Thesis (Ph. D.)--University of Queensland, 2001. / Includes bibliographical references.

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Thesis (Ph. D.)--Oregon State University, 2010. / Printout. Includes bibliographical references (leaves 129-142). Also available on the World Wide Web.

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Cooperative species have long been the focus of much research due to the ‘special difficulty’ cooperation poses to the theory of evolution via natural selection. Despite this long history of scientific interest we actually know relatively little about the evolutionary genetics of cooperative mammalian species, especially in the wild. In this study I use long-term data from the Kalahari Meerkat Project to investigate some aspects of the evolutionary genetics of meerkats (Suricata suricatta). First, I reconstructed a genetically-validated pedigree of the Kalahari meerkat population. 1,494 meerkats (83% of the total known population) were genotyped at a panel of 18 highly variable microsatellite markers. This genetic data, in combination with phenotypic information and two different programs, COLONY2 and MASTERBAYES, was used to infer familial relationships. The resulting pedigree spanned seven generations and included 1,614 individuals of which 1,076 had both parents known. I conclude by discussing the particular merits of using COLONY2 to infer familial relationships for social animals such as meerkats. Second, I investigated the extent of inbreeding and inbreeding depression in early life traits in the Kalahari meerkat population. In the pedigree, 44% of individuals have non-zero (F>0) inbreeding coefficients. Although I found more inbreeding in meerkats than initially expected, there were few cases of inbreeding between very close relatives. Nonetheless, even low to moderate inbreeding appeared to result in inbreeding depression for pup mass at emergence, hind-foot length, growth until independence, and juvenile survival. I also found some tentative evidence for a positive effect of the social environment in ameliorating the effects of inbreeding depression. Third, I conducted a quantitative genetic analysis on mass, skull length, skull width, forearm length, and hind-foot length in up to five key meerkat life stage periods, while accounting for a number of fixed effects, including inbreeding coefficient. By attempting to apportion variance in these traits to a variety of sources I found that birth litter identity often explained much of the variance in morphological traits, although the magnitude of this effect appeared to decline with age. Furthermore, when birth litter was removed from models, the amount of variance explained by additive genetic effects tended to increase. Finally, I conducted a quantitative genetic analysis on two measures of cooperative care and on adult mass. Fixed effects, including inbreeding and relatedness coefficients, were also examined, which revealed that inbred individuals contribute more to pup-feeding, and that helper-recipient relatedness was negatively associated with baby-sitting. I found low heritable variation for baby-sitting (h2 = 0.10) and pup-feeding (h2 = 0.08), and higher heritable variation for adult body mass (h2 = 0.19). I also estimated the magnitude of non-genetic sources of variation in these traits and provide evidence for positive genetic correlations between baby-sitting and pup-feeding, and baby-sitting and adult mass.

A gene is imprinted when its expression is dependent on the sex of the parent from which it was inherited. An increasing number of studies are suggesting that imprinted genes have a major influence on medically, agriculturally and evolutionarily important traits, such as disease severity and livestock production traits. While some genes have a large effect on the traits of an individual, quantitative characters such as height are influenced by many genes and by the environment, including maternal effects. The interaction between these genes and the environment produces variation in the characteristics of individuals. Many quantitative characters are likely to be influenced by a small number of imprinted genes, but at present there is no general theoretical model of the quantitative genetics of imprinting incorporating multiple loci, environmental effects and maternal effects. This research develops models for the quantitative genetics of imprinting incorporating these effects, including deriving expressions for genetic variation and resemblances between relatives. Imprinting introduces both parent-of-origin and generation dependent differences in the derivation of standard quantitative genetic models that are generally equivalent under Mendelian expression. Further, factors such as epistasis, maternal effects and interactions between genotype and environment may mask the effect of imprinting in a quantitative trait. Maternal effects may also mimic a number of signatures in variance and covariance components that are expected in a population with genomic imprinting. This research allows a more comprehensive understanding of the processes influencing an individual�s characteristics.

A 10 x 10 factorial mating design and a ‘common-garden’ rearing approach were employed to examine genetic effects and heritability of growth, carcass-quality traits, and disease resistance, important production traits in the aquaculture of hybrid striped bass (♀ white bass, Morone chrysops, crossed with ♂striped bass, Morone saxatilis). Genotypes at four to ten nuclear-encoded microsatellites were used for parentage assignment and a general, linear-mixed model and a Restricted Maximum Likelihood (REML) algorithm were used to estimate variance components associated with dam, sire, and dam x sire interaction effects. Dam and sire effect on juvenile growth (weight, length and growth rates) were significant, whereas dam by sire interaction effect was not. Estimates of broad-sense heritability for growth, based on family means (h2 f), in dams ranged from 0.60 ± 0.20 to 0.82 ± 0.10 and in sires ranged from 0.43 ± 0.20 to 0.75 ± 0.18. High correlations were found between growth rates measured at two time intervals. Estimates of general combining ability for growth rates differed significantly among dams and among sires, whereas estimates of specific combining ability for each dam × sire combination did not differ significantly from zero. These results suggest that additive-effect genes contributed to the differences in juvenile growth. Dam and sire effect on fillet weight were significant; dam effect on liver weight and sire effect on total viscera weight were also significant. Dam and sire effect on hepatosomatic index and viscerasomatic index were significant, as was dam and sire interaction effect on viscerasomatic index. Phenotypic and genetics correlations between body weight and carcass-quality traits were high (0.85 - 1.00). Phenotypic correlations between body weight and standardized carcass-quality traits were positive but low, ranging from 0.07 to 0.19. Resistance to S. iniae was assessed in a challenge experiment, using the 10 dam x 10 sire factorial mating design. A significant effect of sire on resistance to S. iniae was found, and offspring from one sire had a 2.4 times higher probability of dying than offspring from the ‘average’ sire. Genetic effects on the immune-response parameters and on stress-response parameters assessed were non-significant.

A gene is imprinted when its expression is dependent on the sex of the parent from which it was inherited. An increasing number of studies are suggesting that imprinted genes have a major influence on medically, agriculturally and evolutionarily important traits, such as disease severity and livestock production traits. While some genes have a large effect on the traits of an individual, quantitative characters such as height are influenced by many genes and by the environment, including maternal effects. The interaction between these genes and the environment produces variation in the characteristics of individuals. Many quantitative characters are likely to be influenced by a small number of imprinted genes, but at present there is no general theoretical model of the quantitative genetics of imprinting incorporating multiple loci, environmental effects and maternal effects. This research develops models for the quantitative genetics of imprinting incorporating these effects, including deriving expressions for genetic variation and resemblances between relatives. Imprinting introduces both parent-of-origin and generation dependent differences in the derivation of standard quantitative genetic models that are generally equivalent under Mendelian expression. Further, factors such as epistasis, maternal effects and interactions between genotype and environment may mask the effect of imprinting in a quantitative trait. Maternal effects may also mimic a number of signatures in variance and covariance components that are expected in a population with genomic imprinting. This research allows a more comprehensive understanding of the processes influencing an individual�s characteristics.

When an individual interacts socially with a conspecific, their behavioural phenotype is affected directly by their genotype (‘direct genetic effect’, DGE), but may also be affected indirectly by the genotype of the opposing individual (‘indirect genetic effect’, IGE). While there is no doubt that IGEs occur in various organisms and contexts, it is unknown how properties of the environment may influence the relative magnitude of DGEs, IGEs, and their covariance. To gain insight into this, I examined territorial interactions in Drosophila melanogaster. Due to their short generation time and relatively simple care requirements, D. melanogaster has been used extensively in quantitative genetic research. Using offspring from a half-sib breeding design, I constructed an arena for documenting multiple dyadic territoriality assays with two sizes of a food resource. With this apparatus, 618 territoriality contests between 1,236 individuals were recorded and scored for four key aggressive behaviours. The results revealed significant genetic variation in how opponent effects on focal individuals changed between environments (i.e., genetic variation in the plasticity of IGEs). In addition, changes in DGEs and IGEs between environments were strongly and positively correlated (i.e., there was a DGE × IGE × environment interaction), although confirmation of this result in further studies is warranted because it was non-significant (P = 0.10), likely due to large uncertainties arising in part from some small variance component estimates. As a high throughput system for quantify IGEs in territoriality in Drosophila, my approach holds promise but there are issues to resolve, including automating phenotyping behaviors in place of manual scoring to enable many more trials. Additionally, modifications to increase humidity during trials might result in increased expression of certain territorial behaviours.

Understanding the maintenance of the variation that is typically observed in natural populations has been a central aim of evolutionary biology. In a feral population of Soay sheep on the island of Hirta, St. Kilda there is a phenotypic polymorphism for horns with males growing either normal or reduced (scurred) horns, and females growing either normal, scurred or no (polled) horns, with further variation in horn size within each of the horn types. This thesis examines the potential factors which maintain these polymorphisms. I first present an overview of the literature relating to the factors that potentially maintain variance in traits in natural populations. In chapter two I present an analysis that suggests that polymorphisms in both horn type and horn size may be maintained by trade-offs between allocation to reproductive success and survival in males, and by sexually antagonistic selection between males and females. In chapter three I test the hypothesis that female weaponry may convey an advantage in intrasexual conflicts over resources, rather than just being expressed as a consequence of genetic associations with the male phenotype. Chapter four examines the environmental factors which create variation between individuals in their horn length, revealing that individuals vary in response to the environment. In chapter five I investigate whether the temporally fluctuating environmental conditions of St. Kilda generate fluctuating selection on the horn length of normal-horned males, revealing that this mechanism constrains the evolution of horn length potentially maintaining variance. In chapter six I examine the genetic relationships between morphological traits, revealing that these relationships are dependent upon the environmental conditions experienced during the first year of life. Finally, I discuss the wider implications of these findings for our understanding of the maintenance of trait variation in the wild.