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Witteveen BH, Straley JM, Chenoweth E, Baker CS, Barlow J, Matkin C, Gabriele CM, Neilson J, Steel DJ, von Ziegesar O et al..  2011.  Using movements, genetics and trophic ecology to differentiate inshore from offshore aggregations of humpback whales in the Gulf of Alaska. Endangered Species Research. 14(3):217-225.
Witteveen BH, Straley JM, von Ziegesar O, Steel DJ, Baker CS.  2004.  Abundance and mtDNA differentiation of humpback whales (Megaptera novaeangliae) in the Shumagin Islands, Alaska. Canadian Journal of Zoology. 82:1352-1359.
Wiseman N, Parsons S, Stockin KA, Baker CS.  2011.  Seasonal occurrence and distribution of Bryde's whales in the Hauraki Gulf, New Zealand. Marine Mammal Science. 27(4):E253-E267. 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.
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.
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Tiedemann R, Cipriano F, Morin PA, Hoelzel AR, Palsbøll P, Waples RS, Natoli L, Bachmann L, Postma L, Double MC et al..  2012.  Updated guidelines for DNA data quality control and error rate estimation, for genetic studies relevant to IWC management advice. Report to the Scientific Committee of the International Whaling Commission.
Thompson K, Baker CS, van Helden A, Patel S, Millar C, CONSTANTINE ROCHELLE.  2012.  The world’s rarest whale. Current Biology. 22(21):R905-R906.
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.
Tezanos-Pinto G, Baker CS, Russell K, Martien KK, Baird RW, Hutt A, Stone GS, Mignucci-Giannoni AA, Caballero S, Endo T et al..  2009.  A worldwide perspective on the population structure and genetic diversity of bottlenose dolphins (Tursiops truncatus) in New Zealand. The Journal of Heredity. 100(1):11-24. Abstract
Tezanos-Pinto G, CONSTANTINE ROCHELLE, Brooks L, Jackson JA, Mourão F, Wells S, Baker CS.  2013.  Decline in local abundance of bottlenose dolphins (Tursiops truncatus) in the Bay of Islands, New Zealand. Marine Mammal Science. :n/a-n/a.
Tezanos-Pinto G, Baker CS.  2011.  Short-term reactions and long-term responses of bottlenose dolphins (Tursiops truncatus) to remote biopsy sampling. New Zealand Journal of Marine and Freshwater Research. :1-17. Abstract
Tallmon DA, Gregovich DP, Waples RS, Baker CS, Jackson J, Taylor BL, Archer E, Martien KK, Allendorf FW, Schwartz MK.  2010.  When are genetic methods useful for estimating contemporary abundance and detecting population trends? Molecular Ecology Resources. 10(4):684-692. Abstract
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Sremba AL, Hancock-Hanser B, Branch TA, LeDuc RL, Baker CS.  2012.  Circumpolar Diversity and Geographic Differentiation of mtDNA in the Critically Endangered Antarctic Blue Whale (Balaenoptera musculus intermedia). PLoS ONE. 7(3):e32579.
Slikas B, Baker CS, Clapham P, Frasier TR, Seger J, Valenzuela L, Wade P.  2012.  Proposal to the Scientific Committee: Worldwide genetic diversity and phylogenetic relationships among right whales based on next-generation sequencing of complete mitochondrial geneomes and multiple nuclear loci. Report to the Scientific Committee of the International Whaling Commission.
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.
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Ruegg KC, Anderson EC, Baker CS, Vant MD, Jackson J, Palumbi SR.  2010.  Are Antarctic minke whales unusually abundant because of 20th century whaling? Molecular Ecology. 19(2):281-291.
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.
Rosenbaum H, Brownell RL, Brown MW, Schaeff C, Portway V, White BN, Malik S, Pastene LA, Patenaude NJ, Baker CS et al..  2000.  World-wide genetic differentiation of Eubalaena: questioning the number of right whale species. Molecular Ecology. 9(11):1793-1802.
Robineau D, Goodall RNP, Pichler FB, Baker CS.  2007.  Description of a new subspecies of Commerson's dolphin, Cephalorhynchus commersonii (Lacépède, 1804), inhabiting the coastal waters of the Kerguelen Islands. Mammalia. 71:172-180.
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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
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
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.
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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.
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.
Oremus M, Hamner RM, Stanley M, Brown P, Baker CS, Constantine R.  2012.  Distribution, group characteristics and movements of the Critically Endangered Maui’s dolphin Cephalorhynchus hectori maui. Endangered Species Research. 19(1):1-10.