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Research Papers

Molecular phylogenetics reveals a complex history underlying cryptic diversity in the Bush Squeaker Frog (Arthroleptis wahlbergii) in southern Africa

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Pages 83-97 | Received 08 Mar 2018, Accepted 25 Aug 2018, Published online: 16 Nov 2018

References

  • Bandelt HJ, Forster P, Röhl A. 1999. Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution 16: 37–48. doi: 10.1093/oxfordjournals.molbev.a026036
  • Blackburn DC. 2008. Biogeography and evolution of body size and life history of African frogs: phylogeny of squeakers (Arthroleptis) and long-fingered frogs (Cardioglossa) estimated from mitochondrial data. Molecular Phylogenetics and Evolution 49: 806–826. doi: 10.1016/j.ympev.2008.08.015
  • Blackburn DC. 2009. Description and phylogenetic relationships of two new species of miniature Arthroleptis (Anura: Arthroleptidae) from the Eastern Arc Mountains of Tanzania. Breviora 517: 1–17. doi: 10.3099/0006-9698-515.1.1
  • Blackburn DC, Gvoždík V, Leaché A D. 2010. A new squeaker frog (Arthroleptidae: Arthroleptis) from the mountains of Cameroon and Nigeria. Herpetologica 66: 335–348. doi: 10.1655/HERPETOLOGICA-D-10-00015.1
  • Blackburn DC, Measey, GJ. 2009. Dispersal to or from an African biodiversity hotspot? Molecular Ecology 18: 1904–1915. doi: 10.1111/j.1365-294X.2009.04156.x
  • Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution 17: 540–552. doi: 10.1093/oxfordjournals.molbev.a026334
  • Channing A. 2004. Arthroleptis wahlbergi In: Minter LR, Burger M, Harrison JA, Braack HH, Bishop PJ, Kloepfer D (Eds), Atlas and Red Data Book of the Frogs of South Africa, Lesotho and Swaziland. SI/MAB Series #9. Washington, DC: Smithsonian Institution. pp. 52–53.
  • Cowling RM, Procheş Ş, Partridge TC. 2009. Explaining the uniqueness of the Cape flora: Incorporating geomorphic evolution as a factor for explaining its diversification. Molecular Phylogenetics and Evolution 51: 64–74. doi: 10.1016/j.ympev.2008.05.034
  • da Silva JM, Tolley KA. 2017. Diversification through ecological opportunity in dwarf chameleons. Journal of Biogeography 44: 834–847. doi: 10.1111/jbi.12966
  • deMenocal PB. 1995. Plio-Pleistocene African climate. Science 270: 53–59. doi: 10.1126/science.270.5233.53
  • deMenocal PB. 2004. African climate change and faunal evolution during the Pliocene–Pleistocene. Earth and Planetary Science Letters 220: 3–24. doi: 10.1016/S0012-821X(04)00003-2
  • Dupanloup I, Schneider S, Excoffier L. 2002. A simulated annealing approach to define the genetic structure of populations. Molecular Ecology: 2571–2581. doi: 10.1046/j.1365-294X.2002.01650.x
  • du Preez L, Carruthers V. 2018. Frogs of Southern Africa. A Complete Guide. Struik Nature. Cape Town.
  • Eeley HA, Lawes MJ, Piper SE. 1999. The influence of climate change on the distribution of indigenous forest in KwaZulu-Natal, South Africa. Journal of Biogeography 26: 595–617. doi: 10.1046/j.1365-2699.1999.00307.x
  • Elith J, Phillips SJ, Hastie T, Dudík M, Chee YE, and Yates CJ. 2011. A statistical explanation of MaxEnt for ecologists. Diversity and Distributions 17: 43–57. doi: 10.1111/j.1472-4642.2010.00725.x
  • ESRI. 2014. ArcGIS Desktop. 10.3 Edn. Redlands, CA: Environmental Systems Research Institute
  • Excoffier L, Laval G, Schneider S. 2005. Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evolutionary Bioinformatics 1: 117693430500100003. doi: 10.1177/117693430500100003
  • FitzSimons V. 1930. Descriptions of new South African Reptilia and Batrachia, with distribution records of allied species in the Transvaal Museum collection. Annals of the Transvaal Museum 14: 20–48.
  • Frost DR. 2018. Amphibian Species of the World: an Online Reference. Version 6.0. American Museum of Natural History, New York, USA. Electronic Database accessible at http://research.amnh.org/herpetology/amphibia/index.html. [Accessed 28 February 2018].
  • Harper EB, Measey GJ, Patrick DA, Menegon M, Vonesh JR. 2010. Field Guide to the Amphibians of the Eastern Arc Mountains and Coastal Forests of Tanzania and Kenya. Nairobi, Kenya: Camerapix International.
  • Hijmans RJ, Cameron SE, Parra JL, Jones PG, and Jarvis A. 2005. Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology 25: 1965–1978. doi: 10.1002/joc.1276
  • Jongsma GFM, Barej MF, Barratt CD, Burger M, Conradie W, Ernst R, et al. 2018. Diversity and biogeography of frogs in the genus Amnirana (Family Ranidae) across sub-Saharan Africa. Molecular Phylogenetics and Evolution 120: 274–285. doi: 10.1016/j.ympev.2017.12.006
  • Huelsenbeck JP, Ronquist F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17(8): 754–755. doi: 10.1093/bioinformatics/17.8.754
  • Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, et al. 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 2812: 1647–1649. doi: 10.1093/bioinformatics/bts199
  • Kissling WD, Eiserhardt WL, Baker WJ, Borchsenius F, Couvreur TLP, Balslev H, Svenning J-C. 2012. Cenozoic imprints on the phylogenetic structure of palm species assemblages worldwide. Proceedings of the National Academy of Sciences 109: 7379–7384.
  • Kumar S, Stecher G, Tamura K. 2016. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 33: 1870–1874. doi: 10.1093/molbev/msw054
  • Laurent RF. 1961. Notes on some South African amphibians. Publications de l’Université de l’État a Élisabethville 1: 197–209.
  • Lawes M J, Eeley H A, Piper SE. 2000. The relationship between local and regional diversity of indigenous forest fauna in KwaZulu-Natal Province, South Africa. Biodiversity and Conservation 9: 683–705. doi: 10.1023/A:1008989609581
  • Lawes MJ, Eeley HAC, Findlay NJ, Forbes D. 2007. Resilient forest faunal communities in South Africa: a legacy of palaeoclimatic change and extinction filtering? Journal of Biogeography 34: 1246–1264. doi: 10.1111/j.1365-2699.2007.01696.x
  • Lawson LP. 2013. Diversification in a biodiversity hot spot: Landscape correlates of phylogeographic patterns in the African spotted reed frog. Molecular Ecology 22: 1947–1960. doi: 10.1111/mec.12229
  • Loveridge A. 1954. New frogs of the genera Hyperolius and Arthroleptis from South Africa. Annals of the Natal Museum 13: 95–99.
  • Matthee CA, Tilbury CR, Townsend T. 2004. A phylogenetic review of the African leaf chameleons: genus Rhampholeon (Chamaeleonidae): the role of vicariance and climate change in speciation. Proceedings of the Royal Society of London, Series B. 271: 1967–75.
  • Measey GJ, Galbusera P, Breyne P. Matthysen E. 2007. Gene flow in a direct-developing, leaf litter frog between isolated mountains in the Taita Hills, Kenya. Conservation Genetics 8: 1177–1188. doi: 10.1007/s10592-006-9272-0
  • Measey G, Rödder D, Green S, Kobayashi R, Lillo F, Lobos G, Rebelo R, and Thirion J-M. 2012. Ongoing invasions of the African clawed frog, Xenopus laevis: a global review. Biological Invasions 14: 2255–2270. doi: 10.1007/s10530-012-0227-8
  • Measey GJ, Tolley KA. 2011. Sequential fragmentation of Pleistocene forests in an East Africa biodiversity hotspot: chameleons as a model to track forest history. PLOSOne 6 (10): e26606 doi: 10.1371/journal.pone.0026606
  • Meier R, Shiyang K, Vaidya G, Ng PK. 2006. DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. Systematic Biology 55: 715–728. doi: 10.1080/10635150600969864
  • Miller MP. 2005. Alleles in space (AIS): Computer software for the joint analysis of interindividual spatial and genetic information Journal of Heredity 96: 722–724. doi: 10.1093/jhered/esi119
  • Mittermeier RA, Turner WR, Larsen FW, Brooks TM, Gascon C. 2011. Global biodiversity conservation: the critical role of hotspots. In: Zachos FE, Habel JC (Eds), Biodiversity Hotspots. Berlin, Heidelberg: Springer. pp. 3–22.
  • Mittermeier RA, Robles Gil P, Hoffmann M, Pilgrim J, Brooks T, Goettsch Mittermeier C, Lamoreux J, da Fonseca GAB. 2004. Hotspots revisited. Earth’s Biologically Richest and Most Endangered Terrestrial Ecoregions. Mexico City: CEMEX.
  • Mucina L, Geldenhuys CJ. 2006. Afrotemperate, subtropical and azonal forests. In: Mucina L, Rutherford MC (Eds), The Vegetation of South Africa, Lesotho and Swaziland. Strelitzia 19. Pretoria: South African National Biodiversity Institute. pp. 584–614
  • Mucina L, Rutherford MC. 2006. The Vegetation of South Africa, Lesotho and Swaziland. Strelitzia 19. Pretoria: South African National Biodiversity Institute.
  • Mucina L, Scott-Shaw CR, Rutherford MC, Camp KGT, Matthews WS, Powrie LW, Hoare DB. 2006. Indian Ocean Coastal Belt. In: Mucina L, Rutherford MC (Eds), The Vegetation of South Africa, Lesotho and Swaziland. Strelitzia 19. Pretoria: South African National Biodiversity Institute. pp. 568–582.
  • Otto-Bliesner BL, Brady EC, Clauzet G, Tomas R, Levis S, and Kothavala Z. 2006. Last glacial maximum and Holocene climate in CCSM3. Journal of Climate 19: 2526–2544. doi: 10.1175/JCLI3748.1
  • Palumbi SR, Martin A, Romano S, McMillan WO, Stice L, Grabowski G. 2002. The simple fool’s guide to PCR version 2. University of Hawaii.
  • Pearson RG, Raxworthy CJ, Nakamura M, and Townsend Peterson A. 2007. Predicting species distributions from small numbers of occurrence records: a test case using cryptic geckos in Madagascar. Journal of Biogeography 34: 102–117. doi: 10.1111/j.1365-2699.2006.01594.x
  • Peterson AT, and Nyari AS. 2008. Ecological niche conservatism and Pleistocene refugia in the thrush-like mourner, Schiffornis sp., in the neotropics. Evolution 62: 173–183.
  • Phillips SJ, and Dudík M. 2008. Modelling of species distributions with Maxent: new extensions and a comprehensive evaluation. Ecography 31: 161–175. doi: 10.1111/j.0906-7590.2008.5203.x
  • Posada D. 2008. jModelTest: phylogenetic model averaging. Molecular Biology and Evolution 25(7): 1253–1256. doi: 10.1093/molbev/msn083
  • Poynton JC. 1964. Amphibia of southern Africa: a faunal study. Annals of the Natal Museum 17: 1–334.
  • Poynton JC, Broadley DG. 1985. Amphibia Zambesiaca 1. Scolecomorphidae, Pipidae, Microhylidae, Hemisidae, Arthroleptidae. Annals of the Natal Museum 26: 503–553.
  • Rambaut A, Drummond AJ. 2007. Tracer v1. 4: MCMC trace analyses tool. http://tree.bio.ed.ac.uk/software/tracer.
  • Schreiner C, Rödder D, Measey GJ. 2013. Using modern models to test Poynton’s predictions African Journal of Herpetology 62: 49–62. doi: 10.1080/21564574.2013.794865
  • Schweiger S, Naumann B, Larson JG, Möckel L, Müller H. 2017. Direct development in African squeaker frogs (Anura: Arthroleptidae: Arthroleptis) reveals a mosaic of derived and plesiomorphic characters. Organisms Diversity and Evolution 17: 693–707. doi: 10.1007/s13127-017-0335-5
  • Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688–2690. doi: 10.1093/bioinformatics/btl446
  • Stamatakis A, Hoover P, Rougemont J. 2008. A rapid bootstrap algorithm for the RAxML web servers. Systematic Biology 57: 758–771. doi: 10.1080/10635150802429642
  • Struck TH, Feder JL, Bendiksby M, Birkeland S, Cerca J, Gusarov VI, et al. 2018. Finding evolutionary processes hidden in cryptic species. Trends in Ecology and Evolution 33: 153–163. doi: 10.1016/j.tree.2017.11.007
  • Swets JA. 1988. Measuring the accuracy of diagnostic systems. Science 240: 1285–1293. doi: 10.1126/science.3287615
  • Talavera G, Castresana J. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic Biology 56: 564–577. doi: 10.1080/10635150701472164
  • Tilbury CR, Tolley KA. 2009. A new species of dwarf chameleon (Sauria; Chamaeleonidae, Bradypodion Fitzinger) from KwaZulu-Natal, South Africa with notes on recent climatic shifts and their influence on speciation in the genus. Zootaxa 57: 43–57.
  • Tolley KA, Chase BM, Forest F. 2008. Speciation and radiations track climate transitions since the Miocene Climatic Optimum: A case study of southern African chameleons. Journal of Biogeography 35: 1402–1414. doi: 10.1111/j.1365-2699.2008.01889.x
  • Tolley KA, Tilbury CR, Measey GJ, Menegon M, Branch WR, Matthee CA. 2011. Ancient forest fragmentation or recent radiation? Testing refugial speciation models in chameleons within an African biodiversity hotspot. Journal of Biogeography 38: 1748–1760. doi: 10.1111/j.1365-2699.2011.02529.x
  • Venter JA, Conradie W. 2015. A checklist of the reptiles and amphibians found in protected areas along the South African Wild Coast, with notes on conservation implications. Koedoe 57: 1–25. doi: 10.4102/koedoe.v57i1.1247
  • Wang B, Xie F, Li J, Wang G, Li C, Jiang J. 2017. Phylogeographic investigation and ecological niche modelling of the endemic frog species Nanorana pleskei revealed multiple refugia in the eastern Tibetan Plateau. PeerJ 5: e3770. doi: 10.7717/peerj.3770
  • West A G, Bond W J, Midgley JJ. 2000. Soil carbon isotopes reveal ancient grassland under forest. South African Journal of Science 96: 252–253.
  • Zachos J, Pagani M, Sloan L, Thomas E, Billups K. 2001. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 292: 686–693. doi: 10.1126/science.1059412
  • Zimkus BM, Lawson LP, Barej MF, Barratt CD, Channing A, Dash KM et al. 2017. Leapfrogging into new territory: How Mascarene ridged frogs diversified across Africa and Madagascar to maintain their ecological niche. Molecular Phylogenetics and Evolution 106: 254–269. doi: 10.1016/j.ympev.2016.09.018

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