Dispersal and gene flow in the Southern African endemic Lacertid, Pedioplanis lineoocellata, based on microsatellite and capture-mark-recapture data

Daniels, Ryan Joseph (2014-12)

Thesis (MSc)--Stellenbosch University, 2014.

Thesis

ENGLISH ABSTRACT: Dispersal determines connectivity between populations within a species and is a regulator of genetic differentiation through gene flow. Although the necessity of dispersal for gene flow is clear, for many taxa the relationship between the two is not well understood. Gene flow, or a restriction thereof, may be inferred from population-level genetic divergence estimates. These measures are averages of contemporary and historic gene flow and as such they are not necessarily easily compared to measures of real-time dispersal. Changes in dispersal have been inferred from present day spatial genetic structure for many southern African taxa and further associated with environmental change events. Pedioplanis lineoocellata is a southern African endemic lacertid with a mitochondrial DNA structure that may have been the result of Plio-Pleistocene glacial climatic oscillations. As a wide-spread, open habitat species, P. lineoocellata is an excellent study species for examining the relationship between dispersal and gene flow. In the first data chapter, Chapter 2, nine new microsatellite markers are described for several populations for the purpose of examining gene flow and genetic structure in the species. The possibility of null alleles, population bottlenecks and high inbreeding are investigated as possible explanations for the detected deviation from Hardy-Weinberg equilibrium (HWE). The presence of null alleles and, at one population, relatively high inbreeding best explains the HWE deviations. While null allele frequencies were not excessively high, this caveat should be borne in mind when interpreting results. In Chapter 3 the microsatellite markers were used to assess the geographic genetic patterns for P. lineoocellata across the distribution of the two most wide-spread mitochondrial lineages and to test for evidence of hybridization at a point of clade contact in the Loeriesfontein area. Microsatellite genetic clusters did not match the mtDNA lineages, a possible result of gene flow between clades. However, measures of genetic differentiation and recent migration indicate only weak contemporary long distance gene flow. There was no evidence of genetic admixture at the Loeriesfontein area despite sympatric mtDNA lineages. The complexity of the geographic arrangement of the microsatellite clusters may be attributed to historic range contraction and expansion events for the species. In the last data chapter, evidence for an isolation-by-distance (IBD) pattern was examined within the most widespread mtDNA clade. Sampling over hundreds of kilometres produced an IBD pattern when using spatial autocorrelation while failure to detect IBD using the Mantel test was likely a result of the complex arrangement of microsatellite clusters. A combination of genetic data and demographic data was used to estimate the annual dispersal distances based on the neighbourhood size concept. Results indicated high levels of dispersal that covered distances of a few hundred metres, greater than is expected for a lacertid lizard. Strong dispersal propensity would have influenced gene flow and genetic structure found in this thesis and will further influence future responses to environmental changes for the species.

AFRIKAANSE OPSOMMING: Verspreiding (beweeglikheid) bepaal die verbinding tussen populasies van 'n spesie en is 'n reguleerder van genetiese differensiasie deur middel van gene vloei. Alhoewel die noodsaaklikheid van verspreiding vir baie taksa duidelik is, word die verhouding tussen die twee nie goed verstaan nie. Gene vloei, of 'n beperking daarvan, kan vanaf populasie-genetika divergensie skattings afgelei word. Hierdie maatreëls is gemiddeldes van die huidige en historiese gene vloei, en dus is dit nie maklik vergelykbaar met hedendaagse verspreiding nie. Veranderinge in die verspreiding is afgelei van die huidige geografiese genetiese struktuur vir baie Suider-Afrikaanse taksa en verdere veranderinge wat verband hou met omgewingsgebeurtenisse. Pedioplanis lineoocellata is „n Suider-Afrikaanse endemiese sand-akkedis, met n mitochondriale DNA struktuur wat die gevolg is van Plio-Pleistoseen glacial klimaat ossillasies. As 'n wydverspreide oop habitat spesie, is P. lineoocellata 'n geskikte studie spesies om die verhouding tussen die verspreding en gene vloei te ondersoek. In die eerste data hoofstuk, Hoofstuk 2, word nege nuwe mikrosatelliet merkers vir verskeie populasies beskryf met die doelwit om gene vloei en genetiese struktuur in hierdie spesie te ondersoek. Die moontlikheid van nul allele, populasie knelpunte en hoë-frekwensie inteling word ondersoek as moontlike verklarings vir die afwyking vanaf Hardy-Weinberg ewewig (HWE) wat opgemerk was. Hardy-Weinberg ewewig afwykings word die beste verduidelik deur die teenwoordigheid van nul allele en die relatiewe hoë inteling binne een spesifieke populasie. Alhoewel, alleelfrekwensies nie buitensporig hoog was nie, moet die bogenoemde maatstaf steeds in ag geneem word, wanneer resultate geïnterpreteer word. In Hoofstuk 3 word die mikrosatelliet merkers gebruik om die geografiese genetiese patrone oor die verspreiding van die mees wydverspreide mitochondriale linies te evalueer. Verdere toetse vir die bewys van verbasterigng by n geografiese kontakpunt van twee genetiese groepe in Loeriesfontein was gedoen.Resultate toon dat genetiese groepe nie ooreenstemmend is tussen mikrosatelliet en mtDNA data nie, en dat dit heelmoontlik n gevolg van genevloei tussen klades kan wees. In teenstryding, toon die maatstawwe van genetiese differensiasies en onlangse migrasie swak gene vloei oor langafstande. Daar is geen genetiese vermenging in die Loeriesfontein area nie, ongeag van die simpatriese verspreiding vir twee klades. Die kompleksiteit van die geografiese indeling van die mikrosatelliet groepe kan toegeskryf word aan historiese inkrimping en uitbreiding gebeuternisse van die spesie. In die laaste data hoofstuk, word 'n isolasie-deur-afstand (IBD) patroon binne die mees wydverspreide mtDNA klade ondersoek. Opnames oor honderde kilometres het n IBD patroon getoon wannner ruimtelike outokorrelasie gebruik was, terwyl die gebruik van n Mantel toets gevaal het om `n IBD patroon op te tel, en kan moontlik toegeskryf word aan die komplekse rangskikking van die mikrosatelliet groepe. 'n Kombinasie van genetiese en demografiese data was gebruik om die jaarlikse verspreiding afstande wat gebaseer is op die “buurt-omgewing” grootte konsep te skat. Resultate het hoë vlakke van verspreiding wat afstande van 'n paar honderd meter, groter as wat verwag word vir 'n san-akkedis getoon. Sterk verspreiding geneigdheid sou gene vloei en genetiese struktuur beïnvloed en sal ook verdere impak maak op hoe hierdie spesies in die toekoms sal reageer op omgewingsveranderinge.

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