Giacomo Bernardi's selected publications

Publications

73. Matthieu Leray, Ricardo Beldade, Sally J. Holbrook, Russell J. Schmitt, Serge Planes, and Giacomo Bernardi. 2009. Allopatric divergence and speciation in coral reef fish: the three-spot dascyllus, Dascyllus trimaculatus, species complex. Evolution (in press).

72. Genome 10K community of scientists. 2009. Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species. Journal of Heredity (in press).

71. Jeffrey N. Schinske, Giacomo Bernardi, David K. Jacobs, and Eric J. Routman. 2009. Phylogeography of the diamond turbot (Hypsopsetta guttulata) across the Baja California Peninsula. Marine Biology (in press).

70. Ricardo Beldade, Sally J. Holbrook, Russell J. Schmitt, Serge Planes, and Giacomo Bernardi. 2009. Isolation and characterization of 8 polymorphic microsatellite markers from the orange-fin anemone fish, Amphiprion chrysopterus. Conservation Genetics Resources (in press).

69. Michel Bariche, and Giacomo Bernardi. 2009. Lack of a genetic bottleneck in a recent Lessepsian bioinvader, the blue-barred parrotfish, Scarus ghobban. Molecular Phylogenetics and Evolution 53: 592-595.

68. Ricardo Beldade, Peter Raimondi, Richard Cudney-Bueno, and Giacomo Bernardi. 2009. Isolation and characterization of 13 polymorphic microsatellite markers from the Gulf coney, Epinephelus acanthistius. Molecular Ecology Resources 9: 1375-1429.

67. Joana Robalo, Vitor C. Almada, Andre Levy, Jorg Freyhof, Giacomo Bernardi, Ignacio Doadrio. 2009. Phylogenetic analysis of Peri-Mediterranean blennies of the genus Salaria: molecular insights on the colonization of freshwaters. Molecular Phylogenetics and Evolution 52: 424-431.

66. Giuseppe Bucciarelli, Miriam Di Filippo, Domenico Costagliola, Fernando Alvarez-Valin, Giacomo Bernardi, and Giorgio Bernardi. 2009. Environmental genomics: a tale of two fishes. Molecular Biology and Evolution 26: 1235-1243.

65. Alejandro Vagelli, Martha Burford, and Giacomo Bernardi. 2009. Fine scale dispersal in Banggai Cardinalfish, Pterapogon kauderni, a coral reef species lacking a pelagic larval phase. Marine Genomics 1: 129-134

64. Celine Reisser, Ricardo Beldade, and Giacomo Bernardi. 2009. Multiple paternity and competition in sympatric congeneric reef fishes, Embiotoca jacksoni and E. lateralis. Molecular Ecology 18, 1504-1510

63. Ricardo Beldade, J. B. Heiser, D. Ross Robertson, Joao L. Gasparini, Sergio Floeter and Giacomo Bernardi. 2009. Historical Biogeography and speciation in the Creole wrasses (Labridae, Clepticus). Marine Biology 156: 679-687

62. Giacomo Bernardi. 2009. The name of the Father: Conflict between Louis and Alexander Agassiz, and the Embiotoca surfperch radiation. Journal of Fish Biology 74: 1049-1055.

61. Jan Freiwald, Nathan L. Stewart, Devona C. Yates, and Giacomo Bernardi. 2009. Isolation and characterization of nine polymorphic microsatellite loci of the kelp greenling, Hexagrammos decagrammus, a temperate reef fish. Molecular Ecology Resources 9: 563-565.

60. Marloes Poortvliet, Jeanine L. Olsen, Kimberly A. Selkoe, James A. Coyer, Giacomo Bernardi. 2009. Isolation and characterization of 11 microsatellite primers for a temperate reef fish, the California sheephead (Semicossyphus pulcher). Molecular Ecology Resources 9: 429-430

59. Matthieu Leray, Ricardo Beldade, Sally J. Holbrook, Russell J. Schmitt, Serge Planes, and Giacomo Bernardi. 2009. Isolation and characterization of 13 polymorphic nuclear microsatellite primers for the widespread Indo-Pacific three-spot damselfish, Dascyllus trimaculatus, and closely related D. auripinnis. Molecular Ecology Resources 9: 213-215

58. Giacomo Bernardi. 2008. Isolation and characterization of 12 microsatellites from the black surfperch, Embiotoca jacksoni, a reef fish that lacks a pelagic larval phase. Molecular Ecology Resources 8: 1512-1514.

57. Giacomo Bernardi, Yvette R. Alva-Campbell, Joao L. Gasparini, Sergio R. Floeter. 2008. Molecular ecology, speciation, and evolution of the reef fish genus Anisotremus. Molecular Phylogenetics and Evolution 48: 929-935.

56. Martha O. Burford, and Giacomo Bernardi. 2008. Incipient speciation within a subgenus of rockfish (Sebastosomus) provides evidence of recent radiations within an ancient species flock. Marine Biology 154: 701-717.

55. Vera S. Domingues, Markos Alexandrou, Vitor C. Almada, D. Ross Robertson, Alberto Brito, Ricardo S. Santos, and Giacomo Bernardi 2008. Tropical fishes in a temperate sea: evolution of the wrasse Thalassoma pavo and the parrotfish Sparisoma cretense in the Mediterranean and the adjacent Macaronesian and Cape Verde Archipelagos. Marine Biology 154: 465-474.

54. A. Zvuloni, O. Mokady, M. Al-Zibdah, G. Bernardi, S.D. Gaines and A. Abelson 2008. Local scale genetic structure in coral populations: A signature of selection. Marine Pollution Bulletin 56: 430-438.

53. Marina Ramon, Peter Nelson, Edward DeMartini, William Walsh, and Giacomo Bernardi 2008. Phylogeography, historical demography, and the role of post-settlement ecology in two Hawaiian damselfish species. Marine Biology 153: 1207-1217.

52. Floeter, S.R., L.A. Rocha, D.R. Robertson, J.C. Joyeux, W. Smith-Vaniz, P. Wirtz, A.J. Edwards, J.P. Barreiros, C.E.L. Ferreira, J.L. Gasparini, A. Brito, J.M. Falcon, B.W. Bowen, and G. Bernardi 2008. Atlantic reef fish biogeography and evolution . Journal of Biogeography 35: 22-47.

51. Daniel Golani, Ernesto Azzurro, Maria Corsini-Foka, Manuela Falautano, Franco Andaloro, and Giacomo Bernardi. 2007. Genetic bottlenecks and successful biological invasions: the case of a recent Lessepsian migrant. Biology Letters. 3: 541-545.

50. Karen D. Crow, Hiroyuki Munehara, Ziyusei Kanamoto, Andrey Balanov, Dmitriy Antonenko, and Giacomo Bernardi. 2007. Maintenance of species boundaries despite rampant hybridization between three species of reef fishes (Hexagrammidae): implications for the role of selection. Biological Journal of the Linnnean Society. 91: 135-147.

49. Bernardi G, Ruiz-Campos G, Camarena-Rosales F. 2007. Genetic isolation and evolutionary history opf oases populations of the Baja California killifish, Fundulus lima. Conservation Genetics 8: 547-554.

48. Domingues VS, Almada VC, Santos RS, and Bernardi G. 2007. Phylogeography and evolution of the triplefin Tripterygion delaisi (Pisces, Blennioidei). Marine Biology 150: 509-519.

47. Robertson DR, Karg F, de Moura RL, Victor BC, and Bernardi G. 2006. Mechanisms of speciation and faunal enrichment in Atlantic parrotfishes. Molecular Phylogenetics and Evolution 40: 795-807

46. Azzurro, E., D. Golani, G. Bucciarelli, and G. Bernardi. 2006. Genetics of the early stages of invasion of the Lessepsian rabbitfish Siganus luridus. Journal of Experimental Marine Biology and Ecology 333: 190-201.

45. Bernardi, G. and J. Lape. 2005. Tempo and mode of speciation in the Baja California disjunct fish species Anisotremus davidsonii. Molecular Ecology 14: 4085-4096.

44. Domingues, V., G. Bucciarelli, V.C. Almada, and G. Bernardi. 2005. Historical colonization and demography of the Mediterranean damselfish, Chromis chromis. Molecular Ecology 14: 4051-4063.

43. Bernardi, G. 2005. Phylogeography and demography of sympatric sister species, Embiotoca jacksoni and E. lateralis along the California coast: Historical versus ecological factors. Evolution 59 386-394.

42. Bernardi, G., and Vagelli, A. 2004. Population structure in Banggai Cardinalfish, Pterapogon kauderni, a coral reef fish lacking a pelagic larval phase. Marine Biology 145: 803-810.

41. Crow, K.D., Kanamoto, Z., and Bernardi, G. 2004. Molecular phylogeny of the hexagrammid fishes using a multi-locus approach. Molecular Phylogenetics and Evolution 32: 986-997.

40. Bernardi, G., Bucciarelli, G., Costagliola, D., Robertson, D.R., and Heiser, J.B. 2004. Evolution of coral reef fish Thalassoma spp. (Labridae): 1. Molecular phylogeny and biogeography. Marine Biology 144: 369-375

39. Costagliola, D., Robertson, D.R., Guidetti, P., Stefanni, S., Wirtz, P., Heiser, J.B., and Bernardi, G. 2004. Evolution of the coral reef fish Thalassoma spp. (Labridae): 2. Evolution of the eastern Atlantic species. Marine Biology 144: 377-383

38. Bernardi, G., Holbrook, S.J., Schmitt, R.J., and Crane, N.L. 2003. Genetic evidence for two distinct clades in a French Polynesian population of the coral reef three-spot damselfish Dascyllus trimaculatus. Marine Biology 143: 485-490

37. Bernardi, G., Findley, L., and Rocha-Olivares, A. 2003. Vicariance and dispersal across Baja California in disjunct marine fish populations. Evolution 57:1599-1609.

36. Fauvelot, C., Bernardi, G., and Planes, S. 2003. Reductions in the mitochondrial DNA diversity of coral reef fish provide evidence of population bottlenecks resulting from Holocene sea-level change Evolution 57:1571-1583.

35. Bucciarelli, G., Bernardi, Giacomo. and Bernardi, Giorgio. 2002. An ultracentrifugation analysis of two hundred fish genomes. Gene 295: 153-162.

34. Jones W.J., Quelvog, BD., and Bernardi, G. 2002. Morphological and genetic analysis of the Red Hills roach (Cyprinidae: Lavinia symmetricus). Conservation Genetics 3 (3): 261-276, 2002

33. Bucciarelli, G., Golani, D., and Bernardi, G. 2002. Genetic cryptic species as biological invaders: The case of a Lessepsian fish migrant, the hardyhead silverside Atherinomorus lacunosus. J. Exp. Mar. Biol. Ecol 273:143-149.

32. Bernardi, G., Holbrook, S.J., Schmitt, R.J., Crane, N.L., and DeMartini, E. 2002. Species boundaries, populations, and colour morphs in the coral reef three-spot damselfish (Dascyllus trimaculatus) species-complex. Proc.Roy. Soc. London 269:599-605.

31. Planes, S., Doherty, P., and Bernardi, G. 2001. Unusual case of extreme genetic divergence in a marine fish, Acanthochromis polyacanthus, within the Great Barrier Reef and the Coral Sea. Evolution 55:2263-2273

30. Bernardi G., Holbrook S. J., and Schmitt R. J. 2001. Dispersal of the coral reef three-spot dascyllus,Dascyllus trimaculatus, at three spatial scales. Mar. Biol. 138:457-465.

29. Huang, D., and Bernardi, G. 2001. Disjunct Sea of Cortez - Pacific Ocean Gillichthys mirabilis populations and the evolutionary origin of their paedomorphic relative, Gillichthys seta. Mar. Biol. 138:421-428.

28. Bernardi, G., and Talley, D. 2000. Molecular evidence for reduced dispersal in the coastal California killifish, Fundulus parvipinnis. J. Exp. Mar. Biol. Ecol. 255:187-199.

27. Bernardi, G., Robertson, R., Clifton, K. and Azzuro, E. 2000. Molecular Systematics, Zoography, and Evolutionary Ecology of the Atlantic Parrotfish genus Sparisoma. Mol. Phylo. Evol. 15:292-300.

26. Terry, A., Bucciarelli, G. and Bernardi, G. 2000. Restricted Gene Flow and Incipient Speciation in Disjunct Pacific Ocean and Sea of Cortez Populations of a Reef Fish Species, Girella nigricans. Evolution 54:652-659.

25. Bernardi, G. 2000. Barriers to gene flow in Embiotoca jacksoni, a marine fish lacking a pelagic larval stage. Evolution 54:226-237.

24. Alesandrini, S. and Bernardi, G. 1999. Ancient species flocks and recent speciation events: What can rockfishes teach us about cichlids (and vice-versa)? J. Mol. Evol. 49:814-818.

23. Bernardi, G. and Bucciarelli, G. 1999. Molecular phylogeny and speciation of the surfperches (Embiotocidae, Perciformes). Mol. Phylo. Evol. 13:77-81.

22. Bernardi, G. and Crane, N. 1999. Molecular phylogeny of the Humbug Damselfishes inferred from mtDNA sequences. J. Fish Biology 54:1210-1217.

21. Bernardi, G., Fain, S.R., Gallo-Reynoso, J.P., Figueroa-Carranza, A.L. and LeBoeuf, B.J. 1998. Genetic Variability in Guadalupe fur seals. Journal of Heredity 89:301-305.

20. Bernardi, G. and Goswami, U. 1997. Molecular evidence for cryptic species among the Antarctic fish Trematomus bernacchii and Trematomus hansoni. Antarctic Science 9:381-385.

19. Crow, K., Powers, D.A. and Bernardi, G. 1997. Evidence for multiple maternal contributors in nests of kelp greenling (Hexagrammos decagrammus, Hexagrammidae). Copeia 1997:9-15.

18. Bernardi, G., Fernandez-Delgado, C., Gomez-Chiarri, M. and Powers, D.A. 1995. Origin of a Spanish population of Fundulus heteroclitus inferred by Cytochrome b sequence analysis. Journal of Fish Biology 47:737-740.

17. Bernardi, G. and Powers, D.A. 1995. Phylogenetic relationships among nine species from the genus Fundulus (Cyprinodontiformes, Fundulidae) inferred from sequences of the cytochrome b gene. Copeia 1995:469-473.

16. Zoubak, S., D Onofrio G., Caccio', S, Bernardi, Giacomo and Bernardi, Giorgio. 1995. Specific compositional patterns of synonymous positions in homologous mammalian genes. Journal of Molecular Evolution 40:293-307.

15. Ben-Miled L., Dellagi K., Bernardi, G., Melrose, T.M., Darghouth, M., Bouattour, A., Kinnaird, J., Shiels, B., Tait, A. and Brown, C.G.D. 1994. Genomic and phenotypic diversity of Tunisian Theileria annulata isolates. Parasitology 51-60.

14. Isacchi, A., Bernardi, Giacomo and Bernardi, Giorgio. 1993. Compositional compartmentalization of the nuclear genome of Trypanosoma brucei and Trypanosoma equiperdum. FEBS Letters 181-183.

13. Bernardi, Giacomo , D Onofrio, G., Caccio', S. and Bernardi, Giorgio. 1993. Molecular phylogeny of the bony fishes, based on the amino acid sequence of the growth hormone. Journal of Molecular Evolution 37:644-649.

12. Bernardi, G., Sordino, P. and Powers, D.A. 1993. Concordant mitochondrial and nuclear DNA phylogenies for populations of the teleost fish Fundulus heteroclitus. Proceedings of the National Academy of Sciences, USA 90:9271-9274.

11. Bernardi, G., Sordino, P. and Powers, D.A. 1992. Nucleotide sequence of the 18S Ribosomal Ribonucleic Acid gene from two teleosts and two sharks and their Molecular Phylogeny. Molecular Marine Biology and Biotechnology 1:187-194.

10. Bernardi, G. and Powers, D.A. 1992. Molecular phylogeny of the prickly shark Echinorhinus cookei based on a nuclear (18S rRNA), and a mitochondrial (cytochrome b) gene. Molecular Phylogenetics and Evolution 1:161-167.

9. Bernardi, Giacomo and Bernardi, Giorgio. 1991. Compositional properties of nuclear genes from cold-blooded vertebrates. Journal of Molecular Evolution 33:57-67.

8. Bernardi, Giacomo and Bernardi, Giorgio. 1990. Compositional patterns in the nuclear genome of cold-blooded vertebrates. Journal of Molecular Evolution 31:265-281.

7. Bernardi, Giacomo and Bernardi, Giorgio. 1990. Compositional transitions in the nuclear genome of cold-blooded vertebrates. Journal of Molecular Evolution 31:282-293.

6. Guizani I., Van Eys, G., Bernardi, G., Kroon, N., Schoone, G.J., Ben-Isma_l, R. and Dellagi, K. 1990. Selection of Leishmania major nuclear DNA probes for the characterization of Leishmania strains: Application on Tunisian isolates. Bull. Soc Fr. Parasitol. 8:39.

5. Medrano, L., Bernardi, Giacomo, Couturier, J., Dutrillaux, B. and Bernardi, Giorgio. 1988. Chromosome banding and genome compartmentalization in fishes. Chromosoma 96:178-183.

4. Bernardi, Giorgio, Mouchiroud, D., Gautier, C. and Bernardi, Giacomo. 1988. Compositional patterns in vertebrate genomes: conservation and change in evolution. Journal of Molecular Evolution 28:7-18.

3. Bernardi, Giorgio and Bernardi, Giacomo. 1986. Compositional constraints and genome evolution. Journal of Molecular Evolution 24:1-11.

2. Bernardi, Giacomo, Pizon, V., Cuny, G., Haschemeyer, A. and Bernardi, Giorgio. 1986. ADN et taxonomie des poissons. Oceanis 12:377-380.

1. Bernardi, Giacomo and Bernardi, Giorgio. 1985. Codon usage and genome composition . Journal of Molecular Evolution 22:363-365.

Book Chapters

Giacomo Bernardi, Daniel Golani, and Ernesto Azzurro 2009. The genetics of Lessepsian bioinvasions. In: Fish invasions of the Mediterranean Sea: Change and renewal. D. Golani and B. Applebaum-Golani Eds.

Dawson M., R. Waples, and Bernardi G. 2006. Phylogeography. In The Ecology of Marine Fishes: California and Adjacent Waters - UC Press Larry G. Allen, Daniel J. Pondella, II, and Michael H. Horn Eds.

Bernardi, G. 1997. Molecular phylogeny of the Fundulidae (Teleostei, Cyprinodontiformes) based on the cytochrome b gene. In: Molecular Systematics of Fishes. T. Kocher and C. Stepien, eds. Academic Press, San Diego, CA; pp.189-197.

Powers, D.A., Smith M., Gonzales-Villasenor I., DiMichele L., Crawford D., Bernardi G., and Lauerman T. 1993. A multidisciplinary approach to the selectionist/neutralist controversy using the model teleost Fundulus heteroclitus. In: Oxford Surveys in Evolutionary Biology, Volume 9. D. Futuyama and J. Antonovics, eds. Oxford University Press, Oxford, England; pp. 43-107.

Bernardi, Giorgio, and Bernardi, Giacomo. 1989. Randomness and natural selection in genome evolution. In: Molecules in Physics, Chemistry, and Biology, IV. Jean Maruani, ed. Kluwer Academic Pubs., Norwell, MA; pp. 3-12.

Bernardi, Giorgio and Bernardi, Giacomo. 1987. The role of chance in genome evolution. In: From Enzyme Adaptation to Natural Philosophy : Heritage from Jacques Monod. E. Quagliariello, G. Bernardi, and A. Ullmann, eds. Elsevier, Amsterdam, Holland; pp. 173-185.

Book Reviews

Bernardi, G. 2003. Meselson, Stahl, and the Replication of DNA. by FL Holmes. Book Review. The Quarterly Review of Biology 78: 81-82.

Bernardi, G. 1995. Molecular Biology Frontiers. Biochemistry and Molecular Biology of Fishes. Vol. 2. by P.W. Hochachka, and T.P. Mommsen. Book Review. Copeia 1995:505-506.

Bernardi, G. 1994. Unraveling DNA. by Maxim D. Frank-Kamenetskii. Book Review. The Quarterly Review of Biology 69:513.

Other Publications

Martha Burford, Mark Carr, and G Bernardi. Speciation and Genetic Structure in a Marine Fish with an Extended Pelagic Larval Phase: an Analysis of Both the Juvenile and Adult Populations of Blue Rockfish (Sebastes mystinus). Coastal Environmental Quality Initiative. Paper 039. _http://repositories.cdlib.org/ucmarine/ceqi/039

Bernardi, G. In: Stefanni, Bried and Bettencourt Eds. 2004. Use of Molecular markers for the study of Marine Biodiversity. Acta of the 1st International Workshop in Marine Molecular Phylogenetics.

Bernardi, G and DeVries, A.L. 1994. Cytochrome b gene sequences from two eelpouts (perciformes, zoarcidae) from McMurdo Sound (Antarctica): Implications on the antifreeze gene structure. Antarctic Journal 29:159-161.

Bernardi, Giorgio and Bernardi, Giacomo. 1986. The Human genome and its evolutionary context . Cold Spring Harbor Symp. Quant. Biol. "Molecular Biology of Homo sapiens " 51: 479-487.

Miscellaneous

Sympatric speciation 2006. Science now.

Good Karma in Tropical Paradise 2004. NPR - Jesse Kalisher.

E-mail: bernardi@biology.ucsc.edu