Elucidating patterns of Major Histocompatibility Complex Polymorphism in the Trinidadian Guppy (Poecilia reticulata) using Next Generation Sequencing

Abstract

This thesis describes patterns of Major Histocompatibility Complex (MHC) evolution in natural populations of the guppy (Poecilia reticulata), using Next Generation Sequencing (NGS). I have proposed a redefinition of the molecular and bioinformatic approaches used to gather NGS MHC sequence data, and the theoretical considerations required for accurate interpretation of MHC diversity. The various bioinformatic approaches that are currently implemented in NGS MHC analysis are critically reviewed to provide a clear understanding of how such data should be analyzed. A novel molecular and bioinformatics procedure is introduced to estimate MHC genotypes from NGS data, which performs better than previously used approaches. I also explore the application of NGS to estimate both allelic and loci copy number variation (CNV) among guppy populations. Results suggest that both forms of CNV are widespread among guppies and the complex nature of CNV likely represents an important source of variation both within and among guppy populations. In addition, I provide novel evidence to suggest complex interactions between MHC polymorphism, parasite infection, and male colour, which are implicit in mate choice and believed to be honest signals of immunocompetence. Comparisons among geographic distributions of MHC supertypes and their constitutional alleles provide support for a novel model for how MHC evolution is governed. This identifies a combination of stabilizing selection acting on MHC supertypes (groups of functionally similar/identical MHC alleles) and random genetic drift coupled with Red Queen processes operating on alleles within supertypes. Patterns of population differentiation may be misinterpreted to represent high levels of local adaptation at the allelic level if supertypes are ignored. I propose that MHC supertypes are an important unit of selection and patterns of MHC CNV (or haplotype variation) are likely maintained by balancing selection acting on individual loci (or groups of loci), driven by variable parasite communities. This is summarized as the ‘stabilized supertypes – balanced loci’ model of MHC evolution. Evidence suggests not only that guppies provide a unique system to investigate the interplay between parasite mediated natural selection and sexual selection, but also that the guppy is an ideal model species that can greatly improve our understanding of MHC evolution in natural populations.