Mitochondrial DNA variation of the common hippopotamus: Evidence for a recent population expansion

Heredity

Volumn 95, Issue 3, 2005, Pages 206-215

  Okello, J B A ^a   Nyakaana, S ^a   Masembe, C ^a   Siegismund, H R ^b   Arctander, P ^b  

^a MAKERERE UNIVERSITY   (Uganda)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

Common hippopotamus; Control region; Mitochondrial DNA; Population history; Recent expansion; Variation

Indexed keywords

MITOCHONDRIAL DNA; PRIMER DNA;

GENETIC DIFFERENTIATION; MITOCHONDRIAL DNA; RANGE EXPANSION;

AFRICA SOUTH OF THE SAHARA; ANALYSIS OF VARIANCE; ANIMAL; ARTICLE; ARTIODACTYLA; CLASSIFICATION; CLUSTER ANALYSIS; COMPARATIVE STUDY; DNA SEQUENCE; ENVIRONMENTAL PROTECTION; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; HAPLOTYPE; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; POPULATION DYNAMICS;

AFRICA SOUTH OF THE SAHARA; ANALYSIS OF VARIANCE; ANIMALS; ARTIODACTYLA; BASE SEQUENCE; CLUSTER ANALYSIS; CONSERVATION OF NATURAL RESOURCES; DNA PRIMERS; DNA, MITOCHONDRIAL; GEOGRAPHY; HAPLOTYPES; MOLECULAR SEQUENCE DATA; PHYLOGENY; POPULATION DYNAMICS; SEQUENCE ANALYSIS, DNA; VARIATION (GENETICS);

AFRICA;

HIPPOPOTAMUS AMPHIBIUS; MAMMALIA;

EID: 30744443253     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/sj.hdy.6800711     Document Type: Article

References (72)

1. Amos W, Hoelzel AR (1991). Long-term preservation of whale skin for DNA analysis. In: Hoelzel AR (ed) Genetic Ecology of Whales and Dolphins. International Whaling Commission: Cambridge. pp 99-104.
2. Amrine-Madsen H, Koep KP, Wayne C, Mark S, Springer MS (2003). A new phylogenetic marker, apolipoprotein B, provides compelling evidence for eutherian relationships. Mol Phylogenet Evol 28: 225-240.
3. Arctander P, Johansen C, Coutellec-Vreto MA (1999). Phylogeography of three closely related African bovids (Tribe Alcelaphini). Mol Biol Evol 16: 1724-1739.
4. Avise JC, Neigel JE, Arnold J (1984). Demographic influences on mitochondrial DNA lineage survivorship in animal populations. J Mol Evol 156: 99-105.
5. Banister KE, Clarke MA (1980). A revision of the large Barbus (Pisces, Cyprinidae) of Lake Malawi with a reconstruction of the history of the southern African Rift Valley Lakes. J Nat Hist 14: 483-542.
6. Bell-Cross G (1972). The fish fauna of the Zambezi River system. Arnoldia 29: 1-19.
7. Beuning KRM, Russell KK, Wolfe J, Brent BB (2002). Reassessment of Lake Victoria-Upper Nile River paleohydrology from oxygen isotope records of lake-sediment cellulose. Geology 30: 559-562.
8. 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.
9. Boisserie JR (2005). The phylogeny and taxonomy of Hippopotamidae (Mammalia: Artiodactyla): a review based on morphology and cladistic analysis. Zool J Linn Soc 143: 1-26.
10. Clement M, Posada D, Crandall K (2000). TCS: a computer program to estimate gene genealogies. Mol Ecol 9: 1657-1660.
11. Cooke HBS (1958). Observations relating to Quaternary environments in East Africa. Trans Geo Soc S Afr 60: 1-74.
12. Coryndon SC (1970). The extent of variation in Fossil Hippopotamus from Africa. Symp Zool Soc Lond 26: 135-147.
13. Coryndon SC (1973). Fossil Hippopotamidae from Pliocene/Pleistocene Successions of the Rudolph Basin, Paper for Conference on Stratigraphy, Paleontology and Evolution. Wenner Grenn Foundation: New York.
14. deHeinzelin J (1964). Addendeum. In: Howell FC, Bourlière F (eds) African Ecology and Human Evolution. Viking Foundation Publishers: London. pp 648-654.
15. deMenocal PB (1995). Plio-Pleistocene African climate. Science 270: 53-58.
16. Donnelly MJ, Licht MC, Lehmann T (2001). Evidence for a recent population expansion in the evolutionary history of the malaria vectors Anopheles arabiensis and Anopheles gambiae. Mol Biol Evol 18: 1353-1364.
17. Eltringham SK (1993). The common hippopotamus (Hippopotamus amphibius). In: Oliver WRL (ed) Pigs, Peccaries and Hippos. IUCN: Gland. pp 43-55.
18. Eltringham SK (1999). The Hippos. Academic Press: London.
19. Ewens WJ (1972). The sampling theory of selectively neutral alleles. Theor Popul Biol 3: 87-112.
20. Excoffier L, Smouse PE, Quattro JM (1992). Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131: 479-491.
21. Felsenstein J (1992). Estimating effective population size from samples of sequences: inefficiency of pairwise and segregating sites as compared to phylogenetic estimates. Genet Res 59: 139-147.
22. Felsenstein J (1993). PHYLIP (Phylogeny Inference Package), Version 3.5C. Distributed by the author. University of Washington: Seattle, USA.
23. Flagstad Ø, Syvertsen OP, Stenseth CN, Jakobsen SK (2001). Environmental change and rates of evolution: the phylogeographic pattern within the hartebeest complex as related to climatic variation. Proc R Soc Lond Ser B 268: 667-677.
24. Fu Y-X (1997). Statistical tests of neutrality against population growth, hitchhiking and background selection. Genetics 147: 915-925.
25. Fu Y-X, Li W-H (1993). Statistical tests of neutrality of mutations. Genetics 133: 693-709.
26. Gasse F (2000). Hydrological changes in the African tropics since the Last Glacial Maximum. Quatern Sci Rev 19: 189-211.
27. Gatesy J, Milinkovitch M, Waddell V, Stanhope M (1999). Stability of cladistic relationships between Cetacea and higher-level artiodactyl taxa. Syst Biol 48: 6-20.
28. Grubb P (1993). The Afrotropical Hippopotamus and Hexaprotodon: taxonomy and description. In: Oliver WRL (ed) Pigs, Peccaries and Hippos. IUCN: Gland. pp 41-43.
29. Hall TA (1999). BIOEDIT: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp 41: 95-98.
30. Harpending HC (1994). Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Hum Biol 66: 591-600.
31. Holmgren K, Lee-Thorp JA, Cooper GRJ, Lundblad K, Partridge TC, Scott L et al (2003). Persistent millennial-scale climatic variability over the past 25,000 years in Southern Africa. Quatern Sci Rev 22: 2311-2326.
32. Hudson RR (1990). Gene genealogies and the coalescent process. Oxf Surv Evol Biol 7: 1-44.
33. Johnson TC, Kelts K, Odada E (2000). The holocene history of Lake Victoria. Ambio 29: 2-11.
34. Karesh WB, Smith F, Frazer-Taylor H (1987). A remote method for obtaining skin samples. Conserv Biol 1: 261-262.
35. Kingdon J (1989). East African Mammals. An Atlas of Evolution in Africa (Large Mammals), Vol IIIB. The University of Chicago Press: Chicago.
36. Kingdon J (1997). The Kingdon Field Guide to African Mammals. Academic Press: London.
37. Klingel H (1991). The social organization and behavior of the Hippopotamus amphibius. In: Kayanja FIB, Edroma EL (eds) African Wildlife Research and Management. International Council of Scientific Unions: Paris. pp 73-75.
38. Lamprey RH, Michelmore F (1996). The Wildlife Protected Areas of Uganda. Ministry of Tourism, Wildlife and Antiquities: Kampala, Uganda.
39. Laws RM, Clough G (1966). Observations on reproduction in the hippopotamus Hippopotamus amphibius. Linn Symp Zoo Soc Lond 15: 117-140.
40. Lydekker R (1915). Catalogue of the Ungulate Mammals in the British Museum of Natural History, Vol. 5. British Museum: London.
41. Manly BFJ (1985). The Statistics of Natural Selection on Animal Populations. Chapman & Hall: London.
42. Mantel N (1967). The detection of disease clustering and a generalized regression approach. Cancer Res 27: 209-220.
43. Matthee CA, Burzla JD, Taylor JF, Davis SK (2001). Mining the mammalian genome for artiodactyl systematics. Syst Biol 50: 367-390.
44. Muwanika VB, Nyakaana S, Siegismund HR, Arctander P (2003a). Phylogeography and population structure of the common warthog (Phacochoerus africanus) inferred from variation in mitochondrial DNA sequences and microsatellite loci. Heredity 91: 361-372.
45. Muwanika VB, Siegismund HR, Okello JBA, Masembe C, Arctander P, Nyakaana S (2003b). A recent bottleneck in the warthog and elephant populations of Queen Elizabeth National Park, revealed by a comparative study of four mammalian species in Uganda national parks. Anim Conserv 6: 237-245.
46. Nei M (1987). Molecular Evolutionary Genetics. Columbia University Press: New York.
47. Nersting LG, Arctander P (2001). Phylogeography and conservation of impala and greater kudu. Mol Ecol 10: 711-719.
48. Nyakaana S, Arctander P, Siegismund H (2002). Population structure of the African savannah elephant inferred from mitochondrial control region sequences and nuclear microsatellite loci. Heredity 89: 90-98.
49. Patridge TC, Wood BA, deMenocal PB (1995). The influence of global and regional uplift on large-mammalian evolution in East and Southern Africa. In: Vrba ES, Denton GH, Patridge TC, Burckle LH (eds) Paleoclimate and Evolution, with Emphasis on Human Origins. Yale University Press: New Haven. pp 330-355.
50. Pickford M, Senut B, Hadoto D (1993). Geology and palaeobiology of the Albertine Rift Valley Uganda-Zaire. Pub Occ CIFEG 24: 1-180.
51. Posada D, Crandall KA (1998). MODELTEST 3.06: testing the model of DNA substitution. Bioinformaics 14: 817-818.
52. Ramos-Onsins SE, Rozas J (2002). Statistical properties of the new neutrality test against population growth. Mol Biol Evol 19: 2092-2100.
53. Rodriguez F, Oliver JF, Marin A, Medina JR (1990). The general stochastic model of nucleotide substitutions. J Theor Biol 142: 485-501.
54. Rogers AR (1995). Genetic evidence for a Pleistocene population explosion. Evolution 49: 608-615.
55. Rogers AR (1997). Population structure and modern human origins. In: Donnelly P, Tavar S (eds) Progress in Population Genetics and Human Evolution. Institute for Mathematics and its Applications: University of Minnesota. pp 55-79.
56. Rogers AR, Harpending H (1992). Population growth makes waves in the distribution of pairwise genetic differences. Mol Biol Evol 9: 552-569.
57. Rozas J, Sánchez-DelBarrio JC, Messeguer X, Rozas R (2003). DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19: 2496-2497.
58. Sanger F, Nicklen S, Coulsen AR (1977). DNA sequencing with chain terminating inhibitors. Proc Natl Acad Sci USA 74: 5463-5467.
59. Schneider S, Jean-Mark K, Roessli D, Excoffier L (2000). ARLEQUIN 2.000: A Software for Population Genetic Data Analysis. Genetics and Biometry Laboratory, University of Geneva: Geneva.
60. Seehausen O (2002). Patterns in fish radiation are compatible with Pleistocene desiccation of Lake Victoria and 14,600 yrs history for its chiclid species flock. Proc R Soc Lond Ser B 269: 491-497.
61. Slatkin M (1995). A measure of population subdivision based on microsatellite allele frequencies. Genetics 139: 457-462.
62. Slatkin M, Hudson RR (1991). Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129: 555-562.
63. Stager JC, Reinthal PN, Livingstone DA (1986). A 25000-year history for Lake Victoria, East Africa, and some comments on its significance for the evolution of cichlid fishes. Freshwater Biol 16: 15-19.
64. Stewart KM (2001). The freshwater fish of Neogene Africa (Miocene-Pleistocene): systematics and biogeography. Fish Fish 2: 177-230.
65. Su B, Fu Y, Wang Y, Jin L, Chakraborty R (2001). Genetic diversity and population history in Red Panda (Ailurus fulgens) as inferred from mitochondrial DNA sequence variations. Mol Biol Evol 18: 1070-1076.
66. Swofford DL (1998). PAUP*, Version 4.0b. Phylogenetic Analysis Using Parsimony (*and Other Methods). Sinauer Associates: Sunderland, MA.
67. Tajima F (1989). The effect of change in population size on DNA polymorphism. Genetics 123: 597-601.
68. Templeton AR, Crandall KA, Sing CF (1992). A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics 132: 619-633.
69. Turner A, Wood BA (1993). Comparative palaeotological context for the evolution of the early hominid masticatory system. J Hum Evol 24: 229-236.
70. Ursing BM, Árnason U (1998). Analyses of mitochondrial genomes strongly support a hippopotamus - whale clade. Proc R Soc Lond Ser B 265: 2251-2255.
71. VanCouvering JAH (1982). Fossil Cichlid Fish of Africa, Special Papers in Palaeontology, Vol. 29. Palaeontological Association: London.
72. Verheyen E, Salzburger W, Snoeks J, Meyer A (2003). Origin of the superflock Cichlid fishes from Lake Victoria, East Africa. Science 300: 325-329.