Development is the process by which genes build organisms. It thus determines how genetic variation is translated into phenotypic variation. The dynamics of evolution are therefore determined not only by the action of selection and drift, but also by the processes by which organisms are built. I present a general model with which to study how selection acts on a developmental program. This model explains, and clarifies, the trend towards conservatism in early development. Furthermore, it predicts that this conservatism will be reduced under certain environmental conditions, namely when fitness functions are fluctuating. This leads to the prediction of the pattern of nearshore innovation seen in the fossil record. A more careful test of the theory requires a system in which we have some understanding of the details of development. I provide this in the form of a model of shell growth in mollusks. This model predicts shell form as a function of the interactions between shell producing tissues during growth. Using this system, I test the prediction of the general model that characters that are not correlated with, but not independent of, many other characters should evolve slowly. This prediction is upheld by data gathered from 8 genera of marine gastropods.

Environmental effects on mutation have been documented for many years but have concentrated on agents that directly interact with DNA. Mutation research in its early history investigated a variety of more mundane environmental factors at levels that inhibited biological function and attempted to characterize their mutagenicity. This thesis revisits these old questions armed with more modern methods. It consists of one review chapter and three experimental chapters. The review chapter proposes that biological organization itself acts to direct mutation pressure, and that many mutations are context dependent within this organization. Experimentally, I performed an approximately 1,500-generation mutation accumulation (MA) experiment using the budding yeast Saccharomyces cerevisiae as an evolutionary genetic model. This thesis investigates the rates and distribution of effects of new mutations on fitness when they accumulate under a moderate salt stress. The first experimental section describes the production of the MA lines, measures the diploid fitness traits mitotic growth rate and sporulation, and uses changes in fitness among replicate lines to infer mutation parameters affecting these traits. Mutation rate estimates for these traits were roughly doubled in the salt stress treatment. The proportion of beneficial mutations was high for mutations affecting sporulation in both MA treatments but zero for growth rate. Measurements of haploid viability and haploid growth rate on strains derived from the diploid MA lines were used to infer mutation parameters. Mutation rates affecting haploid growth were ten-fold higher in our salt-line derivatives than those derived from the non-stress treatment. Variance component analysis identified a large fraction of genetic variation arising from differences among haploids within the same tetrad. This component was significantly larger in the salt MA treatment than the non-stress treatment. MA lines were subjected to a novel weak-acid stress. Mutation rate estimates were 38-fold higher in the salt MA treatment when lines were tested under acid stress. Cross-environmental genetic correlation for growth in acid stress versus standard media was significantly different between the two MA treatments suggesting that both MA environment and test environment are important factors when considering mutational effects on fitness.

Thesis (Ph. D.)--University of Missouri-Columbia, 2004. / Typescript. Vita. Includes bibliographical references (leaves 103-129). Also available on the Internet.

Thesis (Ph. D.)--University of Missouri-Columbia, 2004. / Typescript. Vita. Includes bibliographical references (leaves 103-129). Also available on the Internet.

published_or_final_version / Dentistry / Doctoral / Doctor of Philosophy

The <i>Jaera albifrons </i>species group of intertidal isopods is characterised by strong sexual isolation mediated by female discrimination against heterospecific male tactile-stimulatory courtship behaviour.  This is the first study to examine the genetic basis of traits involved in tactile mediated sexual isolation.  To determine the genetic architecture of male secondary sexual characters (species-specific hair traits carried on the legs of males and a carpus leg-segment shape difference) associated with sexual isolation, experimental hybrid populations of <i>J. albifrons </i>and <i>J. ischiosetosa </i>were used to construct AFLP-based genetic linkage maps.  A number of chromosomal differences (Robertsonian fusions) between the parental species were shown to be associated with reduced hybrid fertility.  A quantitative trait locus (QTL) mapping study revealed that the number of hairs and carpus shape have a complex genetic basis, involving a number of QTL showing dominance, epistasis and possible pleiotropic effects.  These QTL mapped largely to putative regions of restricted recombination, especially chromosomal rearrangements. The qualitative difference, however, was shown to be controlled by a single (or several closely linked ) QTL that did not map to a region of restricted recombination.  These findings suggest that introgressive hybridisation played an important role in speciation in the <i>J. albifrons </i>species group and that chromosomal rearrangements allowed incipient species to persist in the face of ongoing gene flow.  The extensive sharing of a single 16S rDNA mitochondrial haplotype supports the assertion that gene flow has been important.  The reinforcement of premating isolating by natural selection against costly hybridisation is suggested as the mechanism of speciation between these species.  The complete dominance of the <i>J. albifrons </i>allele at the QTL controlling the qualitative difference between the species supports this model of speciation.

Hornbills (Aves: family Bucerotidae) are a charismatic group of Palaeotropical birds recognised for their distinctive morphology (casque) and behaviour (nest-sealing). Hornbill diet, habitat use, distribution and social system display pronounced interspecific variation, and their mutualistic interactions with tropical fruits provide vital ecosystem services. A wide range of species of hornbills across the Afrotropics, Indo-Malaya and Melanesia are of conservation concern. However, the evolutionary history of hornbills remains unclear and there are conflicting hypotheses about their origin, tempo of diversification and biogeography. Despite a comprehensive cladistic analysis of phenotypic data, there are unresolved taxonomic uncertainties within the family, and although a gradual accumulation of molecular data has revealed interesting phylogenetic relationships, methodological limitations, and incomplete sampling, has left gaps and produced incongruent results. Hence the evolutionary framework against which to interpret the diversity of this group is incomplete. The aim of this thesis was to construct a well-resolved molecular phylogeny of hornbills, and to use it to address longstanding questions about the evolution and diversification of these remarkable birds. This thesis presents a broad phylogenetic and biogeographic analysis of the family Bucerotidae, based on a coalescence of molecular methods and comparative analyses, largely using historical samples and recently-developed bioinformatic approaches. I provide the first complete species-level molecular phylogeny of hornbills, derived from nuclear adenylate kinase 1 intron 5 and mitochondrial (mtDNA) cytochrome b genes, and also a comprehensive mtDNA phylogeny covering 98% of the taxa, with extensive sampling of Asian geo-isolates. Using these two phylogenetic trees, I sought to determine the tempo of divergence, trace the evolution of traits, identify ancestral areas and colonisation routes, and also calculate genetic divergence. In this part of the work, I stress the importance of (1) using historical samples, (2) calibrating time-trees with fossil and molecular anchor-points, and (3) the use of a complete tree to test models of diversification and reconstruct ancestral states. My findings confirm the monophyly of Bucerotidae, showing nearly distinct African and Asian lineages, with relatively congruent topologies across different phylogenetic methods and genes. In turn, these gene trees were comparable with previous cladistic analysis based on phenotypic data. As a result, I was able to resolve some taxonomic issues and propose generic changes. Comparative analyses of social behaviour revealed that cooperative breeding is an ancestral trait, and its evolution in hornbills (in contrast with some other taxa) is associated with stable environments in combination with frugivory, territoriality and reduced body size. Analysis of the evolution of diet with diversification showed that the shift to frugivory from faunivorous African ancestors influenced the rapid diversification of Afro-Asian forest hornbills, facilitated by their preference for humid forests and mutualistic interactions with , hornbill-dispersed fruits (HDF). This dispersal of frugivorous lineages via the Palaeotropical Biotic Interchange promoted colonisation of Asia, with Sundaland being the centre of radiation for continental and insular Asian species. The gradual eastward colonisation from India to Melanesia matches palaeo-tectonic events that allowed dispersal across Huxley's, Wallace's and Lydekker's lines, and was congruent with historical biogeography of some HDFs. Finally, I used a combined analysis of genetic divergence and a standard scoring system for phenotypic data of Asian geo-isolates to provide evidence for quantitative delineation of species and propose changes in conservation status. My findings reveal the evolutionary history of horn bills from their emergence in the Late Oligocene from African origins, with a switch to frugivory influencing successful colonisation of hornbills and HDFs in Asian forests, which combined to promote sociality. Overall, this thesis demonstrates that access to novel environments and innovations to ecological niche facilitate rapid diversification in an avian lineage, and that this process is further promoted by the interplay of these birds in complex mutualistic interactions with their food, as well as palaeo-climatic and palaeo-tectonic changes.

No description available.

Thesis (doctoral)--Swedish University of Agricultural Sciences, 2004. / Thesis documentation sheet inserted. Appendix reprints five manuscripts and papers co-authored with others. Includes bibliographical references. Also issued electronically via World Wide Web in PDF format; online version lacks appendix.

The transition from cross-fertilization to predominant self-fertilization is considered the most common evolutionary transition in flowering plants. This change in mating system has profound influences on the amounts and patterns of genetic diversity within and among populations, and on key genetic and demographic processes. The main goal of my thesis is to determine the molecular population genetic consequences of this transition in the annual neotropical aquatic plant Eichhornia paniculata (Pontederiaceae) using DNA sequence from individuals sampled from throughout the species’ geographic range. Populations exhibit a wide range of mating patterns associated the evolutionary breakdown of tristyly facilitating specific contrasts between outcrossing and selfing populations. Analysis of molecular variation supported the hypothesis of multiple origins of selfing, including the evolution of two morphologically distinct selfing variants from Central America and the Caribbean. A survey of 10 nuclear loci from 225 individuals sampled from 25 populations demonstrated the joint influence of mating system, population size and demographic bottlenecks in affecting patterns of nucleotide variation. Small selfing populations exhibited significantly lower genetic diversity compared with larger outcrossing and mixed mating populations. There was also evidence for higher population differentiation and a slower decay of linkage disequilibrium in predominately selfing populations from the Caribbean region. Coalescent simulations of the sequence data indicated a bottleneck associated with colonization of the Caribbean from Brazil ∼125,000 years ago. To investigate the consequences of transitions from outcrossing to selfing across the genome, I used high-throughput, short-read sequencing to assemble ~27,000 ESTs representing ∼24Mbp of sequence. Characterization of floral transcriptomes from this dataset identified 269 genes associated with floral development, 22 of which were differentially expressed in three independently derived selfing lineages compared to an outcrossing genotype. Evidence for relaxed selection in selfing lineages was obtained from an analysis of a subset of ~8000 orthologous sequences from each genotype, as predicted by theory. Selfing genomes showed an increase in the proportion of nonsynonymous to synonymous changes and relaxation of selection for codon usage bias. My thesis represents the most detailed investigation to date of the molecular population genetic consequences of intraspecific variation in the mating systems of plants.