Tempo of genetic diversification in southern African rodents: The role of Plio-Pleistocene climatic oscillations as drivers for speciation

Acta Oecologica

Volumn 42, Issue , 2012, Pages 50-57

  Montgelard, Claudine ^a   Matthee, Conrad A ^b  

^a CENTRE D ECOLOGIE FONCTIONNELLE ET EVOLUTIVE   (France)

^b STELLENBOSCH UNIVERSITY   (South Africa)

Author keywords

Climatic fluctuations; Cytochrome b; Diversification rate; Rodents; Southern Africa; Topographic barriers

Indexed keywords

ARIDIFICATION; CALIBRATION; DIVERGENCE; GENETIC ANALYSIS; GENETIC DIFFERENTIATION; HABITAT FRAGMENTATION; PLIOCENE-PLEISTOCENE BOUNDARY; RODENT; SPECIATION (BIOLOGY); TAXONOMY; TOPOGRAPHY; VICARIANCE;

SOUTHERN AFRICA;

AETHOMYS; APODEMUS; BATHYERGIDAE; CRYPTOMYS; GERBILLURUS; MASTOMYS; MURIDAE; MUS; MYA; NESOMYIDAE; OTOMYS; RHABDOMYS; RODENTIA; SACCOSTOMUS; SCIURIDAE; XERUS;

EID: 84863204282     PISSN: 1146609X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.actao.2012.02.001     Document Type: Article

References (48)

1. Bobe R., Eck G. Responses of African bovids to Pliocene climatic change. Paleobiology 2001, 27:1-47.
2. Bobe R., Behrensmeyer K., Chapman R.E. Faunal change, environmental variability and late Pliocene hominin evolution. J. Hum. Evol. 2002, 42:475-497.
3. Chase B.M., Meadows M.E. Late Quaternary dynamics of southern Africa's winter rainfall zone. Earth-Sci. Rev. 2007, 84:103-138.
4. Chevret P., Dobigny G. Systematics and evolution of the subfamily Gerbillinae (Mammalia, Rodentia, Muridae). Mol. Phylogenet. Evol. 2005, 35:674-688.
5. Corti M., Castiglia R., Annesi F., Verheyen W. Mitochondrial sequences and karyotypes reveal hidden diversity in African pouched mice (subfamily Cricetomyinae, genus Saccostomus). J. Zool. 2004, 262:413-424.
6. deMenocal P.B. Plio-Pleistocene African climate. Science 1995, 270:53-59.
7. deMenocal P.B. African climate change and faunal evolution during the Pliocene-Pleistocene. Earth Planet. Sci. Lett. 2004, 220:3-24.
8. Drummond A.J., Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 2007, 7:214.
9. Edwards S., Claude J., Jansen Van Vuuren B., Matthee C.A. Evolutionary history of the Karoo bush rat, Myotomys unisulcatus (Rodentia, Muridae): disconcordance between morphology and genetics. Biol. J. Linn. Soc. 2011, 102:510-526.
10. Faulkes C.G., Verheyen E., Verheyen W., Jarvis J.U.M., Bennett N.C. Phylogeographical patterns of genetic divergence and speciation in African mole-rats (Family: Bathyergidae). Mol. Ecol. 2004, 13:613-629.
11. Felsenstein J. PHYLIP (Phylogeny Inference Package) version 3.6. Seattle: 2004, Department of Genome Sciences, University of Washington.
12. Goldblatt P., Manning J. Cape Plants - A Conspectus of the Cape Flora of South Africa 2000, National Botanical Institute, Pretoria (South Africa).
13. Granjon, L., Montgelard, C. The input of DNA sequences to animal systematics: rodents as study cases. In: Munshi, A. (Ed.), DNA Sequencing. InTech Publisher, in press.
14. Herron M.D., Waterman J.M., Parkinson C.L. Phylogeny and historical biogeography of African ground squirrels: the role of climate change in the evolution of Xerus. Mol. Ecol. 2005, 14:2773-2788.
15. Hewitt G. The genetic legacy of the Quaternary ice ages. Nature 2000, 405:907-913.
16. Hewitt G.M. Genetic consequences of climatic oscillations in the Quaternary. Philos. Trans. Roy. Soc. B 2004, 359:183-195.
17. Ho S.Y.W. Calibrating molecular estimates of substitution rates and divergence times in birds. J. Avian Biol. 2007, 38:409-414.
18. Jansa S.A., Weksler M. Phylogeny of muroid rodents: relationship within and among major lineages as determined by IRBP gene sequence. Mol. Phylogenet. Evol. 2004, 31:256-276.
19. Jansen van Vuuren B., Robinson T.J. Genetic population structure in the yellow mongoose, Cynictis penicillata. Mol. Ecol. 1997, 6:1147-1153.
20. Lecompte E., Aplin K., Denys C., Catzeflis F., Chades M., Chevret P. Phylogeny and biogeography of African Murinae based on mitochondrial and nuclear gene sequences, with a new tribal classification of the subfamily. BMC Evol. Biol. 2008, 8:199.
21. Lecompte E., Granjon L., Peterhans J.K., Denys C. Cytochrome b-based phylogeny of the Praomys group (Rodentia, Murinae): a new African radiation?. C. R. Biol. 2002, 325:827-840.
22. Linder H.P., Johnson S.D., Kuhlmann M., Matthee C.A., Nyffeler R., Swartz E.R. Biotic diversity in the Southern African winter-rainfall region. Curr. Opin. Environ. Sustain. 2010, 2:109-116.
23. Matthee C.A., Flemming A.F. Population fragmentation in the southern rock agama, Agama atra: more evidence for vicariance in Southern Africa. Mol. Ecol. 2002, 11:465-471.
24. Matthee C.A., Robinson T.J. Mitochondrial DNA differentiation among geographic populations of Smith's red rock rabbit, Pronolagus rupestris (Mammalia: Lagomorpha). Heredity 1996, 76:514-523.
25. Matthee C.A., Robinson T.J. Mitochondrial DNA phylogeography and comparative cytogenetics of the springhare, Pedetes capensis (Mammalia: Rodentia). J. Mammal. Evol. 1997, 4:53-73.
26. Montgelard C., Forty E., Arnal V., Matthee C.A. Suprafamilial relationships among Rodentia and the phylogenetic effect of removing fast-evolving nucleotides in mitochondrial, exon and intron fragments. BMC Evol. Biol. 2008, 8:321-336.
27. Mouline K., Granjon L., Galan M., Tatard C., Abdoullaye D., Ag Atteyine S., Duplantier J.-M., Cosson J.-F. Phylogeography of a Sahelian rodent species Mastomys huberti: a Plio-Pleistocene story of emergence and colonization of humid habitats. Mol. Ecol. 2008, 17:1036-1053.
28. Nicolas V., Missoup A.D., Denys C., Kerbis J., Peterhans J.K., Katuala P., Couloux A., Colyn M. The roles of rivers and Pleistocene refugia in shaping genetic diversity in Praomys misonnei in tropical Africa. J. Biogeogr. 2011, 38:191-207.
29. Pisani D. Identifying and removing fast-evolving sites using compatibility analysis: an example from the Arthropoda. Syst Biol. 2004, 53:978-989.
30. Pocok T.N. Pliocene mammalian microfauna from Langebaanweg: a new fossil genus linking the Otomyinae with the Murinae. S. Afr. J. Sci. 1976, 72:58-60.
31. Rambau R.V., Robinson T.J., Stanyon R. Molecular genetics of Rhabdomys pumilio subspecies boundaries: mtDNA phylogeography and karyotypic analysis by fluorescence in situ hybridization. Mol. Phylogenet. Evol. 2003, 28:564-575.
32. Rambaut A., Drummond A.J. Tracer v1.5 2007, Available at:. http://tree.bio.ed.ac.uk/software/tracer/.
33. Randi E. Phylogeography of South European mammals. Phylogeography of Southern European Refugia 2007, 101-126. Springer, The Netherlands. S. Weiss, N. Ferrand (Eds.).
34. Ronquist F., Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
35. Russo I.R.M., Chimimba C.T., Bloomer P. Mitochondrial DNA differentiation between two species of Aethomys (Rodentia: Muridae) from southern Africa. J. Mammal. 2006, 87:545-553.
36. Russo I.R.M., Chimimba C.T., Bloomer P. Bioregion heterogeneity correlates with extensive mitochondrial DNA diversity in the Namaqua rock mouse, Micaelamys namaquensis (Rodentia: Muridae) from southern Africa - evidence for a species complex. BMC Evol. Biol. 2010, 10:307.
37. Schnitzler J., Barraclough T.G., Boatwright J.S., Goldblatt P., Manning J.C., Powell M.P., Rebelo T., Savolainen V. Causes of plant diversification in the cape biodiversity hotspot of South Africa. Syst. Biol. 2011, 60:343-357.
38. Smit H.A., Robinson T.J., Jansen Van Vuuren B. Coalescence methods reveal the impact of vicariance on the spatial genetic structure of Elephantulus edwardii (Afrotheria, Macroscelidea). Mol. Ecol. 2007, 16:2680-2692.
39. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
40. Taberlet P., Fumagalli L., Wust-Saucy A.G., Cosson J.-F. Comparative phylogeography and postglacial colonization routes in Europe. Mol. Ecol. 1998, 7:453-464.
41. Taylor P.J., Maree S., van Sandwyk J., Baxter R., Rambau R.V. When is a species not a species? Uncoupled phenotypic, karyotypic and genotypic divergence in two species of South African laminate-toothed rats (Murinae: Otomyini). J. Zool. 2009, 277:317-332.
42. Trauth M.H., Larrasoan J.C., Mudelsee M. Trends, rhythms and events in Plio-Pleistocene African climate. Quat. Sci. Rev. 2009, 28:399-411.
43. Veyrunes F., Britton-Davidian J., Robinson T.J., Calvet E., Denys C., Chevret P. Molecular phylogeny of the African pygmy mice, subgenus Nannomys (Rodentia, Murinae, Mus): implications for chromosomal evolution. Mol. Phylogenet. Evol. 2005, 36:358-369.
44. Vrba E.S. African Bovidae: evolutionary event since the Miocene. S. Afr. J. 1985, 81:263-266.
45. Vrba E.S. On the connections between paleoclimate and evolution. Paleoclimate and Evolution with Emphasis on Human Origins 1995, 24-45. Yale University Press, New Haven. E.S. Vrba, G.H. Denton, T.C. Partridge, L.H. Burckle (Eds.).
46. Willows-Munro S., Matthee C.A. Linking lineage diversification to climate and habitat heterogeneity: phylogeography of the southern African shrew Myosorex varius. J. Biogeogr. 2011, 38:1976-1991.
47. Wilson D.E., Reeder D.M. Mammal Species of the World. A Taxonomic and Geographic Reference 2005, John Hopkins University Press, Baltimore.
48. Winkler A.J., Denys C., Avery M. Fossil rodents of Africa. Cenozoic Mammals of Africa 2010, 263-304. University of California Press, Baltimore, (Chapter 17). L. Werdelin, W.J. Sanders (Eds.).