Clifford W. Cunningham

Professor in the Department of Biology

227 Bio Sci Bldg, Durham, NC 27708
Campus Box: 
(919) 660-7356

Lab Site:


  • Ph.D. 1991, Yale University

  • B.S. 1983, Yale University

Papers Published

Historical effects on beta diversity and community assembly in Amazonian trees., 5, 2012
Dexter, KG; Terborgh, JW; Cunningham, CW, Proc Natl Acad Sci U S A. 109 vol. (20); pp. 7787-7792

Evolution of life cycle, colony morphology, and host specificity in the family hydractiniidae (hydrozoa, cnidaria), 0, 2012
Miglietta, MP; Cunningham, CW, Evolution. 66 vol. (12); pp. 3876-3901

The spatial scale of genetic subdivision in populations of Ifremeria nautilei, a hydrothermal-vent gastropod from the southwest Pacific., 1, 2011
Thaler, AD; Zelnio, K; Saleu, W; Schultz, TF; Carlsson, J; Cunningham, C; Vrijenhoek, RC; Van Dover, CL, BMC Evol Biol. 11 pp. 372

Using DNA to assess errors in tropical tree identifications: How often are ecologists wrong and when does it matter?, 2010
Dexter, KG; Pennington, TD; Cunningham, CW, Ecological Monographs. (2010) 80 vol. (2); pp. 267-286

Evolution of calcium-carbonate skeletons in the hydractiniidae, 0, 2010
Miglietta, MP; McNally, L; Cunningham, CW, Integrative and Comparative Biology (BioOne). 50 vol. (3); pp. 428-435

Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences, 2010
Regier, JC; Shultz, JW; Zwick, A; Hussey, A; Ball, B; Wetzer, R; Martin, JW; Cunningham, CW, Nature. (2010) 463 vol. (7284); pp. 1079-1083

Reconciling genealogical and morphological species in a worldwide study of the Family Hydractiniidae (Cnidaria, Hydrozoa), 0, 2009
Miglietta, MP; Schuchert, P; Cunningham, CW, Zoologica Scripta. 38 vol. (4); pp. 403-430

Multiple origins of shallow-water corals from deep-sea ancestors, June, 2008
Lindner, A; Cairns, SD; Cunningham, CW, PLOs ONE. (June, 2008) 3 vol. (6); pp. e2429-e2433

From offshore to onshore: Multiple origins of shallow-water corals from deep-dea ancestors, 0, 2008
Lindner, A; Cairns, SD; Cunningham, CW, PloS one. 3 vol. (6);

Ice-age survival of Atlantic cod: Agreement between palaeoecology models and genetics, 0, 2008
Bigg, GR; Cunningham, CW; Ottersen, G; Pogson, GH; Wadley, MR; Williamson, P, Proceedings of the Royal Society of London: Biological Sciences. 275 vol. (1631); pp. 163-172

How to use genetic data to distinguish between natural and human-mediated introduction of Littorina littorea to North America, 0, 2008
Cunningham, CW, Biological Invasions. 10 vol. (1); pp. 1-6

Progressive island colonization and ancient origin of Hawaiian Metrosideros (Myrtaceae), July, 2008
Percy, DM; Garver, AM; Wagner, WL; James, HF; Cunningham, CW; Miller, SE; Fleischer, RC, Proceedings of the Royal Society of London: Biological Sciences. (July, 2008) 275 vol. (1642); pp. 1479-1490

Lessons learned from coordinating research on the North Atlantic (CORONA), November, 2008
Cunningham, CW, Ecology. (November, 2008) 89 vol. (11 SUPPL.); pp. S1

Resolving arthropod phylogeny: Exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence, December, 2008
Regier, JC; Shultz, JW; Ganley, ARD; Hussey, A; Shi, D; Ball, B; Zwick, A; Stajich, JE; Cummings, MP; Martin, JW; Cunningham, CW, Systematic Biology (OUP). (December, 2008) 57 vol. (6); pp. 920-938

Hybridization in postglacial marine habitats, 0, 2007
Riginos, C; Cunningham, CW, Molecular Ecology. 16 vol. (19); pp. 3971-3972

Nearshore fish (Pholis gunnellus) persists across the North Atlantic through multiple glacial episodes., 11, 2006
Hickerson, MJ; Cunningham, CW, Molecular Ecology. 15 vol. (13); pp. 4095-4107

Taking the first steps towards a standard for reporting on phylogenies: Minimum Information about a Phylogenetic Analysis (MIAPA), 0, 2006
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; Zmasek, C, OMICS: A Journal of Integrative Biology. 10 vol. (2); pp. 231-237

Contrasting quaternary histories in an ecologically divergent sister pair of low-dispersing intertidal fish (Xiphister) revealed by multilocus DNA analysis., February, 2005
Hickerson, MJ; Cunningham, CW, Evolution. (February, 2005) 59 vol. (2); pp. 344-360

Invited Review: Local adaptation and species segregation in two mussel (Mytilus edulis X Mytilus trossulus) hybrid zones, February, 2005
Riginos, C; Cunningham, CW, Molecular Ecology. (February, 2005) 14 vol. (2); pp. 381-400

Diversification before the most recent glaciation in Balanus glandula., 2, 2005
Wares, JP; Cunningham, CW, Biological Bulletin. 208 vol. (1); pp. 60-68

Local adaptation and species segregation in two mussel (Mytilus edulis x Mytilus trossulus) hybrid zones., 2, 2005
Riginos, C; Cunningham, CW, Molecular Ecology. 14 vol. (2); pp. 381-400

Diversity in the weapons of sexual selection: Horn evolution in the beetle genus Onthophagus (Coleoptera: Scarabaeidae), 0, 2005
Emlen, DJ; Marangelo, J; Ball, B; Cunningham, CW, Evolution. 59 vol. (5); pp. 1060-1084

Mitochondrial evolution and phylogeography in the hydrozoan Obelia geniculata (Cnidaria), January, 2005
Govindarajan, AF; Halanych, KM; Cunningham, CW, Marine Biology. (January, 2005) 146 vol. (2); pp. 213-222

The right time for synthesis in evolutionary biology, February, 2005
Cunningham, C, BioScience (BioOne). (February, 2005) 55 vol. (2); pp. 99-

Differential patterns of male and female mtDNA exchange across the Atlantic Ocean in the blue mussel, Mytilus edulis., 11, 2004
Riginos, C; Hickerson, MJ; Henzler, CM; Cunningham, CW, Evolution. 58 vol. (11); pp. 2438-2451

Distinguishing between selection and population expansion in an experimental lineage of bacteriophage T7., 5, 2002
Hahn, MW; Rausher, MD; Cunningham, CW, Genetics. 161 vol. (1); pp. 11-20

The effects of nucleotide substitution model assumptions on estimates of nonparametric bootstrap support., 4, 2002
Buckley, TR; Cunningham, CW, Molecular Biology and Evolution. 19 vol. (4); pp. 394-405

Molecular phylogenetic evidence for the independent evolutionary origin of an arthropod compound eye., 2, 2002
Oakley, TH; Cunningham, CW, Proceedings of the National Academy of Sciences of USA. 99 vol. (3); pp. 1426-1430

Molecular phylogeny of the mud lobsters and mud shrimps (Crustacea: Decapoda: Thalassinidea) using nuclear 18S rDNA and mitochondrial 16S rDNA, 0, 2002
Tudge, CC; Cunningham, CW, Invertebrate Systematics. 16 vol. (6); pp. 839-847

Mitochondrial gene rearrangements confirm the parallel evolution of the crab-like form, 0, 2002
Morrison, CL; Harvey, AW; Lavery, S; Tieu, K; Huang, Y; Cunningham, CW, Proceedings of the Royal Society of London: Biological Sciences. 269 vol. (1489); pp. 345-350

Evidence for selection at multiple allozyme loci across a mussel hybrid zone [3], 0, 2002
Riginos, C; Sukhdeo, K; Cunningham, CW, Molecular Biology and Evolution. 19 vol. (3); pp. 347-351

Morphological and genetic evidence for vicariance and refugium in Atlantic and Gulf of Mexico populations of the hermit crab Pagurus longicarpus, 0, 2002
Young, AM; Torres, C; Mack, JE; Cunningham, CW, Marine Biology. 140 vol. (5); pp. 1059-1066

Refuting a controversial case of a human-mediated marine species introduction, 0, 2002
Wares, JP; Goldwater, DS; Kong, BY; Cunningham, CW, Ecology Letters. 5 vol. (4); pp. 577-584

A comparative study of asymmetric migration events across a marine biogeographic boundary., 2, 2001
Wares, JP; Gaines, SD; Cunningham, CW, Evolution. 55 vol. (2); pp. 295-306

Phylogeography and historical ecology of the North Atlantic intertidal., 12, 2001
Wares, JP; Cunningham, CW, Evolution. 55 vol. (12); pp. 2455-2469

Erratum: Dramatic mitochondrial gene rearrangements in the hermit crab Pagurus longicarpus (Crustacea, Anomura) (Molecular Biology and Evolution (17) (639-644)), 0, 2001
Hickerson, MJ; Cunningham, CW, Molecular Biology and Evolution. 18 vol. (12); pp. 2350-

Genetic structure in the sea: from populations to communities, 2001
Grosberg, R.K. and C.W. Cunningham, (2001)

Dramatic mitochondrial gene rearrangements in the hermit crab Pagurus longicarpus (Crustacea, anomura)., 4, 2000
Hickerson, MJ; Cunningham, CW, Molecular Biology and Evolution. 17 vol. (4); pp. 639-644

Independent contrasts succeed where ancestor reconstruction fails in a known bacteriophage phylogeny., 4, 2000
Oakley, TH; Cunningham, CW, Evolution. 54 vol. (2); pp. 397-405

A new perspective on lower metazoan relationships from 18S rDNA sequences [2], 0, 1999
Kim, J; Kim, W; Cunningham, CW, Molecular Biology and Evolution. 16 vol. (3); pp. 423-427

Some limitations of ancestral character-state reconstruction when testing evolutionary hypotheses, 0, 1999
Cunningham, CW, Systematic Biology. 48 vol. (3); pp. 665-674

Reconstructing ancestral character states: a critical reappraisal., 9, 1998
Cunningham, CW; Omland, KE; Oakley, TH, Trends in Ecology & Evolution. 13 vol. (9); pp. 361-366

Best-fit maximum-likelihood models for phylogenetic inference: Empirical tests with known phylogenies, 0, 1998
Cunningham, CW; Zhu, H; Hillis, DM, Evolution. 52 vol. (4); pp. 978-987

Support for a monophyletic Lemuriformes: Overcoming incongruence between data partitions [3], 0, 1998
Stanger-Hall, K; Cunningham, CW, Molecular Biology and Evolution. 15 vol. (11); pp. 1572-1577

Is congruence between data partitions a reliable predictor of phylogenetic accuracy? Empirically testing an iterative procedure for choosing among phylogenetic methods., 9, 1997
Cunningham, CW, Systematic Biology (OUP). 46 vol. (3); pp. 464-478

Can three incongruence tests predict when data should be combined?, 7, 1997
Cunningham, CW, Molecular Biology and Evolution. 14 vol. (7); pp. 733-740

Parallel molecular evolution of deletions and nonsense mutations in bacteriophage T7., 0, 1997
Cunningham, CW; Jeng, K; Husti, J; Badgett, M; Molineux, IJ; Hillis, DM; Bull, JJ, Molecular Biology and Evolution. 14 vol. (1); pp. 113-116

Combining data in phylogenetic analysis, 0, 1996
Huelsenbeck, JP; Bull, JJ; Cunningham, CW, Trends in Ecology and Evolution. 11 vol. (4); pp. 152-158

Class-level relationships in the phylum Cnidaria: Molecular and morphological evidence, 0, 1995
Bridge, D; Cunningham, CW; DeSalle, R; Buss, LW, Molecular Biology and Evolution. 12 vol. (4); pp. 679-689

Application and accuracy of molecular phylogenies, 0, 1994
Hillis, DM; Huelsenbeck, JP; Cunningham, CW, Science. 264 vol. (5159); pp. 671-677

Is character weighting a panacea for the problem of data heterogeneity in phylogenetic analysis?, 0, 1994
Huelsenbeck, JP; Swofford, DL; Cunningham, CW; Bull, JJ; Waddell, PJ, Systematic Biology. 43 vol. (2); pp. 288-291

Experimental molecular evolution of bacteriophage-t7, 8, 1993
Bull, JJ; Cunningham, CW; Molineux, IJ; Badgett, MR; Hillis, DM, Evolution. 47 vol. (4); pp. 993-1007

The evolution of gametic incompatibility in neotropical Echinometra: A reply to McClary, 0, 1993
Lessios, HA; Cunningham, CW, Evolution. 47 vol. (6); pp. 1883-1885

Molecular evidence for multiple episodes of paedomorphosis in the family Hydractiniidae, 0, 1993
Cunningham, CW; Buss, LW, Biochemical Systematics and Ecology. 21 vol. (1); pp. 57-69

Partitioning and combining data in phylogenetic analysis, 0, 1993
Bull, JJ; Huelsenbeck, JP; Cunningham, CW; Swofford, DL; Waddell, PJ, Systematic Biology. 42 vol. (3); pp. 384-397

Evolution of king crabs from hermit crab ancestors, 0, 1992
Cunningham, CW; Blackstone, NW; Buss, LW, Nature. 355 vol. (6360); pp. 539-542

Class-level relationships in the phylum Cnidaria: Evidence from mitochondrial genome structure, 0, 1992
Bridge, D; Cunningham, CW; Schierwater, B; DeSalle, R; Buss, LW, Proceedings of the National Academy of Sciences of USA. 89 vol. (18); pp. 8750-8753

Molecular and geologic evidence of shared history between hermit crabs and the symbiotic genus Hydractinia, 0, 1991
Cunningham, CW; Buss, LW; Anderson, C, Evolution. 45 vol. (6); pp. 1301-1316

Gametic incompatibility between species of the sea urchin Echinometra on the two sides of the Isthmus of Panama, 0, 1990
Lessios, HA; Cunningham, CW, Evolution. 44 vol. (4); pp. 933-941

Recruitment and postrecruitment interactions in a colonial hydroid., 0, 1987
Yund, PO; Cunningham, CW; Buss, LW, Ecology. 68 vol. (4); pp. 971-982

Crab shell-crushing predation and gastropod architectural defense, 0, 1981
Bertness, MD; Cunningham, C, Journal of Experimental Marine Biology and Ecology. 50 vol. (2-3); pp. 213-230

Book Chapters:

Ever since Gould. Book Review of "Stephen Jay Gould: Reflections on his View of Life" in , 0, 2009
C.W. Cunningham