The evolution and phylogeography of the African elephant inferred from mitochondrial DNA sequence and nuclear microsatellite markers

Proceedings of the Royal Society B: Biological Sciences

Volumn 269, Issue 1504, 2002, Pages 1993-2006

  Eggert, Lori S ^a   Rasner, Caylor A ^a   Woodruff, David S ^a  

^a SMITHSONIAN INSTITUTION   (United States)

Author keywords

Forest elephant; Mammal evolution; Molecular scatology; Savannah elephant; Speciation

Indexed keywords

CYTOCHROME B; MICROSATELLITE DNA; MITOCHONDRIAL DNA;

ELEPHANT; EVOLUTION; PHYLOGEOGRAPHY; SPECIATION (BIOLOGY);

ARTICLE; CLIMATE CHANGE; CONTROLLED STUDY; DNA EXTRACTION; DNA SEQUENCE; ECOLOGY; ELEPHANT; EVOLUTION; FECES ANALYSIS; MICROSATELLITE MARKER; NONHUMAN; PHYLOGEOGRAPHY; PRIORITY JOURNAL; SPECIES DIFFERENTIATION; TAXONOMY; WILDLIFE CONSERVATION;

ELEPHANT; ELEPHANTIDAE; LOXODONTA; LOXODONTA AFRICANA; LOXODONTA CYCLOTIS; MAMMALIA;

EID: 53149154500     PISSN: 09628452     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rspb.2002.2070     Document Type: Article

References (65)

1. Akaike, H. 1974 A new look at the statistical model identification. IEEE Trans. Autom. Contr. 19, 716-723.
2. Amos, W., Whitehead, H., Ferrari, M. J., Payne, R. & Gordon, J. 1992 Restrictable DNA from sloughed cetacean skin: its potential for use in population analyses. Mar. Mamm. Sci. 8, 275-283.
3. Ansell, W. F. H. 1971 Order Proboscidea. In The mammals of Africa: an identification manual. Part II (ed. J. Meester & H. W. Setzer), pp. 1-5. Washington, DC: Smithsonian Institution.
4. Arctander, P., Johansen, C. & Coutellec-Vreto, M.-A. 1999 Phylogeography of three closely related African bovids. Mol. Biol. Evol. 16, 1724-1739.
5. Avise, J. C. 1994 Molecular markers, natural history and evolution. New York: Chapman & Hall.
6. Avise, J. C. 2000 Phylogeography: the history and formation of species. Cambridge, MA: Harvard University Press.
7. Barnes, R. F. W., Craig, G. C., Dublin, H. T., Overton, G., Simons, W. & Thouless, C. R. 1999 African elephant database 1998. IUCN Species Survival Commission Occ. paper 22. Gland, Switzerland: IUCN.
8. Barriel, V., Thuet, E. & Tassy, P. 1999 Molecular phylogeny of Elephantidae. Extreme divergence of the extant forest African elephant. Crit. Rev. Acad. Sci. III Life Sci. 322, 447-454.
9. Beden, M. 1983 Family Elephantidae. In Koobi Fora research project. V2. The fossil ungulates: Proboscidea, Perissodactyla, and Suidae (ed. J. M. Harris), pp. 40-129. Oxford University Press.
10. Birungi, J. & Arctander, P. 2000 Large sequence divergence of mitochondrial DNA genotypes of the control region within populations of the African antelope, kob (Kobus kob). Mol. Ecol. 9, 1997-2008.
11. Boom, R., Sol, C. J. A., Salimans, M. M. M., Jansen, C. L., van Dillen Werthein, P. M. E. & van der Noordaa, J. 1990 Rapid and simple method for purification of nucleic acids. J. Clin. Microbiol. 28, 495-503.
12. Cavalli-Sforza, L. L. & Edwards, A. W. F. 1967 Phylogenetic analysis: models and estimation procedures. Am. J. Hum. Genet. 19, 233-257.
13. Cerling, T. E. 1992 Development of grasslands and savannas in East Africa during the Neogene. Palaeogeogr. Palaeoclimatol. Palaeoecol. 97, 241-247.
14. Cobb, M., Huet, M., Lachaise, D. & Veuille, M. 2000 Fragmented forests, evolving flies: molecular variation in African populations of Drosophila teissieri. Mol. Ecol. 9, 1591-1597.
15. deMenocal, P. B. & Bloemendal, J. 1995 Plio-Pleistocene climatic variability in subtropical Africa and the paleoenvironment of hominid evolution: a combined data-model approach. In Paleoclimate and evolution, with emphasis on human origins (ed. E. S. Vrba, G. H. Denton, T. C. Partridge & L. H. Burckle), pp. 262-288. New Haven, CT: Yale University Press.
16. deMenocal, P. B. & Rind, D. 1993 Sensitivity of Asian and African climate to variations in seasonal insolation, glacial ice cover, sea surface temperature, and Asian orography. J. Geophys. Res. 98D4, 7265-7287.
17. Eggert, L. S., Ramakrishnan, U., Mundy, N. I. & Woodruff, D. S. 2000 Polymorphic microsatellite DNA markers in the African elephant (Loxondonta africana) and their use in the Asian elephant (Elephas maximus). Mol. Ecol. 9, 2223-2225.
18. Fernando, P., Pfrender, M. E., Encalada, S. E. & Lande, R. 2000 Mitochondrial DNA variation, phylogeography and population structure of the Asian elephant. Heredity 84, 362-372.
19. Flagstad, O., Syvertsen, P. O., Stenseth, N. Chr. & Jakobsen, K. S. 2001 Environmental change and rates of evolution: the phylogeographic pattern within the hartebeest complex as related to climatic variation. Proc. R. Soc. Lond. B 268, 667-677. (DOI 10.1098/rspb.2000.1416.)
20. Fleischer, R. C., Perry, E. A., Muralidharan, K., Stevens, E. E. & Wemmer, C. M. 2001 Phylogeography of the Asian elephant (Elephas maximus) based on mitochondrial DNA. Evolution 55, 1882-1892.
21. Frade, F. 1955 Ordre des proboscidiens (Proboscidea Illiger, 1811). In Traité de zoologie (ed. P.-P. Grassé), pp. 715-875. Paris: Masson & Cie.
22. Gagneux, P., Wills, C., Gerloff, U., Tautz, D., Morin, P. A., Boesch, C., Fruth, B., Hohmann, G., Ryder, O. & Woodruff, D. S. 1999 Mitochondrial sequences show diverse evolutionary histories of African hominoids. Proc. Natl Acad. Sci. USA 96, 5077-5082.
23. Garcia-Rodriguez, A. I. (and 9 others) 1998 Phylogeography of the West Indian manatee (Trichechus manatus): how many populations and how many taxa? Mol. Ecol. 7, 1137-1149.
24. Georgiadis, N., Bischof, L., Templeton, A., Patton, J., Kresh, W. & Western, D. 1994 Structure and history of African elephant populations. I. Eastern and southern Africa. J. Heredity 85, 100-104.
25. Girman, D. J., Kat, P. W., Mills, M. G. L., Ginsberg, J. R., Borner, M., Wilson, V., Fanshawe, J. H., Fitzgibbon, C., Lau, L. M. & Wayne, R. K. 1993 Molecular genetic and morphological analyses of the African wild dog (Lycaon pictus). J. Heredity 84, 450-459.
26. Goldstein, D. B. & Pollock, D. D. 1997 Launching microsatellites. J. Heredity 88, 3235-3242.
27. Greenwood, A. D. & Pääbo, S. 1999 Nuclear insertion sequences of mitochondrial DNA predominate in hair but not in blood of elephants. Mol. Ecol. 8, 133-137.
28. Groves, C. P. 2000 What are the elephants of west Africa? Elephant 2, 7-8.
29. Grubb, P., Groves, C. P., Dudley, J. P. & Shoshani, J. 2000 Living African elephants belong to two species: Loxodonta africana (Blumenbach, 1797) and Loxodonta cyclotis (Matschie, 1900). Elephant 2, 1-4.
30. Guo, E. A. & Thompson, E. A. 1992 Performing the exact test of Hardy-Weinburg proportions for multiple alleles. Biometrics 48, 361-372.
31. Hare, P. E. 1980 Organic geochemistry of bone and its relation to the survival of bone in the natural environment. In Fossils in the making (ed. A. P. Hill & A. K. Behrensmeyer), pp. 208-219. University of Chicago Press.
32. Hasegawa, M., Kishino, H. & Yano, T. 1985 Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22, 160-174.
33. Hillis, D. M. & Huelsenbeck, J. P. 1992 Signal, noise and reliability in molecular phylogenetic analyses. J. Heredity 83, 189-195.
34. Huelsenbeck, J. P. & Ronquist, F. R. 2001 MrBayes: Bayesian inference of phylogeny. BioInformatics 17, 754-755.
35. Jin, L. & Chakraborty, R. 1993 Estimation of genetic distance and coefficient of gene diversity from single-probe multilocus DNA fingerprinting data. Mol. Biol. Evol. 11, 120-127.
36. Kalb, J. E., Froehlich, D. J. & Bell, G. L. 1996 Palaeobiogeography of late Neogene African and Eurasian Elephantoidea. In The Proboscidea: evolution and palaeoecology of elephants and their relatives (ed. J. Shoshani & P. Tassy), pp. 117-123. Oxford University Press.
37. Kimbel, W. H. 1995 Hominid speciation and Pliocene climate change. In Paleoclimate and evolution, with emphasis on human origins (ed. E. S. Vrba, G. H. Denton, T. C. Partridge & L. H. Burckle), pp. 425-437. New Haven, CT: Yale University Press.
38. Langella, O. 2000 Populations 1.2.19: population genetic software individuals or populations distances, phylogenetic trees. See http://www.cnrs-gif.fr/pge/bioinfo/populations.
39. Lopez, J. V., Yuhki, N., Masuda, R., Modi, W. & O'Brien, S. J. 1994 Numt, a recent transfer and tandem amplification of mitochondrial DNA to the nuclear genome of the domestic cat. J. Mol. Evol. 39, 174-190.
40. Maglio, V. 1973 Origin and evolution of the Elephantidae. Trans. Am. Phil. Soc. 63, 1-149.
41. Maley, J. 1980 Les changements climatiques de la fin du Tertiaire en Afrique: luer conséquence sur l'apparition du Sahara et de sa végétation. In The Sahara and the Nile (ed. M. A. Williams & H. Faure), pp. 63-86. Rotterdam, the Netherlands: Balkema.
42. Maley, J. 1996 The African rain forest-main characteristics of changes in vegetation and climate from the Upper Cretaceous to the Quaternary. Proc. R. Soc. Edin. B 104, 31-73.
43. Martin, C. 1991 The rainforests of West Africa: ecology, threats, conservation. Basel, Switzerland: Birkhäuser.
44. Morley, R. J. 2000 Origin and evolution of tropical rain forests. New York: Wiley.
45. Nyakaana, S. & Arctander, P. 1998 Isolation and characterization of microsatellite loci in the African elephant, Loxodonta africana. Mol. Ecol. 7, 1436-1437.
46. Nyakaana, S. & Arctander, P. 1999 Population genetic structure of the African elephant in Uganda based on variation at mitochondrial and nuclear loci: evidence for male-biased gene flow. Mol. Ecol. 8, 1105-1115.
47. Page, R. D. M. 1996 TreeView: an application to display phylogenetic trees on personal computers. Comp. Appl. Biosci. 12, 357-358.
48. Partridge, T. C., Wood, B. A. & deMenocal, P. B. 1995 The influence of global climatic change and regional uplift on large-mammalian evolution in east and southern Africa. In Paleoclimate and evolution, with emphasis on human origins (ed. E. S. Vrba, G. H. Denton, T. C. Partridge & L. H. Burckle), pp. 331-355. New Haven, CT: Yale University Press.
49. Posada, D. & Crandall, K. A. 1998 Modeltest: testing the model of DNA substitution. BioInformatics 14, 817-818.
50. Raymond, M. & Rousset, F. 1995 Genepop ver. 3.2a: a population genetics software for exact tests and ecumenicism. J. Heredity 86, 248-249.
51. Rice, W. R. 1989 Analyzing tables of statistical tests. Evolution 43, 223-225.
52. Roca, A. L., Georgiadis, N., Pecon-Slattery, J. & O'Brien, S. J. 2001 Genetic evidence for two species of elephant in Africa. Science 293, 1473-1477.
53. Schneider, S., Roessli, D. & Excoffier, L. 2000 Arlequin v. 2.000: a software for population genetics data analysis. University of Geneva, Switzerland: Genetics & Biometry Laboratory.
54. Sikes, S. K. 1971 The natural history of the African elephant. London: Weidenfeld & Nicholson.
55. Spinage, C. 1994 Elephants. London: Poyser.
56. Swofford, D. L. 1998 PAUP*: phylogenetic analysis using parsimony (*and other methods), v. 4. Sunderland, MA: Sinauer.
57. Taberlet, P., Griffin, S., Goossens, B., Questiau, S., Manceau, V., Escaravage, N., Waits, L. P. & Bouvet, J. 1996 Reliable genotyping of samples with very low DNA quantities using PCR. Nucleic Acids Res. 24, 3189-3194.
58. Tassy, P. 1995 Les proboscidiens (Mammalia) fossiles du rift occidental, Ouganda. In Geology and palaeobiology of the Albertine Rift Valley, Uganda-Zaire. II. Palaeobiology (ed. B. Senut & M. Pickford), pp. 217-257. Orléans, France: CIFEG.
59. Thompson, J. D., Higgins, D. G. & Gibson, T. J. 1994 Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
60. Tiedemann, R., Kurt, F., Haberhauer, A. & Hartl, G. B. 1998 Differences in spatial genetic population structure between African and Asian elephant (Loxodonta africana, Elephas maximus) as revealed by sequence analysis of the mitochondrial Cyt b gene. Acta Theriolog. 123, 123-134.
61. Van Hooft, W. F., Groen, A. F. & Prins, H. H. T. 2000 Microsatellite analysis of genetic diversity in African buffalo (Syncerus caffer) populations throughout Africa. Mol. Ecol. 9, 2017-2025.
62. Vrba, E. S. 1995 The fossil record of African antelopes (Mammalia, Bovidae) in relation to human evolution and paleoclimate. In Paleoclimate and evolution, with emphasis on human origins (ed. E. S. Vrba, G. H. Denton, T. C. Partridge & L. H. Burckle), pp. 385-424. New Haven, CT: Yale University Press.
63. Wayne, R. K., Meyer, A., Lehman, N., Van Valkenburgh, B., Kat, P. W., Fuller, R. K., Girman, D. & O'Brien, S. J. 1990 Large sequence divergence among mitochondrial DNA genotypes within populations of eastern African black-backed jackals. Proc. Natl Acad. Sci. USA 87, 1772-1776.
64. Wessleman, H. B. 1995 Of mice and almost-men: regional paleoecology and human evolution in the Turkana Basin. In Paleoclimate and evolution, with emphasis on human origins (ed. E. S. Vrba, G. H. Denton, T. C. Partridge & L. H. Burckle), pp. 356-368. New Haven, CT: Yale University Press.
65. Woodruff, D. S. 2001 Declines of biomes and biotas and the future of evolution. Proc. Natl Acad. Sci. USA 98, 5471-5476.