Cape buffalo mitogenomics reveals a Holocene shift in the African human-megafauna dynamics

Molecular Ecology

Volumn 21, Issue 16, 2012, Pages 3947-3959

  Heller, Rasmus ^a   BrÜniche Olsen, Anna ^b   Siegismund, Hans R ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b UNIVERSITY OF TASMANIA   (Australia)

Author keywords

Cape buffalo; climate change; demographic history; human activities; megafauna

Indexed keywords

AFRICA; ANIMAL; ARTICLE; BAYES THEOREM; BUFFALO; ECOLOGY; GENETIC VARIABILITY; GENETICS; HUMAN; MITOCHONDRIAL GENOME; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; POPULATION DENSITY; POPULATION DYNAMICS;

AFRICA; ANIMALS; BAYES THEOREM; BUFFALOES; ECOLOGY; GENETIC VARIATION; GENOME, MITOCHONDRIAL; HUMANS; MOLECULAR SEQUENCE DATA; POPULATION DENSITY; POPULATION DYNAMICS;

MAMMALIA; SYNCERUS CAFFER CAFFER;

EID: 84864399375     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2012.05671.x     Document Type: Article

References (76)

1. Ambrose SH, (1998) Late Pleistocene human population bottlenecks, volcanic winter and differentiation of modern humans. Journal of Human Evolution, 34, 623-651.
2. Arenas M, Ray N, Currat M, Excoffier L, (2011) Consequences of range contractions and range shifts on molecular diversity. Molecular Biology and Evolution, 29, 207-218.
3. Atkinson QD, Gray RD, Drummond AJ, (2008) mtDNA variation predicts population size in humans and reveals a major southern Asian chapter in human prehistory. Molecular Biology and Evolution, 25, 468-474.
4. Atkinson QD, Gray RD, Drummond AJ, (2009) Bayesian coalescent inference of major human mitochondrial DNA haplogroup expansions in Africa. Proceedings of the Royal Society of Biology, 276, 367-373.
5. Barnosky AD, (2008) Megafauna biomass tradeoff as a driver of Quaternary and future extinctions. PNAS, 105, 11543-11548.
6. Barnosky AD, Koch PL, Feranec RS, Wing SL, Shabel AB, (2004) Assessing the causes of late Pleistocene extinctions on the continents. Science, 306, 70-75.
7. Beaumont MA, (2010) Approximate Bayesian computation in evolution and ecology. Annual Review of Ecology, Evolution and Systematics, 41, 379-405.
8. Brooks N, (2006) Cultural responses to aridity in the Middle Holocene and increased social complexity. Quaternary International, 151, 29-49.
9. de Bruyn M, Hall BL, Chauke LF, Baroni C, Koch PL, Hoelzel AR, (2009) Rapid response of a marine mammal species to Holocene climate and habitat change. PLoS Genetics, 5, e1000554.
10. de Bruyn M, Hoelzel R, Carvalho GR, Hofreiter M, (2011) Faunal histories from Holocene ancient DNA. Trends in Ecology and Evolution, 26, 405-413.
11. Campos P, Willerslev E, Sher A, et al. (2010) Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics. PNAS, 107, 5675-5680.
12. Chan YL, Anderson CNK, Hadly EA, (2006) Bayesian estimation of the timing and severity of a population bottleneck from ancient DNA. PLoS Genetics, 2, 451-460.
13. Chikhi L, Sousa VC, Luisi P, Goossens B, Beaumont MA, (2010) The confounding effects of population structure, genetic diversity and the sampling scheme on the detection and quantification of population size changes. Genetics, 186, 983-995.
14. Cohen AS, Stone JR, Beuning KRM, et al. (2007) Ecological consequences of early Late Pleistocene megadroughts in tropical Africa. PNAS, 104, 16422-16427.
15. Dadi H, Tibbo M, Takahashi Y, Nomura K, Hanada H, Amano T, (2009) Variation in mitochondrial DNA and maternal genetic ancestry of Ethiopian cattle populations. Animal Genetics, 40, 556-559.
16. Drummond AJ, et al,. (2010) Geneious v5.1. Available from.
17. Drummond AJ, Rambaut A, Shapiro B, Pybus OG, (2005) Bayesian coalescent inference of past population dynamics from molecular sequences. Molecular Biology and Evolution, 22, 1185-1192.
18. Drummond AJ, Ho SYW, Phillips MJ, Rambaut A, (2006) Relaxed phylogenetics and dating with confidence. PLoS Biology, 4, e88.
19. Dusseldorp GL, (2010) Prey choice during the South African Middle Stone Age: avoiding dangerous prey or maximising returns? African Archaeological Review, 27, 107-133.
20. Endicott P, Ho SYW, (2008) A Bayesian evaluation of human mitochondrial substitution rates. American Journal of Human Genetics, 82, 895-902.
21. Estes RD, (1991) The Behavior Guide to African Mammals. University of California Press, Berkeley, California, 612 pp.
22. Excoffier L, Schneider S, (1999) Why hunter-gatherer populations do not show signs of Pleistocene demographic expansions. PNAS, 96, 10597-10602.
23. Excoffier L, Foll M, Petit RJ, (2009) Genetic consequences of range expansions. Annual Review of Ecology, Evolution, and Systematics, 40, 481-501.
24. Faith JT, (2008) Eland, buffalo, and wild pigs: were Middle Stone Age humans ineffective hunters? Journal of Human Evolution, 55, 24-36.
25. Finlay EK, Gaillard C, Vahidi SMF, et al. (2007) Bayesian inference of population expansions in domestic bovines. Biology Letters, 3, 449-452.
26. Gignoux CR, Henn BM, Mountain JL, (2011) Rapid, global demographic expansions after the origins of agriculture. PNAS, 108, 6044-6049.
27. Goossens B, Chikhi L, Ancrenaz M, Lackmann-Ancrenaz I, Andau P, Bruford MW, (2006) Genetic signature of anthropogenic population collapse in orang-utans. PLoS Biology, 4, 285-291.
28. Hamilton AC, Taylor D, (1991) History of climate and forests in tropical Africa during the last 8 million years. Climatic Change, 19, 65-78.
29. Heled J, Drummond AJ, (2008) Bayesian inference of population size history from multiple loci. BMC Evolutionary Biology, 8, doi:.
30. Heller R, Lorenzen ED, Okello JBA, Masembe C, Siegismund HR, (2008) Mid-Holocene decline in Cape buffalo inferred from Bayesian coalescent-based analyses of micro-satellites and mitochondrial DNA. Molecular Ecology, 17, 4845-4858.
31. Ho SYW, Shapiro B, (2011) Skyline-plot methods for estimating demographic history from nucleotide sequences. Molecular Ecology, 11, 423-434.
32. Ho SYW, Phillips MJ, Cooper A, Drummond AJ, (2005) Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Molecular Biology and Evolution, 22, 1561-1568.
33. Hoffman JI, Grant SM, Forcada J, Phillips CD, (2011) Bayesian inference of a historical bottleneck in a heavily exploited marine mammal. Molecular Ecology, 20, 3989-4008.
34. Koch PL, Barnosky AD, (2006) Late Quaternary extinctions: state of the debate. Annual Review of Ecology, Evolution and Systematics, 37, 215-250.
35. Li R, Zhu H, Ruan J, et al. (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Research, 20, 265-272.
36. Lorenzen ED, Nogués-Bravo D, Orlando L, et al. (2011) Species-specific responses of Late Quaternary megafauna to climate and humans. Nature, 479, 359-365.
37. MacEachern S, McEwan J, McCulloch A, Mather A, Savin K, Goddard M, (2009) Molecular evolution of the Bovini tribe (Bovidae, Bovinae): is there evidence of rapid evolution or reduced selective constraint in Domestic cattle? BMC Genomics, 10, doi:.
38. Martin PS, (1984) Prehistoric Overkill: The Global Model. In: Quaternary Extinctions: A Prehistoric Revolution (eds, Martin PS, and, Klein RD,), pp. 354-403. University of Arizona Press, Tucson, Arizona.
39. Mayewski PA, Rohling E, Stager JC, et al. (2004) Holocene climate variability. Quaternary Research, 62, 243-255.
40. deMenocal PD, (2001) Cultural responses to climate change during the late Holocene. Science, 292, 667-673.
41. deMenocal PD, Ortiz J, Guilderson T, Sarntheim M, (2000) Coherent high- and low-latitude climate variability during the Holocene warm period. Science, 288, 2198-2202.
42. Minin VN, Bloomquist EW, Suchard MA, (2008) Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics. Molecular Biology and Evolution, 25, 1459-1471.
43. Morin PA, Archer FI, Foote AD, Vilstrup J, Allen EE, (2010) Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species. Genome Research, 20, 908-916.
44. Nabholz B, Glemin S, Galtier N, (2008) Strong variations of mitochondrial mutation rate across mammals-the longevity hypothesis. Molecular Biology and Evolution, 25, 120-130.
45. Nogués-Bravo D, Ohlemüller R, Batra P, Araújo MB, (2010) Climate predictors of Late Quaternary extinctions. Evolution, 64, 2442-2449.
46. Ogutu JO, Piepho HP, Dublin HT, Bhola N, Reid RS, (2008) Rainfall influences on ungulate population abundance in the Mara-Serengeti ecosystem. Journal of Animal Ecology, 77, 814-829.
47. Okello JBA, Wittemeyer G, Rasmussen HB, Arctander P, Nyakaana S, Douglas-Hamilton I, Siegismund HR, (2008) Effective population size dynamics reveal impacts of historic climate events and recent anthropogenic pressure in African elephants. Molecular Ecology, 17, 3788-3799.
48. Pannell JR, (2003) Coalescence in a metapopulation with recurrent local extinction and recolonization. Evolution, 57, 949-961.
49. Peter MB, Wegmann D, Excoffier L, (2010) Distinguishing between population bottleneck and population subdivision by a Bayesian model choice procedure. Molecular Ecology, 19, 4648-4660.
50. Pond SLK, Posada D, Gravenor MB, Woelk CH, Frost SDW, (2006) Automated phylogenetic detection of recombination using a genetic algorithm. Molecular Biology and Evolution, 23, 1891-1901.
51. Posada D, (2008) jModelTest: phylogenetic model averaging. Molecular Biology and Evolution, 25, 1253-1256.
52. Pritchard JK, Seielstad MT, Perez-Lezaun A, Feldman MW, (1999) Population growth of human Y chromosome microsatellites. Molecular Biology and Evolution, 16, 1791-1798.
53. Rampino MP, Self S, (1992) Volcanic winter and accelerated glaciation following the Toba super-eruption. Nature, 359, 50-52.
54. Ray N, Currat M, Excoffier L, (2003) Intra-deme molecular diversity in spatially expanding populations. Molecular Biology and Evolution, 29, 76-86.
55. Rozas J, Sánches-DelBarrio JC, Messeguer X, Rozas R, (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19, 2496-2497.
56. Rozen S, Skaletsky HJ, (2000) Primer3 on the WWW for General Users and for Biologist Programmers. In: Bioinformatics Methods and Protocols: Methods in Molecular Biology (eds, Krawetz S, and, Misener S,), pp. 365-386. Humana Press, Totowa, New Jersey.
57. Scheinfeldt LB, Soib S, Tishkoff SA, (2010) Working toward a synthesis of archaeological, linguistic, and genetic data for inferring African population history. PNAS, 107, 8931-8938.
58. Schierup MH, Hein J, (2000) Consequences of recombination on traditional phylogenetic analysis. Genetics, 156, 879-891.
59. Scholz CA, Johnson C, Cohen AS, et al. (2007) East African megadroughts between 135 and 75 thousand years ago and bearing on early-modern human origins. PNAS, 104, 16416-16421.
60. Shapiro B, Drummond J, Rambaut A, et al. (2004) Rise and fall of the Beringian steppe bison. Science, 306, 1561-1565.
61. Simonsen BT, Siegismund HR, Arctander P, (1998) Population structure of Cape buffalo inferred from mtDNA sequences and microsatellite loci: high variation but low differentiation. Molecular Ecology, 7, 225-237.
62. Sinclair ARE, (1977) The African Buffalo: A Study of Resource Limitation of Populations. University of Chicago Press, Chicago, Illinois, 355 pp.
63. Soares P, Alshamali F, Pereira JB, et al. (2012) The expansion of mtDNA haplogroup L3 within and out of Africa. Molecular Biology and Evolution, 29, 915-927.
64. Städler T, Haubold B, Merino C, Stephan W, Pfaffelhuber P, (2009) The impact of sampling schemes on the site frequency spectrum in nonequilibrium subdivided populations. Genetics, 182, 205-216.
65. Stanley JD, Krom MD, Cliff RA, Woodward JC, (2003) Nile flow failure at the end of the Old Kingdom, Egypt: Strontium isotopic and petrologic evidence. Geoarchaeology, 18, 395-402.
66. Storz JF, Beaumont MA, Alberts SC, (2002) Genetic evidence for long-term population decline in a savannah-dwelling primate: inferences from a hierarchical Bayesian model. Molecular Biology and Evolution, 19, 1981-1990.
67. Thompson LG, Mosley-Thompson E, Davis ME, et al. (2002) Kilimanjaro ice core records: evidence of Holocene climate change in tropical Africa. Science, 298, 589-593.
68. Thompson LG, Mosley-Thompson E, Brecher H, et al. (2006) Abrupt tropical climate change: past and present. PNAS, 103, 10536-10543.
69. Tierney JE, Russell JM, Huang Y, (2010) A molecular perspective on Late Quaternary climate and vegetation change in the Lake Tanganyika basin, East Africa. Quaternary Science Reviews, 29, 787-800.
70. Van Hooft WF, Groen AF, Prins HHT, (2002) Phylogeography of the Cape buffalo based on mitochondrial and Y-chromosomal loci: Pleistocene origin and population expansion of the Cape buffalo subspecies. Molecular Ecology, 11, 267-279.
71. Wakeley J, (1999) Non-equilibrium migration in human history. Genetics, 153, 1836-1871.
72. Wakeley J, (2001) The coalescent in an island model of population subdivision with variation among demes. Theoretical Population Biology, 59, 133-144.
73. Wang Z, Shen X, Liu B, et al. (2010) Phylogeographical analyses of domestic and wild yaks based on mitochondrial DNA: new data and reappraisal. Journal of Biogeography, 37, 2332-2344.
74. Wegmann D, Leuenberger C, Neuenschwander S, Excoffier L, (2010) ABCtoolbox: a versatile toolkit for approximate Bayesian computations. BMC Bioinformatics, 11, 116.
75. Williams MAJ, Talbot MR, (2009) Late Quaternary Environments in the Nile Basin. In: The Nile: Origin, Environments, Limnology and Human Use (ed., Dumont HJ,), pp. 61-72. Springer Science + Business Media B. V., Dordrecht, Netherlands.
76. Wolff C, Haug GH, Timmermann A, et al. (2011) Reduced interannual rainfall variability in East Africa during the Last Ice Age. Science, 333, 743-747.