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Indiana University-Purdue University Indianapolis (IUPUI) / Chromosomal mechanisms of sex determination vary greatly in phylogenetically closely related species, indicative of rapid evolutionary rates. Sex chromosome karyotypes are generally conserved within families; however, many species have derived sex chromosome configurations. Insects display a plethora of sex chromosome systems due to rapid diversification caused by changes in evolutionary processes within and between species. A good example of such a system are insects in the blow fly family Calliphoridae. While cytogenetic studies observe that the karyotype in blow flies is highly conserved (five pairs of autosomal chromosomes and one pair sex chromosome), there is variation in sex determining mechanisms and sex chromosome structure within closely related species in blow flies. The evolutionary history of sex chromosomes in blow fly species have not been fully explored. Therefore, the objective of this research was to characterize the sex chromosome structures in four species of blow flies and investigate the selective forces which have played a role in shaping the diverse sex chromosome system observed in blow flies. The blow fly species used in this study are Phormia regina, Lucilia cuprina, Chrysomya rufifacies and Chrysomya albiceps. Phormia regina,and Lucilia cuprina have a heteromorphic sex chromosome system and are amphogenic (females produce both male and female offspring in equal ratio). In contrast, Chrysomya rufifacies and Chrysomya albiceps, have a homomorphic sex chromosome system, are monogenic (females produce unisexual progeny), have two types of females (arrhenogenic females – male producers and thelygenic females – female producers), and sex of the offspring is determined by the maternal genotype. To accomplish these tasks, a total of nine male and female individual draft genomes for each of the four species (including three individual draft genomes of Chrysomya rufifacies – male, and the two females) were sequenced and assembled providing genomic data to explore sex chromosome evolution in blow flies. Whole genome analysis was utilized to characterize and identify putative sex chromosomal sequences of the four blow fly species. Genomic evidence confirmed the presence of genetically differentiated sex chromosomes in P. regina and L. cuprina; and genetically undifferentiated sex chromosomes in C. rufifacies and C. albiceps. Furthermore, comparative analysis of the ancestral Dipteran sex chromosome (Muller element F in Drosophila) was determined to be X-linked in P. regina and L. cuprina contributing to sex chromosome differentiation but not sex-linked in C. rufifacies and C. albiceps. Evolutionary pressures are often quantified by the ratio of substitution rates at non-synonymous (dN) and synonymous (dS) sites. Substitution rate ratio analysis (dN/dS) of homologous genes indicated a weaker purifying selection may have contributed to the loss of sex-linked genes in Muller element F genes of the undifferentiated sex chromosome as compared to the differentiated sex chromosome system. Overall, the results presented herein greatly expands our knowledge in sex chromosome evolution within blow flies and will reinforce the study of sex chromosome evolution in other species with diverse sex chromosome systems.

Rapidly accumulating genomic data as a result of high-throughput sequencing has necessitated development of efficient computational methods to decode the biological information underlying these data. DNA composition varies across structurally or functionally different regions of a genome as well as those of distinct evolutionary origins. We adapted an integrative framework that combines a top-down, recursive segmentation algorithm with a bottom-up, agglomerative clustering algorithm to decipher compositionally distinct regions in genomes. The recursive segmentation procedure entails fragmenting a genome into compositionally distinct segments within a statistical hypothesis testing framework. This is followed by an agglomerative clustering procedure to group compositionally similar segments within the same framework. One of our main objectives was to decipher distinctive evolutionary patterns in sex chromosomes via unraveling the underlying compositional heterogeneity. Application of this approach to the human X-chromosome provided novel insights into the stratification of the X chromosome as a consequence of punctuated recombination suppressions between the X and Y from the distal long arm to the distal short arm. Novel "evolutionary strata" were identified particularly in the X conserved region (XCR) that is not amenable to the X-Y comparative analysis due to massive loss of the Y gametologs following recombination cessation. Our compositional based approach could circumvent the limitations of the current methods that depend on X-Y (or Z-W for ZW sex determination system) comparisons by deciphering the stratification even if only the sequence of sex chromosome in the homogametic sex (i.e. X or Z chromosome) is available. These studies were extended to the plant sex chromosomes which are known to have a number of evolutionary strata that formed at the initial stage of their evolution, presenting an opportunity to examine the onset of stratum formation on the sex chromosomes. Further applications included detection of horizontally acquired DNAs in extremophilic eukaryote, Galdieria sulphuraria, which encode variety of potentially adaptive functions, and in the taxonomic profiling of metagenomic sequences. Finally, we discussed how the Markovian segmentation and clustering method can be made more sensitive and robust for further applications in biological and biomedical sciences in future.

Much of modern population genetics revolves around neutral genetic differences among individuals, populations, and species. In this dissertation, I study how sex-specific life history traits affects neutral diversity levels within populations (polymorphism) and between species (divergence) on autosomes and sex chromosomes. In chapter 1, I consider the effects of sex specific life histories, and particularly generation times, on substitution rates along the great ape phylogeny. Using a model that approximates features of the mutational process in most mammals, and fitting the model on data from pedigree-studies in humans, I predict the effects of life history traits on specific great ape lineages. As I show, my model can account for a number of seemingly disparate observations: notably, the puzzlingly low X-to-autosome ratios of substitution rates in humans and chimpanzees and differences in rates of autosomal substitutions among great ape lineages. The model further suggests how to translate pedigree-based estimates of human mutation rates into split times among extant apes, given sex-specific life histories. In so doing, it largely bridges the gap reported traditional fossil-based estimates of mutation rates, and recent pedigree-based estimates. In chapter 2, I consider the effects of sex- and age- dependent mortalities, fecundities, reproductive variances and mutation rates on polymorphism levels in humans. Using a coalescence framework, I provide closed formulas for the expected polymorphism rate, accounting for life history effects. These formulas generalize and simplify previous models. Applying the model to humans, my results suggest that the effects of life history – and of sex differences in generation times in particular – attenuate how changes in historical population sizes affect X to autosome polymorphism ratios. Applying these results to observations across human populations, I find that life history effects and demographic histories can largely explain the reduction in X to autosome polymorphism ratios outside Africa. More generally, my work elucidates the major role of sex-specific life history traits – and male and female generation times in particular – in shaping patterns of neutral genetic diversity within and between species.

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Thesis (Ph. D.)--University of Chicago, Committe on Genetics, December 2003. / Includes bibliographical references. Also available on the Internet.

No description available.

Thesis (Ph.D.)--University of Florida, 2004. / Typescript. Title from title page of source document. Document formatted into pages; contains 102 pages. Includes Vita. Includes bibliographical references.

Sex chromosomes represent a unique part of the genome in many eukaryotic organisms. They differ significantly from autosomes by their evolution, specific features, and meiotic behaviour. Recent advances in the knowledge of sex chromosomes in non-model organisms have been largely enabled by modern cytogenetic methods. The present study explores several topics related to sex chromosomes in Lepidoptera, the largest group of animals with female heterogamety, using methods of molecular cytogenetics, immunocytogenetics, and molecular biology. These topics include physical mapping of chromosomes by BAC-FISH, molecular differentiation and composition of the W chromosome, differences in the evolution of the W and Z chromosome, and meiotic sex chromosome inactivation. The results obtained brought new information not only about the W and Z chromosomes in Lepidoptera, but also about the evolution and specific features of sex chromosomes in general.

6 Abstract Scincoidean lizards, i.e. cordylids, gerrhosaurids, skinks and xantusiids, are known for their remarkable ecological and morphological variability. It was hypothesized that, at least in skinks, sex determining systems are highly variable as well. In the other three families, evidence for presence or absence of sex chromosomes has been scarce, with two species of night lizards with ZZ/ZW sex chromosomes being the exception. In this thesis, conventional and molecular cytogenetic methods, including C-banding, fluorescence in situ hybridization (FISH) with probes for telomeric motifs and rDNA loci and comparative genomic hybridization (CGH) were used to identify cytogenetically distinguishable sex chromosomes. Although most studied species showed no sex-specific differences by cytogenetic examination, some did. Tracheloptychus petersi has accumulations of rDNA loci on a pair of macrochromosomes and a pair of microchromosomes in males, while again on a pair of macrochromosomes and a single microchromosome in females. This distribution suggests a ZZ/ZW system in this species, which is the first report of sex chromosomes in any gerrhosaurid lizard. In Zonosaurus madagascariensis, CGH was able to identify the W chromosome in females, which is the second report of sex chromosomes in this family....