Evolutionary Drivers of Diversification and Distribution of a Southern Temperate Stream Fish Assemblage: Testing the Role of Historical Isolation and Spatial Range Expansion

PLoS ONE

Volumn 8, Issue 8, 2013, Pages

  Chakona, Albert ^a,b   Swartz, Ernst R ^a   Gouws, Gavin ^a  

^a SOUTH AFRICAN INSTITUTE FOR AQUATIC BIODIVERSITY   (South Africa)

^b RHODES UNIVERSITY   (South Africa)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME B; MITOCHONDRIAL DNA;

ARTICLE; DNA SEQUENCE; FRESHWATER FISH; GALAXIAS; GENETIC VARIABILITY; GEOGRAPHIC DISTRIBUTION; HAPLOTYPE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PHYLOGEOGRAPHY; POPULATION ABUNDANCE; PSEUDOBARBUS BURCHELLI; SANDELIA CAPENSIS; SPECIES DISTRIBUTION; SPECIES DIVERSITY; STREAM (RIVER); UNINDEXED SEQUENCE;

EID: 84881243052     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0070953     Document Type: Article

References (78)

1. Rüber L, Britz R, Zardoya R, (2006) Molecular phylogenetics and evolutionary diversification of labyrinth fishes (Perciformes: Anabantoidei). Syst Biol 55: 374-397.
2. Price BW, Barker NP, Villet MH, (2007) Patterns and processes underlying evolutionary significant units in the Platypleura stridula L. species complex (Hemiptera: Cicadidae) in the Cape Floristic Region, South Africa. Mol Ecol 16: 2574-2588.
3. Verboom GA, Archibald JK, Bakker FT, Bellstedt DU, Conrad F, et al. (2009) Origin and diversification of the Greater Cape flora: Ancient species repository, hot-bed of recent radiation, or both? Mol Phylogenet Evol 51: 44-53.
4. Barber BR, Klicka J, (2010) Two pulses of diversification across the Isthmus of Tehuantepec in a montane Mexican bird fauna. Proc R Soc Lond B 277: 2675-2681.
5. Klaus S, Selvandran S, Goh JW, Wowor D, Brandis D, et al. (2013) Out of Borneo: Neogene diversification of Sundaic freshwater crabs (Crustacea: Brachyura: Gecarcinucidae: Parathelphusa). J Biogeogr 40: 63-74.
6. Cooke GM, Chao NL, Beheregaray LB (2012a) Five cryptic species in the Amazonian catfish Centromochlus existimatus identified based on biogeographic predictions and genetic data. PlosOne 7(11).
7. Hawlitschek O, Hendrich L, Espeland M, Toussaint EFA, Genner MJ, et al. (2012) Pleistocene climate change promoted rapid diversification of aquatic invertebrates in Southeast Australia. BMC Evol Biol 12: 142.
8. Chakona A, Swartz ER, Gouws G, Bloomer P, (2013) A freshwater fish defies ancient mountain ranges and drainage divides: extrinsic and intrinsic influences on the evolutionary history of a recently identified galaxiid. J Biogeogr 40: 1399-1412.
9. Waters JM, Allibone RM, Wallis GP, (2006) Geological subsidence, river capture, and cladogenesis of galaxiid fish lineages in central New Zealand. Biol J Linn Soc 88: 367-376.
10. Burridge CP, Craw D, Waters JM, (2006) River capture, range expansion, and cladogenesis: the genetic signature of freshwater vicariance. Evolution 60: 1038-1049.
11. Burridge CP, Craw D, Waters JM, (2007) An empirical test of freshwater vicariance via river capture. Mol Ecol 16: 1883-1895.
12. Berendzen PB, Gambles T, Simons AM, (2008) Phylogeography of the bigeye chub Hybopsis amblops (Teleostei: Cypriniformes): early Pleistocene diversification and post-glacial range expansion. J Fish Biol 73: 2021-2039.
13. Swartz ER, Skelton PH, Bloomer P, (2007) Sea-level changes, river capture and the evolution of populations of the Eastern Cape and fiery redfins (Pseudobarbus afer and Pseudobarbus phlegethon, Cyprinidae), across multiple river systems in South Africa. J Biogeogr 34: 2086-2099.
14. Swartz ER, Skelton PH, Bloomer P, (2009) Phylogeny and biogeography of the genus Pseudobarbus (Cyprinidae): shedding light on the drainage history of rivers associated with the Cape Floristic Region. Mol Phylogent Evol 51: 75-84.
15. McCulloch GA, Wallis GP, Waters JM, (2010) Onset of glaciation drove simultaneous vicariant isolation of Alpine insects in New Zealand. Evolution 64-7: 2033-2043.
16. Barber BR, Unmack PJ, Pérez-Losada M, Johnson J, Crandall K, (2011) Different processes lead to similar patterns: a test of codivergence and the role of sea level and climate changes in shaping a southern temperate freshwater assemblage. BMC Evol Biol 11: 343.
17. Goldblatt P, Manning JC (2000) Cape Plants. A Conspectus of the cape Flora of South Africa. National botanic Institute, Pretoria.
18. Linder HP, (2003) The radiation of the Cape flora, southern Africa. Biol Rev 78: 597-638.
19. Kreft H, Jetz W, (2007) Global patterns and determinants of vascular plant diversity. P Natl Acad Sci USA 104: 5925-5930.
20. Wishart MJ, Day JA, (2002) Endemism of the freshwater fauna of the south-western Cape, South Africa. Verh Internat Verein Limnol 28: 1-5.
21. Thieme ML, Abell R, Stiassny MLJ, Skelton PH, Lehner B, et al. (2005) Freshwater Ecoregions of Africa and Madagascar. Island Press.
22. Linder HP, Johnson SD, Kuhlmann M, Matthee CA, Nyffeler R, et al. (2010) Biotic diversity in the Southern African winter-rainfall region. Curr Opin Env Sust 2: 109-116.
23. Waters JM, Cambray JA, (1997) Intraspecific phylogeography of the Cape galaxias from South Africa: evidence from mitochondrial DNA sequences. J Fish Biol 50: 1329-1338.
24. Bloomer P, Impson ND, (2000) Mitochondrial DNA differentiation in the critically endangered Berg River Redfin (Pseudobarbus burgi). J Hered 91: 122-127.
25. Wishart M, Hughes J, Stewart B, Impson D, (2006) Extreme levels of intra-specific divergence among Cape Peninsula populations of the Cape galaxias, Galaxias zebratus Castelnau 1861, reveals a possible species complex. Afr J Aquat Sci 31: 99-106.
26. Swartz ER, Flemming AF, Mouton P le FN, (2004) Contrasting genetic patterns and population histories in three threatened redfin species (Cyprinidae) from the Olifants River System, western South Africa. J Fish Biol 64: 1153-1167.
27. Barnard KH, (1943) Revision of the indigenous freshwater fishes of the S.W. Cape Region. Ann S Afr Mus 36: 101-263.
28. Skelton PH, (1986) Distribution patterns and biogeography of non-tropical southern African freshwater fishes. Palaeoecol Afr 17: 211-230.
29. Wishart MJ, Hughes JM, (2001) Exploring patterns of population subdivision in the net-winged midge, Elporia barnardi (Diptera: Blephariceridae), in mountain streams of the south-western Cape, South Africa. Freshwater Biol 46: 479-490.
30. Siesser WG, Dingle RV, (1981) Tertiary sea-level movements around southern Africa. J Geol 89: 83-96.
31. Hendey QB (1983) Cenozoic geology and palaeogeography of the fynbos region. In: Deacon HJ, Hendey QB, Lambrechts JJN, editors. Fynbos Palaeoecology: A Preliminary Synthesis. South African National Scientific Programmes Report No. 75. CSIR, Pretoria, 35-60.
32. Partridge TC, Maud RR, (1987) Geomorphic evolution of southern Africa since the Mesozoic. S Afr J Geol 90: 179-208.
33. Partridge TC, Maud RR (2000) Macro-scale geomorphic evolution of southern Africa. In: Partridge TC, Maud RR, editors. The Cenozoic of Southern Africa. Oxford University Press, New York, 3-18.
34. Partridge TC, Scott L, Hamilton JE, (1999) Synthetic reconstructions of southern African environments during the Last Glacial Maximum (21-18 kyr) and the Holocene Altithermal (8-6 kyr). Quatern Int 57/58: 207-214.
35. Marlow JR, Lange CB, Wefer G, Rosell-Melè A, (2000) Upwelling intensification as part of the Pliocene-Pleistocene climate transition. Science 290: 2288-2291.
36. Zachos J, Pagani M, Sloan L, Thomas E, Billups K, (2001) Trends, rhythms, aberrations in global climate 65 Ma to present. Science 292: 686-693.
37. Cowling RM, Procheş Ş, Partridge TC, (2009) Explaining the uniqueness of the Cape Flora: Incorporating geomorphic evolution as a factor for explaining its diversification. Mol Phylogenet Evol 51: 64-74.
38. Deacon HJ, Jury MR, Ellis F (1992) Selective regime and time. In: Cowling RM, editor. The ecology of fynbos: Nutrients, fire and diversity. Oxford University Press, Cape Town, 6-22.
39. Tyson PD, Partridge TC (2000) Evolution of Cenozoic climates. In: Partridge TC, Maud RM, editors. Cenozoic of Southern Africa. Oxford University Press, New York, 371-387.
40. Miller KG, Kominz MA, Browning JV, Wright JD, Mountain GS, et al. (2005) The Phanerozoic record of global sea-level change. Science 310: 1293-1298.
41. Siesser WG (1978) Leg 40 results in relation to continental shelf and onshore geology. In: Bolli HM, Ryan WBF, et al., editors. Initial Reports of the Deep Sea Drilling Project, Volume 40: Washington, U.S. Government Printing Offi ce, 40, 965-979.
42. Skelton P (2001) A complete guide to the freshwater fishes of Southern Africa. Struik Publishers, Cape Town.
43. Roos H (2004) Genetic diversity in the anabantids Sandelia capensis and S. bainsii: A phylogeographical and phylogenetic investigation. Unpublished MSc dissertation, University of Pretoria, South Africa.
44. Van Niekerk R (2004) Phylogeography of the Cape galaxias Galaxias zebratus. Unpublished MSc dissertation, University of Pretoria, South Africa.
45. Bermingham E, Martin AP, (1998) Comparative mtDNA phylogeography of neotropical freshwater fishes: testing shared history to infer the evolutionary landscape of lower Central America. Mol Ecol 7: 499-517.
46. Machordom A, Doadrio I, (2001) Evidence of a cenozoic Betic-Kabilian connection based on freshwater fish phylogeography (Luciobarbus, Cyprinidae). Mol Phylogenet Evol 18: 252-263.
47. Kocher TD, Thomas WK, Meyer A, Edwards SV, Paabo S, et al. (1989) Dynamics in the mitochondrial DNA evolution in animals: Amplification and sequencing with conserved primers. P Natl Acad Sci USA 86: 6196-6200.
48. Librado P, Rozas J, (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.
49. Posada D, Crandall KA, (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817-818.
50. Lanave C, Preparata G, Saccone C, Serio G, (1984) A new method for calculating evolutionary substitution rates. J Mol Evol 20: 86-93.
51. Posada D, Crandall KA, (2001) Selecting Models of Nucleotide Substitution: An Application to Human Immunodeficiency Virus 1 (HIV-1). Mol Biol Evol 18: 897-906.
52. Ronquist F, Huelsenbeck JP, (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
53. Rambaut A, Drummond AJ (2007) Tracer v.1.4. Available: http://beast.bio.ed.ac.uk/Tracer/.
54. Swofford DL (2003) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Assoc. Inc., Sunderland, Massachusetts.
55. Clement M, Posada D, Crandall KA, (2000) TCS: a computer program to estimate gene genealogies. Mol Ecol 9: 1657-1659.
56. Fu Y-X, (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking, and background selection. Genetics 147: 915-925.
57. Excoffier L, Laval G, Schneider S, (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinform 1: 47-50.
58. Drummond AJ, Rambaut A, (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7: 214.
59. Zardoya R, Doadrio I, (1999) Molecular evidence on the evolutionary and biogeographical patterns of European cyprinids. J Mol Evol 49: 227-237.
60. Bowen BW, Bass AL, Rocha LA, Grant WS, Robertson DR, (2001) Phylogeography of the trumpetfishes (Aulostomus): ring species complex on a global scale. Evolution 55: 1029-1039.
61. Perdices A, Doadrio I, (2001) The molecular systematics and biogeography of the European cobitids based on mitochondrial DNA sequences. Mol Phylogenet Evol 19: 468-478.
62. Near TJ, Benard M (2004) Rapid allopatric speciation in logperch darters (Percidae: Percina). Evolution 58 2798-2808.
63. Swartz ER (2005) Phylogeography, phylogenetics and evolution of the redfins (Teleostei, Cyprinidae, Pseudobarbus) in southern Africa. PhD thesis, Department of Genetics, University of Pretoria, South Africa.
64. Near TJ, Kassler TW, Koppelman JB, Dillman CB, Philipp D, (2003) Speciation in North American Black Basses, Micropterus (Actinopterygii: Centrachidae). Evolution 57: 1610-1621.
65. De Bruyn M, Mather PB, (2007) Molecular signatures of Pleistocene sea-level changes that affected connectivity among freshwater shrimp in Indo-Australian waters. Mol Ecol 16: 4295-4307.
66. Cooke GM, Chao NL, Beheregaray LB, (2012b) Marine incursions, cryptic species and ecological diversification in Amazonia: the biogeographic history of the croaker genus Plagioscion (Sciaenidae). J Biogeogr 39: 724-738.
67. Ruzzante DE, Walde SJ, Gosse JC, Cussac VE, Habit E, et al. (2008) Climate control on ancestral population dynamics: insight from patagonian fish phylogeography. Mol Ecol 17: 2234-2244.
68. Zemlak TS, Habit EM, Walde SJ, Battini MA, Adams EDM, et al. (2008) Across the southern Andes on fin: glacial refugia, drainage reversals and a secondary contact zone revealed by the phylogeographical signal of Galaxias platei in Patagonia. Mol Ecol 17: 5049-5061.
69. Martínez OA, Kutschker A, (2011) The 'Rodados Patagónicos' (Patagonian shingle formation) of Eastern Patagonia: environmental conditions of gravel sedimentation. Biol J Linn Soc 103: 336-345.
70. Ponce JF, Rabassa J, Coronato A, Borromei AM, (2011) Paleogeographic evolution of the Atlantic coast of Pampa and Patagonia since the Last Glacial Maximum to the Middle Holocene. Biol J Linn Soc 103: 363-379.
71. Ruzzante DE, Walde SJ, Macchi PJ, Alonso M, Barriga JP, (2011) Phylogeography and phenotypic diversification in the Patagonian fish Percichthys trucha: the roles of Quaternary glacial cycles and natural selection. Biol J Linn Soc 103: 514-529.
72. Cooke GM, Chao NL, Beheregaray LB, (2012c) Natural selection in the water: freshwater invasion and isolation by adaptation to water colour in the Amazonian pufferfish. J Evol Biol 25: 1305-132.
73. Cooke GM, Chao NL, Beheregaray LB, (2012d) Divergent natural selection with gene flow along major environmental gradients in Amazonia: insights from genome scans, population genetics and phylogeography of the characin fish Triportheus albus. Mol Ecol 21: 2410-2427.
74. Thacker CE, Unmack PJ, Matsui L, Rifenbark N, (2007) Comparative phylogeography of five sympatric Hypseleotris species (Teleostei: Eleotridae) in south-eastern Australia reveals a complex pattern of drainage basin exchanges with little congruence across species. J Biogeogr 34: 1518-1533.
75. Craw D, Burridge CP, Upton P, Rowe DL, Waters JM, (2008) Evolution of biological dispersal corridors through a tectonically active mountain range in New Zealand. J Biogeogr 35: 1790-1802.
76. Chakona A, Swartz ER, (2012) Contrasting habitat associations of imperilled endemic stream fishes from a global biodiversity hot spot. BMC Ecol 12: 19.
77. Avise JC (2000) Phylogeography: the history and formation of species. Harvard University Press, Cambridge, MA.
78. Donoghue MJ, Moore BR, (2003) Towards an integrative historical biogeography. Integr Comp Biol 43: 261-270.