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
  - 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
  - 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 (2010): 1079-1083. 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
  - 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 of the Royal Society B: Biological Sciences 275, no. 1631 (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
  - Lindner, A, Cairns, SD, and Cunningham, CW. "From offshore to onshore: Multiple origins of shallow-water corals from deep-dea ancestors." PLoS ONE 3, no. 6 (2008). Full Text Open Access Copy
  - 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 of the Royal Society B: Biological Sciences 275, no. 1642 (2008): 1479-1490. 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 (2008): 920-938. 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 (2006): 231-237. 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 59, no. 2 (February 2005): 344-360. Link to Item
  - 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." Mol Ecol 14, no. 2 (February 2005): 381-400. (Review) Full Text Link to Item
  - Wares, JP, and Cunningham, CW. "Diversification before the most recent glaciation in Balanus glandula." Biol Bull 208, no. 1 (February 2005): 60-68. Full Text Link to Item
  - Cunningham, C. "The right time for synthesis in evolutionary biology." BioScience 55, no. 2 (2005): 99--.
  - 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 59, no. 5 (2005): 1060-1084.
  - 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. Link to Item
  - Buckley, TR, and Cunningham, CW. "The effects of nucleotide substitution model assumptions on estimates of nonparametric bootstrap support." Mol Biol Evol 19, no. 4 (April 2002): 394-405. Full Text Link to Item
  - 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 of the Royal Society B: Biological Sciences 269, no. 1489 (2002): 345-350. Full Text
  - Riginos, C, Sukhdeo, K, and Cunningham, CW. "Evidence for selection at multiple allozyme loci across a mussel hybrid zone [3]." Molecular Biology and Evolution 19, no. 3 (2002): 347-351.
  - 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)." Mol Biol Evol 17, no. 4 (April 2000): 639-644. Full Text Link to Item
  - 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." Syst Biol 46, no. 3 (September 1997): 464-478. Link to Item
  - Cunningham, CW. "Can three incongruence tests predict when data should be combined?." Mol Biol Evol 14, no. 7 (July 1997): 733-740. Full Text Link to Item
  - 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 and Evolution 11, no. 4 (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.
  - 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, Blackstone, NW, and Buss, LW. "Evolution of king crabs from hermit crab ancestors." Nature 355, no. 6360 (1992): 539-542. Full Text
  - 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 2018
- 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

Some information on this profile has been compiled automatically from Duke databases and external sources. (Our About page explains how this works.) If you see a problem with the information, please write to Scholars@Duke and let us know. We will reply promptly.

Education, Training, & Certifications

Duke Appointment History

Selected Grants

Selected Publications

Journal Articles

Recent Courses

Presentations & Appearances

Service to the Profession