Scholars@Duke
Clifford W. Cunningham

Clifford W. Cunningham

Professor of Biology
Biology
cliff@duke.edu
Box 90338, Biology Department, Durham, NC 27708-0338
371C Bio Sci Bldg, Durham, NC 27708

Selected Publications

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

Journal Article Deep-Sea Research Part II: Topical Studies in Oceanography · March 1, 2017 Pliocardiin (vesicomyid) clams rely on microbial symbionts for nutrition and are obligate inhabitants of deep-sea chemosynthetic ecosystems. Unlike many other invertebrate hosts of chemosynthetic microbes, pliocardiin clams are found in every ocean in a va ... Full text Cite

Evolution of life cycle, colony morphology, and host specificity in the family Hydractiniidae (Hydrozoa, Cnidaria).

Journal Article Evolution; international journal of organic evolution · December 2012 Biased transitions are common throughout the tree of life. The class hydrozoa is no exception, having lost the feeding medusa stage at least 70 times. The family hydractiniidae includes one lineage with pelagic medusae (Podocoryna) and several without (e.g ... Full text Cite

Historical effects on beta diversity and community assembly in Amazonian trees.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · May 2012 We present a unique perspective on the role of historical processes in community assembly by synthesizing analyses of species turnover among communities with environmental data and independent, population genetic-derived estimates of among-community disper ... Full text Cite

The spatial scale of genetic subdivision in populations of Ifremeria nautilei, a hydrothermal-vent gastropod from the southwest Pacific.

Journal Article BMC evolutionary biology · December 2011 BackgroundDeep-sea hydrothermal vents provide patchy, ephemeral habitats for specialized communities of animals that depend on chemoautotrophic primary production. Unlike eastern Pacific hydrothermal vents, where population structure has been stud ... Full text Cite

Evolution of calcium-carbonate skeletons in the Hydractiniidae.

Journal Article Integr Comp Biol · September 2010 Biomineralization has mostly been studied in the class Anthozoa (Phylum Cnidaria), but very little is known about the evolution of the calcified skeleton in the class Hydrozoa or about the processes leading to its formation. The evolution of the calcified ... Full text Link to item Cite

Using DNA to assess errors in tropical tree identifications: How often are ecologists wrong and when does it matter?

Journal Article Ecological Monographs · May 1, 2010 Ecological surveys of tropical tree communities have provided an important source of data to study the forces that generate and maintain tropical diversity. Accurate species identification is central to these studies. Incorrect lumping or splitting of spec ... Full text Cite

Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences.

Journal Article Nature · February 2010 The remarkable antiquity, diversity and ecological significance of arthropods have inspired numerous attempts to resolve their deep phylogenetic history, but the results of two decades of intensive molecular phylogenetics have been mixed. The discovery tha ... Full text Cite

Reconciling genealogical and morphological species in a worldwide study of the Family Hydractiniidae (Cnidaria, Hydrozoa)

Journal Article Zoologica Scripta · July 1, 2009 The Hydractiniidae are a family of globally distributed marine hydrozoans (class Hydrozoa, phylum Cnidaria). Despite being one of the most well-studied families of the Hydrozoa, their genus and species-level taxonomy is unsettled and disputed. The taxonomi ... Full text Cite

Progressive island colonization and ancient origin of Hawaiian Metrosideros (Myrtaceae).

Journal Article Proceedings. Biological sciences · July 2008 Knowledge of the evolutionary history of plants that are ecologically dominant in modern ecosystems is critical to understanding the historical development of those ecosystems. Metrosideros is a plant genus found in many ecological and altitudinal zones th ... Full text Cite

From offshore to onshore: multiple origins of shallow-water corals from deep-sea ancestors.

Journal Article PloS one · June 2008 Shallow-water tropical reefs and the deep sea represent the two most diverse marine environments. Understanding the origin and diversification of this biodiversity is a major quest in ecology and evolution. The most prominent and well-supported explanation ... Full text Open Access Cite

How to use genetic data to distinguish between natural and human-mediated introduction of Littorina littorea to North America

Journal Article Biological Invasions · January 1, 2008 The rapid range southward expansion of the periwinkle Littorina littorea from the Canadian maritimes has fueled a long-running debate over whether this species was introduced to North America by human activity. A reappraisal of the mitochondrial DNA sequen ... Full text Cite

Ice-age survival of Atlantic cod: agreement between palaeoecology models and genetics.

Journal Article Proceedings. Biological sciences · January 2008 Scant scientific attention has been given to the abundance and distribution of marine biota in the face of the lower sea level, and steeper latitudinal gradient in climate, during the ice-age conditions that have dominated the past million years. Here we e ... Full text Cite

Hybridization in postglacial marine habitats.

Journal Article Molecular ecology · October 2007 Within the last few million years, repeated invasions from the North Pacific have brought evolutionarily divergent lineages of Macoma balthica clams into contact in the marginal and inland seas of northern Europe (Strelkov et al. 2007). These divergent M. ... Full text Cite

Nearshore fish (Pholis gunnellus) persists across the North Atlantic through multiple glacial episodes.

Journal Article Molecular ecology · November 2006 The intertidal biota of the North Atlantic is characterized by two disjunct communities (North American and European) exposed to different climatic regimes during the Pleistocene and in the Holocene. We collect multilocus DNA sequence data from the nearsho ... Full text Cite

Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA).

Journal Article Omics : a journal of integrative biology · January 2006 In the eight years since phylogenomics was introduced as the intersection of genomics and phylogenetics, the field has provided fundamental insights into gene function, genome history and organismal relationships. The utility of phylogenomics is growing wi ... Full text Cite

Diversity in the weapons of sexual selection: horn evolution in the beetle genus Onthophagus (Coleoptera: Scarabaeidae).

Journal Article Evolution; international journal of organic evolution · May 2005 Both ornaments and weapons of sexual selection frequently exhibit prolific interspecific diversity of form. Yet, most studies of this diversity have focused on ornaments involved with female mate choice, rather than on the weapons of male competition. With ... Full text Cite

Diversification before the most recent glaciation in Balanus glandula.

Journal Article The Biological bulletin · February 2005 A deep genetic cline between southern populations of the barnacle Balanus glandula (from about Monterey Bay southward) and northern populations (from northern California through Alaska) has recently been described. If this pattern is due to historical isol ... Full text Cite

Contrasting quaternary histories in an ecologically divergent sister pair of low-dispersing intertidal fish (Xiphister) revealed by multilocus DNA analysis.

Journal Article Evolution; international journal of organic evolution · February 2005 Recurrent glacial advances have shaped community histories across the planet. While biogeographic responses to glaciations likely varied with latitude, the consequences for temperate marine communities histories are less clear. By coalescent analyses of mu ... Full text Cite

Local adaptation and species segregation in two mussel (Mytilus edulis x Mytilus trossulus) hybrid zones.

Journal Article Molecular ecology · February 2005 Few marine hybrid zones have been studied extensively, the major exception being the hybrid zone between the mussels Mytilus edulis and Mytilus galloprovincialis in southwestern Europe. Here, we focus on two less studied hybrid zones that also involve Myti ... Full text Cite

Mitochondrial evolution and phylogeography in the hydrozoan Obelia geniculata (Cnidaria)

Journal Article Marine Biology · January 1, 2005 The distribution and genetic structure of many marine invertebrates in the North Atlantic have been influenced by the Pleistocene glaciation, which caused local extinctions followed by recolonization in warmer periods. Mitochondrial DNA markers are typical ... Full text Cite

The right time for synthesis in evolutionary biology

Journal Article BioScience · January 1, 2005 Full text Cite

Differential patterns of male and female mtDNA exchange across the Atlantic Ocean in the blue mussel, Mytilus edulis.

Journal Article Evolution; international journal of organic evolution · November 2004 Comparisons among loci with differing modes of inheritance can reveal unexpected aspects of population history. We employ a multilocus approach to ask whether two types of independently assorting mitochondrial DNAs (maternally and paternally inherited: F- ... Full text Cite

Molecular phylogeny of the mud lobsters and mud shrimps (Crustacea: Decapoda: Thalassinidea) using nuclear 18S rDNA and mitochondrial 16S rDNA

Journal Article Invertebrate Systematics · December 1, 2002 Partial sequences of the 18S nuclear and 16S mitochondrial ribosomal genes were obtained for 14 species of thalassinidean shrimp (families Callianassidae, Laomediidae, Strahlaxiidae, Thalassinidae and Upogebiidae) and a further six species in related decap ... Full text Cite

Morphological and genetic evidence for vicariance and refugium in Atlantic and Gulf of Mexico populations of the hermit crab Pagurus longicarpus

Journal Article Marine Biology · December 1, 2002 The number and wide variety of southeastern United States marine taxa with significant differentiation between Gulf of Mexico and Atlantic Ocean populations suggests that these taxa may have experienced major vicariance events, whereby populations were sub ... Full text Cite

Refuting a controversial case of a human-mediated marine species introduction

Journal Article Ecology Letters · August 10, 2002 Human activities have strongly impacted natural communities through the introduction of non-native species in historical times. A frequently cited marine example is Littorina littorea, a common intertidal gastropod that was first reported in North America ... Full text Cite

Distinguishing between selection and population expansion in an experimental lineage of bacteriophage T7.

Journal Article Genetics · May 2002 Experimental evolution of short-lived organisms offers the opportunity to study the dynamics of polymorphism over time in a controlled environment. Here, we characterize DNA polymorphism data over time for four genes in bacteriophage T7. Our experiment ran ... Full text Cite

The effects of nucleotide substitution model assumptions on estimates of nonparametric bootstrap support.

Journal Article Molecular biology and evolution · April 2002 The use of parameter-rich substitution models in molecular phylogenetics has been criticized on the basis that these models can cause a reduction both in accuracy and in the ability to discriminate among competing topologies. We have explored the relations ... Full text Cite

Evidence for selection at multiple allozyme loci across a mussel hybrid zone.

Journal Article Molecular biology and evolution · March 2002 Full text Cite

Molecular phylogenetic evidence for the independent evolutionary origin of an arthropod compound eye.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · February 2002 Eyes often take a central role in discussions of evolution, with debate focused on how often such complex organs might have evolved. One such debate is whether arthropod compound eyes are the product of single or multiple origins. Here we use molecular phy ... Full text Cite

Mitochondrial gene rearrangements confirm the parallel evolution of the crab-like form.

Journal Article Proceedings. Biological sciences · February 2002 The repeated appearance of strikingly similar crab-like forms in independent decapod crustacean lineages represents a remarkable case of parallel evolution. Uncertainty surrounding the phylogenetic relationships among crab-like lineages has hampered evolut ... Full text Cite

Phylogeography and historical ecology of the North Atlantic intertidal.

Journal Article Evolution; international journal of organic evolution · December 2001 Recent glaciation covered the full extent of rocky intertidal habitat along the coasts of New England and the Canadian Maritimes. To test whether this glaciation in fact caused wholesale extinction of obligate rocky intertidal invertebrates, and thus requi ... Full text Cite

A comparative study of asymmetric migration events across a marine biogeographic boundary.

Journal Article Evolution; international journal of organic evolution · February 2001 In many nonclonal, benthic marine species, geographic distribution is mediated by the dispersal of their larvae. The dispersal and recruitment of marine larvae may be limited by temperature gradients that can affect mortality or by ocean currents that can ... Full text Cite

Independent contrasts succeed where ancestor reconstruction fails in a known bacteriophage phylogeny.

Journal Article Evolution; international journal of organic evolution · April 2000 Methods of ancestor reconstruction are important tools for evolutionary inference that are difficult to test empirically because ancestral states are rarely known with certainty. We evaluated reconstruction methods for continuous phenotypic characters usin ... Full text Cite

Dramatic mitochondrial gene rearrangements in the hermit crab Pagurus longicarpus (Crustacea, anomura).

Journal Article Molecular biology and evolution · April 2000 The entire mitochondrial gene order of the crustacean Pagurus longicarpus was determined by sequencing all but approximately 300 bp of the mitochondrial genome. We report the first major gene rearrangements found in the clade including Crustacea and Insect ... Full text Cite

A new perspective on lower metazoan relationships from 18S rDNA sequences.

Journal Article Molecular biology and evolution · March 1999 Full text Cite

Support for a monophyletic Lemuriformes: Overcoming incongruence between data partitions

Journal Article Molecular Biology And Evolution · November 1998 Cite

Reconstructing ancestral character states: a critical reappraisal.

Journal Article Trends in ecology & evolution · September 1998 Using parsimony to reconstruct ancestral character states on a phylogenetic tree has become a popular method for testing ecological and evolutionary hypotheses. Despite its popularity, the assumptions and uncertainties of reconstructing the ancestral state ... Full text Cite

Best-fit maximum-likelihood models for phylogenetic inference: Empirical tests with known phylogenies

Journal Article Evolution · 1998 Despite the proliferation of increasingly sophisticated models of DNA sequence evolution, choosing among models remains a major problem in phylogenetic reconstruction. The choice of appropriate models is thought to be especially important when there is lar ... Cite

Is congruence between data partitions a reliable predictor of phylogenetic accuracy? Empirically testing an iterative procedure for choosing among phylogenetic methods.

Journal Article Systematic biology · September 1997 The relationship between phylogenetic accuracy and congruence between data partitions collected from the same taxa was explored for mitochondrial DNA sequences from two well-supported vertebrate phylogenies. An iterative procedure was adopted whereby accur ... Full text Cite

Can three incongruence tests predict when data should be combined?

Journal Article Molecular biology and evolution · July 1997 Advocates of conditional combination have argued that testing for incongruence between data partitions is an important step in data exploration. Unless the partitions have had distinct histories, as in horizontal gene transfer, incongruence means that one ... Full text Cite

Parallel molecular evolution of deletions and nonsense mutations in bacteriophage T7.

Journal Article Molecular biology and evolution · January 1997 Full text Cite

Combining data in phylogenetic analysis.

Journal Article Trends in ecology & evolution · April 1996 Systematists have access to multiple sources of character information in phylogenetic analysis. For example, it is not unusual to have nucleotide sequences from several different genes, or to have molecular and morphological data. How should diverse data b ... Full text Cite

Class-level relationships in the phylum Cnidaria: molecular and morphological evidence.

Journal Article Molecular biology and evolution · July 1995 The evolutionary history of cnidarian life cycles has been debated since the 1880s, with different hypotheses favored even by current textbooks. Contributing to the disagreement is the fact that the systematic relationships of the four cnidarian classes ha ... Full text Cite

Application and accuracy of molecular phylogenies.

Journal Article Science (New York, N.Y.) · April 1994 Molecular investigations of evolutionary history are being used to study subjects as diverse as the epidemiology of acquired immune deficiency syndrome and the origin of life. These studies depend on accurate estimates of phylogeny. The performance of meth ... Full text Cite

Experimental molecular evolution of bacteriophage-t7

Journal Article Evolution · August 1993 Cite

Molecular evidence for multiple episodes of paedomorphosis in the family Hydractiniidae

Journal Article Biochemical Systematics and Ecology · January 1, 1993 Reduction of complex life cycles in the Hydrozoa is commonly achieved by the heterochronic reduction of the medusa from a free-living to a sessile stage. Two competing traditions of hydroid taxonomy dating from the last century disagree about whether the d ... Full text Cite

Partitioning and combining data in phylogenetic analysis

Journal Article Systematic Biology · January 1, 1993 Full text Cite

Class-level relationships in the phylum Cnidaria: evidence from mitochondrial genome structure.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · September 1992 The phylogenetic relationships of the Recent cnidarian classes remain one of the classic problems in invertebrate zoology. We survey the structure of the mitochondrial genome in representatives of the four extant cnidarian classes and in the phylum Ctenoph ... Full text Cite

Evolution of king crabs from hermit crab ancestors.

Journal Article Nature · February 1992 King crabs (Family Lithodidae) are among the world's largest arthropods, having a crab-like morphology and a strongly calcified exoskeleton. The hermit crabs, by contrast, have depended on gastropod shells for protection for over 150 million years. Shell-l ... Full text Cite

Molecular and geologic evidence of shared history between hermit crabs and the symbiotic genus Hydractinia

Journal Article Evolution · January 1, 1991 The paleobiogeographic histories of three North Atlantic hermit crab lineages were compared with a single-copy DNA-DNA hybridization phylogeny of their symbiotic hydroid genus Hydractinia. Two vicariance events in the Quaternary are apparently responsible ... Full text Cite

Gametic incompatibility between species of the sea urchin Echinometra on the two sides of the Isthmus of Panama

Journal Article Evolution · January 1, 1990 The genus Echinometra has E. vanbrunti in the E Pacific, and E. lucunter and E. viridis in the Caribbean. E. viridis is morphologically distinct from the other two species, leading to the conclusion that E. lucunter and E. vanbrunti constitute a geminate p ... Full text Cite

Recruitment and postrecruitment interactions in a colonial hydroid.

Journal Article Ecology · January 1, 1987 The colonial athecate hydroid Hydractinia echinata encrusts gastropod shells inhabited by hermit crabs (genus Pagurus). In field samples recruits were found clustered in specific locations on the undersurface of Urosalpinx cinerea shells. Assays of the beh ... Full text Cite

Crab shell-crushing predation and gastropod architectural defense

Journal Article Journal of Experimental Marine Biology and Ecology · March 16, 1981 The shell-breaking behavior of the crabs Ozius verreauxii Saussure 1853 and Eriphia squamata, Stimpson 1859 from the Bay of Panama is described. The master claws of both these crabs are well designed for breaking shells. Small shells, relative to the size ... Full text Cite