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Baker CS, Gilbert DA, Weinrich MT, Lambertsen RH, Calambokidis J, McArdle B, Chambers GK, O'Brien SJ.  1993.  Population characteristics of DNA fingerprints in humpback whales (Megaptera novaeangliae). The Journal of heredity. 84(4):281-90. Abstract
Dalebout ML, Steel DJ, Baker CS.  2008.  Phylogeny of the beaked whale genus Mesoplodon (Ziphiidae: Cetacea) revealed by nuclear introns: implications for the evolution of male tusks. Systematic Biology. 57(6):857-75. Abstract
Constantine R, Russell K, Gibbs N, Childerhouse S, Baker CS.  2007.  Photo-identification of humpback whales in New Zealand waters and their migratory connections to breeding grounds of Oceania. Marine Mammal Science. 23:715-720.
Oremus M, Poole MM, Albertson RG, Baker CS.  2012.  Pelagic or insular? Genetic differentiation of rough-toothed dolphins in the Society Islands, French Polynesia Journal of Experimental Marine Biology and Ecology. 432-433:37-46.
Carroll EL, CHILDERHOUSE SIMONJ, CHRISTIE MARK, Lavery S, PATENAUDE NATHALIE, Alexander A, Constantine R, Steel DJ, BOREN LAURA, Baker CS.  2012.  Paternity assignment and demographic closure in the New Zealand southern right whale. Molecular Ecology. 21(16):3960-3973.
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Garrigue C, Dodemont R, Steel DJ, Baker CS.  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.
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Thompson KF, Millar CD, Baker CS, Dalebout M, Steel DJ, van Helden AL, CONSTANTINE ROCHELLE.  2013.  A novel conservation approach provides insights into the management of rare cetaceans. Biological Conservation. 157:331-340.
Dalebout ML, Baker CS, Steel DJ, Thompson K, Robertson KM, Chivers SJ, Perrin WF, Goonatilake M, Anderson RC, Mead JG et al..  2012.  A Newly Recognised Beaked Whale (Ziphiidae) in the Tropical Indo-Pacific: Mesoplodon hotaula or M. ginkgodens hotaula. Report to the Scientific Committee of the International Whaling Commission.
Hickey AJR, Lavery S, Hannan DA, Baker CS, Clements KD.  2009.  New Zealand triplefin fishes (family Tripterygiidae): contrasting population structure and mtDNA diversity within a marine species flock. Molecular Ecology. 18(4):680-96. Abstract
Dalebout ML, Mead JG, Baker CS, Baker AN, Helden AL.  2002.  A New Species of Beaked Whale Mesoplodon perrini sp. n. (cetecea: ziphiidae) Discovered Through Phylogenetic Analyses of Mitochondrial DNA Sequences. Marine Mammal Science. 18(3):577-608.
Madon B, Gimenez O, McArdle B, Baker CS, Garrigue C.  2011.  A new method for estimating animal abundance with two sources of data in capture-recapture studies. Methods in Ecology and Evolution. 2(4):390-400. Abstract
Laikre L, Allendorf FW, Aroner LC, Baker CS, Gregovich DP, Hansen MM, Jackson J, Kendall KC, McKelvey K, Neel MC et al..  2010.  Neglect of Genetic Diversity in Implementation of the Convention on Biological Diversity. Conservation Biology. 24(1):86-88.
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Jackson JA, Anderson M, Steel DJ, Brooks L, Baverstock P, Burns D, Clapham P, Constantine R, Franklin W, Franklin T et al..  2012.  Multistate measurements of genotype interchange between east Australia and Oceania (IWC breeding sub-stocks E1, E2, E3 and F) between 1999 and 2004. Report to the Scientific Committee of the International Whaling Commission.
Garrigue C, Constantine R, Poole MM, Hauser N, Clapham P, Donoghue M, Russell K, Paton D, Mattila DK, Robbins J et al..  2011.  Movement of individual humpback whales between wintering grounds of Oceania (South Pacific), 1999 to 2004. Journal of Cetacean Research and Management. (Special Issue 3):275-82.
Caballero S, Jackson J, Mignucci-Giannoni AA, Barrios-Garrido H, Beltrán-Pedreros S, Montiel-Villalobos MAG, Robertson KM, Baker CS.  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(1):252-68. Abstract
Baker CS, Cipriano F, Palumbi SR.  1996.  Molecular genetic identification of whale and dolphin products from commercial markets in Korea and Japan. Molecular Ecology. 5(5):671-685.
Pimper LE, Baker CS, Goodall NRP, Olavarria C, Remis MI.  2010.  Mitochondrial DNA variation and population structure of Commerson’s dolphins (Cephalorhynchus commersonii) in their southernmost distribution. Conservation Genetics. 11(6):2157-2168. Abstract
Patenaude NJ, Portway V, Schaeff C, Bannister JL, Best P, Payne R, Rowntree V, Rivarola M, Baker CS.  2007.  Mitochondrial DNA diversity and population structure among southern right whales (Eubalaena australis). Journal of Heredity. 98:147-157.
Hollatz C, Flach L, Baker CS, Santos FR.  2011.  Microsatellite data reveal fine genetic structure in male Guiana dolphins (Sotalia guianesis) in two geographically close embayments at south-eastern coast of Brazil. Marine Biology. 158(4):927-933. Abstract
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Schmitt NT, Double MC, Baker CS, Steel DJ, Jenner KCS, Jenner MN, Paton D, Gales R, Jarman SN, Gales N et al..  2012.  Low levels of genetic differentiation characterize Australian humpback whale (Megaptera novaeangliae) populations. Report to the Scientific Committee of the International Whaling Commission.
Alexander A, Steel DJ, Slikas B, Hoekzema K, Carraher C, Parks M, Cronn R, Baker CS.  2013.  Low Diversity in the Mitogenome of Sperm Whales Revealed by Next-Generation Sequencing. Genome Biology and Evolution. 5(1):113-129.
Baker CS, Hamner RM, Cooke J, Heimeier D, Vant M, Steel DJ, Constantine R.  2012.  Low abundance and probable decline of the critically endangered Maui's dolphin estimated by genotype capture-recapture. Animal Conservation.
Pichler FB, Baker CS.  2000.  Loss of genetic diversity in the endemic Hector's dolphin due to fisheries-related mortality. Proceedings. Biological sciences / The Royal Society. 267(1438):97-102. Abstract
Mizroch SA, Tillman MF, Jurasz S, Straley JM, von Ziegesar O, Herman LM, Pack AA, Baker CS, Darling J, Glockner-Ferrari D et al..  2010.  Long-term survival of humpback whales radio-tagged in Alaska from 1976 through 1978. Marine Mammal Science. 27(1):217-229.
Ruegg K, Rosenbaum HC, Anderson EC, Engel M, Rothschild A, Baker CS, Palumbi SR.  2013.  Long-term population size of the North Atlantic humpback whale within the context of worldwide population structure. Conservation Genetics. 14(1):103-114.