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Hamner RM, CONSTANTINE ROCHELLE, Oremus M, Stanley M, Brown P, Baker CS.  2013.  Long-range movement by Hector's dolphins provides potential genetic enhancement for critically endangered Maui's dolphin. Marine Mammal Science. :n/a-n/a.
Olavarria C, Balbontin F, Bernal R, Baker CS.  2006.  Lack of divergence in the mitochondrial cytochrome b gene between Macruronus species (Pisces: Merlucciidae) in the Southern Hemisphere. New Zealand Journal of Marine and Freshwater Research. 40:299-304.
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Oremus M, Poole MM, Steel DJ, Baker CS.  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.
Oremus M, Poole MM, Steel DJ, Baker CS.  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.
Campbell R, Gales NJ, Lento GM, Baker CS.  2008.  Islands in the sea: extreme female natal site fidelity in the Australian sea lion, Neophoca cinerea. Biology Letters. 4(1):139-42. Abstract
Campbell R, Gales NJ, Lento GM, Baker CS.  2007.  Islands in the sea: extreme female natal site fidelity in the Australian sea lion, Neophoca cinerea. Biology Letters. 4(1):139-142.
Calambokidis J, Steiger GH, Evenson JR, Flynn KR, Balcomb KC, Claridge DE, Bloedel P, Straley JM, Baker CS, von Ziegesar O et al..  1996.  INTERCHANGE AND ISOLATION OF HUMPBACK WHALES OFF CALIFORNIA AND OTHER NORTH PACIFIC FEEDING GROUNDS. Marine Mammal Science. 12(2):215-226.
Baker CS, Palumbi SR, Lambertsen RH, Weinrich MT, Calambokidis J, O'Brien SJ.  1990.  Influence of seasonal migration on geographic distribution of mitochondrial DNA haplotypes in humpback whales. Nature. 344(6263):238-40. Abstract
Weinrich MT, Rosenbaum H, Baker CS, Blackmer AL, Whitehead H.  2006.  The influence of maternal lineages on social affiliations among humpback whales (Megaptera novaeangliae) on their feeding grounds in the Southern Gulf of Maine. Journal of Heredity. 97:226-234.
Baker CS, Lukoschek V, Lavery S, Dalebout ML, Ma Y-un, Endo T, Funahashi N.  2006.  Incomplete reporting of whale, dolphin and porpoise ‘bycatch' revealed by molecular monitoring of Korean markets. Animal Conservation. 9:474-482.
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Barlow J, Calambokidis J, Falcone EA, Baker CS, Burdin AM, Clapham PJ, Ford JKB, Gabriele CM, LeDuc R, Mattila DK et al..  2011.  Humpback whale abundance in the North Pacific estimated by photographic capture-recapture with bias correction from simulation studies. Marine Mammal Science. 27(4):793-818.
Jackson J, Patenaude NJ, Carroll EL, Baker CS.  2008.  How few whales were there after whaling? Inference from contemporary mtDNA diversity Molecular Ecology. 17(1):236-51. Abstract
Wade PR, Baker CS.  2012.  High plausibility of Hypothesis III for stock structure of the western North Pacific minke. Report to the Scientific Committee of the International Whaling Commission.
Baker CS, Slade RW, Bannister JL, Abernethy RB, Weinrich MT, Lien J, Urbán-Ramirez J, Corkeron P, Calambokidis J, Vasquez O et al..  1994.  Hierarchical structure of mitochondrial DNA gene flow among humpback whales Megaptera novaeangliae, world-wide. Molecular Ecology. 3(4):313-327.
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Jackson JA, Laikre L, Baker CS, Kendall KC.  2012.  Guidelines for collecting and maintaining archives for genetic monitoring. Conservation Genetics Resources. 4(2):527-536.
Baker CS, Dalebout ML, Lento GM, Funahashi N.  2002.  Gray whale products sold in commercial markets along the Pacific coast of Japan. Marine Mammal Science. 18(1):295-300.
Oremus M, Gales R, Kettles H, Baker CS.  2013.  Genetic Evidence of Multiple Matrilines and Spatial Disruption of Kinship Bonds in Mass Strandings of Long-finned Pilot Whales, Globicephala melas. Journal of Heredity.
Baker CS, Steel DJ, Choi Y, Lee H, Kim KS, Choi SK, Ma Y-un, Hambleton C, Psihoyos L, Brownell RL et al..  2010.  Genetic evidence of illegal trade in protected whales links Japan with the US and South Korea. Biology Letters. Abstract
Hamner RM, Pichler FB, Heimeier D, CONSTANTINE ROCHELLE, Baker CS.  2012.  Genetic differentiation and limited gene flow among fragmented populations of New Zealand endemic Hector’s and Maui’s dolphins. Conservation Genetics. 13(4):987-1002.
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Garrigue C, Franklin T, Constantine R, Russell K, Burns D, Poole MM, Paton D, Hauser N, Oremus M, Childerhouse S et al..  2011.  First assessment of interchange of humpback whales between Oceania and the east coast of Australia. Journal of Cetacean Research and Management. (Special Issue 3):269-74.
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Baker CS, Cooke J, Lavery S, Dalebout ML, Ma Y-un, Funahashi N, Carraher C, Brownell, Jr. RL.  2007.  Estimating the number of whales entering trade using DNA profiling and capture-recapture analysis of market products. Molecular Ecology. 13:2617-2626.
Hamner RM, Oremus M, Stanley M, Brown P, Constantine R, Baker CS.  2012.  Estimating the abundance and effective population size of Maui’s dolphins using microsatellite genotypes in 2010–11, with retrospective matching to 2001–07.
Jackson J, Pinsky ML, Baker CS.  2009.  Erratum. How few whales were there after whaling? Inference from contemporary mtDNA diversity. Molecular Ecology. 18(19):4134-5.
D
Baker CS, Vant MD, Dalebout ML, Lento GM, O'Brien SJ, Yuhki N.  2006.  Diversity and duplication of DQB and DRB-like genes of the MHC in baleen whales (Suborder: Mysticeti). Immunogenetics. 58:283-296.
Dalebout ML, Baker CS, Steel DJ, Robertson KM, Chivers SJ, Perrin WF, Mead JG, Grace RV, Schofield TD.  2007.  A divergent mtDNA lineage among Mesoplodon beaked whales: Molecular evidence for a new species in the tropical pacific? Marine Mammal Science. 23:954-966.