Bigg, G. R., C. W. Cunningham, G. Ottersen, G. H. Pogson, M. R. Wadley, and P. Williamson. 2008. Ice-age survival of Atlantic cod: agreement between palaeoecology models and genetics. Proceedings of the Royal Society B: Biological Sciences 275:163-172.

Cunningham, C. W. 2008. How to use genetic data to distinguish between natural and human-mediated introduction of Littorina littorea to North America. Biological Invasions 10:1-6.

Riginos, C., and C. W. Cunningham. 2007. Hybridization in postglacial marine habitats. Molecular Ecology 16:3971-3972.

Hickerson, M. J., and C. W. Cunningham. 2006 Nearshore fish (Pholis gunnellus) persists across the North Atlantic through multiple glacial episodes. Molecular Ecology 15:4095-4107.

Emlen, DJ, J. Marengalo, B. Ball, and C.W. Cunningham 2005 Diversity in the weapons of sexual selection: horn evolution in the beetle genus Onthophagus (Coleoptera: Scarabaeidae)
Evolution 59:1060-1084

Hickerson, M.J. and C.W. Cunningham 2005 Contrasting Quaternary Histories in an Ecologically Divergent Sister-Pair of Low-Dispersing Intertidal Fish (Xiphister) Revealed by Multi-Locus DNA Analysis Evolution 59:344-360

Riginos, C. and C.W. Cunningham 2005 Invited Review: Local Adaptation and Species Segregation in Two Mussel (Mytilus edulis x M. trossulus) Hybrid Zones
Molecular Ecology 14:381-400

Govindarajan, A.F., K.M. Halanych and C.W. Cunningham 2005 Mitochondrial Evolution and Phylogeography in the Hydrozoan Obelia geniculata
Marine Biology 146:213-222

Wares, J.P, C.W. Cunningham 2005 Diversification before the most recent glaciation in Balanus glandula
Biological Bulletin 208 60-68

Riginos, C., Hickerson, J.J., Henzler, C.M. and C.W. Cunningham 2004 Differential Patterns of Male and Female mtDNA Exchange Across the Atlantic Ocean in the Blue Mussel, Mytilus edulis
Evolution 58:2438-2451

Wares, J.P, D.S. Goldwater, B.Y.Kong and C.W. Cunningham 2002 Refuting a Controversial Case of a Human Marine Species Introduction.
Ecology Letters 5:577-584

Hahn, M. W., M. D. Rausher, and C. W. Cunningham 2002 Distinguishing Between Selection and Population Expansion in an Experimental Lineage of Bacteriophage T7.
Genetics 161:11-20

Buckley, T. R., and C. W. Cunningham 2002 The Effects of Nucleotide Substitution Model Assumptions on Estimates of Nonparametric Bootstrap Support.
Systematic Biology 39:394-405

Young, A., C. Torres and C. W. Cunningham 2002 Evidence for vicariance and refugium shown by morphological and genetic differentiation in the hermit crab Pagurus longicarpus Say in the Atlantic and Gulf of Mexico
Marine Biology 140: 1059-1066

Oakley, Todd H. and Clifford W. Cunningham  2002 Molecular phylogenetic evidence for the independent evolutionary origin of an arthropod compound eye.
PNAS 99: 1426-1430

Riginos, Cynthia, Kumar Sukhdeo, and Clifford W. Cunningham 2002 Evidence for Selection at Multiple Allozyme Loci Across a Mussel Hybrid Zone
MBE 19: 347-351

Morrison, C. L., A. W. Harvey, S. Lavery, K. Tieu, Y. Huang and C.W. Cunningham 2002 Mitochondrial gene rearrangements confirm the parallel evolution of the crab-like form
Proc. Roy. Acad. Ser. B. 269: 345-350

Tudge C.C, C.W. Cunningham 2002 Molecular phylogeny of the mud lobsters and mud shrimps (Crustacea : Decapoda : Thalassinidea) using nuclear 18S rDNA and mitochondrial 16S rDNA
Invertebrate Sytematics 16: 839-847

J.P. Wares and C. W. Cunningham 2001 Phylogeography and historical ecology of the North Atlantic intertidal
Evolution 55:2455-2469.

J. P Wares, Gaines, S.D. and Cunningham, C. W. 2001 A comparative study of asymmetric migration events across a marine biogeographic boundary.
Evolution 55:295-306

Grosberg, R. K. and C. W. Cunningham 2001 Genetic structure in the sea: from populations to communities.  Pages 61-84 in Marine Community Ecology (M. D. Bertness, S. Gaines, and M. E. Hay, eds.), Sinauer Associates, Sunderland, MA.

Hickerson, M.J. and Cunningham, C. W. 2000 Dramatic Mitochondrial Gene Rearrangements in the Hermit Crab Pagurus longicarpus (Crustacea, Anomura).
MBE 17:639-644

Oakley, T. and Cunningham, C. W. 2000 Ancestor state reconstruction fails where independent contrasts succeed in a known viral phylogeny.
Evolution 54:397-405

Cunningham, C. W. 1999 Some limitations of ancestral character state reconstruction when testing evolutionary hypotheses.
Systematic Biology 48:665-674

Kim, J., W. Kim, and C. W. Cunningham. 1999 A new perspective on lower metazoan relationships from 18S rDNA sequences.
MBE 16:423-427

Stanger-Hall, K., and C. W. Cunningham. 1998 Support for a monophyletic Lemuriformes: Overcoming incongruence between data partitions.
MBE 15:1572-1577

C.W. Cunningham, K. Omland , and T. Oakley 1998 Reconstructing ancestral states, a critical reappraisal.
TREE 13: 361-368

C.W. Cunningham, H. Zhu and D. M. Hillis 1998 Best-fit maximum likelihood models for phylogenetic inference: Empirical tests with known phylogenies.
Evolution 52:978-987

C.W. Cunningham and T. Collins, 1998 Beyond area relationships: Extinction and recolonization in marine molecular biogeography. pp. 297-322 in Molecular Approaches to Ecology and Evolution (R. DeSalle, Schierwater, B., eds.). Birkhauser Verlag, Basel, Switzerland.

C. W. Cunningham, 1997a. Is congruence between data partitions a reliable predictor of phylogenetic accuracy? Empirically testing an iterative procedure for choosing among phylogenetic methods.
Systematic Biology 46: 464-478

C. W. Cunningham, 1997b. Can three incongruence tests predict when data should be combined?
MBE 14:733-740

C. W. Cunningham, K. Jeng, J. Husti, M. Badgett, I. Molineux, D. M. Hillis, and J. J. Bull. 1997.
Parallel molecular evolution of deletions and nonsense mutations.
MBE 14:113-11614

J. P. Huelsenbeck, J. J. Bull, and C. W. Cunningham, 1996. Combining data in phylogenetic analysis. TREE 11:152-157

D. Bridge, C.W. Cunningham, L. Buss, and R. DeSalle 1995. Class-level relationships in the Phylum Cnidaria: Molecular and Morphological Evidence.
MBE 12:679-689

C.W. Cunningham and T. Collins 1994. Developing model systems for molecular biogeography: vicariance and interchange in marine invertebrates . pp. 405-433 in Molecular Ecology and Evolution: Approaches and Applications (R. DeSalle, Schierwater, B., G. Wagner eds.). Birkhauser Verlag, Basel, Switzerland.

D.M. Hillis, J. Huelsenbeck, and C. Cunningham 1994. Application and accuracy of molecular phylogenies.
Science 264:671-676

Lessios, H.A. and C.W. Cunningham 1994. Gametic incompatibility in the sea urchin Echinometra: reply to McClary.
Evolution 47:1883-1885

Huelsenbeck, J.P., D.L. Swofford, C.W. Cunningham, J.J. Bull, and P.W. Waddell 1994. Is character weighting a panacea for the problem of data heterogeneity in phylogenetic analysis?
Systematic Biology 43: 288-291

Bull, J.J., J. Huelsenbeck, C.W. Cunningham, D.L. Swofford, and P. Waddell. 1993. Partitioning and Combining Data in Phylogenetic Analysis.
Systematic Biology 42: 384-3979.

Bull, J.J., C.W. Cunningham, I.J. Molineux, M.R. Badgett, and D.M. Hillis. 1993. Experimental Molecular Evolution of Bacteriophage T7.
Evolution 47:993-1007

Cunningham, C.W. and L.W. Buss 1993. Molecular evidence for multiple episodes of paedomorphosis in the Family Hydractiniidae.
Biochemical Systematics and Ecology 21:57-69.

Bridge, D., C.W. Cunningham, B. Schierwater, R. DeSalle, and L.W. Buss, 1992. Mitochondrial DNA Structure and Cnidarian Phylogeny.
PNAS. 89:8750-8753.

Cunningham, C.W., N.W. Blackstone, and L.W. Buss, 1992. Evolution of king crabs from hermit crab ancestors.
Nature 335:539-542.

Cunningham, C.W., L.W. Buss, and C. Anderson, 1991. Molecular and geologic evidence of shared history between hermit crabs and the genus Hydractinia.
Evolution 46:1301-1316.

Lessios, H.A. and C.W. Cunningham, 1990. Gametic incompatibility between species of the sea urchin Echinometra on the two sides of the isthmus of Panama.
Evolution 44:933-941.

Yund, P.O., C.W. Cunningham, and L.W. Buss, 1987. Recruitment and post-recruitment interactions in a colonial hydroid.
Ecology 68:971-982.

Bertness, M.D. and C.W. Cunningham, 1981. Crab shell crushing predation and gastropod architectural defense.
Journal of Experimental Marine Biology and Ecology 50:213-230.

 New Regier Data