Phylogeny and historical biogeography of African ground squirrels: The role of climate change in the evolution of Xerus

Molecular Ecology

Volumn 14, Issue 9, 2005, Pages 2773-2788

  Herron, M D ^a,b   Waterman, J M ^a   Parkinson, C L ^a  

^a UNIVERSITY OF CENTRAL FLORIDA   (United States)

^b University of Arizona   (United States)

Author keywords

Climate change; Nested clade analysis; Phylogeography; Sciuridae; Southern Africa; Xerus

Indexed keywords

SCIURIDAE; SPERMOPHILUS; XERUS; XERUS INAURIS; XERUS PRINCEPS;

CYTOCHROME B; PRIMER DNA;

AFRICA; ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; CLIMATE; COMPARATIVE STUDY; DEMOGRAPHY; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; HAPLOTYPE; MOLECULAR EVOLUTION; PHYLOGENY; POPULATION DYNAMICS; SCIURIDAE; SPECIES DIFFERENCE;

AFRICA; ANIMALS; BAYES THEOREM; CLIMATE; CYTOCHROMES B; DEMOGRAPHY; DNA PRIMERS; EVOLUTION, MOLECULAR; GEOGRAPHY; HAPLOTYPES; MODELS, GENETIC; PHYLOGENY; POPULATION DYNAMICS; SCIURIDAE; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; VARIATION (GENETICS);

EID: 24944520034     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2005.02630.x     Document Type: Article

References (80)

1. Abdo Z, Crandall KA, Joyce P (2004) Evaluating the performance of likelihood methods for detecting population structure and migration. Molecular Ecology, 13, 837-851.
2. Alien GM (1939) A checklist of African mammals. Bulletin of the Museum of Comparative Zoology, 83, 1-761.
3. Arbogast BS (1999) Mitochondrial DNA phylogeography of the New World flying squirrels (Glaucomys): implications for Pleistocene biogeography. Journal of Mammalogy, 80, 142-155.
4. Arbogast BS, Slowinski JB (1998) Pleistocene speciation and the mitochondrial DNA clock. Science, 282, 1955a.
5. Axelrod DI, Raven PH (1978) Late Cretaceous and Tertiary vegetation history of Africa. In: Biogeography and Ecology of Southern Africa (ed. Werger MJA), pp. 77-130. Dr. W. Junk Publishers, The Hague, The Netherlands.
6. Barnard P, Brown CJ, Jarvis AM, Robertson A, Rooyen LV (1998) Extending the Namibian protected area network to safeguard hotspots of endemism and diversity. Biodiversity and Conservation, 7, 531-547.
7. Baskevich MI (1997) Karyology and systematics of rodents of the Ethiopian Rift Valley. In: Tropical Biodiversity and Systematics Proceedings of the International Symposium on Biodiversity and Systematics in Tropical Ecosystems, Bonn, 1994 (ed. Ulrich H), pp. 119-123. Zoologisches Forschungsinstitut und Museum Alexander Koenig, Bonn, Germany.
8. Beerli P, Felsenstein J (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, USA, 98, 4563-4568.
9. Clement M, Posada D, Crandall KA (2000) TCS: a computer program to estimate gene genealogies. Molecular Ecology, 9, 1657-1659.
10. Crandall K (1996) Multiple interspecies transmissions of human and simian T-cell leukemia/lymphoma virus type I sequences. Molecular Biology and Evolution, 13, 115-131.
11. De Winter B (1971) Floristic relationships between the northern and southern arid areas in Africa. Mitteilungen der Botanischen Staatssammlung München, 10, 424-437.
12. Denys C, Viriot L, Daams R et al. (2003) A new Pliocene sciurid (Rodentia) from Kossom Bougoudi, Chad. Journal of Vertebrate Paleontology, 23, 676-687.
13. Dobigny G, Nomao A, Gautun J-C (2002) A cytotaxonomic survey of Rodents from Niger: implications for systematics, biodiversity and biogeography. Mammalia, 66, 495-523.
14. Dorst J, Dandelot P (1970) Order Rodentia. In: A Field Guide to the Larger Mammals of Africa, pp. 22-33. Houghton Mifflin Company, Boston, Massachusetts.
15. Edwards S (1997) Relevance of microevolutionary processes to higher level molecular systematics. In: Avian Molecular Evolution and Systematics (ed. Mindell DP), pp. 251-278. Academic Press, San Diego, California.
16. Eisentraut VM (1975) Das gaumenfaltenmuster bei afrikanischen Sciuriden. Zeitschrifte für Säugetierkunde, 40, 133-141.
17. Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplo-types: application to human mitochondrial DNA restriction data. Genetics, 131, 479-491.
18. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution, 17, 368-376.
19. Funk DJ, Omland KE (2003) Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annual Review of Ecology, Evolution, and Systematics, 34, 397-423.
20. Gaggiotti OE, Excoffier L (2000) A simple method of removing the effect of a bottleneck and unequal population sizes on pairwise genetic distances. Proceedings of the Royal Society of London. Series B, Biological Sciences, 267, 81-87.
21. Goossens B, Waits LP, Taberlet P (1998) Plucked hair samples as a source of DNA: reliability of dinucleotide microsatellite geno- typing. Molecular Ecology, 7, 1237-1241.
22. de Graaff G (1981) The Rodents of Southern Africa. Butterworths, Pretoria, South Africa.
23. Griffin M (1999) Checklist and provisional conservation status of amphibians, reptiles and mammals known or expected to occur in Namibia. Ministry of Environment and Tourism, Government of Namibia, Windhoek.
24. Haim A, Skinner JD, Robinson TJ (1987) Bioenergetics, thermoregulation and urine analysis of squirrels of the genus Xerus from an arid environment. South African Journal of Zoology, 22, 45-49.
25. Herron MD, Castoe TA, Parkinson CL (2004) Sciurid phytogeny and the paraphyly of Holarctic ground squirrels (Spermophilus). Molecular Phylogenetics and Evolution, 31, 1015-1030.
26. Herzig-Straschil B, Herzig A (1989) Biology of Xerus princeps (Rodentia, Sciuridae). Madoqua, 16, 41-46.
27. Herzig-Straschil B, Herzig A, Winkler H (1991) A morphometric analysis of the skulls of Xerus inauris and Xerus princeps (Rodentia; Sciuridae). Zeitschrifte für Säugetierkunde, 56, 177-187.
28. Huelsenbeck JP, Crandall KA (1997) Phylogeny estimation and hypothesis testing using maximum likelihood. Annual Review of Ecology and Systematics, 28, 437-466.
29. Irwin D, Kocher T, Wilson A (1991) Evolution of the cytochrome b gene in mammals. Journal of Molecular Evolution, 32, 37-55.
30. Jacobson KM, Lester E (2003) A first assessment of genetic variation in Welwitschia mirabilis Hook. Journal of Heredity, 94, 212-217.
31. Jürgens N (1997) Floristic biodiversity and history of African arid regions. Biodiversity and Conservation, 6, 495-514.
32. Kern WF, Bland JR (1948) Solid Mensuration with Proofs, 2nd edn. Wiley, New York.
33. Knoch K, Schulze A (1956) Niederschlag, Teperatur und Schwüle in Africa. Falk Verlag, Hamburg.
34. Knowles LL (2001) Did the Pleistocene glaciations promote divergence? Tests of explicit refugial models in montane grasshoppers. Molecular Ecology, 10, 691-701.
35. Knowles LL, Maddison WP (2002) Statistical phylogeography. Molecular Ecology, 11, 2623-2635.
36. Kotlik P, Bogutskaya NG, Ekmekçi FG (2004) Circum-Black Sea phylogeography of Barbus freshwater fishes: divergence in the Pontic glacial refugium. Molecular Ecology, 13, 87-95.
37. Kuhner MK, Yamato J, Felsenstein J (1998) Maximum likelihood estimation of population growth rates based on the coalescent. Genetics, 149, 429-434.
38. Linn I, Key G (1996) Use of space by the African striped ground squirrel Xerus erythropus. Mammalian Review, 26, 9-26.
39. Maddison WP, Maddison DR (2004) MESQUITE: a modular system for evolutionary analysis. http://mesquiteproject.org.
40. Maggs GL, Craven P, Kolberg HH (1998) Plant species richness, endemism, and genetic resources in Namibia. Biodiversity and Conservation, 7, 435-446.
41. Mantel NA (1967) The detection of disease clustering and a generalized regression approach. Cancer Research, 27, 209-220.
42. Matthee CA, Robinson TJ (1996) Mitochondrial DNA differentiation among geographical populations of Pronolagus rupestris, Smith's red rock rabbit (Mammalia: Lagomorpha). Heredity, 76, 514-523.
43. Matthee CA, Hemming AF (2002) Population fragmentation in the southern rock agama, Agama atra: more evidence for vicariance in southern Africa. Molecular Ecology, 11, 465-471.
44. de Menocal PB (1995) Plio-Pleistocene African climate. Science, 270, 53-59.
45. de Menocal PB (2004) African climate change and faunal evolution during the Pliocene-Pleistocene. Earth and Planetary Science Letters, 220, 3-24.
46. Mercer JM, Roth VL (2003) The effects of Cenozoic global change on squirrel phylogeny. Science, 299, 1568-1572.
47. Moore JC (1959) Relationships among the living squirrels of the Sciurinae. Bulletin of the American Museum of Natural History, 118, 159-206.
48. Moore JC (1961) Geographic variation in some reproductive characteristics of diurnal squirrels. Bulletin of the American Museum of Natural History, 122, 1-32.
49. Nicholas KB, Nicholas HB Jr (1997) GENEDOC: a tool for editing and annotating multiple sequence alignments. Distributed by the authors.
50. O'Shea T (1991) Xerus rutilus. Mammalian Species, 370, 1-5.
51. Pocock RI (1923) The classification of the Sciuridae. Proceedings of the Zoological Society of London, 1923, 209-246.
52. Posada D, Crandall K (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics, 14, 817-818.
53. Posada D, Crandall KA (2001) Selecting the best-fit model of nucleotide substitution. Systematic Biology, 50, 580-601.
54. Posada D, Crandall KA, Templeton AR (2000) GEODIS: a program for the cladistic nested analysis of the geographical distribution of genetic haplotypes. Molecular Ecology, 9, 487-488.
55. Prinsloo P, Robinson T (1992) Geographic mitochondrial DNA variation in the rock hyrax, Procavia capensis. Molecular Biology and Evolution, 9, 447-456.
56. Raymond M, Rousset F (1995) An exact test for population differentiation. Evolution, 49, 1280-1283.
57. Robertson A, Jarvis AM, Brown CJ, Simmons RE (1998) Avian diversity and endemism in Namibia: patterns from the Southern African Bird Atlas Project. Biodiversity and Conservation, 7, 495-511.
58. Robinson TJ, Skinner JD, Haim AS (1986) Close chromosomal congruence in two species of ground squirrel: Xerus inauris and X. princeps (Rodentia: Sciuridae). South African Journal of Zoology, 21, 100-105.
59. Ronquist F, Huelsenbeck JP (2003) MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572-1574.
60. Rosevear DR (1969) The Rodents of West Africa. Trustees of the British Museum (Natural History), London.
61. Saiki R, Gelfand DH, Stoeffl S et al. (1988) Primer-directed enzymatic amplification of DNA with thermostable DNA polymerase. Science, 239, 487-491.
62. Sambrook J, Russell DW (2001) Molecular Cloning: A Laboratory Manual, 3rd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
63. Schneider SD, Roessli D, Excoffier L (2000) ARLEQUIN: a software for population genetics data analysis, Version 2.000. Genetics and Biometry Laboratory, Department of Anthropology, University of Geneva, Switzerland.
64. Slatkin M (1987) Gene flow and the geographic structure of natural populations. Science, 236, 787-792.
65. Smith CI, Farrell BD (2005) Range expansion in the flightless longhorn cactus beetles, Moneilema gigas and Moneilerna armatum, in response to Pleistocene climate changes. Molecular Ecology, 14, 1025-1044.
66. Steppan SJ, Storz BL, Hoffmann RS (2004) Nuclear DNA phylogeny of the squirrels (Mammalia: Rodentia) and the evolution of arboreality from c-myc and RAG1. Molecular Phylogenetics and Evolution, 30, 703-719.
67. Swofford DL (2002) PAUP * : Pliylogenetic Analysis Using Parsimony ( * and Other Methods). Sinauer Associates, Sunderland, Massachusetts.
68. Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution, 10, 512-526.
69. Templeton AR (2004) Statistical phylogeography: methods of evaluating and minimizing inference errors. Molecular Ecology, 13, 789-809.
70. Templeton A, Boerwinkle E, Sing C (1987) A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. I. Basic theory and an analysis of alcohol dehydrogenase activity in Drosophila. Genetics, 117, 343-351.
71. Templeton AR, Sing CF (1993) A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. IV. Nested analyses with cladogram uncertainty and recombination. Genetics, 134, 659-669.
72. Waterman JM (1995) The social organization of the Cape ground squirrel (Xerus inauris; Rodentia: Sciuridae). Ethology, 101, 130-147.
73. Waterman JM (1997) Why do male Cape ground squirrels live in groups? Animal Behaviour, 53, 809-817.
74. Watterson GA (1975) On the number of segregating sites in genetical models without recombination. Theoretical Population Biology, 7, 256-276.
75. Werger MJA (1978) The Karoo-Namib Region. In: Biogeography and Ecology of Southern Africa (ed. Werger MJA), pp. 231-299. Dr. W. Junk Publishers, The Hague, The Netherlands.
76. Wilson DE, Reeder DM (1993) Mammal Species of the World. Smithsonian Institution Press, Washington, D.C.
77. Zheng X, Arbogast BS, Kenagy GJ (2003) Historical demography and genetic structure of sister species: deermice (Peromyscus) in the North American temperate rain forest. Molecular Ecology, 12, 711-724.
78. van Zinderen Bakker EM (1969) The 'arid corridor' between south-western Africa and the Horn of Africa. Palaeoecology of Africa, 4, 139-140.
79. van Zinderen Bakker EM (1978) Quaternary vegetation changes in southern Africa. In: Biogeography and Ecology of Southern Africa (ed. Werger MJA), pp. 131-143. Dr. W. Junk Publishers, The Hague, The Netherlands.
80. Zumpt I (1970) The ground squirrel. African Wild Life, 24, 115-121.