Heimeier, D., C.S. Baker, P.J. Duignan, K. Russell, A. Hutt and G.S. Stone. 2009. Confirmed expression of MHC class I and class II genes in the New Zealand endemic Hector's dolphin (Cephalorhynchus hectori). Marine Mammal Science. 25:68-90.

Tezanos-Pinto, G., C.S. Baker, K. Russell, K. Martien, R.W. Baird, A. Hutt, G. Stone, A.A. Mignucci-Giannoni, S. Caballero, T. Endo, S. Lavery, M. Oremus, C. Olavarria and C. Garrigue. 2009. A worldwide perspective on the population structure and genetic diversity of bottlenose dolphins (Tursiops truncatus) in New Zealand. Journal of Heredity. 100:11-24.

Dalebout, M.L., D. Steel, and C.S. Baker, 2008. Phylogeny of the beaked whale genus Mesoplodon (Ziphiidae: Cetacea) revealed by nuclear introns: implications for the evolution of male tusks. Systematic Biology. 57:857-875.

Baker, C.S., 2008. A truer measure of the market: the molecular ecology of fisheries and wildlife trade. Molecular Ecology. 17:3985-3998.

Endo, T., Y. Hisamichit, O. Kimurar, K. Haraguchi and C.S. Baker. 2008. Contamination Levels of Mercury and Cadmium in Melon-headed Whales (Peponocephala electra) from a Mass Stranding on the Japanese Coast. Science of the Total Environment. 401:73-80.

Campbell, R.A., N.J. Gales, G.M. Lento and C.S. Baker. Islands in the sea: extreme female natal site fidelity in the Australian sea lion, Neophoca cinerea. 2008. Biology Letters 4:139-142.

Caballero, S., J. Jackson, A.A. Mignucci-Giannoni, H. Barrios-Garrido, S. Beltran-Pedreros, M.a.G. Montiel-Villalobos, K.M. Robertson and C.S. Baker. 2008. Molecular systematics of South American dolphins Sotalia: Sister taxa determination and phylogenetic relationships, with insights into a multi-locus phylogeny of the Delphinidae. Molecular Phylogenetics and Evolution. 46:252-268.

Oremus, M., M.M. Poole, D. Steel and C.S. Baker. 2007. Isolation and interchange among insular spinner dolphin communities in the South Pacific revealed by individual identification and genetic diversity. Marine Ecology Progress Series. 336:275-289.

Caballero, S., F. Trujillo, J.A. Vianna, H. Barrios-Garrido, M.G. Montiel, S. Beltran-Pedreros, M. Marmontel, M.C. Santos, M. Rossi, F.R. Santo and C.S. Baker. 2007. Taxonomic status of the genus Sotalia: species level ranking for “tucuxi” (Sotalia fluviatilis) and “costero” (Sotalia guianensis) dolphins. Marine Mammal Science. 23:358-386.

Olavarría, C., C.S. Baker, C. Garrigue, M. Poole, N. Hauser, S. Caballero, L. Flórez-González, M. Brasseur, J. Bannister, J. Capella, P.J. Clapham, R. Dodemont, M. Donoghue, C. Jenner, M.N. Jenner, D. Moro, M. Oremus, D.A. Paton and K. Russell. 2007. Population structure of humpback whales throughout the South Pacific and the origins of the eastern Polynesian breeding grounds. Marine Ecology Progress Series 330:257-268.

Patenaude, N, V. Portway, C. Schaeff, J. Bannister, P. Best, R. Payne, V. Rowntree, M. Rivarola and C.S. Baker. 2007. Mitochondrial DNA diversity and population structure among southern right whales (Eubalaena australis). Journal of Heredity 98:147-157.

Baker, C.S., J. Cooke, S. Lavery, M.L. Dalebout, Y.-U. Ma, N. Funahashi, C. Carraher and R.L. Brownell Jr. 2007. Estimating the number of whales entering trade using DNA profiling and capture-recapture analysis of market products. Molecular Ecology. 13:2617-2626.

Robineau, D., R.N.P. Goodall, F. Pichler and C.S. Baker. 2007. Description of a new subspecies of Commerson's dolphin, Cephalorhynchus commersonii (Lacépède, 1804), inhabiting the coastal waters of the Kerguelen Islands. 2007. Mammalia 71:172-180.

Constantine R, Russell K, Gibbs N, Childerhouse S, Baker C.S. Photo-identification of humpback whales in New Zealand waters and their migratory connections to breeding grounds of Oceania. 2007. Marine Mammal Science 23:715-720.

Baker, C.S. Vant, M. D., Dalebout, M. L. Lento, G. M., O'Brien, S.J. and Yuhki, N. Diversity and duplication of DQB and DRB-like genes of the MHC in baleen whales (Suborder: Mysticeti). 2006. Immunogenetics. 58:283-296.

Baker, C.S., Lukoschek, V., Lavery, S., Dalebout, M. L., Yong-un, M., Endo, T. & Funahashi, N. Incomplete reporting of whale, dolphin and porpoise ‘bycatch' revealed by molecular monitoring of Korean markets. 2006. Animal Conservation. 9:474-482.

Olavarria, C., Balbontin, F., Bernal, R., and Baker, C.S. Lack of divergence in the mitochondrial cytochrome b gene between Macruronus species (Pisces: Merlucciidae) in the Southern Hemisphere. 2006. New Zealand Journal of Marine and Freshwater Research. 40:299-304.

Weinrich, M. T., Rosenbaum, H., Baker, C.S., Blackmer, A. L., and Whitehead, H. The influence of maternal lineages on social affiliations among humpback whales (Megaptera novaeangliae) on their feeding grounds in the Southern Gulf of Maine. 2006. Journal of Heredity. 97:226-234.

Garrigue, C., R. Dodemont, D. Steel, and C.S. Baker. 2004. Organismal and 'gametic' capture-recapture using microsatellite genotyping confirm low abundance and reproductive autonomy of humpback whales on the wintering grounds of New Caledonia. Marine Ecology Progress Series 274, 251-262.

Witteveen, B. H., J. M. Straley, O. von Ziegesar, D. Steel, and C.S. Baker, 2004. Abundance and mtDNA differentiation of humpback whales (Megaptera novaeangliae) in the Shumagin Islands, Alaska. Canadian Journal of Zoology. 82:1352-1359.