Phylogenetic and morphological analysis of the Afroedura nivaria (Reptilia: Gekkonidae) species complex in South Africa

Makhubo, Buyisile Getrude (2013-03)

Thesis (MSc)--Stellenbosch University, 2013.

Thesis

ENGLISH ABSTRACT: The Afroedura nivaria complex is one of the six recognized species complexes within a southern African endemic genus, Afroedura. The A. nivaria complex is a morphologically conservative group of medium-sized geckos endemic to South Africa though they are unevenly distributed in the Eastern Cape, Free State and KwaZulu-Natal provinces. The complex comprises the following five species: A. nivaria (Boulenger 1894), A. amatolica (Hewitt 1925), A. karroica (Hewitt 1925), A. tembulica (Hewitt 1926) and A. halli (Hewitt 1935). These nocturnal and rupicolous geckos shelter in narrow rock crevices on outcrops. It is currently unknown whether a) the described species are valid and b) if additional lineages are present on isolated outcrops. I investigated the hypothesis that endemics with a narrow distribution, that is, A. amatolica and A. tembulica are valid species but that isolated populations in the widespread species (A. nivaria, A. karroica and A. halli) demonstrate genetic variation at the species level. Fragments of two mitochondrial genes (16S rRNA and ND4) and a single nuclear marker (KIAA) were sequenced and analysed using Bayesian inference, maximum parsimony and maximum likelihood. All analyses strongly supported the genetic distinctiveness of the described species. The A. nivaria complex is not monophyletic, A. karroica appeared to be outside the species complex and A. pondolia (thought to be outside the A. nivaria complex) consistently nested within A. nivaria complex. Additional clades recovered in the phylogeny within A. halli and A. nivaria had large genetic divergences and no spatial overlap. Narrowly distributed A. amatolica showed to have two highly diverged clades. Clades recovered in the phylogeny highlight geographical structuring. These findings suggest the existence of up to four additional cryptic lineages within the complex. I used morphometric data (ecologically relevant morphological traits) to investigate whether the genetic lineages would present morphological conservatism. Multivariate analyses of 19 variables showed variation within the A. nivaria species complex was accounted for mostly by differences in locomotor apparatus (limbs and feet) and head dimensions. These traits are mostly related to microhabitat usage and/or dietary specialization in lizards. There were no significant differences for body dimensions between species within the complex, indicative of morphological conservatism. It appears genetic divergence has been achieved among the different clades within A. nivaria complex, but with much similarity in phenotype being retained because of fragmented but similar habitats occupied.

AFRIKAANSE OPSOMMING: Die Afroedura nivaria kompleks is een van ses herkende spesies komplekse binne die endemiese suidelike Afrika genus, Afroedura. Die A. nivaria kompleks is ‘n morfologiese konserwatiewe groep bestaande uit medium grootte geitjies endemies tot Suid Afrika, alhoewel hulle oneweredig verspreid is in die Oos Kaap, Vrystaat en Kwazulu-Natal provinsies. Die kompleks bestaan uit die volgende vyf spesies: A. nivaria (Boulenger 1894), A. amatolica (Hewitt 1925), A. karroica (Hewitt 1925), A. tembulica (Hewitt 1926) and A. halli (Hewitt 1935). Hierdie geitjies kom snags voor en skuil tussen nou skeure op klip koppies. Dit is tans onbekend of a) die beskryfde spesies geldig is en b) of die addisionele afstammelinge voorkom op geisoleerde koppies. Met die studie het ek die hipotese ondersoek dat endemiese spesies met ‘n noue verspreiding (A. amatolica en A. tembulica) geldige spesies is, maar dat spesies met ‘n wye verspreiding (A. nivaria, A. karroica and A. halli) genetiese variasie op spesie vlak wys. Fragmente van twee mitochondriale gene (16S rRNA and ND4) en ‘n enkele nuklêre merker (KIAA) se basispaaropeenvolgingsdata was verkry en geanaliseer deur Bayesian inferensie, maksimum parsimonie en maksimum waarskynlikheid. Alle analise het die genetiese kenmerkendheid van die beskryfde spesies sterk ondersteun. Die A. nivaria kompleks is monofileties, A. karroica het geblyk om buite die spesies kompleks voor te kom en A. pondolia (voorheen beskryf as buite die A. nivaria kompleks) het voortdurend binne die A. nivaria kompleks voorgekom. Addisionele klades afkomstig vanaf die filogenië van A. halli en A. nivaria het vir beide spesies groot genetiese divergensie met geen ruimtelike oorvleuling gewys. Afroedura amatolica, met sy noue verspreiding, het twee hoogs divergente klades getoon. Die klades onthul deur die filogenie beklemtoon ‘n geografiese struktuur. Hierdie bevindings blyk die bestaan van tot vier ekstra kriptiese afstammelinge binne die kompleks. Ek het morfometriese data (ekologiese relevante morfologiese eienskappe) gebruik om vas te stel of die genetiese afstammelinge morphologies konserwatief sal wees. Meerveranderlike analises op 19 veranderlikes het variasie binne die A. nivaria spesies kompleks getoon. Hierdie veranderinge was meestal gevind in die beweeglikheidsapparatuur (ledemate en voete) en kop dimensies. Die verskeie eienskappe hou meestal verband met die mikrohabitatte wat gebruik word en/of dieët spesialisering in akkedisse. Daar was geen noemenswaardige verskille in liggaamsdimensies tussen spesies in die kompleks nie, beduidend op ‘n konserwatiewe morfologie. Dit wil blyk of genetiese divergensie tussen die verskeie klades van die A. nivaria kompleks bewerkstellig is met ooreenstemming in die fenotipes as gevolg van gefragmenteerde maar soortgelyke habitat verbruik.

Please refer to this item in SUNScholar by using the following persistent URL: http://hdl.handle.net/10019.1/79808
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