The persistence of sex is a recurrent conundrum in evolutionary biology because sex is costly. These costs may be accounted for by looking at the outcome of sex, namely that sex causes genetic mixing. Recombination is one of the processes by which sex causes genetic mixing; determining when recombination is advantageous may alleviate some of the costs of sex. The advantages of recombination are in the effects of recombination and the influences thereupon. The first experiment focuses on the effects of recombination on the mean fitness and variance in fitness. A second experiment examines the influences on recombination by addressing whether recombination is a general response to poor condition. Specifically, the impact on recombination rate of genotypes with variable fitness is investigated. Differing fitness effects are not correlated to recombination rates. Conversely, coincidence, a recombination related trait, is positively correlated with fitness.

The persistence of sex is a recurrent conundrum in evolutionary biology because sex is costly. These costs may be accounted for by looking at the outcome of sex, namely that sex causes genetic mixing. Recombination is one of the processes by which sex causes genetic mixing; determining when recombination is advantageous may alleviate some of the costs of sex. The advantages of recombination are in the effects of recombination and the influences thereupon. The first experiment focuses on the effects of recombination on the mean fitness and variance in fitness. A second experiment examines the influences on recombination by addressing whether recombination is a general response to poor condition. Specifically, the impact on recombination rate of genotypes with variable fitness is investigated. Differing fitness effects are not correlated to recombination rates. Conversely, coincidence, a recombination related trait, is positively correlated with fitness.

Theory predicts that sexual reproduction confers an advantage over asexual reproduction due to the generation and maintenance of genetic variation afforded by the processes of recombination and segregation. However, this prediction has rarely been empirically tested. Oenothera is a flowering plant genus whose evolutionary history is punctuated with numerous transitions from sexual reproduction to a form of functionally asexual reproduction known as Permanent Translocation Heterozygosity (PTH). In Ch. 2, a greenhouse experiment examined patterns of phenotypic and genetic variation within and between populations across eight Oenothera species, representing four independent transitions to PTH. I found some evidence for a decrease in heritability and an increase in population differentiation in phenotypic traits associated with the loss of sex. Ch. 3 explored the possibility that rare outcrossing events represent a mechanism for the maintenance of variation in a PTH species. Analysis of microsatellite markers showed evidence for extremely low rates of outcrossing in natural populations (< 1%) of O. biennis, a PTH species.

Theory predicts that sexual reproduction confers an advantage over asexual reproduction due to the generation and maintenance of genetic variation afforded by the processes of recombination and segregation. However, this prediction has rarely been empirically tested. Oenothera is a flowering plant genus whose evolutionary history is punctuated with numerous transitions from sexual reproduction to a form of functionally asexual reproduction known as Permanent Translocation Heterozygosity (PTH). In Ch. 2, a greenhouse experiment examined patterns of phenotypic and genetic variation within and between populations across eight Oenothera species, representing four independent transitions to PTH. I found some evidence for a decrease in heritability and an increase in population differentiation in phenotypic traits associated with the loss of sex. Ch. 3 explored the possibility that rare outcrossing events represent a mechanism for the maintenance of variation in a PTH species. Analysis of microsatellite markers showed evidence for extremely low rates of outcrossing in natural populations (< 1%) of O. biennis, a PTH species.

Naturally competent bacterial species, which self-induce the recombination mechanism of transformation, are wide spread across the bacterial tree-of-life. However, it remains unclear why competence has evolved in these bacteria. Although it is likely that exact explanations will be different for each species, a common selective factor cannot be excluded. Currently, three dominant hypotheses, which focus on the transformation function, try to explain the benefits of competence. Firstly, competence is thought to increase the rate of adaptation by combining beneficial alleles in single genotypes. Secondly, competence can repair DNA-damage by replacing the damaged DNA fragments with undamaged ones. Thirdly, the DNA uptake during competence is used to recycle environmental DNA fragments for nutrients. One of the naturally competent species is the Gram-positive Streptococcus pneumoniae, which is an opportunistic pathogen generally inhabiting the naso-pharyngeal area of young children. Competence in S. pneumoniae is regulated via density dependent extracellular signaling peptide. Here I use a combination of experiments designed around knockout mutants of the signaling mechanism and next-generation sequencing methods to test the first two hypotheses in S. pneumoniae. First, I extend on the DNA-for-repair hypothesis by showing that competent populations of S. pneumoniae are better protected not only against a DNA-damaging agent, but also against protein synthesis inhibitors. However, the mechanisms underlying this protection differ between types of stress. DNA-damage requires the full process of transformation, while protection against protein synthesis inhibitors only requires the activation of the competent cell state. This shows that benefits of competence cannot be totally explained by the benefits of transformation. Second, I use a long-term evolution experiment, where competent and non-competent strains are kept in the presence and absence of periodic stress, to determine the importance of competence for the generation of genetic variation. I find that competence does not increase the rate of adaptation in S. pneumoniae. The fitness of evolved competent populations was significantly lower than those of non-competent populations evolved over the same period of time. However, the intrinsic costs of competence are mitigated by the addition of short periods of stress exposure. These results confirm the prediction of the fitness associated recombination (FAR) hypothesis that competence is favoured in low-fitness situations. Thirdly, whole genome re-sequencing of the evolved populations allowed me to explore genomic evolution next to fitness changes. The genomic data revealed that competence reduces the mutational load of deleterious mutations rather than generating combinations of beneficial alleles. In addition I show several case of parallel genomic evolution within each treatment and across treatments. This shows that parallel evolution is not restricted by genotypic background (competence) or environment (periodic stress). Finally, these results show that competence has evolved in populations of S. pneumoniae as a mechanism to deal with various forms of stress.

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第20956号 / 理博第4408号 / 新制||理||1633(附属図書館) / 京都大学大学院理学研究科生物科学専攻 / (主査)准教授 渡辺 勝敏, 教授 曽田 貞滋, 教授 中川 尚史 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

<p>What evolutionary processes and ecological patterns underlie the maintenance of asexual reproduction in natural populations? Although a vast body of literature offers theory to explain the existence of sexual and asexual reproduction, there has been little study of these forms of reproduction in the natural environment. In this dissertation I use a combination of field experiments, greenhouse studies, and genetic techniques to answer this question in the model plant system Boechera. </p><p>In Chapter 1, I review the utility of this system for studying ecological and evolutionary questions in general. Boechera offers an array of genetic and genomic tools, facilitated in part by a close evolutionary relationship with the model plant Arabidopsis thaliana, as well as undisturbed ecology and habitat that extends across much of North America. Additionally, the presence of apomixis (asexual reproduction via parthenogenetic formation of seeds) at the diploid level makes Boechera an ideal system for studying sex without the often-confounding factor of polyploidy; Boechera is one of very few plant groups in which this is possible. </p><p>In Chapter 2, I use a combination of microsatellite markers, flow cytometry, chromosome squashes, and morphological work to characterize apomixis, polyploidy, and species diversity in over 100 natural populations collected from central Idaho and western Montana. As in many other apomictic systems, I find that apomixis in Boechera is strongly linked to hybridization between species or between genetically divergent intraspecific lineages. I then explore associations between apomixis and ecological and topographical variables, as well as variables underlying differentiation between apomictic and sexual lineages. I find that ecological variables associated with apomixis are largely in congruence with the hypothesis of geographic parthenogenesis, and that geographic parthenogenesis is likely driven by the consequences of interspecific hybridization. We also find that apomixis is linked with disturbance and slope, with apomicts occurring in flatter locations than sexuals. </p><p>In Chapter 3, I use a large-scale field experiment comprising three years of data from two cohorts of sexual and asexual lineages to compare fitness between these two groups. I find that, despite herbivory levels that are much higher in apomicts than sexuals, apomictic fitness is consistently higher than sexual. Viability selection strongly favors apomicts, which results in a total fitness advantage for apomicts, despite variable fecundity selection. Selection varies in intensity between cohorts and among gardens. The results of a complementary greenhouse experiment show that the effects of herbivory differ by reproductive mode. Together, these experiments suggest that Red Queen dynamics may contribute to the coexistence of sex and asex in this group.</p><p>In Chapter 4, I use inter- and intraspecific F2 crosses to conduct a greenhouse study and a field experiment to explore the effects of hybridization and heterozygosity on fitness. I find that heterozygosity is favored in the field, with viability selection strongly favoring outcrossed over inbred lineages. However, hybridization results in lower survival, reproduction, and total fitness of interspecific F2 crosses, although hybrids that do reproduce produce more fruits than selfed parental lineages of both species, resulting in fecundity selection for hybrids. It is clear that the benefits of apomixis are due to hybridization, as hybrids are less fit overall. Evidence for both heterosis and outbreeding depression, dependent on lineage and on trait, are found in the field; these phenomena are not clearly associated with geographic distance between parental populations. Ongoing SNP genotyping will facilitate assessment of heterozygosity-fitness correlations as well as correlation of fitness and heterozygosity.</p> / Dissertation

It is known that chromosomal rearrangements play an important role in speciation by limiting gene flow within and between species. Furthermore, this effect may be enhanced by involvement of sex chromosomes that are known to undergo fast evolution compared to autosomes and play a special role in speciation due to their engagement in postzygotic reproductive isolation. The work presented in this study uses various molecular-genetic and cytogenetic techniques to describe karyotype and sex chromosome evolution of two groups of Lepidoptera, namely selected representatives of the family Tortricidae and Leptidea wood white butterflies of the family Pieridae. The acquired knowledge points to unexpected evolutionary dynamics of lepidopteran karyotypes including the presence of derived neo-sex chromosome systems that originated as a result of chromosomal rearrangements. We discuss the significance of these findings for radiation and subsequent speciation of both lepidopteran groups.

Evolution of sex determining mechanisms in squamate reptiles (Reptilia: Squamata) Martina Pokorná Ph.D. thesis Abstract This Ph.D. thesis is focused on the evolution of sex determining mechanisms and genomes in squamate reptiles. It is based on three published articles and two manuscripts. The evolution of sex determining mechanisms, sex chromosomes and genomes, and their organisation, was studied on a wide phylogenetic scale of the whole group of squamate reptiles and some lineages of other Sauropsids, as well as on the small phylogenetic range as a detailed comparative study inside individual lineages of squamates. This thesis is based upon the use of classical cytogenetic methods, methods of molecular cytogenetic (especially fluorescent in situ hybridisation) and the results were analysed using phylogenetic approaches. The results and outputs of this study represent an important contribution to the general knowledge of the principals of sex determination and the evolution of these phenomena not only in squamate reptiles but also in the whole group of amniotes. Using the results obtained during the work on this thesis we can conclude that sex chromosomes evolved in particular lineages of amniotes independently. This origin was in some cases followed by accumulation of microsatellite sequences on sex...

Three aspects of Xanthoparmelia cumberlandia and Xanthoparmelia coloradoënsis populations found at two elevations are explored: clustering of secondary chemicals and the resulting implications for taxonomic distinctions, the usefulness of thallus size as an indirect measure of sexual fecundity, and the frequency of sexual reproduction. First, we use clustering of 46 chemicals produced by X. cumberlandia and X. coloradoënsis to evaluate the adequacy of the current taxonomic distinction between them. Using principal components analysis and UPGMA, we find that the currently recognized species boundaries indicated by the presence of stictic acid in X. cumberlandia and salazinic acid in X. coloradoënsis are supported by distinct differences in their chemotypes (combinations of secondary chemicals). Norstictic acid, which the literature also associates with X. cumberlandia, is found frequently in both X. cumberlandia and X. coloradoënsis, and is not a good distinguishing characteristic. No chemical difference between sexually fecund and sterile individuals was found. Second, we test the claim that thallus size can be used as an indirect measure of sexual fecundity. By comparing the number of apothecia, the total area of the apothecia, and the presence or absence of apothecia with thallus area, we found positive correlations between these measures of sexual fecundity and thallus size which are statistically significant. However, the total variation explained by these predictors is limited, and is significantly affected by elevation and micro-environmental features such as proximity to trees. We conclude that size is not a reliable synonym for sexual fecundity in X. cumberlandia and X. coloradoënsis. Third, we make inferences concerning the frequency of sexual reproduction based on the frequency of sexual structures, rare chemicals, and unique chemotypes. We predicted that sexual reproduction would be more frequent at lower elevations, consistent with a common pattern found in plants and animals. The frequency of sexual structures indicates that sexual reproduction is more common at the lower elevation, while frequency of rare chemicals and chemotypes implies that outcrossing is more common at the upper elevation. Since these indicators lead to opposing conclusions, we encourage the use of molecular markers to estimate the frequency of outcrossing directly.