Journal of Archaeological Method and Theory

, Volume 20, Issue 3, pp 495–524 | Cite as

A Late Holocene Population Bottleneck in California Tule Elk (Cervus elaphus nannodes): Provisional Support from Ancient DNA

  • Jack M. Broughton
  • R. Kelly Beck
  • Joan B. Coltrain
  • Dennis H. O’ Rourke
  • Alan R. Rogers


Zooarchaeological analyses have suggested a possible case of late Holocene resource depression in California tule elk (Cervus elaphus nannodes). We develop and conduct a preliminary independent test of this here based on trends in genetic diversity derived from ancient DNA extracted from archaeological elk bone. Mitochondrial DNA sequence data from 24 tule elk temporally dispersed across the late Holocene deposits of the Emeryville Shellmound, California, provide provisional support for a decline in genetic diversity and a population bottleneck beginning about 1600 B.P. Final confirmation of this pattern must await complete replication of the sequences. Stable isotope analyses of the elk bone provide a record of change in the terrestrial environment across the period of deposition and no suggestion that climate change may have played a role in an elk population decline. The analysis has implications for our understanding of change in human behavior and biology during late Holocene of central California, the methodology of resource depression analyses, and the conservation biology of tule elk.


Tule elk Late Holocene Ancient DNA Resource depression Climate change 



We thank the College of Social and Behavioral Sciences and the Vice President for Research, University of Utah, for seed grants that funded this research. We also thank J. Knudsen and the staff of the Phoebe Hearst Museum of Anthropology for access to, and assistance in acquiring, the elk samples from Emeryville. We thank C. Darwent, V. Butler and M. O’Brien for organizing and chairing the symposium in which this paper was originally presented and for the work organizing the special JAMT volume. We also thank them, Bruce Winterhalder, Ben Sacks, Eric Bartleink and two anonymous reviewers for very helpful comments on the manuscript. Finally, JMB thanks Richard E. Broughton for discussions in 2000 that led to the conception of this project.


  1. Adam, D. P. (1975). A late Holocene pollen record from Pearson’s Pond, Weeks Creek Landslide, San Francisco Peninsula, California. United States Geological Survey Journal of Research, 3, 721–731.Google Scholar
  2. Ambrose, S. H. (1990). Preparation and characterization of bone and tooth collagen for isotopic analysis. Journal of Archaeological Science, 17, 431–451.CrossRefGoogle Scholar
  3. Anderson, M. K. (2005). Tending the wild: Native American knowledge and the management of California’s natural resources. Berkeley: University of California Press.Google Scholar
  4. Anderson, R. S., & Smith, S. J. (1994). Paleoclimatic interpretations of meadow sediment and pollen stratigraphies from California. Geology, 22, 723–726.CrossRefGoogle Scholar
  5. Barnes, I. P., Matheus, B., Shapiro, B., Jensen, D., & Cooper, A. (2002). Dynamics of Pleistocene population extinctions in Beringian brown bears. Science, 295, 2267–2270.CrossRefGoogle Scholar
  6. Bartelink, E. J. (2006). Resource intensification in pre-contact central California: A bioarchaeological perspective on diet and health patterns among hunter-gatherers from the Lower Sacramento Valley and San Francisco Bay. Ph.D. dissertation, Department of Anthropology, Texas A&M University, College Station, TX.Google Scholar
  7. Bayham, F. E. (1979). Factors influencing the Archaic pattern of animal utilization. Kiva, 44, 219–235.Google Scholar
  8. Bayham, F. E. (1982). A diachronic analysis of prehistoric animal exploitation at Ventana Cave. Ph.D. dissertation, Department of Anthropology, Arizona State University, Tempe, Arizona. University Microfilms, Ann Arbor.Google Scholar
  9. Beck, R. K. (2009). The molecular genetics of prey choice: using ancient DNA to infer prehistoric population histories. California Archaeology, 1, 253–268.Google Scholar
  10. Bensasson, D., Zhang, D.-X., Hartl, D. L., & Hewitt, G. M. (2001). Mitochondrial pseudogenes: evolution’s misplaced witnesses. Trends in Ecology & Evolution, 16(6), 314–321.CrossRefGoogle Scholar
  11. Benson, L., Kashgarian, M., Rye, R., Lund, S., Paillet, F., Smoot, J., et al. (2002). Holocene multidecadal and multicentennial droughts affecting northern California and Nevada. Quaternary Science Reviews, 21, 659–682.CrossRefGoogle Scholar
  12. Berkes, F. (2004). Rethinking community-based conservation. Conservation Biology, 18, 621–630.CrossRefGoogle Scholar
  13. Berkes, F., Folke, C., & Gadgil, M. (1995). Traditional ecological knowledge, biodiversity, resilience and sustainability. In C. A. Perrings et al. (Eds.), Biodiversity conservation (pp. 281–299). Netherlands: Kluwer Academic Publishers.CrossRefGoogle Scholar
  14. Blackburn, T. C., & Anderson, M. K. (Eds.). (1993). Before the wilderness: environmental management by Native Californians. Menlo Park: Ballena.Google Scholar
  15. Bon, C., Berthonaud, V., Fosse, P., Gély, B., Maksud, F., Vitalis, R., et al. (2011). Low regional diversity of late cave bears mitochondrial DNA at the time of Chauvet Aurignacian paintings. Journal of Archaeological Science, 38, 1886–1895.CrossRefGoogle Scholar
  16. Braje, T. J. (2010). Modern oceans, ancient sites: archaeology and marine conservation on San Miguel Island, California. Salt Lake City: University of Utah Press.Google Scholar
  17. Braje, T. J., Kennett, D. J., Erlandson, J. M., & Culleton, B. J. (2007). Human impacts on nearshore shellfish taxa: a 7000 year record from Santa Rosa Island, California. American Antiquity, 41, 117–128.Google Scholar
  18. Broughton, J. M. (1994). Declines in mammalian foraging efficiency during the late Holocene, San Francisco Bay, California. Journal of Anthropological Archaeology, 13, 371–401.CrossRefGoogle Scholar
  19. Broughton, J. M. (1999). Resource depression and intensification during the Late Holocene, San Francisco Bay: Evidence from the Emeryville Shellmound vertebrate fauna. University of California Anthropological Records 32. Berkeley: University of California Press.Google Scholar
  20. Broughton, J. M. (2002). Prey spatial structure and behavior affect archaeological tests of optimal foraging models: examples from the Emeryville Shellmound vertebrate fauna. World Archaeology, 34, 60–83.CrossRefGoogle Scholar
  21. Broughton, J. M. (2004). Prehistoric human impacts on California birds: evidence from the Emeryville Shellmound avifauna. Ornithological Monographs, 56.Google Scholar
  22. Broughton, J. M., & Bayham, F. E. (2003). Showing off, foraging models, and the ascendance of large game hunting in the California Middle Archaic. American Antiquity, 68, 783–789.CrossRefGoogle Scholar
  23. Broughton, J. M., Mullins, D., & Ekker, T. (2007). Avian resource depression or intertaxonomic variation in bone density? A test with San Francisco Bay avifaunas. Journal of Archaeological Science, 34, 374–391.CrossRefGoogle Scholar
  24. Broughton, J. M., Byers, D., Bryson, R., Eckerle, W., & Madsen, D. (2008). Did climatic seasonality control late Quaternary artiodactyl densities in western North America? Quaternary Science Reviews, 37, 1916–1937.CrossRefGoogle Scholar
  25. Broughton, J. M., Cannon, M., & Bartelink, E. (2010). Evolutionary ecology, resource depression, and niche construction theory: applications to central California hunter-gatherers and Mimbres-Mogollon agriculturalists. Journal of Archaeological Method and Theory, 17, 371–421.CrossRefGoogle Scholar
  26. Broughton, J. M., Cannon, M. D., Bayham, F. E., & Byers, D. (2011). Prey body size and ranking in zooarchaeology: theory, empirical evidence and applications from the northern Great Basin. American Antiquity, 76, 403–428.CrossRefGoogle Scholar
  27. Byers, D. A., & Broughton, J. M. (2004). Holocene environmental change, artiodactyl abundances, and human hunting strategies in the Great Basin. American Antiquity, 69, 235–255.CrossRefGoogle Scholar
  28. California Fish and Game. (2011). http:// Accessed 10 September 2011.
  29. Calvignac, S., Hughes, S., Tougard, C., Michaux, J., Thevenot, M., Philippe, M., et al. (2008). Ancient DNA evidence for the loss of a highly divergent brown bear clade during historical times. Molecular Ecology, 17, 1962–1970.CrossRefGoogle Scholar
  30. Campos, P., Willerslev, E., Sher, A., Ludovic, O., Axelsson, E., Tikhonov, A., et al. (2010). Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics. Proceedings of the National Academy of Sciences, 107, 5675–5680.CrossRefGoogle Scholar
  31. Cannon, M. D. (2001). Archaeofaunal relative abundance, sample size, and statistical methods. Journal of Archaeological Science, 28, 185–195.CrossRefGoogle Scholar
  32. Coltrain, J. B., & Leavitt, S. W. (2002). Climate and diet in Fremont prehistory: economic variability and abandonment of maize agriculture in the Great Salt Lake Basin. American Antiquity, 67, 453–485.CrossRefGoogle Scholar
  33. Coltrain, J. B., Janetski, J., & Carlyle, S. (2007). The stable and radio-isotope chemistry of western Basketmaker burials: implications for early Puebloan diets and origins. American Antiquity, 72, 301–321.CrossRefGoogle Scholar
  34. Cronin, M. A., Renecker, L. A., & Patton, J. C. (2009). Genetic variation in domestic and wild elk (Cervus elaphus). Journal of Animal Science, 87, 829–834.CrossRefGoogle Scholar
  35. de Bruyn, M., Hoelzel, A. R., Carvalho, G. R., & Hofreiter, M. (2011). Faunal histories from Holocene ancient DNA. Trends in Ecology & Evolution, 26(8), 405–413.CrossRefGoogle Scholar
  36. Ehleringer, J. R., & Monson, R. K. (1993). Evolutionary and ecological aspects of photosynthetic pathway variation. Annual Review of Ecology and Systematics, 24, 411–439.CrossRefGoogle Scholar
  37. Erlandson, J. M., & Rick, T. C. (2010). Archaeology meets marine ecology: the antiquity of maritime cultures and human impacts on marine fisheries and ecosystems. Annual Reviews of Marine Science, 2, 165–185.Google Scholar
  38. Estes, J. A. (1996). Predators and ecosystem management. Wildlife Society Bulletin, 24, 390–396.Google Scholar
  39. Evans, R. D., & Ehleringer, J. R. (1994). Water and nitrogen dynamics in an arid woodland. Oecologia, 99, 233–242.CrossRefGoogle Scholar
  40. Farquhar, G. D., Ehleringer, J. R., & Hubick, K. T. (1989). Carbon isotope discrimination and photosynthesis. Annual Review of Plant Physiology and Molecular Biology, 40, 503–537.CrossRefGoogle Scholar
  41. Frankham, R. (1996). Relationship of genetic variation to population size in wildlife. Conservation Biology, 10, 1500–1508.CrossRefGoogle Scholar
  42. Frankham, R., Ballou, J. D., Briscoe, D. A., & McInnes, K. H. (2002). Introduction to conservation genetics. New York: Cambridge University Press.CrossRefGoogle Scholar
  43. Fu, Y.-X. (1997). Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147, 915–925.Google Scholar
  44. Gilbert, M. T. P., Willerlev, E., Hansen, A. J., Barnes, I., Rudbeck, L., Lynnerup, N., et al. (2003). Distribution patterns of postmortem damage in human mitochondrial DNA. American Journal of Human Genetics, 72, 32–47.CrossRefGoogle Scholar
  45. Gilbert, M. T. P., Bandelt, H.-J., Hofreiter, M., & Barnes, I. (2005a). Assessing ancient DNA studies. Trends in Ecology & Evolution, 20(10), 541–544.CrossRefGoogle Scholar
  46. Gilbert, M. T. P., Shapiro, B., Drummond, A. J., & Cooper, A. (2005b). Post-mortem DNA damage hotspots in Bison (Bison bison) provide evidence for both damage and mutational hotspots in human mitochondrial DNA. Journal of Archaeological Science, 32, 1053–1060.CrossRefGoogle Scholar
  47. Gilbert, M. T. P., Hansen, A. J., Willerlev, E., Turner-Walker, G., & Collins, M. (2006). Insights into the process behind the contamination of degraded human teeth and bone samples with exogenous sources of DNA. International Journal of Osteoarchaeology, 16, 156–164.CrossRefGoogle Scholar
  48. Gilliam, H. (2002). Weather of the San Francisco Bay region. Berkeley: University of California Press.Google Scholar
  49. Glenn, T. C., Stephan, W., & Braun, M. J. (1999). Effects of a population bottleneck on whooping crane mitochondrial DNA variation. Conservation Biology, 13, 1097–1107.CrossRefGoogle Scholar
  50. Goman, M., Malamud-Roam, F., & Ingram, B. L. (2008). Holocene environmental history and evolution of a tidal salt marsh in San Francisco Bay, California. Journal of Coastal Research, 24, 1126–1137.CrossRefGoogle Scholar
  51. Graham, N. E., Hughes, M. K., Ammann, C. M., Cobb, K. M., Hoerling, M. P., Kennett, D. J., et al. (2007). Tropical Pacific—mid-latitude teleconnections in medieval times. Climatic Change, 83, 241–285.CrossRefGoogle Scholar
  52. Grayson, D. K. (2001). The archaeological record of human impacts on animal populations. Journal of World Prehistory, 15, 1–68.CrossRefGoogle Scholar
  53. Grigorenko, A. P., Borinskaya, S. A., Yankovsky, N. K., & Rogaev, E. I. (2009). Achievements and peculiarities in studies of ancient DNA and DNA from complicated forensic specimens. Acta Naturae, 1, 58–69.Google Scholar
  54. Hadly, E. A., Kohn, M. H., Leonard, J. A., & Wayne, R. K. (1998). A genetic record of population isolation in pocket gophers during Holocene climate change. Proceedings of the National Academy of Sciences, 95, 6893–6896.CrossRefGoogle Scholar
  55. Hartl, D. L., & Clark, A. G. (1997). Principles of population genetics (3rd ed.). Sunderland: Sinauer Associates, Inc.Google Scholar
  56. Hawkes, K. (1991). Showing off: tests of an hypothesis about men’s hunting goals. Ethology and Sociobiology, 12, 29–54.CrossRefGoogle Scholar
  57. Hawkes, K., O’Connell, J. F., & Blurton Jones, N. G. (1991). Hunting income patterns among the Hadza: big game, common goods, foraging goals and the evolution of the human diet. Philosophical Transactions: Biological Sciences, 334(1270), 243–250.CrossRefGoogle Scholar
  58. Heaton, T. H. E. (1987). The 15N/14N ratios of plants in South Africa and Namibia: relationship to climate and coastal/saline environments. Oecologia, 74, 236–246.CrossRefGoogle Scholar
  59. Hildebrandt, W. R., & Jones, T. L. (1992). Evolution of marine mammal hunting: a view from the California and Oregon coasts. Journal of Anthropological Archaeology, 11, 360–401.CrossRefGoogle Scholar
  60. Hildebrandt, W. R., & Jones, T. L. (2002). Depletion of prehistoric pinniped populations along the California and Oregon coasts: were humans the cause? In C. E. Kay & R. T. Simmons (Eds.), Wilderness and political ecology: aboriginal influences and the original state of nature (pp. 72–110). Salt Lake City: University of Utah Press.Google Scholar
  61. Hoelzel, A. R., Fleischer, R. C., Campagna, C., LeBoeuf, B. J., & Alvord, G. (2002). Impact of a population bottleneck on symmetry and genetic diversity in the northern elephant seal. Journal of Evolutionary Biology, 15, 567–575.CrossRefGoogle Scholar
  62. Hofreiter, M., Serre, D., Poinar, H., Kuch, M., & Pääbo, S. (2001). Ancient DNA. Nature Reviews Genetics, 2, 353–359.CrossRefGoogle Scholar
  63. Hofreiter, M., Jaenicke, V., Serre, S., von Haeseler, A., & Pääbo, S. (2001). DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. Nucleic Acids Research, 29, 4793–4799.CrossRefGoogle Scholar
  64. Hofreiter, M., Capelli, C., Krings, M., Waits, L., Conards, N., Münzel, S., et al. (2002). Ancient DNA analyses reveal high mitochondrial DNA sequence diversity and parallel morphological evolution of late Pleistocene cave bears. Molecular Biology and Evolution, 19, 1244–1250.CrossRefGoogle Scholar
  65. Howell, J. A., Brooks, G. C., Semenoff-Irving, M., & Greene, C. (2002). Population dynamics of tule elk at Point Reyes National Seashore, California. Journal of Wildlife Management, 66, 478–490.CrossRefGoogle Scholar
  66. Ingram, B. L., Ingle, J. C., & Conrad, M. E. (1996). Stable isotope record of late Holocene salinity and river discharge in San Francisco Bay, California. Earth and Planetary Science Letters, 141, 237–247.CrossRefGoogle Scholar
  67. Kaestle, F. A., & Horsburgh, K. A. (2002). Ancient DNA in anthropology: methods, applications, and ethics. Yearbook of Physical Anthropology, 45, 92–130.CrossRefGoogle Scholar
  68. Kay, C. E. (1994). Aboriginal overkill: the role of Native Americans in structuring western ecosystems. Human Nature, 5, 359–396.CrossRefGoogle Scholar
  69. Kay, C. E. (1998). Are ecosystems structured from the top-down or bottom-up? A new look at an old debate. Wildlife Society Bulletin, 26, 484–498.Google Scholar
  70. Kay, C. E. (2002). False gods, ecological myths, and biological reality. In C. E. Kay & R. T. Simmons (Eds.), Wilderness and political ecology: aboriginal influences and the original state of nature (pp. 238–261). Salt Lake City: University of Utah Press.Google Scholar
  71. Kay, C. E. (2007). Were native people keystone predators? A continuous-time analysis of wildlife observations made by Lewis and Clark in 1804–1806. The Canadian Field Naturalist, 121, 1–16.Google Scholar
  72. Kuhn, T. S., McFarlane, K. A., Groves, P., Mooers, A. Ø., & Shapiro, B. (2010). Modern and ancient DNA reveal recent partial replacement of caribou in the southwest Yukon. Molecular Ecology, 19, 312–323.Google Scholar
  73. Larson, S., Jameson, R., Etnier, M., Fleming, M., & Bentzen, P. (2002). Loss of genetic diversity in sea otters (Enhydra lutris) associated with fur trade of the 18th and 19th centuries. Molecular Ecology, 11, 1899–1903.CrossRefGoogle Scholar
  74. Leonard, J. A. (2008). Ancient DNA applications for wildlife conservation. Molecular Ecology, 17, 4186–4196.CrossRefGoogle Scholar
  75. Leonard, J. A., Wayne, R. K., & Cooper, A. (2000). Population genetics of Ice Age brown bears. Proceedings of the National Academy of Sciences, 97, 1651–1654.CrossRefGoogle Scholar
  76. Levin, N. E., Cerling, T. E., Passy, B. H., Harris, J. M., & Ehleringer, J. R. (2006). A stable isotope aridity index for terrestrial environments. Proceedings of the National Academy of Sciences, 103, 11201–11205.CrossRefGoogle Scholar
  77. Librado, P., & Rozas, J. (2009). DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25, 1451–1452.CrossRefGoogle Scholar
  78. Lyman, R. L. (1988). Significance for wildlife management of the late Quaternary biogeography of mountain goats (Oreamnos americanus) in the Pacific Northwest U.S.A. Arctic and Alpine Research, 20, 13–23.CrossRefGoogle Scholar
  79. Lyman, R. L. (1994a). The Olympic mountain goat controversy: a different perspective. Conservation Biology, 8, 898–901.CrossRefGoogle Scholar
  80. Lyman, R. L. (1994b). Vertebrate taphonomy. Cambridge: Cambridge University Press.Google Scholar
  81. Lyman, R. L. (1996). Applied zooarchaeology: the relevance of faunal analysis to wildlife management. World Archaeology, 28, 110–125.CrossRefGoogle Scholar
  82. Lyman, R. L. (2008). Quantitative Paleozoology. Cambridge: Cambridge University Press.CrossRefGoogle Scholar
  83. Lyman, R. L. (2011). Paleozoological data suggest Euroamerican settlement did not displace ursids and North American elk from lowlands to highlands. Environmental Management, 47, 899–906.CrossRefGoogle Scholar
  84. Lyman, R. L., & Cannon, K. P. (Eds.). (2004). Zooarchaeology and conservation biology. Salt Lake City: University of Utah Press.Google Scholar
  85. Malamud-Roam, F., & Ingram, B. P. (2004). Late Holocene d 13C and pollen records of paleosalinity from tidal marshes in the San Francisco Bay estuary, California. Quaternary Research, 62, 134–145.CrossRefGoogle Scholar
  86. Malamud-Roam, F., Dettinger, M., Ingram, B. L., Hughes, M. K., & Florsheim, J. L. (2007). Holocene climates and connections between the San Francisco Bay estuary and its watershed: a review. San Francisco Estuary and Watershed Science, 5(1).Google Scholar
  87. Martin, W. (2003). Gene transfer from organelles to the nucleus: frequent and in big chunks. Proceedings of the National Academy of Science, 100, 8612–8614.CrossRefGoogle Scholar
  88. McCullough, D. R. (1969). The tule elk: Its history, behavior, and ecology (Vol. 88). Berkeley: University of California Publications in Zoology.Google Scholar
  89. McCullough, D. R., Fischer, J. K., & Ballou, J. D. (1996). From bottleneck to metapopulation: recovery of the tule elk in California. In D. R. McCullough (Ed.), Metapopulations and wildlife conservation (pp. 375–403). Covelo: Island Press.Google Scholar
  90. McGann, M. (2008). High-resolution foraminiferal, isotopic, and trace element records from Holocene estuarine deposits of San Francisco Bay, California. Journal of Coastal Research, 24, 1092–1109.CrossRefGoogle Scholar
  91. Meredith, E. P., Rodzen, J. A., Banks, J. D., Schaefer, R., Ernest, H. B., Famula, T. R., et al. (2007). Microsatellite analysis of three subspecies of elk (Cervus elaphus) in California. Journal of Mammalogy, 88, 801–808.CrossRefGoogle Scholar
  92. Montgomery, M., Woodworth, L., Nurthen, R., Gilligan, D., Briscoe, D., & Frankham, R. (2000). Relationship between population size and loss of genetic diversity: comparisons of experimental results with theoretical predictions. Conservation Genetics, 1, 33–43.CrossRefGoogle Scholar
  93. Mourier, T., Hansen, A. J., Willerslev, E., & Arctander, P. (2001). The Human Genome Project reveals a continuous transfer of large mitochondrial fragments to the nucleus. Molecular Biology and Evolution, 18(9), 1833–1837.CrossRefGoogle Scholar
  94. Nei, M. (1987). Molecular evolutionary genetics. New York: Columbia University Press.Google Scholar
  95. O’Rourke, D. H., Hayes, M. G., & Carlyle, S. W. (2000). Ancient DNA studies in physical anthropology. Annual Review of Anthropology, 29, 217–242.CrossRefGoogle Scholar
  96. Pääbo, S., Poinar, H., Serre, D., Jaenicke-Despres, V., Hebler, J., Rohland, N., et al. (2004). Genetic analyses from ancient DNA. Annual Review of Genetics, 38, 645–679.CrossRefGoogle Scholar
  97. Pate, F. D. (1994). Bone chemistry and paleodiet. Journal of Archaeological Method and Theory, 1, 161–209.CrossRefGoogle Scholar
  98. Patton, C. P. (1956). Climatology of summer fogs in the San Francisco Bay area. University of California Publications in Geography, 10, 113–200.Google Scholar
  99. Paxinos, E. E., James, H. L., Olson, S. L., Ballou, J. D., Leonard, J. A., & Fleischer, R. C. (2002). Prehistoric decline of genetic diversity in the nene. Science, 296, 1827.CrossRefGoogle Scholar
  100. Pilot, M., Branicki, W., Jędrzejewski, W., Goszczyński, J., Jędrzejewska, Dykyy, I., et al. (2010). Phylogeographic history of grey wolves in Europe. BMC Evolutionary Biology, 10, 104.CrossRefGoogle Scholar
  101. Polziehn, R. O., & Strobeck, C. (2002). A phylogentic comparison of red deer and wapiti using mitochondrial DNA. Molecular Phylogenetics and Evolution, 22, 342–356.CrossRefGoogle Scholar
  102. Polziehn, R. O., Hamr, J., Mallory, F. F., & Strobeck, C. (1998). Phylogenetic status of North American wapiti (Cervus elaphus) subspecies. Canadian Journal of Zoology, 76, 998–1010.CrossRefGoogle Scholar
  103. Polziehn, R. O., Hamr, J., Mallory, F. F., & Strobeck, C. (2000). Microsatellite analysis of North American wapiti (Cervus elaphus) populations. Molecular Ecology, 9, 1561–1576.CrossRefGoogle Scholar
  104. Porcasi, J. F., Jones, T. L., & Rabb, M. L. (2000). Trans-Holocene marine mammal exploitation on San Clemente Island, California: a tragedy of the commons revisited. Journal of Anthropological Archaeology, 19, 200–220.CrossRefGoogle Scholar
  105. Preston, W. (1998). Serpent in the garden: environmental change in colonial California. In R. A. Gutierrez & R. J. Orsi (Eds.), Contested Eden: California before the old Rush (pp. 260–298). Berkeley: University of California Press.Google Scholar
  106. Raab, L. M., & Jones, T. L. (2004). Prehistoric California: Archaeology and the myth of paradise. Salt Lake City: University of Utah Press.Google Scholar
  107. Rick, T. C. (2011). Weathering the storm: coastal subsistence and ecological resilience on late Holocene Santa Rosa Island, California. Quaternary International, 239, 135–146.CrossRefGoogle Scholar
  108. Rogers, A. R. (1995). Genetic evidence for a Pleistocene population explosion. Evolution, 49, 608–615.CrossRefGoogle Scholar
  109. Rogers, A. R., Fraley, A. E., Bamshad, M. J., Watkins, W. S., & Jorde, L. B. (1996). Mitochondrial mismatch analysis is insensitive to the mutational process. Molecular Biology and Evolution, 13, 895–902.CrossRefGoogle Scholar
  110. Rozen, S., & Shaletsky, H. J. (2000). Primer3 on the WWW for general users and for biologist programmers. In S. Krawetz & S. Misener (Eds.), Bioinformatics methods and protocols: Methods in molecular biology (pp. 365–386). Totowa: Humana Press.Google Scholar
  111. Schwarcz, H. P., Dupras, T. L., & Fairgrieve, S. I. (1999). 15N enrichment in the Sahara: in search of a global relationship. Journal of Archaeological Science, 26, 629–636.CrossRefGoogle Scholar
  112. Sealey, J. C., van der Merwe, N. J., Lee-Thorp, J. A., & Lanham, J. L. (1987). Nitrogen isotopic ecology in Southern Africa: implications for environmental and dietary tracing. Geochimica et Cosmochimica, 51, 2707–2717.CrossRefGoogle Scholar
  113. Shapiro, B., Drummond, A. J., Rambaut, A., Wilson, M. C., Matheus, P. E., Sher, A. V., et al. (2004). Rise and fall of Beringian steppe bison. Science, 306, 1561–1565.CrossRefGoogle Scholar
  114. Sponheimer, M., & Lee-Thorp, J. A. (1999). Oxygen isotopes in enamel carbonate and their ecological significance. Journal of Archaeological Science, 26, 723–728.CrossRefGoogle Scholar
  115. Starratt, S. W. (2008). The tangled web: records of the Medieval Climate Anomaly (A.D. 900–1350) from northern San Francisco Bay marshes. Geological Society of America Abstracts with Programs, 40, 227.Google Scholar
  116. Stephens, D. W., & Krebs, J. R. (1986). Foraging theory. Princeton: Princeton University Press.Google Scholar
  117. Tajima, F. (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585–595.Google Scholar
  118. Testa, J. W. (2004). Population dynamics and life history trade-offs of moose (Alces alces) in south-central Alaska. Ecology, 85, 1439–1452.CrossRefGoogle Scholar
  119. Ugan, A., & Coltrain, J. B. (2011). Variation in stable nitrogen values in black-tailed jackrabbits (Lepus californicus) in relation to small-scale differences in climate, soil and topography. Journal of Archaeological Science, 38, 1417–1429.CrossRefGoogle Scholar
  120. Wake, T. A. (2003). Mammal remains from the Emeryville Shellmound (CA-ALA-309) and CA-ALA-310. Unpublished manuscript. University of California, Los Angeles: Cotsen Institute.Google Scholar
  121. Watterson, G. (1975). On the number of segregating sites in genetical models without recombination. Theoretical Population Biology, 7, 256–276.CrossRefGoogle Scholar
  122. Weber, D., Stewart, B., & Lehman, N. (2004). Genetic consequences of a severe population bottleneck in the Guadalupe fur seal (Arctocephalus townsendi). Journal of Heredity, 95, 144–153.CrossRefGoogle Scholar
  123. Willerslev, E., & Cooper, A. (2005). Ancient DNA. Proceedings of the Royal Society of London, Series B, 272, 3–16.CrossRefGoogle Scholar
  124. Williams, C. L., Lundrigan, B., & Rhodes, O. E. (2004). Microsatellite DNA variation in tule elk. Journal of Wildlife Management, 68, 109–119.CrossRefGoogle Scholar
  125. Winterhalder, B., & Lu, F. (1997). A forager-resource population ecology model and implications for indigenous conservation. Conservation Biology, 11, 1354–1364.CrossRefGoogle Scholar
  126. Yang, D. Y., & Watt, K. (2005). Contamination controls when preparing archaeological remains for ancient DNA analysis. Journal of Archaeological Science, 32, 331–336.CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2012

Authors and Affiliations

  • Jack M. Broughton
    • 1
  • R. Kelly Beck
    • 1
    • 2
  • Joan B. Coltrain
    • 1
  • Dennis H. O’ Rourke
    • 1
  • Alan R. Rogers
    • 1
  1. 1.Department of AnthropologyUniversity of UtahSalt Lake CityUSA
  2. 2.SWCA Environmental ConsultantsSalt Lake CityUSA

Personalised recommendations