Dexter, K., T. Pennington, and C. W. Cunningham. 2010. Using DNA to assess errors in tropical tree identifications: How often are ecologists wrong and when does it matter? Ecological Monographs 80:267-286.

Regier, J. C., J. W. Shultz, A. Zwick, A. Hussey, B. Ball, R. Wetzer, J. W. Martin, and C. W. Cunningham. 2010. Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature 463:1079-1083

C. W. Cunningham 2009
Ever since Gould. Book Review of “Stephen Jay Gould: Reflections on his View of Life”
Trends in Ecology and Evolution 24: 645-646.

Miglietta, M. P., P. Schuchert, and C. W. Cunningham 2009
Reconciling genealogical and morphological species in a worldwide study of the Family Hydractiniidae (Cnidaria, Hydrozoa).
Zoologica Scripta 38: 403-430.

Regier, J. C., J. W. Shultz, A. Ganley, A. Hussey, D. Shi, B. Ball, A. Zwick, J. Stajich, M. P. Cummings, J. W. Martin, and C. W. Cunningham 2008
Resolving arthropod phylogeny: Exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence.
Systematic Biology.

Cunningham, C.W. 2008.
Lessons Learned from Coordinating Research on the North Atlantic (CORONA).
Ecology 89:S1-S2.

Cunningham C.W. 2008.
Guest Editor of: Coordinating Research on the North Atlantic.
Ecology, Special Issue 11, Volume 89
Click for free links to Special Issue

Lindner, A., S. D. Cairns, and C. W. Cunningham 2008
Multiple origins of shallow-water corals from deep-sea ancestors.
PLOs One 

Percy, D. M., A. M. Garver, W. L. Wagner, H. F. James, C. W. Cunningham, S. E. Miller, and R. C. Fleischer. 2008.
Progressive island colonization and ancient origin of Hawaiian Metrosideros (Myrtaceae).
Proc. Roy.Soc. B

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.
Proc. Roy.Soc. B

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 

Riginos, C., and C. W. Cunningham. 2007
Hybridization in postglacial marine habitats.
Molecular Ecology

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

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

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

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 and C.W. Cunningham 2005
Diversification before the most recent glaciation in Balanus glandula. Bio. Bull. 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

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

Hahn, M. W., M. D. Rausher, and C. W. Cunningham 2002 Distinguishing Between Selection and Population Expansion in an Experimental Lineage of Bacteriophage T7.

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

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, T. H. and C. W. Cunningham� 2002 Molecular phylogenetic evidence for the independent evolutionary origin of an arthropod compound eye.
 99: 1426-1430

Riginos, C., K. Sukhdeo, and C. W. Cunningham 2002
Evidence for Selection at Multiple Allozyme Loci Across a Mussel Hybrid Zone.
Mol. Biol. Evol. 
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 and 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.

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

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).
Mol. Biol. Evol.

Oakley, T. and Cunningham, C. W. 2000
Ancestor state reconstruction fails where independent contrasts succeed in a known viral phylogeny.

Cunningham, C. W. 1999
Some limitations of ancestral character state reconstruction when testing evolutionary hypotheses.
Systematic Biology

Kim, J., W. Kim, and C. W. Cunningham. 1999
A new perspective on lower metazoan relationships from 18S rDNA sequences.
Mol. Biol. Evol.

Stanger-Hall, K., and C. W. Cunningham. 1998
Support for a monophyletic Lemuriformes: Overcoming incongruence between data partitions.
Mol. Biol. Evol.

C.W. Cunningham, K. Omland , and T. Oakley 1998
Reconstructing ancestral states, a critical reappraisal.
Trends in Ecology and Evolution 
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.

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?
Mol. Biol. Evol.

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.
Mol. Biol. Evol.

J. P. Huelsenbeck, J. J. Bull, and C. W. Cunningham, 1996.
Combining data in phylogenetic analysis.
Trends in Ecology and Evolution 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.
Mol. Biol. Evol.

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.

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.

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.

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

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.