Biogeography and host-related factors trump parasite life history: Limited congruence among the genetic structures of specific ectoparasitic lice and their rodent hosts

Molecular Ecology

Volumn 22, Issue 20, 2013, Pages 5185-5204

  du Toit, Nina ^a   Van Vuuren, Bettine J ^b   Matthee, Sonja ^a   Matthee, Conrad A ^a  

^a STELLENBOSCH UNIVERSITY   (South Africa)

^b UNIVERSITY OF JOHANNESBURG   (South Africa)

Author keywords

comparative phylogeography; cophylogeny; mtDNA; Polyplax; Rhabdomys; southern Africa

Indexed keywords

ANOPLURA; PHTHIRAPTERA; POLYPLAX; POLYPLAX ARVICANTHIS; RHABDOMYS; RODENTIA;

MITOCHONDRIAL DNA;

AFRICA; ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; CELL NUCLEUS; COMPARATIVE PHYLOGEOGRAPHY; COPHYLOGENY; EVOLUTION; GENETICS; HAPLOTYPE; HOST RANGE; LOUSE; METHODOLOGY; MUTATION RATE; PARASITE; PARASITOLOGY; PHYLOGENY; PHYLOGEOGRAPHY; POLYPLAX; POPULATION GENETICS; RHABDOMYS; RODENT; SOUTHERN AFRICA;

COMPARATIVE PHYLOGEOGRAPHY; COPHYLOGENY; MTDNA; POLYPLAX; RHABDOMYS; SOUTHERN AFRICA;

AFRICA, SOUTHERN; ANIMALS; BAYES THEOREM; BIOLOGICAL EVOLUTION; CELL NUCLEUS; DNA, MITOCHONDRIAL; GENETICS, POPULATION; HAPLOTYPES; HOST SPECIFICITY; MODELS, GENETIC; MUTATION RATE; PARASITES; PHTHIRAPTERA; PHYLOGENY; PHYLOGEOGRAPHY; RODENTIA;

EID: 84885578804     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.12459     Document Type: Article

References (132)

1. Akaike H, (1973) Information theory and an extention of the maximum likelihood principle. In: Second International Symposium on Information Theory (eds, Petrov PN, &, Csaki F,), pp. 267-281. Budapest, Adad. Kiado.
2. Althoff DM, Segraves KA, Smith CI, Leebens-Mack J, Pellmyr O, (2012) Geographic isolation trumps coevolution as a driver of yucca and yucca moth diversification. Molecular Phylogenetics and Evolution, 62, 898-906.
3. Banks JC, Paterson AM, (2005) Multi-host parasite species in cophylogenetic studies. International Journal for Parasitology, 35, 741-746.
4. Barrett LG, Thrall PH, Burdon JJ, Linde CC, (2008) Life history determines genetic structure and evolutionary potential of host-parasite interactions. Trends in Ecology and Evolution, 23, 678-685.
5. Bauer AM, Lamb T, Branch WR, (2006) A revision of the Pachydactylus serval and P. weberi groups (Reptilia: Gekkota: Gekkonidae) of Southern Africa, with the description of eight new species. Proceedings of the California Academy of Sciences, 57, 595-709.
6. Blouin MS, Yowell CA, Courtney CH, Dame JB, (1995) Host movement and the genetic structure of populations of parasitic nematodes. Genetics, 141, 1007-1014.
7. Bohonak AJ, (2002) IBD (isolation by distance): a program of analyses of isolation by distance. Journal of Heredity, 93, 153-154.
8. Brooks DR, (1979) Testing the context and extent of host-parasite coevolution. Systematic Zoology, 28, 299-307.
9. Brooks DR, Ferrao AL, (2005) The historical biogeography of co-evolution: emerging infectious diseases are evolutionary accidents waiting to happen. Journal of Biogeography, 32, 1291-1299.
10. Brooks DR, McLennan DA, (1993) Parascript. Parasites and the language of evolution Smithsonian Institution Press, Washington, District of Columbia
11. Burnham KP, Anderson DA, (2004) Multi-model inference: understanding AIC and BIC in model selection. Sociological Methods & Research, 33, 261-304.
12. Charleston MA, (2011) TreeMap 3b. Available from [http://sites.google. com/site/cophylogeny].
13. Charleston MA, Perkins SL, (2006) Traversing the tangle: algorithms and applications for cophylogenetic studies. Journal of Biomedical Informatics, 39, 62-71.
14. Clayton DH, (1990) Host specificity of Strigiphilus owl lice (Ischnocera: Philopteridae), with the description of new species and host associations. Journal of Medical Entomology, 27, 257-265.
15. Clayton DH, Johnson KP, (2003) Linking coevolutionary history to ecological process: doves and lice. Evolution, 57, 2335-2341.
16. Clayton DH, Al-Tamimi S, Johnson KP, (2003) The ecological basis of coevolutionary history. In: Tangled Trees: Phylogeny, Cospeciation, and Coevolution (ed., Page RDM,), pp. 330-350. University of Chicago Press, Chicago.
17. Clayton DH, Bush SE, Johnson KP, (2004) Ecology of congruence: Past meets present. Systematic Biology, 53, 165-173.
18. Clement M, Posada D, Crandall KA, (2000) TCS: a computer program to estimate gene genealogies. Molecular Ecology, 9, 1657-1659.
19. Conow C, Fielder D, Ovadia Y, Libeskind-Hadas R, (2010) Jane: a new tool for the cophylogeny reconstruction problem. Algorithms for Molecular Biology, 5, 16.
20. Corander J, Tang J, (2007) Bayesian analysis of population structure based on linked molecular information. Mathematical Biosciences, 205, 19-31.
21. Corander J, Marttinen P, Sirén J, Tang J, (2008) Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations. BMC Bioinformatics, 9, 539.
22. Criscione CD, Blouin MS, (2005) Effective sizes of macroparasite populations: a conceptual model. Trends in Parasitology, 21, 212-217.
23. Criscione CD, Poulin R, Blouin MS, (2005) Molecular ecology of parasites: elucidating ecological and microevolutionary processes. Molecular Ecology, 12, 2247-2257.
24. De Vienne DM, Refrégier G, Lõpez-Villavicencio M, Tellier A, Hood ME, Giraud T, (2013) Cospeciation vs host-shift speciation: methods for testing, evidence from natural associations and relation to coevolution. New Phytologist, 198, 347-385.
25. Demastes JW, Spradling TA, Hafner MS, et al,. (2012) Cophylogeny on a fine scale: Geomydoecus chewing lice and their pocket gopher hosts, Pappogeomys bulleri. Journal of Parasitology, 98, 262-270.
26. Dilcher M, Hasib L, Lechner M, et al,. (2011) Genetic characterization of Tribeč virus and Kemerovo virus, two tick-transmitted human-pathogenic Orbiviruses. Virology, 423, 68-76.
27. Drummond CS, Hamilton MB, (2007) Hierarchical components of genetic variation at a species boundary: population structure in two sympatric varieties of Lupinus microcarpus (Leguminosae). Molecular Ecology, 16, 753-769.
28. Drummond AJ, Ho S, Phillips M, Rambaut A, (2006) Relaxed phylogenetics and dating with confidence. PLOS Biology, 4, e88.
29. Drummond AJ, Suchard MA, Xie D, Rambaut A, (2012) Bayesian phylogenetics with BEAUTi and the BEAST 1.7. Molecular Biology and Evolution, 29, 1969-1973.
30. Dupont LM, (2006) Late Pliocene vegetation and climate in Namibia (southern Africa) derived from palynology of ODP Site 1082. Geochemistry, Geophysics, Geosystems, 7, 1-15.
31. Durden LA, Musser GG, (1994) The sucking lice (Insecta, Anoplura) of the world: a taxonomic checklist with records of Mammalian hosts and geographical distributions. Bulletin of the American Museum of Natural History, 218, 1-90.
32. Ellery WN, Scholes RJ, Mentis MT, (1991) An initial approach to predicting the sensitivity of the grassland biome to climate change. South African Journal of Science, 87, 499-503.
33. Engelbrecht A, Taylor PJ, Daniels SR, Rambau RV, (2011) Cryptic speciation in the southern African vlei rat Otomys irroratus complex: evidence derived from mitochondrial cyt b and niche modelling. Biological Journal of the Linnean Society, 104, 192-206.
34. Excoffier L, Lischer HEL, (2010) arlequin suite ver 3.5: a new series of programs to perform population genetic analyses under Linux and Windows. Molecular Ecology Resources, 10, 564-567.
35. 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.
36. Frankham R, Ballou JD, Briscoe DA, (2002) Introduction to Conservation Genetics. Cambridge University Press, Cambridge.
37. Frantz AC, Cellina S, Krier A, Schley L, Burke T, (2009) Using spatial Bayesian methods to determine the genetic structure of a continuously distributed population: clusters or isolation by distance ? Journal of Applied Ecology, 46, 493-505.
38. Ganem G, Meynard CN, Perigault M, et al,. (2012) Environmental correlates of co-occurrence of three mitochondrial lineages of striped mice (Rhabdomys) in the Free State Province (South Africa). Acta Oecologica, 42, 30-40.
39. Guindon S, Gascuel O, (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology, 52, 696-704.
40. Hafner MS, Sudman PD, Villablanca FX, et al,. (1994) Disparate rates of molecular evolution in cospeciating hosts and parasites. Science, 265, 1087-1090.
41. Halas D, Zamparo D, Brooks DR, (2005) A historical biogeographical protocol for studying diversification by taxon pulses. Journal of Biogeography, 32, 249-260.
42. Hall T, (2005) ioEdit, Biological sequence alignment editor for Win95/98/NT/2K/XP. Available from http://www.mbio.ncsu.edu/BioEdit/bioedit.html.
43. Heled J, Drummond AJ, (2010) Bayesian inference of species trees from multilocus data. Molecular Biology and Evolution, 27, 570-580.
44. Hoberg EP, Brooks DR, (2008) A macroevolutionary mosaic: episodic host-switching, geographical colonization and diversification in complex host-parasite systems. Journal of Biogeography, 35, 1533-1550.
45. Hoberg EP, Klassen GJ, (2002) Revealing the faunal tapestry: co-evolution and historical biogeography of hosts and parasites in marine systems. Parasitology, 124, 3-22.
46. Hopkins GHE, (1949) The host association of the lice of mammals. Proceedings of the Zoological Society, London, 119, 387-604.
47. Huyse T, Poulin R, Theron A, (2005) Speciation in parasites: a population genetics approach. Trends in Parasitology, 21, 469-475.
48. Jensen JL, Bohonak AJ, Kelley ST, (2005) Isolation by distance, web service. BMC Genetics, 6, 13.
49. Jerome CA, Ford BA, (2002) Comparative population structure and genetic diversity of Arceuthobium americanum (Viscaceae) and its Pinus host species: insight into host-parasite evolution in parasitic angiosperms. Molecular Ecology, 11, 407-420.
50. Johnson KP, Clayton DH, (2004) Untangling coevolutionary history. Systematic Biology, 53, 92-94.
51. Johnson KP, Williams BL, Drown DM, Adams RJ, Clayton DH, (2002) The population genetics of host specificity: genetic differentiation in dove lice (Insecta: Phthiraptera). Molecular Ecology, 11, 25-38.
52. Johnson KP, Adams RJ, Page RDM, Clayton DH, (2003) When do parasites fail to speciate in response to host speciation? Systematic Biology, 52, 37-47.
53. Keller-Schmidt S, Wieseke N, Klemm K, Middendorf M, (2011) Evaluation of host parasite reconciliation methods using a new apporach for cophylogeny generation. Working paper from Bioinformatics Leipzig. Available from http://www.bioinf.uni-leipzig.de/working/11-013.
54. Kim KC, (1985) Coevolution of Parasitic Arthropods and Mammals. John Wiley, New York.
55. Kim KC, (2006) Blood-sucking lice (Anoplura) of small mammals: True parasites. In: Micromammals and Macroparasites: From Evolutionary Ecology to Management (eds, Morand S, Krasnov BR, &, Poulin R,), pp. 141-160. Springer-Verlag, Tokyo.
56. Lamb T, Bauer AM, (2000) Relationships of the Pachydactylus rugosus group of geckos (Reptilia: Squamata: Gekkonidae). African Zoology, 35, 55-67.
57. Ledger JA, (1980) The Arthropod Parasites of Vertebrates in Africa south of the Sahara. Volume IV. Phthiraptera (Insecta). Publications of the South African Institute for Medical Research No. 56. South African Institute for Medical Research, Johannesburg, South Africa.
58. Legendre P, Legendre L, (1998) Numerical Ecology, 2nd edn. Elsevier, New York.
59. Legendre P, Desdevises Y, Bazin E, (2002) A statistical test for host-parasite coevolution. Systematic Biology, 51, 217-234.
60. Librado P, Rozas J, (2009) dnasp v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25, 1451-1452.
61. Light JE, Hafner MS, (2007) Disparate rates of evolution in sympatric lineages of chewing lice on pocket gophers. Molecular Phylogenetics and Evolution, 45, 997-1013.
62. Light JE, Hafner MS, (2008) Codivergence in Heteromyid rodents (Rodentia: Heteromyidae) and their sucking lice of the genus Fahrenholzia (Phthiraptera: Anoplura). Systematic Biology, 57, 449-465.
63. Mantel N, (1967) The detection of disease clustering and a generalized regression approach. Cancer Research, 27, 209-220.
64. Marshall AG, (1981) The Ecology of Ectoparasitic Insects. Aberdeen University Academic Press, London.
65. Matthee CA, Flemming AF, (2002) Population fragmentation in the southern rock agama, Agama atra: more evidence for vicariance in Southern Africa. Molecular Ecology, 11, 465-471.
66. Matthee S, Horak IG, Beaucournu J-C, et al,. (2007) Epifaunistic arthropod parasites of the four-striped mouse, Rhabdomys pumilio, in the Western Cape Province, South Africa. Journal of Parasitology, 93, 47-59.
67. Matthee S, McGeoch MA, Krasnov B, (2010) Parasite-specific variation and the extent of male-biased parasitism; an example with a South African rodent and ectoparasitic arthropods. Parasitology, 137, 651-660.
68. McCoy KD, (2003) Sympatric speciation in parasites-what is sympatry? Trends in Parasitology, 19, 400-404.
69. McCoy KD, Boulinier T, Tirard C, Michalakis Y, (2003) Host-dependant genetic structure of parasite populations: differential dispersal of seabird tick host races. Evolution, 57, 288-296.
70. Meier-Kolthoff JP, Auch AF, Huson DH, Göker M, (2007) Copycat: Co-phylogenetic Analysis Tool. Bioinformatics, 23, 898-900.
71. Meirmans PG, (2012) The trouble with isolation by distance. Molecular Ecology, 21, 2839-2846.
72. Mendlová M, Desdevises Y, Civáňová K, Pariselle A, Šimková A, (2012) Monogeneans of West African cichlid fish: evolution and cophylogenetic interactions. PLoS ONE, 7, e37268.
73. Merkle D, Middendorf M, Wieseke N, (2010) A parameter-adaptive dynamic programming aproach for inferring cophylogenies. BMC Bioinformatics, 11, S60.
74. Montgelard C, Matthee CA, (2012) Tempo of genetic diversification in southern African rodents: The role of Plio-Pleistocene climatic oscillations as drivers for speciation. Acta Oecologica, 42, 50-57.
75. Mucina L, Rutherford MC, (2006) The Vegetation of South Africa. Lesotho and Swaziland, South African National Biodiversity Institute, Pretoria.
76. Nadler SA, (1995) Microevolution and the genetic structure of parasite populations. Journal of Parasitology, 81, 395-403.
77. Nieberding CM, Morand S, (2006) Comparative phylogeography: The use of parasites for insights into host history. In: Micromammals and Macroparasites: From Evolutionary Ecology to Management (eds, Morand S, Krasnov BR, &, Poulin R,), pp. 277-293. Springer-Verlag, Tokyo.
78. Nieberding CM, Olivieri I, (2007) Parasites: proxies for host genealogy and ecology? Trends in Ecology & Evolution, 22, 156-165.
79. Nieberding CM, Durette-Desset MC, Vanderpoorten A, et al,. (2008) Geography and host biogeography matter for understanding the phylogeography of a parasite. Molecular Phylogenetics and Evolution, 47, 538-554.
80. Nieberding CM, Jousselein E, Desdevises Y, (2010) The use of co-phylogeographic patterns to predict the nature of host-parasite interactions, and vice versa. In: The Biogeography of Host-Parasite Interactions (eds, Morand S, &, Krasnov BR,), pp. 59-69. Oxford University Press, Oxford.
81. Page RDM, (2003) Tangled trees: Phylogeny, Cospeciation, and Coevolution. University of Chicago press, Chicago.
82. Page DM, Hafner MS, (1996) Molecular phylogenies and host-parasite co-speciation: gophers and lice as a model system. In: New Uses for New Phylogenies (eds, Harvey PH, Brown AJL, Smith JM, &, Nee S,), pp. 255-270. Oxford University Press, Oxford.
83. Page RDM, Lee PLM, Becher SA, Griffiths R, Clayton DH, (1998) A different tempo of mitochondrial DNA evolution in birds and their parasitic lice. Molecular Phylogenetics and Evolution, 9, 276-293.
84. Page RDM, Cruickshank RH, Dickens M, et al,. (2004) Phylogeny of "Philoceanus complex" seabird lice (Phthiraptera: Ischnocera) inferred from mitochondrial DNA sequences. Molecular Phylogenetics and Evolution, 30, 633-652.
85. Partridge TC, (1997) Evolution of landscapes. In: Vegetation of Southern Africa (eds, Cowling RM, Richardson DM, &, Pierce SM,), pp. 5-20. Cambridge University Press, Cambridge.
86. Paterson AM, Banks J, (2001) Analytical approaches to measuring cospeciation of host and parasites: through a looking glass, darkly. International Journal for Parasitology, 31, 1012-1022.
87. Paterson AM, Wallis GP, Wallis LJ, Gray RD, (2000) Seabird and louse co-evolution: complex histories revealed by 12S rDNA sequences and reconciliation analyses. Systematic Biology, 49, 383-399.
88. Peakall ROD, Smouse PE, (2006) genalex 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes, 6, 288-295.
89. Peakall R, Smouse PE, (2012) genalex 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics, 28, 2537-2539.
90. Peakall R, Ruibal M, Lindenmayer DB, (2003) Spatial autocorrelation analysis offers new insights into gene flow in the Australian bush rat, Rattus fuscipes. Evolution, 57, 1182-1195.
91. Posada D, (2004) collapse 1.2: Describing haplotypes from sequence alignments. Available from http://darwin.uvigo.es/software/collapse.html.
92. Posada D, (2008) jModelTest: Phylogenetic model averaging. Molecular Biology and Evolution, 25, 1253-1256.
93. Poulin R, Keeney DB, (2007) Host specificity under molecular and experimental scrutiny. Trends in Parasitology, 24, 24-28.
94. Rambaut A, Drummond AJ, (2007) Tracer v1.5. Available from http://beast.bio.ed.ac.uk/Tracer.
95. Rannala B, Michalakis Y, (2003) Population genetics and cospeciation: from process to pattern. In: Tangled trees. Phylogeny, Cospeciation and Coevolution (ed., Page RDM,), pp. 120-143. Chicago University Press, Chicago.
96. Redman GT, Hamer ML, (2003) The distribution of southern African Harpagophoridae Attems, 1909 (Diplopoda: Spirostreptida). African Invertebrates, 44, 213-226.
97. Reed DL, Smith VS, Hammond SL, Rogers AR, Clayton DH, (2004) Genetic analysis of lice supports direct contact between modern and archaic humans. PLOS Biology, 2, 1972-1983.
98. Rice WR, (1989) Analyzing tables of statistical tests. Evolution, 43, 223-225.
99. Rivas LR, (1964) A reinterpretation of the concepts "sympatric" and "allopatric" with proposal of the additional terms "syntopic" and "allotopic". Systematic Zoology, 13, 42-43.
100. Ronquist F, Teslenko M, van der Mark P, et al,. (2012) mrbayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology, 61, 539-542.
101. Rosenblueth M, Sayavedra L, Sámano-Sánchez H, Roth A, Martínez-Romero E, (2013) Evolutionary relationships of flavobacterial and enterobacterial endosymbionts with their scale insect hosts (Hemiptera: Coccoidea). Journal of Evolutionary Biology, 25, 2357-2368.
102. Safner T, Miller MP, McRae BH, Fortin M-J, Manel S, (2011) Comparison of Bayesian clustering and edge detection methods for inferring boundaries in landscape genetics. International Journal of Molecular Sciences, 12, 865-889.
103. Schradin C, Pillay N, (2005) Intraspecific variation in the spatial and social organization of the African striped mouse. Journal of Mammalogy, 86, 99-107.
104. Schradin C, Scantlebury M, Pillay N, König B, (2009) Testosterone levels in dominant sociable males are lower than in solitary roamers: physiological differences between three male reproductive tactis in a socially flexible mammal. The American Naturalist, 173, 376-388.
105. Scott L, Nyakale M, (2002) Pollen indicators of Holocene palaeoenvironments at Florisbad in the central Free State, South Africa. The Holocene, 12, 497-503.
106. Scott L, Anderson HM, Anderson JM, (1997) Vegetation history. In: Vegetation of Southern Africa (eds, Cowling RM, Richardson DM, &, Pierce SM,), pp. 62-84. Cambridge University Press, Cambridge.
107. Shimodaira H, Hasegawa M, (1999) Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution, 16, 1114-1116.
108. Silvestro D, Michalak K, (2012) raxmlGUI: a graphical front-end for RAxML. Organisms Diversity & Evolution, 12, 335-337.
109. Skinner JD, Chimimba CT, (2005) The Mammals of the South African subregion, 3rd edn. Cambridge University Press, Cambridge.
110. Smit HA, Robinson TJ, Jansen van Vuuren B, (2007) Coalescence methods reveal the impact of vicariance on the spatial genetic structure of Elephantulus edwardii (Afrotheria, Macroscelidea). Molecular Ecology, 16, 2680-2692.
111. Smouse PE, Long JC, (1992) Matrix correlation-analysis in anthropology and genetics. Yearbook Of Physical Anthropology, 35, 187-213.
112. Smouse PE, Peakall R, (1999) Spatial autocorrelation analysis of individual multiallele and multilocus genetic structure. Heredity, 82, 561-573.
113. Smouse PE, Long JC, Sokal RR, (1986) Multiple regression and correlation extensions of the Mantel test of matrix correspondence. Systematic Zoology, 35, 627-632.
114. Solmsen N, Johannesen J, Schradin C, (2011) Highly asymmetric fine-scale genetic structure between sexes of African striped mice and indication for condition dependent alternative male dispersal tactics. Molecular Ecology, 20, 1624-1634.
115. Stadler T, (2010) Sampling-through-time in birth-death trees. Journal of Theoretical Biology, 267, 396-404.
116. Stamatakis A, (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analysis with thousands of taxa and mixed models. Bioinformatics, 22, 2268-2690.
117. Stamatakis A, Auch AF, Meier-Kolthoff JP, Göker M, (2007) AxPcoords & parallel AxParafit: statistical co-phylogenetic analyses on thousands of taxa. BMC Bioinformatics, 8, 405.
118. Štefka J, Hypša V, (2008) Host specificity and genealogy of the louse Polyplax serrata on field mice, Apodemus species: a case of parasite duplication or colonization? International Journal for Parasitology, 38, 731-741.
119. Štefka J, Hoeck PEA, Keller LF, Smith VS, (2011) A hitchhikers guide to the Galápagos: co-phylogeography of Galápagos mockingbirds and their parasites. BMC Evolutionary Biology, 11, 284.
120. Stephens M, Scheet P, (2005) Accounting for decay of linkage disequilibrium in haplotype inference and missing data imputation. American Journal of Human Genetics, 76, 449-462.
121. Stephens M, Smith NJ, Donnelly P, (2001) A new statistical method for haplotype reconstruction from population data. American Journal of Human Genetics, 68, 978-989.
122. Swofford DL, (2000) PAUP: Phylogenetic Analysis Using Parsimony (and other methods). Sinauer Associates, Sunderland, Massachusetts.
123. du Toit N, Jansen van Vuuren B, Matthee S, Matthee CA, (2012) Biome specificity of distinct genetic lineages within the four-striped mouse Rhabdomys pumilio (Rodentia: Muridae) from southern Africa with implications for taxonomy. Molecular Phylogenetics and Evolution, 65, 75-86.
124. du Toit N, Matthee S, Matthee CA, (2013) The sympatric occurrence of two genetically divergent lineages of sucking louse, Polyplax arvicanthis (Phthiraptera: Anoplura), on the four-striped mouse genus, Rhabdomys (Rodentia: Muridae). Parasitology, 140, 604-616.
125. Tolley KA, Tilbury CR, Branch WR, Matthee CA, (2004) Phylogenetics of the southern African dwarf chameleons, Bradypodion (Squamata:Chamaeleonidae). Molecular Phylogenetics and Evolution, 30, 354-365.
126. Tolley KA, Braae A, Cunningham M, (2010) Phylogeography of the Clicking Stream Frog Strongylopus grayii (Anura, Pyxicephalidae) reveals cryptic divergence across climatic zones in an abundant and widespread taxon. African Journal of Herpetology, 59, 17-32.
127. Tyson PD, Partridge TC, (2000) The evolution of Cenozoic climates. In: The Cenozoic of Southern Africa (eds, Partridge TC, &, Maud RR,), pp. 371-387. Oxford University Press, New York.
128. Weckstein JD, (2004) Biogeography explains cophylogenetic patterns in toucan chewing lice. Systematic Biology, 53, 154-164.
129. Whiteman NK, Parker PG, (2005) Using parasites to infer host population history: a new rationale for parasite conservation. Animal Conservation, 8, 175-181.
130. Willows-Munro S, Matthee CA, (2011) Linking lineage diversification to climate and habitat heterogeneity: phylogeography of the southern African shrew Myosorex varius. Journal of Biogeography, 38, 1976-1991.
131. Wirth T, Meyer A, Achtman M, (2005) Deciphering host migrations and origins by means of their microbes. Molecular Ecology, 14, 3289-3306.
132. Zachos J, (2001) Trends, rhythms, and aberrations in global climate 65 Ma to present. Science, 292, 686-693.