Phylogenetic analyses in the african fish genus nothobranchius in relation to landscape evolution

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dc.contributor.advisorBellstedt, Dirk U.en_ZA
dc.contributor.advisorCotterill, Fenton P. D. en_ZA
dc.contributor.advisorSchliewen, Ulrich Kurten_ZA
dc.contributor.authorVan der Merwe, Pieter De Weten_ZA
dc.contributor.otherStellenbosch University. Faculty of Science. Dept. of Biochemistry.en_ZA
dc.date.accessioned2023-03-03T08:11:27Z
dc.date.accessioned2023-05-18T07:15:24Z
dc.date.available2023-03-03T08:11:27Z
dc.date.available2023-05-18T07:15:24Z
dc.date.issued2023-03
dc.descriptionThesis (PhD)--Stellenbosch University, 2023. en_ZA
dc.description.abstractENGLISH ABSTRACT: Nothobranchius is a genus of short-lived annual to semi-annual African freshwater fishes that are found in smaller seasonal ephemeral wetlands or pools and not in larger open lakes or non-seasonal river systems. The waterbodies in which they are found are situated on vertisol-type soils that have a large capacity to absorb and retain water which is slowly released upon drying. Eggs are fertilized and are deposited into the vertisol-type substrate of the waterbody. As the soil dries during the dry season cracks are formed and the eggs, which up to that point have been in an anoxic environment, are exposed to oxygen which stimulates them to develop. Several complicated pathways exist through which the eggs develop, which can lead to full development, or to several types of delayed development called diapauses. Some will remain dormant for subsequent rainy seasons ensuring that the species can survive extended droughts. Nothobranchius hatch quickly after the rainy season starts and subsequently grow very rapidly to reach maturity to repeat the life cycle. Sequencing of two mitochondrial and three nuclear genes of the majority of the species in Nothobranchius and appropriate outgroups was used to generate suitable sequence matrices which were analysed extensively using maximum likelihood and Bayesian Inference to generate robust phylogenies and dated phylogenies of the genus. A dated phylogeny was used in a biogeographic analysis to determine dispersal routes and establish that the ancestral area of Nothobranchius is in the Nilo-Sudan. Using the recently developed technique, double digest RAD sequencing, an even greater sequence data matrix of the species in Nothobranchius and appropriate outgroups was generated and analysed using the same techniques as described above. This resulted in an even more robust phylogenetic hypothesis for the genus. From this dated phylogeny landscape evolution in a tectonically active area on south central Africa could be inferred. Four key landscape evolutionary events in this area could be inferred and dated: (i) landscape warping, faulting and rifting in the Luapula river drainage, (ii), formation of the Upemba rift in the Lufira-Lualaba river drainage system, and (iii) formation of the Congo-Zambezi Watershed between the Kafue and Luapula drainage systems disrupting the ancient Palaeo-Chambeshi river drainage system, (iv) drainage of Palaeo Lake Mweru, from a previous maximum level of 1200 masl to the present-day level of 917 masl. Lastly, this research resulted in the identification of 15 new Nothobranchius species which were described in the course of this study. .en_ZA
dc.description.abstractAFRIKAANSE OPSOMMING: Nothobranchius is ‘n genus van kortlewende eenjarige tot halfjaarlikse Afrika-varswatervisse wat in kleiner seisoenale, nie-standhoudende vleilande of poele aangetref word en nie in groter oop mere of nie-seisoenale rivierstelsels nie. Die waterliggame waarin hulle gevind word, is geleë op vertisol-tipe gronde wat 'n kapasiteit het om water te absorbeer en te behou, wat stadig vrygestel word wanneer dit droog word. Eiers word bevrug en word in die vertisol-tipe substraat van die waterliggame begrawe. Soos die grond tydens die droë seisoen verdroog, word krake gevorm en die eiers, wat tot op daardie stadium in 'n anoksiese omgewing was, word aan suurstof blootgestel wat hulle stimuleer om te ontwikkel ,war kan lei tot volle of verskeie parsiële ontwikkelingstipes wat diapouses genoem word. Sommige sal rustend bly tot daaropvolgende reënseisoene om te verseker dat die spesies langdurige droogtes kan oorleef. Nothobranchius broei vinnig uit nadat die reënseisoen begin het en groei daarna baie vinnig om volwassenheid te bereik om die lewensiklus te herhaal. DNS-volgordebepalings van twee mitochondriale en drie nukluêre gene van die meerderheid van die spesies in Nothobranchius, en toepaslike buitegroepe, is gebruik om geskikte volgordematrikse te genereer wat breedvoerig ontleed is deur gebruik te maak van “maximum likelihood en “Bayesian Inference” om robuuste filogenieë en gedateerde filogenieë van die genus te genereer. ’n Gedateerde filogenie is gebruik om vas te stel dat die oorsprongsgebied van Nothobranchius in die Nilo-Soedan-streek is en dat hulle deur oorstromingsgebeurtenisse oor die landskap versprei is. Nuwe populasies is op vertisol-tipe grond waterliggame gevestig. Daaropvolgende landskap-evolusionêre veranderinge het daartoe gelei dat populasies geïsoleer is, wat gelei het tot allopatriese spesiasie en die vorming van nuwe afstammelinge en spesies. 'n Gedateerde filogenie is in 'n biogeografiese analise gebruik om verspreidingsroetes te bepaal en vas te stel dat die oorsprongebied van Nothobranchius in die Nilo-Soedan is. Deur gebruik te maak van relatief nuwe tegnologie, dubbelverteerde “RAD”-volgordebepalings is ‘n groter volgordematriks gegenereer en ontleed deur middel van die bogenoemde filogenetiese programmatuur. Dit het tot ‘n meer robuuste filogenetiese hipotese gelei vir die genus. Uit hierdie gedateerde filogenie kon landskapevolusie in 'n tektonies aktiewe gebied op suid-sentraal-Afrika afgelei word. Vier belangrike landskap-evolusionêre gebeurtenisse in hierdie gebied kon afgelei en gedateer word: (i) landskapsverbuiging, verskuiwings en skeuring in die Luapula- rivierdreineringstelsel, (ii), vorming van die Upemba-skeur in die Lufira-Lualaba- rivierdreineringstelsel, en (iii) ) vorming van die Kongo-Zambezi-waterskeiding tussen die Kafue- en Luapula-dreineringstelsels wat die antieke Palaeo-Chambeshi-rivierdreineringstelsel opgebreek het, (iv) dreinering van Palaeo-meer Mweru, vanaf 'n vorige maksimum vlak van 1200 meter bo seevlak tot die huidige vlak van 917 meter bo seevlak. Laastens het hierdie navorsing gelei tot die identifikasie van 15 nuwe Nothobranchius spesies deur die loop van die navorsing.af_ZA
dc.description.versionDoctoralen_ZA
dc.format.extentxxx, 423 : illustrations (some color), mapsen_ZA
dc.identifier.urihttp://hdl.handle.net/10019.1/127310
dc.language.isoen_ZAen_ZA
dc.publisherStellenbosch : Stellenbosch Universityen_ZA
dc.rights.holderStellenbosch Universityen_ZA
dc.subject.lcshPhylogenetic analysisen_ZA
dc.subject.lcshNothobranchius -- Geneticsen_ZA
dc.subject.lcshFishes -- Phylogenyen_ZA
dc.subject.lcshPhylogenetic analysesen_ZA
dc.subject.nameUCTDen_ZA
dc.titlePhylogenetic analyses in the african fish genus nothobranchius in relation to landscape evolutionen_ZA
dc.typeThesisen_ZA
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