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<p>Sex chromosomes have evolved independently multiple times in plants and animals. Sex chromosome evolution theory predicts the gradual degeneration of the sex-specific sex chromosome due to suppression of recombination, which lowers the efficacy of natural selection. Suppressed recombination also acts to resolve sexual conflict and ensure proper segregation of sex-specific alleles. However, sex chromosome degeneration is not always the case, and evolutionarily old, and young, but homomorphic (nondegenerate) sex chromosomes have been observed. African clawed frogs (<em>Xenopus</em> and <em>Silurana</em>) have homomorphic sex chromosomes due to a recent turnover event. However, occasional recombination between the sex chromosomes may contribute to the maintenance of homomorphic sex chromosomes in African clawed frogs. Mechanisms that prevent divergence of sex chromosomes may be related to polyploidization, which is frequently observed in African clawed frogs. The studies herein construct a phylogenetic framework to test alternative hypotheses for selection on sex-linked and autosomal genes involved in sex determination, map sex chromosomes and compare sex chromosomes across African clawed frogs. I have also explored the relationship between phenomena like recent turnover events, recombination and polyploidization to sex chromosome degeneration (or lack thereof). In this dissertation, I have discussed the potential for multiple mechanisms of sex determination and the unique pseudoautosomal nature of sex chromosomes within this group of frogs. This body of work provides a comprehensive study of sex chromosomes in a group lacking phylogenetic resolution and sheds light on the origin and evolution of sex chromosomes in other organisms.</p> / Doctor of Philosophy (PhD)

<div>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. </div><div>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.</div><div><br></div>

Thesis (MScMedSc (Obstetrics and Gynaecology))--University of Stellenbosch, 2005. / CHAPTER 1 presents comprehensive background information regarding all aspects addressed in this thesis. Special attention was given to literature on paternal influences on embryonic development, the role of sperm RNA, sperm chromatin and sperm functional aspects i.e. morphology and acrosomal status and size. The experimental design and all relevant methods used during the study as well as the material that were used are presented in CHAPTER 2. The results of the different techniques and evaluations are provided in CHAPTER 3. It was found that 70% of the embryos that showed no developmental potential were Y-chromosome bearing embryos. The sperm selection process for ICSI based on the approach of choosing the “best looking“ spermatozoon in the ejaculate seem to provide cells that can be classified as normal based on the length width ratio set by the WHO for normal cells. The chromatin packaging quality of the sperm correlated significantly and negatively with the percentage normal cells in the ejaculates. CHAPTER 4 comprises of a general discussion of the results and short summary of the major findings during the project. The discussion section focused on the paternal influence on the embryonic development and provided a suggestion for future research that can possibly lead to the use of X-chromosome bearing sperm in case of severe male factor cases. CHAPTER 5 contains the bibliographical information of the study.

Sex chromosomes experience distinct evolutionary environments, due to their unusual pattern of inheritance, and studies of sex chromosome evolution can shed light on the fundamental evolutionary forces acting across the genome as a whole. Here, I combine genomic and transcriptomic data across a wide range of avian species to explore the evolutionary processes governing sex chromosome evolution. Birds are female heterogametic and therefore it is possible, via comparisons with male heterogametic species, to identify the fundamental factors driving sex chromosome evolution, versus those associated with sex. In this thesis, I uncover a complex mosaic of recombination suppression between the Z and W chromosomes, characterized by repeated and independent divergence of gametologs, together with ongoing genetic exchange. Additionally, I highlight the role of mating system, and interplay between evolutionary forces, in driving coding and expression evolution on the Z and W chromosomes. My findings indicate that although the Z chromosome is masculinized for male-specific effects, the magnitude of genetic drift acting on Z-linked genes is elevated in promiscuous relative to monogamous mating systems. In contrast, evolution of the female-limited W chromosome is governed predominately by purifying selection. Together, my results suggest that the role of the Z chromosome in encoding sexual dimorphisms may be limited, but that W-linked genes play a significant role in female-specific fitness. In conclusion, my findings reveal the power of mating system in shaping broad patterns of genome evolution.

The effect of 17α-methyltestosterone a 17β-estradiol on sex of livebearer fish Poecilia reticulata and P. wingei was studied. Solution of 2.5 mg testosterone was added in the aquarium the first and fifteenth day after delivery of new fry. Estrogen was administered in food to gravid females (400 mg per 1 kg food). Sex of all individuals was determined in one, two and three months. Administration of neither testosterone nor estrogen caused sex reversal; in the second case reproduction of almost all females was stopped.

Les mécanismes de détermination génétique du sexe, qui requièrent la présence de régions chromosomiques non recombinantes ou bien de chromosomes sexuels, ont émergé de manière indépendante et répétée au sein de plusieurs lignées d'eucaryotes. La plupart des connaissances acquises dans ce domaine portent sur un nombre limité de groupes d'eucaryotes. La disponibilité d'une espèce modèle pour le groupe des algues brunes, Ectocarpus siliculosus, dont le génome a été séquencé, permet de disposer des outils nécessaires pour étudier ces mécanismes au sein d'une lignée phylogénétiquement éloignée des modèles classiquement étudiés. L'un des premiers défis a été d'identifier les chromosomes sexuels dans le génome d'E. siliculosus et de réaliser l'analyse comparative de ces structures. Par la suite, l'analyse de l'expression des gènes entre individus mâles et femelles à différents stades du cycle de vie a permis d'identifier les gènes différentiellement exprimés, de caractériser leurs fonctions et d'analyser leur évolution moléculaire. Les nombreuses données générées afin de réaliser ces différentes analyses ont permis de proposer une nouvelle version de l'assemblage du génome et de l'annotation structurale et fonctionnelle de l'ensemble des gènes codants et non-codants d'E. siliculosus. Ces différents travaux ont permis d'apporter une importante contribution sur les connaissances dans le domaine de l'analyse fonctionnelle et évolutive du déterminisme sexuel chez les algues brunes ainsi qu'une importante actualisation des ressources génomiques du modèle Ectocarpus. / Genetically determined sex determination mechanisms, which are controlled by non-recombinant chromosome regions or sex chromosomes, have emerged independently and repeatedly across several eukaryotic lineages. Most of the knowledge acquired in this area has been obtained for a limited number of eukaryotic groups. The availability of a model organism for the brown algae, Ectocarpus, whose genome has been sequenced, allows the development of tools to study these mechanisms in a lineage that is phylogenetically distant from classically studied models. One of the first challenges was to identify the sex chromosomes in Ectocarpus and to carry out a comparative analysis of these genomic structures. Analysis of gene expression in males and females at different stages of the life cycle then allowed the identification of differentially expressed genes. The functions and molecular evolution of these sex-biased genes was then studied. The large amount of data generated during the course of these analyses allowed the establishment of a new version of the genome assembly and refined structural and functional annotation of both coding and non-coding genes in Ectocarpus. This work helped made a significant contribution to knowledge in the field of functional and evolutionary analysis of sex determination in brown algae and a significantly updated the genomic resources available for the model organism Ectocarpus.

Le déterminisme génétique du sexe nécessite souvent l’évolution d’une région non-recombinante (NR) formant ainsi paire de chromosomes sexuels. Bien que la reproduction sexuée ait une origine commune à tous les eucaryotes, l’évolution des chromosomes sexuels s’est quant à elle effectuée de manière répétée et indépendante. Les chromosomes du sexe ont été particulièrement étudiés dans les systèmes diploïdes (chromosomes sexuels XY et ZW) des plantes et animaux. Le récent séquençage du génome d’Ectocarpus, modèle d’étude des algues brunes, donne non seulement une chance unique d’analyser les chromosomes sexuels dans un groupe phylogénétiquement distant des opisthocontes et de la lignée verte ; mais il donne aussi l’opportunité d’examiner un système haploïde de chromosomes sexuels (système UV). Chez Ectocarpus l’expression du sexe a lieu pendant la phase haploïde du cycle de vie, avec les chromosomes U et V, respectivement spécifiques aux femelles et aux mâles. L’analyse des chromosomes sexuels chez Ectocarpus a montré que la taille de la région NR est restée modeste pour un système vieux de plus de 70 millions d’années. Une analyse des dimorphismes sexuels a été effectuée ainsi que l’étude comparative des transcriptomes mâle et femelle d’Ectocarpus. Le développement parthénogénétique est, dans certaines populations d’Ectocarpus, un dimorphisme sexuel. Le lien génétique entre parthénogenèse et sexe a été analysé et suggère qu’un locus contrôlant la parthénogenèse est localisé au niveau de la partie recombinante du chromosome sexuel d’Ectocarpus. De plus, une analyse de fitness indique que le locus de la parthénogenèse est soumis à une sélection antagoniste entre les deux sexes. / Genetic sex determination is usually controlled by sex chromosomes carrying a non-recombining sex-determining region (SDR). Despite the common origin of sex (meiosis) in Eukaryotes, the evolution of sex chromosomes has evolved repeatedly and independently. Our knowledge in sex chromosomes comes mainly from the analysis of diploid systems (XY and ZW sex chromosomes) in animals and land plants. However the recent genome sequencing of the brown alga Ectocarpus, not only opens up the possibility of studying sex chromosomes in a phylogenetic distant group but also of analysing a haploid sex chromosome system (UV sex chromosomes). Indeed in Ectocarpus sex is expressed during the haploid phase of the life cycle, where U and V sex chromosomes are restricted to female and male, respectively. The Ectocarpus sex chromosomes have some unusual evolutionary features such as the size of the non-recombining region, which is surprisingly small for a 70 million year old system. Also the evolutionary aspect of sexual dimorphism was studied by analyzing male and female transcriptomes and by identifying several subtle sexual dimorphic traits. Parthenogenetic capacity is a sexual dimorphic trait in some populations of Ectocarpus. The genetic link between parthenogenesis and sex was analysed and a locus that controls parthenogenetic was located to the Ectocarpus sex chromosome, in the recombining pseudoautosomal region. Fitness analysis strongly suggested that the parthenogenetic locus is a sexual antagonistic locus

Cromossomos sexuais evoluíram repetidas vezes independentemente nos grandes grupos de vertebrados. Sistemas sexuais altamente diferenciados e antigos são caracterizados por grandes diferenças morfológicas e de conteúdo gênico entre os dois cromossomos homólogos onde a recombinação é restrita a uma pequena região homóloga. Os sistemas recentes característicos de peixes caracterizam-se pela similaridade entre os cromossomos X e Y (ou Z e W), nos quais as diferenças observadas freqüentemente envolvem a presença de heterocromatina, translocações e inversões. A recombinação ocorre entre o par sexual na maior parte de sua extensão, sendo inibida apenas na região diretamente relacionada com a determinação sexual. Notavelmente, sistemas diferentes de determinação podem ser encontrados em espécies, ou mesmo populações. O gênero Eigenmannia compreende grupos de espécies crípticas do ponto de vista morfológico que exibem variação no número cromossômico e podem apresentar sistemas sexuais XY ou ZW, incluindo sistemas múltiplos (com translocação Y-autossomo). Estes sistemas estão entre os mais recentes descritos (<16ma) e estão dispostos de forma desordenada em árvores de relações filogenéticas, sugerindo origens múltiplas. No presente estudo, a técnicas de pintura cromossômica usando sondas obtidas por microdissecção de cromossomos sexuais foram empregadas para testar a homologia de dois sistemas XY encontrados nos citótipos (ou espécies) E. virescens e E. sp.2. Os resultados mostram que, de fato, ambos são não homólogos. A fusão Y-autossomo provavelmente ocorreu após a separação de E. sp.2 com sua espécie irmã, E. sp.1 uma vez que um evento de fusão independente, envolvendo um dos cromossomos homólogos ao Y, foi detectado em E. sp.1. A hibridação in sit&#956; do cromossomo X de E. virescens em sua população mais próxima (também com 38 cromossomos, mas sem cromossomos sexuais heteromórficos) mostrou que o cromossomo X é homólogo a um par de acrocêntricos, condizente com o modelo proposto de diferenciação por acúmulo de heterocromatina. Essa heterocromatina foi caracterizada e mostrou um padrão complexo de seqüências CG-ricas. Dois fragmentos de DNA repetitivo GC-ricos presentes no cromossomo X foram isolados e seqüenciados. Não foram detectadas similaridades em comparações com bases de dados e entre os fragmentos obtidos. Estes mostraram-se concentrados nas regiões cromomicina-positivas de E. virescens, incluindo regiões periteloméricas de sete pares e os dois maiores blocos heterocromáticos (nos cromossomos X e par n. 8), além de um cromossomo acrocêntrico, possivelmente o Y. Curiosamente, essas seqüências foram detectadas em apenas três pares cromossômicos na população mais próxima, incluindo um par acrocêntrico de morfologia semelhante à condição ancestral do X, sugerindo que processos dinâmicos de expansão e homogenização genômica ocorreram após a separação dessas populações / Sex chromosomes have evolved independently several times in all major groups of vertebrates. Highly differentiated sex chromosomes are characterized by extensive differences in morphology and gene content, whereas recombination is restricted to a small homologous region. Recent sex chromosomes are characteristic of fish, and display a high level of homology between X and Y (or Z and W) chromosomes, recombination is restricted only in a small sex determining region. Notably, different sex chromosome systems can be found in closely related groups, such as species or even populations. The genus Eigenmannia comprises a group of morphologically cryptic species that display a variety of diploid numbers and different sex chromosome systems, including XY, ZW and a multiple XY system (with a Y-autosome fusion). These systems are among the most recent known (<16ma) and occur with a lack of phylogenetic pattern, whereas frequently populations bearing heteromorphic sex chromosomes are closest related to populations displaying no sex chromosomes. In the present study, chromosome painting using probes derived from the microdissection of two different sex chromosomes where used to investigate the homology of both systems. Results show that, in fact, they are non-homologous and evolved independently. The Y-autosome hypothesis gained further support from the observation that a chromosome homologous to the Y in a close population is involved in yet a different fusion event. The X chromosome present in the E. virescens karyotype was found to be homologous to acrocentric chromosomes in all populations analyzed, thus supporting the notion that its differentiations is mainly due to the accumulation of heterochromatin. The X heterochromatic block was shown to form a complex pattern of GC-rich sequences, different from what was previously described. Two GC-rich fragments were isolated and sequenced; both showed no similarities to known sequences and to one another. These sequences were shown to be concentrated viii on the two largest heterochromatic blocks, those of the X and n.8 chromosomes besides peri-telomeric regions of seven additional pairs and the putative Y. Curiously, these sequences were detected in only three pairs in the closest population, including an acrocentric pair morphologically similar to undifferentiated sex pair. This suggests that dynamic evolutionary processes of expansion and genomic homogenization have occurred after the separation of these populations.