PL EN


Preferencje help
Widoczny [Schowaj] Abstrakt
Liczba wyników
2012 | 42 | 4 |

Tytuł artykułu

DNA barcoding reveals micro-evolutionary changes and river system-level phylogeographic resolution of African silver catfish, Schilbe intermedius (Actinopterygii: Siluriformes: Schilbeidae) from seven populations across different African river

Warianty tytułu

Języki publikacji

EN

Abstrakty

EN
Background. Under the tropics, less than 40% of known fishes are identified to species-level. Further, the ongoing global change poses unprecedented threat to biodiversity, and several taxa are likely to go extinct even before they could be described. Traditional ecological theory suggests that species would escape extinction risk posed by global threats (e.g., climate change) only by migrating to new environments. In this study, we hypothesise that micro-evolutionary changes (evolution within species and populations) are also important mechanisms for the survival of Schilbe intermedius in Africa, a continent subjected to uneven distribution of climate severity. Materials and Methods. Using the mitochondrial cytochrome c oxidase subunit I (COI) gene, known as animal DNA barcode, we tested this hypothesis by analysing the genetic diversity and phylogenetic relations between seven populations of S. intermedius across different African river systems. Results. We reveal a clear geographical patterning in genetic variations, with three clear clusters (southern Africa, eastern Africa, and western Africa). In southern Africa, the South African population is distinct from that of Namibia and Botswana. In addition, within Nigerian populations of silver catfish, two sub-clusters emerged from two isolated river systems. We suggest that the phylogeographic pattern within African silver catfish populations mirror the past effects of selection and gene flow, and that the split within Nigerian silver catfish populations might be the result of micro-evolutionary adaptive responses to local selection pressures. Conclusion. We suggest that the strong genetic difference in African silver catfish among geographically isolated river systems might be the result of in situ micro-evolutionary adaptive responses to changing environments, and that DNA barcode has potential beyond species delimitation.

Słowa kluczowe

Wydawca

-

Rocznik

Tom

42

Numer

4

Opis fizyczny

p.307–320,fig.,ref.

Twórcy

  • Department of Zoology, African Centre for DNA Barcoding (ACDB), Kingsway Campus, P.O.Box 524, Auckland Park, 2006, Republic of South Africa
  • Department of Zoology, African Centre for DNA Barcoding (ACDB), Kingsway Campus, P.O.Box 524, Auckland Park, 2006, Republic of South Africa
autor
  • Department of Botany and Plant Biotechnology, University of Johannesburg, African Centre for DNA Barcoding (ACDB), Kingsway Campus, P.O.Box 524, Auckland Park, 2006, Republic of South Africa
autor
  • Department of Botany and Plant Biotechnology, University of Johannesburg, African Centre for DNA Barcoding (ACDB), Kingsway Campus, P.O.Box 524, Auckland Park, 2006, Republic of South Africa

Bibliografia

  • Abban E.K., Skibinski D.O.F. 1988. Protein variation In Schilbe mystus (L.) and Eutropius niloticus (Rüppel) (Pisces siluriformes) in the Volta Basin of Ghana, West Africa.Aquaculture Research 19 (1): 25–37.DOI: 10.1111/j.1365-2109.1988.tb00330.x
  • Alfaro M.E., Holder M.T. 2006. The posterior and the prior In Bayesian phylogenetics. Annual Review of Ecology,Evolution, and Systematics 37: 19–42.DOI: 10.1146/annurev.ecolsys.37.091305.110021
  • Ashley M.V., Wilson M.F., Pergams O.R.W., O’Dowd D.J.,Gende S.M., Brown J.S. 2003. Evolutionarily enlightened management. Biological Conservation 111 (2): 115–123.DOI: 10.1016/S0006-3207(02)00279-3
  • Bell-Cross G. 1972. The fish fauna of the Zambezi River System. Arnoldia (Rhodesia) 5 (29) 1–19.
  • Bell-Cross G., Minshull J.L. 1988. The fishes of Zimbabwe.Trustees of the National Museums and Monuments of Zimbabwe, Harare.
  • Bowmaker A.P., Jackson P.N., Jubb R.A. 1978. Freshwater fishes. Pp. 1181–1230 In:WergerM.J.A. (ed.) Biogeography and ecology of southern Africa. W.H. Junk, The Hague.
  • Brown J.H., Kodric-Brown A. 1977. Turnover rates in insula biogeography: Effect of immigration on extinction. Ecology 58 (2): 445–449. DOI: 10.2307/1935620
  • Brown S.D.J., Collins R.A., Boyer S., Lefort M.-C.,Malumbres-Olarte J., Vink C.J., Cruickshank R.H. 2012. Spider: An R package for the analysis of species identity and evolution, with particular reference to DNA barcoding.Molecular Ecology Resources 12 (3): 562–565.DOI: 10.1111/j.1755-0998.2011.03108.x
  • Caddy J., Garibaldi L. 2000. Apparent changes in the trophic composition of wild marine harvest: The perspective from FAO capture database. Ocean and Coastal Management 43:615–655.
  • Dankwa H.R., Abban E.K., Teugels G.G. 1999. Freshwater fishes of Ghana: identification, distribution, ecological and economic importance. Koninklijk Museum voor Midden-Afrika Tervuren, België. Annalen Zoloögische Wetenschappen. Vol. 283.
  • De Vos L. 1984. Preliminary data of a systematic revision of the African species of the family Schilbeidae (Pisces,Siluriformes). Revue de Zoologie Africaine 98: 424–433.
  • De Vos L., Leveque C. 1983. Etude systématique et morphologique du genre Eutropius en Afrique de L’ouest (Pisces, Schilbeidae). Revue de Zoologie Africaine 97 (3):469–532.
  • De Vos L., Skelton P. 1990. Name changes for two common African catfishes. Rehabilitation of Schilbe intermedius Rüppel, 1832 (Siluriformes, Schilbeidae). Cybium 14 (4):323–326.
  • Edgar R.C. 2004. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32 (5): 1792–1797.DOI: 10.1093/nar/gkh340
  • Endler J.A. 1986. Natural selection in the wild. Princeton University Press, Princeton, NJ, USA.
  • Ernst A., Becker S., Wollenzien U.I.A., Postius C. 2003.Ecosystem-dependent adaptive radiation of picocyanobacteria inferred from 16S rRNA and ITS-1 sequences analysis. Microbiology 149 (1): 217–228.DOI: 10.1099/mic.0.25475-0
  • Faith D.P. 1992. Conservation evaluation and phylogenetic diversity. Biological Conservation 61 (1): 1–10.DOI: 10.1016/0006-3207(92)91201-3
  • Fitch W.M. 1971. Towards defining the course of evolution:minimum change for a specific tree topology. Systematic Zoology 20 (4): 406–416.
  • Forest F., Grenyer R., Rouget M., Davies T.J., Cowling R.M.,Faith D.P., Balmford A., Manning J.C., Procheş Ş., Van der Bank M., Reeves G., Hedderson T.A.J., Savolainen V. 2007. Preserving the evolutionary potential of floras in biodiversity hotspots. Nature 445 (7129): 757–760.DOI: 10.1038/nature05587.
  • Froese R., Pauly D. (eds.) 2012. FishBase. [version 04/2012] http://www.fishbase.org
  • Gaigher I.G., Pott R.Mc.C. 1973. Distribution of fishes In southern Africa. South African Journal of Science 69 (1):25–27.
  • Geber M.A., Dawson T.E. 1993. Evolutionary responsem of plants to global change. Pp. 179–197. In: Kareiva P.M.,Kingsolver J.G., Huey R.B. (eds.). Biotic interactions and global change. Sinauer, Sunderland, MA, USA.
  • Gilpin M.E., Soulé M.E. 1986. Minimum viable populations:processes of species extinction. Pp. 19–34. In: Soule M.E.(ed.). Conservation biology: the science and scarcity of diversity. Sinauer, Sunderland, MA, USA.
  • Goldstein P.Z., Desalle R. 2003. Calibrating phylogenetic species formation in a threatened insect using DNA from historical specimens. Molecular Ecology 12 (7): 1993–1998.DOI: 10.1046/j.1365-294X.2003.01860.x
  • Greenwood P.H. 1983. The zoogeography of African freshwater fishes: bioaccountancy or biogeography? Pp. 179–199.In: Sims R.W., Price J.H., Whalley P.E.S. (eds.) Evolution,time and space: The emergence of the biosphere. Academic Press, London, UK.
  • Hajibabaei M., Janzen D.H., Burns J.M., Hallwachs W.,Hebert P.D.N. 2006a. DNA barcodes distinguish species of tropical Lepidoptera. Proceedings of the National Academy of Sciences of the United States of America 103 (4):968–971.DOI: 10.1073/pnas.0510466103
  • Hajibabaei M., Smith M.A., Janzen D.H., Rodriguez J.J.,Whitfield J.B., Hebert P.D.N. 2006b. A minimalist barcode can identify a specimen whose DNA is degraded.Molecular Ecology Notes 6 (4): 959–964.DOI: 10.1111/j.1471-8286.2006.01470.x
  • Hajibabaei M., Singer G.A.C., Clare E.L., Hebert P.D.N.2007. Design and applicability of DNA arrays and DNA barcodes in biodiversity monitoring. BMC Biology 5: 24.DOI: 10.1186/1741-7007-5-24
  • Hardman M. 2005. The phylogenetic relationships among nondiplomystid catfishes as inferred from mitochondrial cytochrome b sequences; the search for the ictalurid sister taxon (Otophysi: Siluriformes). Molecular Phylogenetics and Evolution 37 (3): 700–720.DOI: 10.1016/j.ympev.2005.04.029,
  • Hebert P.D.N., Stoeckle M.Y., Zemlak T.S., Francis C.M.2004. Identification of birds through DNA barcodes. PLoS Biology 2 (10): E312.DOI: 10.1371/journal.pbio.0020312
  • Hillis D.M., Bull J.J. 1993. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis.Systematic Biology 42 (2): 182–92.DOI: 10.1093/sysbio/42.2.182
  • Hughes J.B., Daily G.C., Ehrlich P.R. 1997. Population diversity: Its extent and extinction. Science 278 (5338): 689–692.DOI: 10.1126/science.278.5338.689
  • Kembel S.W., Cowan P.D., Helmus M.R., Cornwell W.K.,Morlon H., Ackerly D.D., Blomberg S.P., Webb C.O.2010. Picante: R tools for integrating phylogenies and ecology.Bioinformatics 26 (11): 1463–1464.DOI: 10.1093/bioinformatics/btq166
  • Kettlewell M.G. 1972. The evolution of melanism. Oxford University Press, Oxford, UK.
  • Kinnison M.T., Hendry A.P. 2001. The pace of modern life II:from rates of contemporary microevolution to pattern and process. Genetica 112–113 (1): 145–164.DOI: 10.1023/A:1013375419520
  • Loarie S.R., Duffy P.B., Hamilton H., Asner G.P., Field C.B.,Ackerly D.D. 2009. The velocity of climate change. Nature 462 (7276): 1052–1055.DOI: 10.1038/nature08649
  • Mace G., Masundire H., Baillie J.E.M. 2005. Biodiversity.Pp. 77–122. In: Hassan R., Scholes R., Ash N. (eds.)Ecosystems and human well-being: Current state and trends:findings of the condition and trends working group. Island Press, Washington, DC, USA.
  • Meusnier I., Singer G.A.C., Landry J.-F., Hickey D.A.,Hebert P.D.N., Hajibabaei M. 2008. A universal DNA mini-barcode for biodiversity analysis. BMC Genomics 9:1–4.DOI: 10.1186/1471-2164-9-214
  • Nelson J.S. 1994. Fishes of the world, 3rd edn. Wiley, New York, NY, USA.
  • Nwani C.D., Becker S., Braid H.E., Ude E.F., Okogwu O.I.,Hanner R. 2011. DNA barcoding discriminates freshwater fishes from southeastern Nigeria and provides river systemlevel phylogeographic resolution within some species.Mitochondrial DNA 22 (S1): 43–51.DOI: 10.3109/19401736.2010.536537
  • Olwoch J.M., Van Jaarsveld A.S., Scholtz C.H., Horak I.G.2007. Climate change and the genus Rhipicephalus (Acari:Ixodidae) in Africa. Onderstepoort Journal of Veterinary Research 74 (1): 45–72.DOI: 10.4102/ojvr.v74i1.139
  • Paradis E., Claude J., Strimmer K. 2004. Ape: analyses of phylogenetics and evolution in R language. Bioinformatics 20 (2): 289–290.DOI: 10.1093/bioinformatics/btg412
  • Partridge T.C., Maud R.R. 1987. Geomorphic evolution of southern Africa since the Mesozoic. South African Journal of Geology 90 (2): 165–184.
  • Pimm S.L., Russell G.J., Gittleman J.L., Brooks T.M. 1995.The future of biodiversity. Science 269 (5222): 347–350.DOI: 10.1126/science.269.5222.347
  • Posada D. 2008. jModelTest: phylogenetic model averaging.Molecular Biology and Evolution 25 (7): 1253–1256.DOI: 10.1093/molbev/msn083
  • Posada D., Buckley T.R. 2004. Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Systematic Biology 53 (5): 793–808.DOI: 10.1080/10635150490522304
  • Radulovici A.E., Archambault P., Dufresne F. 2010. DNA Barcodes for marine biodiversity: Moving fast forward?Diversity 2 (4): 450–472.DOI: 10.3390/d2040450
  • Rice K.J., Emery N.C. 2003. Managing microevolution:Restoration in the face of global change. Frontiers in Ecology and the Environment 1 (9): 469–478.
  • Roberts T.R. 1975. Geographical distribution of African freshwater fishes. Zoological Journal of the Linnean Society 57 (4):249–319.DOI: 10.1111/j.1096-3642.1975.tb01893.x
  • Ronquist F., Huelsenbeck J.P. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (12): 1572–1574.DOI: 10.1093/bioinformatics/btg180
  • Sandel B., Arge L. Dalsgaard B., Davies R.G., Gaston K.J.,Sutherland W.J., Svenning J.-C. 2011. The Influence of late quaternary climate-change velocity on species endemism. Science 334 (6056): 660–664.DOI: 10.1126/science.1210173
  • Sanderson M.J. 2002. Estimating absolute rates of molecular evolution and divergence times: A penalized likelihood approach. Molecular Biology and Evolution 19 (1):101–109.
  • Stockwell C.A., Hendry A.P., Kinnison M.T. 2003.Contemporary evolution meets conservation biology.Trends in Ecology and Evolution 18 (2): 94–101.DOI: 10.1016/S0169-5347(02)00044-7
  • Swofford D.L. 2003. PAUP*4.0: Phylogenetic Analysis Rusing Parsimony (andOther Methods). Sinauer Associates Inc.,Sunderland, MA, USA.
  • Tajima F. 1983. Evolutionary relationship of DNA sequences in finite populations. Genetics 105 (2): 437–460.
  • Trauth M.H., Maslin M.A., Deino A., Strecker M.R. 2005.Late cenozoic moisture history of East Africa. Science 309 (5743): 2051–2053.DOI: 10.1126/science.1112964
  • Van der Bank F.H., Engelbrecht G.D., Sauer-Gürth H.,Wink M., Mulder P.F.S. 1998. Allozyme and DNA sequence data support speciation between northern and southern populations of the silver catfish Schilbe intermedius (Rüppel, 1832). Comparative biochemistry and physiology. Part A: Molecular and Integrative Physiology 120 (3): 531–543.DOI: 10.1016/S1095-6433(98)10063-6
  • Wandeler P., Hoeck P.E.A., Keller L.F. 2007. Back to the future: museum specimens in population genetics. Trends In Ecology Evolution 22 (12): 634–642. DOI: 10.1016/j.tree.2007.08.017
  • Ward R.D., Zemlak T.S., Innes B.H., Last P.R., Hebert P.D.N.2005. DNA barcoding Australia’s fish species.Philosophical Transactions of the Royal Society Part B:Biological Sciences 360 (1462): 1847–1857.DOI: 10.1098/rstb.2005.1716
  • Wellington J.H. 1955. Southern Africa—A geographic study.Vol. 1. Physical geography. Cambridge University Press,Cambridge, UK.
  • Western D. 2001. Human-modified ecosystems and future evolution.Proceedings of the National Academy of Sciences of the United States of America 98 (10): 5458–5465.DOI: 10.1073/pnas.101093598
  • Wilcox T.P., Zwickl D.J., Heath T.A., Hillis D.M. 2002.Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support. Molecular Phylogenetics and Evolution 25 (2):361–371.DOI: 10.1016/S1055-7903(02)00244-0
  • Willis C.G., Ruhfel B., Primack R.B., Miller-Rushing A.J.,Davis C.C. 2008. Phylogenetic patterns of species loss in Thoreau’s woods are driven by climate change. Proceedings of the National Academy of Sciences USA 105 (44):17029–17033.DOI: 10.1073/pnas.0806446105
  • Willis C.G., Ruhfel B.R., Primack R.B., Miller-Rushing A.J.,Losos J.B., Davis C.C. 2010. Favourable climate change response explains non-native species’ success in Thoreau’s Woods. PLoS ONE 5 (1): e8878.DOI: 10.1371/journal.pone.0008878
  • Yessoufou K., Daru B.H., Davies T.J. 2012 Phylogenetic patterns of extinction risk in the Eastern Arc Ecosystems, an African biodiversity hotspot. PLoS ONE 7 (10): e47082.DOI: 10.1371/journal.pone.0047082

Uwagi

PL
Rekord w opracowaniu

Typ dokumentu

Bibliografia

Identyfikatory

Identyfikator YADDA

bwmeta1.element.agro-ac1c9993-4f38-4575-9b7b-ff74bf8aba4f
JavaScript jest wyłączony w Twojej przeglądarce internetowej. Włącz go, a następnie odśwież stronę, aby móc w pełni z niej korzystać.