. Full Text
  - Cunningham, CW. "Can three incongruence tests predict when data should be combined?." Molecular Biology and Evolution 14, no. 7 (July 1997): 733-740. Full Text
  - Cunningham, CW, Jeng, K, Husti, J, Badgett, M, Molineux, IJ, Hillis, DM, and Bull, JJ. "Parallel molecular evolution of deletions and nonsense mutations in bacteriophage T7." Molecular biology and evolution 14, no. 1 (1997): 113-116.
  - Huelsenbeck, JP, Bull, JJ, and Cunningham, CW. "Combining data in phylogenetic analysis." Trends in Ecology & Evolution 11, no. 4 (April 1996): 152-158. Full Text
  - Bridge, D, Cunningham, CW, DeSalle, R, and Buss, LW. "Class-level relationships in the phylum Cnidaria: Molecular and morphological evidence." Molecular Biology and Evolution 12, no. 4 (1995): 679-689.
  - Hillis, DM, Huelsenbeck, JP, and Cunningham, CW. "Application and accuracy of molecular phylogenies." Science 264, no. 5159 (1994): 671-677.
  - Huelsenbeck, JP, Swofford, DL, Cunningham, CW, Bull, JJ, and Waddell, PJ. "Is character weighting a panacea for the problem of data heterogeneity in phylogenetic analysis?." Systematic Biology 43, no. 2 (1994): 288-291.
  - Bull, JJ, Cunningham, CW, Molineux, IJ, Badgett, MR, and Hillis, DM. "Experimental molecular evolution of bacteriophage-t7." Evolution 47, no. 4 (August 1993): 993-1007. (Academic Article)
  - Bull, JJ, Huelsenbeck, JP, Cunningham, CW, Swofford, DL, and Waddell, PJ. "Partitioning and combining data in phylogenetic analysis." Systematic Biology 42, no. 3 (1993): 384-397.
  - Cunningham, CW, and Buss, LW. "Molecular evidence for multiple episodes of paedomorphosis in the family Hydractiniidae." Biochemical Systematics and Ecology 21, no. 1 (1993): 57-69. Full Text
  - Lessios, HA, and Cunningham, CW. "The evolution of gametic incompatibility in neotropical Echinometra: A reply to McClary." Evolution 47, no. 6 (1993): 1883-1885.
  - Cunningham, CW, Blackstone, NW, and Buss, LW. "Evolution of king crabs from hermit crab ancestors." Nature 355, no. 6360 (February 1992): 539-542. Full Text
  - Bridge, D, Cunningham, CW, Schierwater, B, DeSalle, R, and Buss, LW. "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 (1992): 8750-8753.
  - Cunningham, CW, Buss, LW, and Anderson, C. "Molecular and geologic evidence of shared history between hermit crabs and the symbiotic genus Hydractinia." Evolution 45, no. 6 (1991): 1301-1316.
  - Lessios, HA, and Cunningham, CW. "Gametic incompatibility between species of the sea urchin Echinometra on the two sides of the Isthmus of Panama." Evolution 44, no. 4 (1990): 933-941.
  - Yund, PO, Cunningham, CW, and Buss, LW. "Recruitment and postrecruitment interactions in a colonial hydroid." Ecology 68, no. 4 (1987): 971-982.
  - Bertness, MD, and Cunningham, C. "Crab shell-crushing predation and gastropod architectural defense." Journal of Experimental Marine Biology and Ecology 50, no. 2-3 (1981): 213-230. Full Text
Teaching & Mentoring
Recent Courses
- BIOLOGY 207: Organismal Evolution 2018
- BIOLOGY 293: Research Independent Study 2018
- BIOLOGY 493: Research Independent Study 2018
- BIOLOGY 790S: Special Topics Seminar 2017
- BIOLOGY 791T: Tutorial 2016
- BIOLOGY 792: Research 2016
Scholarly, Clinical, & Service Activities
Presentations & Appearances
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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Education, Training, & Certifications

Duke Appointment History

Selected Grants

Selected Publications

Journal Articles

Recent Courses

Presentations & Appearances

Service to the Profession