PART VII. Balaenoptera physalus / The End of Nature

 

 

 

 

 

Chapter 3

 

The paper Veronica is talking about here is Shimamura et al. 1997, but the discussion of whale phylogeny is based on many other sources, as well.

 

 

Chapter 4

 

Much of the history Graham relates here is treated in his extraordinary book, The Sounding of the Whale.

 

 

Chapter 5

 

While estimating population size from population genetic data is rather magical, it's important to understand the complexities and limitations. See in particular Nabholz et al. 2008 and Wares et al. 2009. For a good introduction to coalescent models, see Hudson 1991 or Wakeley 2009.

 

 

Sources

 

Arnason, U., Gullberg, A. and Janke, A., 2004. Mitogenomic analyses provide new insights into cetacean origin and evolution. Gene, 333: 27-34.

 

Baker, C.S. and Clapham, P.J., 2004. Modelling the past and future of whales and whaling. Trends in Ecology & Evolution, 19(7): 365-371.

 

Baumgartner, M.F., Mullin, K.D., May, L.N. and Leming, T.D., 2001. Cetacean habitats in the northern Gulf of Mexico. Fishery Bulletin, 99(2): 219-239.

 

Bejder, L. and Hall, B.K., 2002. Limbs in whales and limblessness in other vertebrates: mechanisms of evolutionary and developmental transformation and loss. Evolution & Development, 4(6): 445-458.

 

Buntjer, J.B., Hoff, I.A. and Lenstra, J.A., 1997. Artiodactyl interspersed DNA repeats in cetacean genomes. Journal of Molecular Evolution, 45(1): 66-69.

 

Burnett, D.G., 2012. The Sounding of the Whale: Science and Cetaceans in the Twentieth Century. University of Chicago Press.

 

Gatesy, J. and O'leary, M.A., 2001. Deciphering whale origins with molecules and fossils. Trends in Ecology & Evolution, 16(10): 562-570.

 

Gingerich, P.D., 2003. Land-to-sea transition in early whales: evolution of Eocene Archaeoceti (Cetacea) in relation to skeletal proportions and locomotion of living semiaquatic mammals. Paleobiology, 29(3): 429-454.

 

Graur, D. and Higgins, D.G., 1994. Molecular Evidence for the Inclusion of Cetaceans within the Order Artiodactyla. Molecular Biology and Evolution, 11(3): 357-364.

 

Hasegawa, M., Adachi, J. and Milinkovitch, M.C., 1997. Novel phylogeny of whales supported by total molecular evidence. Journal of Molecular Evolution, 44: S117-S120.

 

Holt, S.J., 2004. Counting whales in the North Atlantic. Science, 303(5654): 39-39.

 

Hudson, R.R., 1991. Gene genealogies and the coalescent process. Oxford Surveys in Evolutionary Biology, 7: 1-44.

 

Lubick, N., 2003. Ecology - New count of old whales adds up to big debate. Science, 301(5632): 451-451.

 

McClellan, D.A., Palfreyman, E.J., Smith, M.J., Moss, J.L., Christensen, R.G. and Sailsbery, A.K., 2005. Physicochemical evolution and molecular adaptation of the cetacean and artiodactyl cytochrome b proteins. Molecular Biology and Evolution, 22(3): 437-455.

 

Messenger, S.L. and Mcguire, J.A., 1998. Morphology, molecules, and the phylogenetics of cetaceans. Systematic Biology, 47(1): 90-124.

 

Milinkovitch, M.C., Orti, G. and Meyer, A., 1995. Novel Phylogeny of Whales Revisited but Not Revised. Molecular Biology and Evolution, 12(3): 518-520.

 

Milinkovitch, M.C. and Thewissen, J.G.M., 1997. Evolutionary biology - Even-toed fingerprints on whale ancestry. Nature, 388(6643): 622-624.

 

Mitchell, E.D., 2004. Counting whales in the North Atlantic. Science, 303(5654): 39-40.

 

Nikaido, M., Hamilton, H., Makino, H., Sasaki, T., Takahashi, K., Goto, M., Kanda, N., Pastene, L.A. and Okada, N., 2006. Baleen whale phylogeny and a past extensive radiation event revealed by SINE insertion analysis. Molecular Biology and Evolution, 23(5): 866-873.

 

Nikaido, M., Matsuno, F., Hamilton, H., Brownell, R.L., Cao, Y., Ding, W., Zuoyan, Z., Shedlock, A.M., Fordyce, R.E., Hasegawa, M. and Okada, N., 2001. Retroposon analysis of major cetacean lineages: The monophyly of toothed whales and the paraphyly of river dolphins. Proceedings of the National Academy of Sciences of the United States of

America, 98(13): 7384-7389.

 

 

Nikaido, M., Piskurek, O. and Okada, N., 2007. Toothed whale monophyly reassessed by SINE insertion analysis: The absence of lineage sorting effects suggests a small population of a common ancestral species. Molecular Phylogenetics and Evolution, 43(1): 216-224.

 

O'leary, M.A., 2001. The phylogenetic position of cetaceans: Further combined data analyses, comparisons with the stratigraphic record and a discussion of character optimization. American Zoologist, 41(3): 487-506.

 

O'leary, M.A., Gatesy, J. and Novacek, M.J., 2003. Are the dental data really at odds with the molecular data? Morphological evidence for whale phylogeny (re) reexamined. Systematic Biology, 52(6): 853-864.

 

Palumbi, S.R. and Roman, J., 2004. Counting whales in the North Atlantic - Response. Science, 303(5654): 40-40.

 

Roman, J. and Palumbi, S.R., 2003. Whales before whaling in the North Atlantic. Science (Washington D C), 301(5632): 508-510.

 

Sasaki, T., Nikaido, M., Hamilton, H., Goto, M., Kato, H., Kanda, N., Pastene, L.A., Cao, Y., Fordyce, R.E., Hasegawa, M. and Okada, N., 2005. Mitochondrial phylogenetics and evolution of mysticete whales. Systematic Biology, 54(1): 77-90.

 

Shimamura, M., Abe, H., Nikaido, M., Ohshima, K. and Okada, N., 1999. Genealogy of families of SINEs in cetaceans and artiodactyls: The presence of a huge superfamily of tRNA(Glu)-derived families of SINEs. Molecular Biology and Evolution, 16(8): 1046-1060.

 

Shimamura, M., Yasue, H., Ohshima, K., Abe, H., Kato, H., Kishiro, T., Goto, M., Munechika, I. and Okada, N., 1997. Molecular evidence from retroposons that whales form a clade within even-toed ungulates. Nature (London), 388(6643): 666-670.

 

Thewissen, J.G.M., Cohn, M.J., Stevens, L.S., Bajpai, S., Heyning, J. and Horton, W.E., 2006. Developmental basis for hind-limb loss in dolphins and origin of the cetacean bodyplan. Proceedings of the National Academy of Sciences of the United States of America, 103(22): 8414-8418.

 

Thewissen, J.G.M., Cooper, L.N., Clementz, M.T., Bajpai, S. and Tiwari, B.N., 2007. Whales originated from aquatic artiodactyls in the Eocene epoch of India. Nature, 450(7173): 1190-U1.

 

Thewissen, J.G.M. and Williams, E.M., 2002. The early radiations of cetacea (Mammalia): Evolutionary pattern and developmental correlations. Annual Review of Ecology and Systematics, 33: 73-90.

 

Thewissen, J.G.M., Williams, E.M., Roe, L.J. and Hussain, S.T., 2001. Skeletons of terrestrial cetaceans and the relationship of whales to artiodactyls. Nature, 413(6853): 277-281.

 

Uhen, M.D., 2007. Evolution of marine mammals: Back to the sea after 300 million years. Anatomical Record-Advances in Integrative Anatomy and Evolutionary Biology, 290(6): 514-522.

 

Wakeley, J., 2009. Coalescent Theory: An Introduction. Roberts & Company Publishers.

 

Wares, J.P., 2010. Natural Distributions of Mitochondrial Sequence Diversity Support New Null Hypotheses. Evolution, 64(4): 1136-1142.