| Summary: | Determining the molecular mechanisms underlying variation in morphology, physiology and behaviour is a prime focus in the field of evolutionary genetics. This thesis investigates the molecular genetics of the unusual alternative male reproductive morphs of a shorebird, the ruff (Philomachus pugnax). Ruffs possess three distinct alternative reproductive morphs: i) territorial dark-plumed ‘Independents’, ii) non-territorial white-plumed ‘Satellites’, and iii) small unplumed female-like males called ‘Faeders’. Independent and satellite morph development is determined by an autosomal genetic polymorphism at the Satellite locus, and a dominant autosomal allele of unknown location also controls development of the female-mimicking faeders. To investigate the molecular genetics of alternative reproductive morphs in this non-model organism, I used several analytical approaches and molecular techniques, including: developing two microsatellite libraries and characterizing microsatellite markers, constructing a first-generation linkage map of the ruff genome, attempting to specifically map behavioural and plumage loci on this map, and sequencing the melanocortin-1 receptor (Mc1r) gene to investigate its role in plumage polymorphism.I characterize 102 microsatellite markers from the ruff and present 7 linkage groups and 5 single marker loci homologous to chicken and zebra finch chromosomes. Through linkage analysis, I identified the chromosomal location of Faeder, the locus that controls development of the female mimic morph and find it to be unlinked to the Satellite locus. This preliminary data appear to support a two-locus epistatic model of male morph determination, although further studies are needed to confirm this finding. I demonstrated that sequence variation in the coding region of Mc1r is not solely responsible for the dark and white plumage polymorphism in ruffs, and that other melanin–based colouration, regulatory, or structural genes likely contribute to the plumage polymorphism observed in this species. One non-synonymous SNP, His207Arg, located in the transmembrane region of Mc1r, may be under selection, with the possibility of a lethal in ruffs maintained by overdominance, or else gene duplication. This thesis broadens and brings together previous areas of research in the ruff and sets the stage for further genomic work addressing questions of evolutionary interest in this enigmatic shorebird.
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