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University of California Berkeley (2011)

Pathogen-mediated evolution of immunogenetic variation in plains zebra (Equus quagga) of southern Africa

Kamath, Pauline Lalitha

Titre : Pathogen-mediated evolution of immunogenetic variation in plains zebra (Equus quagga) of southern Africa

Auteur : Kamath, Pauline Lalitha

Université de soutenance : University of California Berkeley

Grade : Doctor of Philosophy (PhD) 2011

Résumé partiel
Investigating patterns of variability in functional protein-coding genes is fundamental to identifying the basis for population and species adaptation and ultimately, for predicting evolutionary potential in the face of environmental change. The Major Histocompatibility Complex (MHC), a family of immune genes, has been one of the most emphasized gene systems for studying selection and adaptation in vertebrates due to its significance in pathogen recognition and consequently, in eliciting host immune response. Pathogen evasion of host resistance is thought to be the primary mechanism preserving extreme levels of MHC polymorphism and shaping immunogenetic patterns across host populations and species. In this thesis, I examined the evolution of two equine MHC genes, DRA and DQA, over the history of the genus Equus and across free-ranging plains zebra (E. quagga) populations of southern Africa : Etosha National Park (ENP), Namibia and Kruger National Park (KNP), South Africa. Furthermore, I evaluated the relationships between the DRA locus and parasite intensity in E. quagga of ENP, to elucidate the mechanisms by which parasites have shaped diversity at the MHC. In equids, the full extent of diversity and selection on the MHC in wild populations is unknown. Therefore, in this study, I molecularly characterized MHC diversity and selection across equid species to shed light on its mode of evolution in Equus and to identify specific sites under positive selection. Both the DRA and DQA exhibited a high degree of polymorphism and more intriguingly, greater allelic diversity was observed at the DRA than has previously been shown in any other vertebrate taxon. Global selection analyses of both loci indicated that the majority of codon sites are under purifying selection which may be explained by functional constraints on the protein. However, maximum likelihood based codon models of selection, allowing for heterogeneity in selection across codons, suggested that selective pressures varied across sites. Furthermore, at the DQA locus, all sites predicted to be under positive selection were antigen binding sites, implying that a few selected amino acid residues may play a significant role in equid immune function. Observations of trans-species polymorphisms and elevated genetic diversity were concordant with the hypothesis that balancing selection is acting on these genes. Over the past half century, the role of neutral versus selective processes in shaping genetic diversity has been at the center of an ongoing dialogue among evolutionary biologists. To determine the relative influence of demography versus selection on the DRA and DQA loci, I contrasted diversity patterns of neutral and MHC data across the E. quagga populations of ENP and KNP. Neutrality tests, along with observations of elevated diversity and low differentiation across populations relative to nuclear intron data, provided further evidence for balancing selection at these loci among E. quagga populations. However, at the DRA locus, differentiation was comparable to results at microsatellite loci. Furthermore, zebra in ENP exhibited reduced levels of diversity relative to KNP due to a highly skewed allele frequency distribution that could not be explained by demography. These findings were indicative of spatially heterogeneous selection and suggested directional selection and local adaptation at the DRA locus.

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Page publiée le 1er février 2016, mise à jour le 30 septembre 2017