Publications of Clifford W. Cunningham    :chronological  alphabetical  combined  bibtex listing:

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Papers Published

  1. LaBella, AL; Van Dover, CL; Jollivet, D; 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, vol. 137 (March, 2017), pp. 307-317, Elsevier BV [doi]  [abs].
  2. Miglietta, MP; Cunningham, CW, Evolution of life cycle, colony morphology, and host specificity in the family Hydractiniidae (Hydrozoa, Cnidaria)., Evolution; international journal of organic evolution, vol. 66 no. 12 (December, 2012), pp. 3876-3901 [doi]  [abs].
  3. Dexter, KG; Terborgh, JW; Cunningham, CW, Historical effects on beta diversity and community assembly in Amazonian trees., Proceedings of the National Academy of Sciences of the United States of America, vol. 109 no. 20 (May, 2012), pp. 7787-7792 [22547831], [doi]  [abs].
  4. Thaler, AD; Zelnio, K; Saleu, W; Schultz, TF; Carlsson, J; Cunningham, C; Vrijenhoek, RC; 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, vol. 11 (December, 2011), pp. 372 [22192622], [doi]  [abs].
  5. Miglietta, MP; McNally, L; Cunningham, CW, Evolution of calcium-carbonate skeletons in the Hydractiniidae., Integr Comp Biol, vol. 50 no. 3 (September, 2010), pp. 428-435 [doi]  [abs].
  6. Dexter, KG; Pennington, TD; Cunningham, CW, Using DNA to assess errors in tropical tree identifications: How often are ecologists wrong and when does it matter?, Ecological Monographs, vol. 80 no. 2 (May, 2010), pp. 267-286, WILEY [doi]  [abs].
  7. Regier, JC; Shultz, JW; Zwick, A; Hussey, A; Ball, B; Wetzer, R; Martin, JW; Cunningham, CW, Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences., Nature, vol. 463 no. 7284 (February, 2010), pp. 1079-1083 [doi]  [abs].
  8. Miglietta, MP; Schuchert, P; Cunningham, CW, Reconciling genealogical and morphological species in a worldwide study of the Family Hydractiniidae (Cnidaria, Hydrozoa), Zoologica Scripta, vol. 38 no. 4 (July, 2009), pp. 403-430, WILEY [doi]  [abs].
  9. Regier, JC; Schultz, JW; Ganley, ARD; Hussey, A; Shi, D; Ball, B; Zwick, A; Stajich, JE; Cummings, MP; Martin, JW; Cunningham, CW, Resolving Arthropod Phylogeny: Exploring Phylogenetic Signal within 41 kb of Protein-Coding Nuclear Gene Sequence, Systematic Biology, vol. 57 no. 6 (December, 2008), pp. 920-938 [doi]  [abs].
  10. Cunningham, CW, Lessons learned from coordinating research on the North Atlantic (CORONA)., edited by C.W. Cunningham, Ecology, vol. 89 no. 11 Suppl (November, 2008), pp. S1-S2 [doi] .
  11. Percy, DM; Garver, AM; Wagner, WL; James, HF; Cunningham, CW; Miller, SE; Fleischer, RC, Progressive island colonization and ancient origin of Hawaiian Metrosideros (Myrtaceae)., Proceedings. Biological sciences, vol. 275 no. 1642 (July, 2008), pp. 1479-1490 [doi]  [abs].
  12. Lindner, A; Cairns, SD; Cunningham, CW, Multiple origins of shallow-water corals from deep-sea ancestors, PLOs ONE, vol. 3 no. 6 (June, 2008), pp. e2429-e2433 .
  13. Lindner, A; Cairns, SD; Cunningham, CW, From offshore to onshore: multiple origins of shallow-water corals from deep-sea ancestors., PloS one, vol. 3 no. 6 (June, 2008), pp. e2429 [repository], [doi]  [abs].
  14. Bigg, GR; Cunningham, CW; Ottersen, G; Pogson, GH; Wadley, MR; Williamson, P, Ice-age survival of Atlantic cod: agreement between palaeoecology models and genetics., Proceedings. Biological sciences, vol. 275 no. 1631 (January, 2008), pp. 163-172 (I was the major author of this paper, but we chose alphabetical order..) [doi]  [abs].
  15. Cunningham, CW, How to use genetic data to distinguish between natural and human-mediated introduction of Littorina littorea to North America, Biological Invasions, vol. 10 no. 1 (January, 2008), pp. 1-6, Springer Nature [doi]  [abs].
  16. Riginos, C; Cunningham, CW, Hybridization in postglacial marine habitats., Molecular ecology, vol. 16 no. 19 (October, 2007), pp. 3971-3972 [doi]  [abs].
  17. Hickerson, MJ; Cunningham, CW, Nearshore fish (Pholis gunnellus) persists across the North Atlantic through multiple glacial episodes., Molecular ecology, vol. 15 no. 13 (November, 2006), pp. 4095-4107 [17054505], [doi]  [abs].
  18. 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, Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA)., Omics : a journal of integrative biology, vol. 10 no. 2 (January, 2006), pp. 231-237 [doi]  [abs].
  19. Emlen, DJ; Marangelo, J; Ball, B; Cunningham, CW, Diversity in the weapons of sexual selection: horn evolution in the beetle genus Onthophagus (Coleoptera: Scarabaeidae)., Evolution; international journal of organic evolution, vol. 59 no. 5 (May, 2005), pp. 1060-1084 [doi]  [abs].
  20. Hickerson, MJ; Cunningham, CW, Contrasting quaternary histories in an ecologically divergent sister pair of low-dispersing intertidal fish (Xiphister) revealed by multilocus DNA analysis., Evolution; international journal of organic evolution, vol. 59 no. 2 (February, 2005), pp. 344-360 [15807420], [doi]  [abs].
  21. Riginos, C; Cunningham, CW, Invited Review: Local adaptation and species segregation in two mussel (Mytilus edulis X Mytilus trossulus) hybrid zones, Molecular Ecology, vol. 14 no. 2 (February, 2005), pp. 381-400 [15660932], [doi]  [abs].
  22. Wares, JP; Cunningham, CW, Diversification before the most recent glaciation in Balanus glandula., The Biological bulletin, vol. 208 no. 1 (February, 2005), pp. 60-68 [15713813], [doi]  [abs].
  23. Riginos, C; Cunningham, CW, Local adaptation and species segregation in two mussel (Mytilus edulis x Mytilus trossulus) hybrid zones., Molecular ecology, vol. 14 no. 2 (February, 2005), pp. 381-400 [15660932], [doi]  [abs].
  24. Cunningham, C, The right time for synthesis in evolutionary biology, BioScience, vol. 55 no. 2 (January, 2005), pp. 99, Oxford University Press (OUP) [doi] .
  25. Govindarajan, AF; Halanych, KM; Cunningham, CW, Mitochondrial evolution and phylogeography in the hydrozoan Obelia geniculata (Cnidaria), Marine Biology, vol. 146 no. 2 (January, 2005), pp. 213-222, Springer Nature [doi]  [abs].
  26. Riginos, C; Hickerson, MJ; Henzler, CM; Cunningham, CW, Differential patterns of male and female mtDNA exchange across the Atlantic Ocean in the blue mussel, Mytilus edulis., Evolution; international journal of organic evolution, vol. 58 no. 11 (November, 2004), pp. 2438-2451 [15612287], [doi]  [abs].
  27. Young, AM; Torres, C; Mack, JE; 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, vol. 140 no. 5 (December, 2002), pp. 1059-1066, Springer Nature [doi]  [abs].
  28. Tudge, CC; Cunningham, CW, Molecular phylogeny of the mud lobsters and mud shrimps (Crustacea: Decapoda: Thalassinidea) using nuclear 18S rDNA and mitochondrial 16S rDNA, Invertebrate Systematics, vol. 16 no. 6 (December, 2002), pp. 839-847, CSIRO PUBLISHING [doi]  [abs].
  29. Wares, JP; Goldwater, DS; Kong, BY; Cunningham, CW, Refuting a controversial case of a human-mediated marine species introduction, Ecology Letters, vol. 5 no. 4 (August, 2002), pp. 577-584, WILEY [doi]  [abs].
  30. Hahn, MW; Rausher, MD; Cunningham, CW, Distinguishing between selection and population expansion in an experimental lineage of bacteriophage T7., Genetics, vol. 161 no. 1 (May, 2002), pp. 11-20 [12019219], [doi]  [abs].
  31. Buckley, TR; Cunningham, CW, The effects of nucleotide substitution model assumptions on estimates of nonparametric bootstrap support., Molecular biology and evolution, vol. 19 no. 4 (April, 2002), pp. 394-405 [11919280], [doi]  [abs].
  32. Riginos, C; Sukhdeo, K; Cunningham, CW, Evidence for selection at multiple allozyme loci across a mussel hybrid zone., Molecular biology and evolution, vol. 19 no. 3 (March, 2002), pp. 347-351 [doi] .
  33. Morrison, CL; Harvey, AW; Lavery, S; Tieu, K; Huang, Y; Cunningham, CW, Mitochondrial gene rearrangements confirm the parallel evolution of the crab-like form., Proceedings. Biological sciences, vol. 269 no. 1489 (February, 2002), pp. 345-350 [doi]  [abs].
  34. Oakley, TH; Cunningham, CW, Molecular phylogenetic evidence for the independent evolutionary origin of an arthropod compound eye., Proceedings of the National Academy of Sciences of the United States of America, vol. 99 no. 3 (February, 2002), pp. 1426-1430 [11818548], [doi]  [abs].
  35. Hickerson, MJ; 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, vol. 18 no. 12 (December, 2001), pp. 2350 .
  36. Wares, JP; Cunningham, CW, Phylogeography and historical ecology of the North Atlantic intertidal., Evolution; international journal of organic evolution, vol. 55 no. 12 (December, 2001), pp. 2455-2469 [11831661], [doi]  [abs].
  37. Wares, JP; Gaines, SD; Cunningham, CW, A comparative study of asymmetric migration events across a marine biogeographic boundary., Evolution; international journal of organic evolution, vol. 55 no. 2 (February, 2001), pp. 295-306 [11308087], [doi]  [abs].
  38. Grosberg, R.K. and C.W. Cunningham, Genetic structure in the sea: from populations to communities, in Marine Community Ecology, pp.61-84, edited by M.D. Bertness, S. Gaines, and M.E. Hay (2001), Sinauer Associates, Sunderland, MA .
  39. Hickerson, MJ; Cunningham, CW, Dramatic mitochondrial gene rearrangements in the hermit crab Pagurus longicarpus (Crustacea, anomura)., Molecular biology and evolution, vol. 17 no. 4 (April, 2000), pp. 639-644 [10742054], [doi]  [abs].
  40. Oakley, TH; Cunningham, CW, Independent contrasts succeed where ancestor reconstruction fails in a known bacteriophage phylogeny., Evolution; international journal of organic evolution, vol. 54 no. 2 (April, 2000), pp. 397-405 [10937216], [doi]  [abs].
  41. Kim, J; Kim, W; Cunningham, CW, A new perspective on lower metazoan relationships from 18S rDNA sequences., Molecular biology and evolution, vol. 16 no. 3 (March, 1999), pp. 423-427 [doi] .
  42. Cunningham, CW, Some limitations of ancestral character-state reconstruction when testing evolutionary hypotheses, Systematic Biology, vol. 48 no. 3 (January, 1999), pp. 665-674, Oxford University Press (OUP) [doi] .
  43. Stanger hall, K; Cunningham, CW, Support for a monophyletic Lemuriformes: Overcoming incongruence between data partitions, Molecular Biology And Evolution, vol. 15 no. 11 (November, 1998), pp. 1572-1577 [doi] .
  44. Cunningham, CW; Omland, KE; Oakley, TH, Reconstructing ancestral character states: a critical reappraisal., Trends in ecology & evolution, vol. 13 no. 9 (September, 1998), pp. 361-366 [21238344], [doi]  [abs].
  45. Cunningham, CW; Zhu, H; Hillis, DM, Best-fit maximum-likelihood models for phylogenetic inference: Empirical tests with known phylogenies, Evolution, vol. 52 no. 4 (1998), pp. 978-987, JSTOR [doi]  [abs].
  46. Cunningham, CW, Is congruence between data partitions a reliable predictor of phylogenetic accuracy? Empirically testing an iterative procedure for choosing among phylogenetic methods., Systematic biology, vol. 46 no. 3 (September, 1997), pp. 464-478 [11975330], [doi]  [abs].
  47. Cunningham, CW, Can three incongruence tests predict when data should be combined?, Molecular biology and evolution, vol. 14 no. 7 (July, 1997), pp. 733-740 [9214746], [doi]  [abs].
  48. Cunningham, CW; Jeng, K; Husti, J; Badgett, M; Molineux, IJ; Hillis, DM; Bull, JJ, Parallel molecular evolution of deletions and nonsense mutations in bacteriophage T7., Molecular biology and evolution, vol. 14 no. 1 (January, 1997), pp. 113-116 [doi] .
  49. Huelsenbeck, JP; Bull, JJ; Cunningham, CW, Combining data in phylogenetic analysis., Trends in ecology & evolution, vol. 11 no. 4 (April, 1996), pp. 152-158 [doi]  [abs].
  50. Bridge, D; Cunningham, CW; DeSalle, R; Buss, LW, Class-level relationships in the phylum Cnidaria: molecular and morphological evidence., Molecular biology and evolution, vol. 12 no. 4 (July, 1995), pp. 679-689 [doi]  [abs].
  51. Hillis, DM; Huelsenbeck, JP; Cunningham, CW, Application and accuracy of molecular phylogenies., Science (New York, N.Y.), vol. 264 no. 5159 (April, 1994), pp. 671-677 [doi]  [abs].
  52. Huelsenbeck, JP; Swofford, DL; Cunningham, CW; Bull, P; Waddell, PJ, Is character weighting a panacea for the problem of data heterogeneity in phylogenetic analysis?, Systematic Biology, vol. 43 no. 2 (January, 1994), pp. 288-291, Oxford University Press (OUP) [doi] .
  53. Bull, JJ; Cunningham, CW; Molineux, IJ; Badgett, MR; Hillis, DM, Experimental molecular evolution of bacteriophage-t7, Evolution, vol. 47 no. 4 (August, 1993), pp. 993-1007 .
  54. Lessios, HA; Cunningham, CW, The evolution of gametic incompatibility in neotropical Echinometra: A reply to McClary, Evolution, vol. 47 no. 6 (January, 1993), pp. 1883-1885, WILEY [doi] .
  55. Bull, JJ; Huelsenbeck, JP; Swofford, DL; Cunningham, CW; Waddell, PJ, Partitioning and combining data in phylogenetic analysis, Systematic Biology, vol. 42 no. 3 (January, 1993), pp. 384-397, Oxford University Press (OUP) [doi] .
  56. Cunningham, CW; Buss, LW, Molecular evidence for multiple episodes of paedomorphosis in the family Hydractiniidae, Biochemical Systematics and Ecology, vol. 21 no. 1 (January, 1993), pp. 57-69, Elsevier BV [doi]  [abs].
  57. Bridge, D; Cunningham, CW; Schierwater, B; DeSalle, R; 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, vol. 89 no. 18 (September, 1992), pp. 8750-8753 [doi]  [abs].
  58. Cunningham, CW; Blackstone, NW; Buss, LW, Evolution of king crabs from hermit crab ancestors., Nature, vol. 355 no. 6360 (February, 1992), pp. 539-542 [doi]  [abs].
  59. Cunningham, CW; Buss, LW; Anderson, C, Molecular and geologic evidence of shared history between hermit crabs and the symbiotic genus Hydractinia, Evolution, vol. 45 no. 6 (January, 1991), pp. 1301-1316, WILEY [doi]  [abs].
  60. Lessios, HA; Cunningham, CW, Gametic incompatibility between species of the sea urchin Echinometra on the two sides of the Isthmus of Panama, Evolution, vol. 44 no. 4 (January, 1990), pp. 933-941, WILEY [doi]  [abs].
  61. Yund, PO; Cunningham, CW; Buss, LW, Recruitment and postrecruitment interactions in a colonial hydroid., Ecology, vol. 68 no. 4 (January, 1987), pp. 971-982, WILEY [doi]  [abs].
  62. Bertness, MD; Cunningham, C, Crab shell-crushing predation and gastropod architectural defense, Journal of Experimental Marine Biology and Ecology, vol. 50 no. 2-3 (March, 1981), pp. 213-230, Elsevier BV [doi]  [abs].

Edited Volumes

  1. C. W. Cunningham, Coordinating Research on the North Atlantic, Ecology, vol. 89 no. 11 (November, 2008) (I edited this special volume, the only special volume of Ecology accepted in the past 8 years..) .

Book Reviews

  1. C.W. Cunningham, Ever since Gould. Book Review of "Stephen Jay Gould: Reflections on his View of Life", Trends in Ecology and Evolution, vol. 24 (2009), pp. 645-646 .