The characterization of MHC Class II genes of the Nile crocodile (Crocodylus niloticus) : an investigation of mechanisms that shape genetic diversity in natural populations

Master Thesis


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University of Cape Town

Genes within the Major Histocompatibility Complex (MHC) of vertebrates code for proteins that are involved in antigen recognition and activation of the adaptive immune response. The hallmark of the MHC is the extremely high levels of polymorphism found at loci. A diverse array of mechanisms have been proposed to explain the generation and maintenance of diversity at MHC loci, including the processes of gene conversion, genetic drift and selection; in the presence of many pathogens balancing selection is thought to be the dominant mechanism by which selection operates. Amino acid substitutions within the peptide-binding region (PBR) of MHC genes further supports the hypothesis that positive selection enhances amino acid diversity in the PBR, such that natural selection will favour PBR diversity in natural populations. This study investigated mechanisms that shape genetic diversity of MHC class II genes in a natural population of the Nile crocodile, Crocodylus niloticus. Using PCR-cloning-sequencing methodology, allelic diversity at MHC Class II genes was investigated and provides evidence for at least two Class II 13 gene families in the Nile crocodile. The Crni-OAB family is homologous to classical Class II vertebrate genes; high levels of both allelic and amino acid diversity characterise this gene family and a strong signal of balancing selection acts to maintain functional diversity. The second family, Crni-OBB, most likely represents a non-classical Class II locus in crocodiles and was characterized by reduced levels of diversity. Analysis suggests that Crni-OBB loci have evolved in a divergent manner to those of the Crni-OAB as balancing selection was not detected within the putative PBR. Results from this study suggest that duplication followed by a recombination event has most likely led to the formation of two distinct crocodilian Class II 13 gene families. Secondly, the relative contributions of balancing selection and random genetic drift in the evolution of extant MHC diversity are examined in a natural population of the Nile crocodile. Temporal variation in allele frequencies for MHC and microsatellite loci was assessed in four successive cohorts of crocodiles from the Okavango Delta, Botswana. Results from this study suggest that a combination of short-term neutral forces such as random genetic drift, together with longer-term selection influence variation at Class II loci in the Okavango Nile crocodile. Loci within the MHC of the Nile crocodile appear to be evolving within a dynamic framework of selection, random genetic drift and recombination. This study is the first of its kind to investigate the respective influence of demography and selection on allele frequencies in a natural population of crocodilians.

Includes abstract.

Includes bibliographical references (leaves 66-77).