The history of whales read from DNA

Whales, Whaling, and Ocean Ecosystems

Volumn , Issue , 2007, Pages 102-115

  Palumbi, Stephen R ^a   Roman, Joe ^b  

^a STANFORD UNIVERSITY   (United States)

^b UNIVERSITY OF VERMONT   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84872872149     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (68)

1. Abdo, Z., K. A. Crandall, and P. Joyce. 2004. Evaluating the performance of likelihood methods for detecting population structure. Molecular Ecology 13: 837-851.
2. Andersen, L., E. Born, R. Dietz, T. Haug, N. øien, and C. Bendixen. 2003. Genetic population structure of minke whales Balaenoptera acutorostrata from Greenland, the North East Atlantic and the North Sea probably reflects different ecological regions. Marine Ecology Progress Series 247: 263-280.
3. Angliss, R. P., D. J. Rugh, D. E. Withrow, and R. C. Hobbs. 1995. Evaluations of aerial photogrammetric length measurements of the Bering-Chukchi-Beaufort Seas stock of bowhead whales (Balaena mysticetus). Report of the International Whaling Commission 45: 313-324.
4. Arnason, U., A. Gullberg, and B. Widegren. 1993. Cetacean mitochondrial-DNA control region: sequences of all extant baleen whales and 2 sperm whale species. Molecular Biology and Evolution 10: 960-970.
5. Avise, J. 1994. Molecular Markers, Natural History and Evolution. NY: Chapman and Hall.
6. Avise, J., R. Ball, and J. Arnold. 1988. Current versus historical population sizes in vertebrate species with high gene flow: a comparison based on mitochondrial DNA lineages and inbreeding theory for neutral mutations. Molecular Biology and Evolution 5: 331-344.
7. Baker, C., L. Medrano-Gonzalez, J. Calambokidis, A. Perry, F. Pichler, H. Rosenbaum, J. Straley, J. Urban-Ramirez, M. Yamaguchi, and O. Von Ziegesar. 1998. Population structure of nuclear and mitochondrial DNA variation among humpback whales in the North Pacific. Molecular Ecology 7: 695-707.
8. Baker, C., A. Perry, J. Bannister, M. Weinrich, R. Abernethy, J. Calambokidis, J. Lien, R. Lambertsen, J. Ramirez, O. Vasquez, P. Clapham, A. Alling, S. O'Brien, and S. Palumbi. 1993. Abundant mitochondrial-DNA variation and world-wide population structure in humpback whales. Proceedings of the National Academy of Sciences 90: 8239-8243.
9. Baker, C., R. Slade, J. Bannister, R. Abernethy, M. Weinrich, J. Lien, J. Urban, P. Corkeron, J. Calmabokidis, O. Vasquez, and S. Palumbi. 1994. Hierarchical structure of mitochondrial- DNA gene flow among humpback whales Megaptera novaeangliae, worldwide. Molecular Ecology 3: 313-327.
10. Bakke, I., S. Johansen, O. Bakke, and M. ElGewely. 1996. Lack of population subdivision among the minke whales (Balaenoptera acutorostrata) from Icelandic and Norwegian waters based on mitochondrial DNA sequences. Marine Biology 125:1-9.
11. Baum, J. K., R. A. Myers, D. G. Kehler, B. Worm, J. Harley, and P.A. Doherty. 2003. Collapse and conservation of shark populations in the northwest Atlantic. Science 299: 389-392.
12. Beerli, P. and J. Felsenstein. 2001. Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proceedings of the National Academy of Sciences 98: 4563-4568.
13. Bérubé, M., A. Aguilar, D. Dendanto, F. Larsen, G. Di Sciara, R. Sears, J. Sigurjónsson, J. Urban-Ramirez, and P. Palsbøll. 1998. Population genetic structure of North Atlantic, Mediterranean Sea and Sea of Cortez fin whales, Balaenoptera physalus (Linnaeus 1758): analysis of mitochondrial and nuclear loci. Molecular Ecology 7: 585-599.
14. Bérubé, M., J. Urban, A. Dizon, R. Brownell, and P. Palsbøll. 2002. Genetic identification of a small and highly isolated population of fin whales (Balaenoptera physalus) in the Sea of Cortez, Mexico. Conservation Genetics 3: 183-190.
15. Chittleborough, R. 1965. Dynamics of two populations of the humpback whale, Megaptera novaeangliae (Borowski). Australian Journal of Marine and Freshwater Research 16: 33-128.
16. Clapham, P. J. 1996. The social and reproductive biology of humpback whales: an ecological perspective. Mammal Review 26: 27-49.
17. Clapham, P. J. 2002. Humpback whale, in Encyclopedia of marine mammals. W. F. Perrin, B. Wursig, and J. G. M. Thewissen, eds. San Diego: Academic Press, pp.
18. Clapham, P., P. Palsbøll, L. Pastene, T. Smith and L. Walløe. 2004. Estimating pre-whaling abundance. Report of the Scientific Committee. International Whaling Commission. Annex S.
19. Cooke. J. 1999. Improvement of fishery-management advice through simulation testing of harvest algorithms. ICES Journal of Marine Science 56: 797-810.
20. Frankham, R. 1995. Effective population size/adult population size ratios in wildlife: a review. Genetical Research 66: 95-107.
21. Frankham, R. 1996. Relationship of genetic variation to population size in wildlife. Conservation Biology 10: 1500-1508.
22. Franz, G., D. Tautz, and G. Dover. 1985. Conservation of major nuclease S1-sensitive sites in the non-conserved spacer region of ribosomal DNA in Drosophila species. Journal of Molecular Biology 183: 519-527.
23. Hare, M., F. Cipriano, and S. R. Palumbi. 2003. Genetic evidence on the demography of specuation in ailopatric dolphin species. Evolution 56: 804-816.
24. Hartl, D. and A. Clark. 1997. Principles of population genetics. Sunderland, MA: Sinauer Associates.
25. Holt, S. 2004. Counting whales in the North Atlantic. Science 303: 39b-40.
26. Horwood, J. 1990. Biology and exploitation of the minke whale. Boca Raton, FL: CRC Press.
27. Howell, N., C. B. Smejkal, D. A. Mackey, P. F. Chinnery, D. M. Turnbull, and C. Herrnstadt. 2003. The pedigree rate of sequence divergence in the human mitochondrial genome: There is a difference between phylogenetic and pedigree rates. American Journal of Human Genetics 72: 659-670.
28. IUCN. 1994. 1994 IUCN Red List of threatened species. Gland, Switzerland: World Conservation Union.
29. IWC. 2003. Report of the Subcommittee on the Comprehensive Assessment of Humpback Whales. Journal of Cetacean Research and Management 5 (Suppl.): 293-323.
30. Jackson, J. B. C. 1997. Reefs since Columbus. Coral Reefs 16 (Suppl.): S23-S32.
31. Jackson, J. B. C., M. X. Kirby, W. H. Berger, K. A. Bjorndal, L.W. Botsford, B. J. Bourque, R. Bradbury, R. Cooke, J. Erlandson, J. A. Estes, T. P. Hughes, S. Kidwell, C. B. Lange, H. S. Lenihan, J. M. Pandolfi, C. H. Peterson, R. S. Steneck, M. J. Tegner, and R. Warner. 2001. Historical overfishing and the recent collapse of coastal ecosystems. Science 293: 629-638.
32. Kimura, T. and T. Ozawa. 2002. A new cetothere (Cetacea: Mysticeti) from the early Miocene of Japan. Journal of Vertebrate Paleontology 22: 684-702.
33. Li, W. 1997. Molecular evolution. Sunderland, MA: Sinauer Associates.
34. Lockyer, C. 1984. Review of baleen whale (Mysticeti) reproduction and implications for management. Report of the International Whaling Commission (Special Issue) 6: 27-50.
35. Mace, G. and R. Lande. 1991. Assessing extinction threats: toward a reevaluation of IUCN threatened species categories. Conservation Biology 5: 148-157.
36. MacLean, S., G. Sheehan, and A. Jensen. 2002. Inuit and marine mammals, in Encyclopedia of marine mammals. W. F. Perrin, B. Wursig, and J. G. M. Thewissen, eds. San Diego: Academic Press, pp.
37. Martin, A., B. Kessing, and S. Palumbi. 1990. Accuracy of estimating genetic-distance between species from short sequences of mitochondrial-DNA. Molecular Biology and Evolution 7: 485-488.
38. Mitchell, E. and R. R. Reeves. 1983. Catch history, abundance, and present status of northwest Atlantic humpback whales. Report of the International Whaling Commission (Special Issue) 5: 153-212.
39. Myers, R. A. and B. Worm. 2003. Rapid worldwide depletion of predatory fish communities. Nature 423: 280-283.
40. Nei, M. and D. Graur. 1984. Extent of protein polymorphism and the neutral mutation theory. Evolutionary Biology 17: 73-118.
41. Nunney, L. 1993. The influence of mating system and overlapping generations on effective population-size. Evolution 47: 1329-1341.
42. Nunney, L. 2000. The limits to knowledge in conservation genetics: the value of effective population size. Evolutionary Biology 32: 179-194.
43. Palsbøll, P., P. Clapham, D. Mattila, F. Larsen, R. Sears, H. Siegismund, J. Sigurjónsson, O. Vasquez, and P. Arctander. 1995. Distribution of mtDNA haplotypes in North-Atlantic humpback whales: the influence of behavior on population-structure. Marine Ecology-Progress Series 116: 1-10.
44. Palsbøll, P., M. Bérubé, J. Robbins, A. Nettel-Hernanz, P. J. Clapham, and D. Mattila. 2004. Whales before whaling in the North Atlantic: nuclear DNA markers. Paper SC/56/O25 presented to the International Whaling Commission Scientific Committee.
45. Palumbi, S. R. and C. S. Baker. 1994. Contrasting population structure from no clear intron sequences and mtDNA of humpback whales. Molecular Biology and Evolution 11: 426-435.
46. Palumbi, S. R., F. Cipriano and M. Hare. 2001. Predicting nuclear gene coalescence from mitochondrial data: the three-times rule. Evolution 55: 859-868.
47. Perrin W. and R. Brownell. 2002. Minke whales, in Encyclopedia of marine mammals.W. F. Perrin, B. Wursig, and J. G. M. Thewissen, eds. San Diego: Academic Press, pp.
48. Posada, D., and K. Crandall. 1998. Model test: testing the model of DNA substitution. Bioinformatics 14: 817-818.
49. Reeves, R. R. 2002. The origins and character of "aboriginal subsistence" whaling: a global review. Mammal Review 32: 71-106.
50. Roman, J. and S. R. Palumbi. 2003. Whales before whaling in the North Atlantic. Science 301: 508-510.
51. Rosenbaum, H., M. Egan, P. Clapham, R. Brownell, S. Malik, M. Brown, B. White, P. Walsh, and R. Desalle. 2000. Utility of North Atlantic right whale museum specimens for assessing changes in genetic diversity. Conservation Biology 14: 1837-1842.
52. Rychel, A. L., T.W. Reeder, and A. Berta. 2004. Phylogeny of mysticete whales based on mitochondrial and nuclear data. Molecular Phylogenetics and Evolution 32: 892-901.
53. Scammon, C. M. 1874. The marine mammals of the north-western coast of North America, described and illustrated with an account of the American whale- fishery. New York: John H. Carmany and Co. Reprint, Riverside, CA: Manessier, 1969.
54. Sergeant, D. E. 1977. Stocks of fin whales Balenoptera physalus L. in the North Atlantic Ocean. Report of the International Whaling Commission 27: 460-473.
55. Shapiro, B., A. J. Drummond, and 25 others. 2004. The rise and fall of the Beringian Steppe bison. Science 306: 1561-1565.
56. Smith, T. D., and R. R. Reeves. 2002. Estimating historical humpback whale removals from the North Atlantic. Journal of Cetacean Research and Management 4 (Supplement): 242-255.
57. Smith, T. D.. 2003. Estimating historical humpback whale removals from the North Atlantic: an update. Journal of Cetacean Research and Management 5 (Supplement): 301-311.
58. Soulé, M. 1976. Allozyone variation: its determinants in space and time. in Molecular evolution. F. J. Ayala, ed. Sunderland, MA: Sinauer, pp. 60-77.
59. Springer, A. M., J. A. Estes, G. B. van Vliet, T.M. Williams, D. F. Doak, E.M. Danner, K. A. Forney, and B. Pfister. 2003. Sequential megafaunal collapse in the North Pacific Ocean: an ongoing legacy of industrial whaling? Proceedings of the National Academy of Sciences 100: 12223-12228.
60. Stevick, P. T., J. Allen, P. J. Clapham, N. Friday, S.K. Katona, F. Larsen, J. Lien, D. K. Mattila, P. J. Palsbøll, J. Sigurjónsson, T. D. Smith, N. øien, and P. S. Hammond. 2003. North Atlantic humpback whale abundance and rate of increase four decades after protection from whaling. Marine Ecology Progress Series 258:263-273.
61. Tajima, F. 1989. The effect of change in population size on DNA polymorphism. Genetics 123: 597-601.
62. Takahata, N. 1995. A genetic perspective on the origin and history of humans. Annual Review of Ecology and Systematics 26: 343-372.
63. Wada, S. and K. Numachi. 1991. Allozyme analyses of genetic differentiation among the populations and species of the Balaenoptera. Report of the International Whaling Commission (Special Issue) 13: 125-154.
64. Waldick, R., S. Kraus, M. Brown, and B. White. 2002. Evaluating the effects of historic bottleneck events: an assessment of microsatellite variability in the endangered, North Atlantic right whale. Molecular Ecology 11: 2241-2250.
65. Weller, D., A. Burdin, B. Wursig, B. Taylor, and R. Brownell. 2002. The western gray whale: a review of past exploitation, current status and potential threats. Journal of Cetacean Research and Management 4: 7-12.
66. Whitehead, H. 2000. Density-dependent habitat selection and the modeling of sperm whale (Physeter macrocephalus) exploitation. Canadian Journal of Fisheries and Aquatic Sciences 57: 223-230.
67. Whitehead, H. 2002. Estimates of the current global population size and historical trajectory for sperm whales. Marine Ecology Progress Series 242: 295-304.
68. Wu, C. -I. and W. -H. Li. 1985. Evidence for higher rates of nucleotide substitution in rodents than in man. Proc. Nat. Acad. Sci. (USA) 82: 1741-1745.