As deleterious variants continually arise in a population, they tend to be purged via purifying selection, leading to distortions in the shapes of genealogies relative to neutral expectations. In recent years, a mounting body of evidence has arisen suggesting that this can have significant implications for the patterns of diversity seen in natural populations. However, existing theory has not yet fully characterized the effects of these distortions on the structure of genealogies. The focus of this thesis is on exploring this gap, and developing an analytical description of the distortions that arise in genealogies due to purifying selection. / Physics

Siglecs and CEA are two families of cell surface proteins belonging to the immunoglobulin superfamily. They are thought to be involved in cell-cell interactions and have various other biological functions. We used the GENECONV program that applies statistical tests to detect gene conversion events in each family of five primate species. For the Siglec family, we found that gene conversions are frequent between CD33rSiglec genes, but are absent between their conserved Siglec genes. For the CEA family, half of gene conversion events detected are located in coding regions. A significant positive correlation was found between the length of the conversions and the similarity of the converted regions only in the Siglec gene family. Moreover, we found an increase in GC-content and similarity in converted regions compared to non-converted regions of the two families. Furthermore, in the two families, gene conversions occur more frequently in the extracellular domains of proteins, and rarely in their transmembrane and cytoplasmic regions. Finally, these two families appear to be evolving neutrally or under negative selection.

Siglecs and CEA are two families of cell surface proteins belonging to the immunoglobulin superfamily. They are thought to be involved in cell-cell interactions and have various other biological functions. We used the GENECONV program that applies statistical tests to detect gene conversion events in each family of five primate species. For the Siglec family, we found that gene conversions are frequent between CD33rSiglec genes, but are absent between their conserved Siglec genes. For the CEA family, half of gene conversion events detected are located in coding regions. A significant positive correlation was found between the length of the conversions and the similarity of the converted regions only in the Siglec gene family. Moreover, we found an increase in GC-content and similarity in converted regions compared to non-converted regions of the two families. Furthermore, in the two families, gene conversions occur more frequently in the extracellular domains of proteins, and rarely in their transmembrane and cytoplasmic regions. Finally, these two families appear to be evolving neutrally or under negative selection.

Siglecs and CEA are two families of cell surface proteins belonging to the immunoglobulin superfamily. They are thought to be involved in cell-cell interactions and have various other biological functions. We used the GENECONV program that applies statistical tests to detect gene conversion events in each family of five primate species. For the Siglec family, we found that gene conversions are frequent between CD33rSiglec genes, but are absent between their conserved Siglec genes. For the CEA family, half of gene conversion events detected are located in coding regions. A significant positive correlation was found between the length of the conversions and the similarity of the converted regions only in the Siglec gene family. Moreover, we found an increase in GC-content and similarity in converted regions compared to non-converted regions of the two families. Furthermore, in the two families, gene conversions occur more frequently in the extracellular domains of proteins, and rarely in their transmembrane and cytoplasmic regions. Finally, these two families appear to be evolving neutrally or under negative selection.

African clawed frogs (Xenopus) have been scientific and medical model species for decades. These frogs present many curious features, and their genomic history is no exception. As such, a variety of evolutionary genomic questions can be addressed with these species in a comparative framework, owing to the great array of genetic tools available and a large number of abundant species. The sex chromosomes of this group are evolutionarily young, and this thesis establishes that there has been an additional change in what constitutes the sex chromosomes in one species of Xenopus. This allows us to compare the evolutionary trajectory of newly established sex chromosomes. By exploring the genetic content of these systems, profiling their recombinational activity, and assessing the extent of nucleotide divergence between the sex chromosomes, we find that sex chromosome evolution may be predictable in some aspects, and highly unpredictable in others. In addition, this genus is uncharacteristic for vertebrates in the frequency with which lineages undergo whole genome duplication. In this thesis, we explore the selective dynamics operating on duplicate genes over time, and the rate at which duplicate copies are purged from the genome from multiple Xenopus species. These investigations provide an animal perspective on the subject of biased subgenome evolution, characteristic of allopolyploids. The last two chapters of this thesis redefine the species boundaries for the most intensively studied Xenopus species (X. laevis), and explore the genetic extent of hybridization between the common X. laevis and the endangered X. gilli. Overall, this thesis provides a broad look at several aspects of Xenopus evolutionary genomics, providing novel contributions to the fields of sex chromosome research, whole genome duplication, and speciation and hybridization. / Thesis / Doctor of Philosophy (PhD)

Submitted by (ana.araujo@ufrpe.br) on 2016-07-07T12:58:08Z No. of bitstreams: 1 Juliana Katia da Silva.pdf: 2299995 bytes, checksum: 786d6f38a091474c4b7f97d00ef069a9 (MD5) / Made available in DSpace on 2016-07-07T12:58:08Z (GMT). No. of bitstreams: 1 Juliana Katia da Silva.pdf: 2299995 bytes, checksum: 786d6f38a091474c4b7f97d00ef069a9 (MD5) Previous issue date: 2009-02-16 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / The understanding of the central mechanisms favouring sex and recombination in real populations is one of the fundamental issues in evolutionary biology. Based on a previous stochastic formulation to the study of sex, here we aim to investigate the conditions under which epistasis favours the fixation of the sexual mode of reproduction in a given population. Besides, we try to identify the evolutionary forces which contribute to this process. Our model considers a finite population model which assumes the existence of a recombination modifier allele which can activate the recombination mechanism. We have found that sex is very little favoured in a scenario of antagonistic epistasis, and this advantage only takes place in a narrow range of values of the selection coefficient, sd. On the other hand, synergistic epistasis favours recombination in a very broad domain. However, the major mechanism contributing to the spreading of the modifier allele depends on the range of values of sd. At large sd background selection favours recombination since it increases the efficacy of selection, while at low sd Muller’s ratchet is the leading mechanism. / O entendimento dos mecanismos centrais que favorecem o sexo e a recombinação nas populações é um das questões fundamentais, e que ainda se encontra indefinida, na Biologia Evolucionária. Diversos modelos e teorias têm sido propostos de forma a melhor compreender a predominância do sexo e recombinação na natureza. Uma teoria de sucesso deve ser capaz de mostrar que existem mecanismos que contrabalanceiem os custos imediatos associados à reprodução sexuada. Aqui nesta dissertação de mestrado fazemos uma extensão de um modelo estocástico para o estudo do sexo, de forma agora a verificarmos em que condições a epistasia (interação entre genes) favorece a fixação do modo de reprodução sexuado, e que mecanismos evolucionários contribuem para isto. Consideramos um modelo de população finita que assume a existência de um alelo modificador de recombinação que é então inserido em uma população inicialmente assexuada. O destino desse alelo é então analisado. Verificamos que o sexo é pouco favorecido quando consideramos o relevo com epistasia antagonística, tornando-se vantajoso em um pequeno intervalo de valores do parâmetro seletivo sd. Já no caso da epistasia sinergística, observamos uma grande vantagem para a recombinação em duas regiões distintas: uma para pequenos valores de sd, e neste caso é a Catraca de Muller o mecanismo responsável pela vantagem; e na segunda região para grandes valores de sd, o mecanismo responsável é o efeito Hill-Robertson, em que a recombinação atua de forma a aumentar a eficácia da seleção purificadora.

Os mosquitos (Culicidae) compreendem um grupo monofilético, mas algumas relações dentro da família ainda não estão totalmente resolvidas. O objetivo deste trabalho foi elaborar uma hipótese filogenética para os gêneros de Culicidae baseada nos caracteres de variabilidade genética e perfil proteico. Além disso, foi analisado como a forma da asa evoluiu dentro desse grupo. Utilizou-se 76 espécies diferentes abrangendo 20 gêneros. O formato alar mostrou-se um bom marcador taxonômico, já que as análises em cada tribo ou gênero revelaram grupos naturais. Análises com genes nucleares mostraram Anophelinae como grupo irmão de todos os outros Culicinae. A topologia construída com genomas mitocondriais revelou grupos bem suportados, com alguns discordantes da filogenia atual. Foram identificados 24 biomarcadores nas espécies analisadas usando espectrometria MALDI-TOF, que podem ter potencial na identificação taxonômica. A morfologia, a genética e os perfis proteicos não foram concordantes, e isso pode estar ocorrendo devido a taxas evolutivas distintas entre eles. / Mosquitoes (Culicidae) comprise a monophyletic group, but some relationships within the family are not fully resolved. The aim of this study was to elaborate a phylogenetic hypothesis for the genera Culicidae based on the characters of genetic variability and protein profile. In addition, it was analyzed how wing shape evolved within this group. It was used 76 different species covering 20 genera. The wing shape showed to be a good taxonomic marker, because the analyzes in each tribe or genus revealed natural groups. Analyzes with nuclear genes showed Anophelinae as sister group of all other Culicinae. The topology constructed with mitochondrial genomes revealed well supported groups, with some discordant of the current phylogeny. Twenty-four biomarkers were identified in the species analyzed using MALDI-TOF spectrometry, which may have potential in taxonomic identification. Morphology, genetics, and protein profiles were inconsistent, and this may be occurring due to distinct evolutionary rates between them.

Cis-regulatory changes in e.g. promoters or enhancers that affect the expression of a linked focal gene have long been thought to be important for adaptation. In this thesis, I investigate the selective importance and genomic correlates of cis-regulatory variation and divergence in the genus Capsella, using massively parallel sequencing data. This genus provides an opportunity to investigate cis-regulatory changes in response to polyploidization and mating system shifts, as it harbors three diploid species, the outcrosser Capsella grandiflora and the selfers Capsella orientalis and Capsella rubella, as well as the tetraploid Capsella bursa-pastoris. We first identify cis-regulatory changes associated with adaptive floral evolution in connection with the recent switch to self-fertilization in C. rubella and show that cis-regulatory changes between C. rubella and its outcrossing close relative C. grandiflora are associated with differences in transposable element content. Second, we show that variation in positive and purifying selection is important for the distribution of cis-regulatory variation across the genome of C. grandiflora. Interestingly, the presence of polymorphic transposable elements is strongly associated with cis-regulatory variation in C. grandiflora. Third, we show that the tetraploid C. bursa-pastoris is of hybrid origin and investigate the contribution of both parental species to gene expression. We show that gene expression in the tetraploid is partly explained by cis-regulatory divergence between the parental species. Nonetheless, within C. bursa-pastoris there is a great deal of variation in homeolog expression. In summary, this thesis explores the role of cis-regulatory changes for adaptive morphological changes in connection to a shift in mating system, the role of cis-regulatory divergence between progenitor species for an allopolyploid as well as the impact of positive and purifying selection on cis-regulatory variation within a species.

Les plantes produisent une remarquable diversité de métabolites pour faire face aux contraintes d’un environnement en constante fluctuation. Cependant la manière dont les plantes ont atteint un tel degré de complexité métabolique et les forces responsables de cette diversité chimique reste largement incomprise. On considère généralement que le mécanisme de duplication des gènes contribue pour une grande part à l’évolution naturelle. En absence de transfert horizontal, les gènes d’évolution récente se cantonnent généralement chez quelques espèces et sont soumis à une évolution rapide, alors que les gènes conservés et plus anciens ont une distribution beaucoup plus large et sont porteurs de fonctions essentielles. Il est donc intéressant d’étudier l’adaptation des plantes en analysant parallèlement les gènes qui présentent soit une large distribution taxonomique, soit une distribution plus restreinte, de type lignée-spécifique. Les cytochromes P450 (CYP) constituent l’une des plus vastes familles de protéines chez les plantes, présentant des phylogénies très conservées ou très branchées qui illustrent la plasticité métabolique et la diversité chimique. Pour illustrer l’évolution des fonctions des cytochromes P450 dans le métabolisme végétal, nous avons sélectionné trois gènes, l’un très conservé au cours de l’évolution, CYP715A1 et les deux autres, CYP98A8 et CYP98A9, très récemment spécialisés de manière lignée spécifique chez les Brassicaceae. Les gènes appartenant à la famille CYP715 ont évolué avant la divergence entre gymnospermes et angiospermes, et sont le plus souvent présent en copie unique dans les génomes végétaux. Ceci suggère que leur fonction est essentielle et très conservée chez les plantes à graines (spermaphytes). Sur la base d’une analyse transcriptionnelle et de l’expression du gène GUS sous le contrôle du promoteur de CYP715A1, il est apparu que ce gène est spécifiquement exprimé au cours du développement floral, dans les cellules tapétales des jeunes boutons floraux ainsi que dans les filaments lors de l’anthèse. CYP715A1 est également fortement induit dans les cellules du péricycle de la zone d’élongation racinaire en réponse au stress salin. L’induction par le sel nécessite une région promotrice située entre 2 et 3 kb en amont de la région codante (i.e ; codon START), ce qui suggère la présence d’un facteur cis à cet endroit. Afin de déterminer la fonction de CYP715A1 chez Arabidopsis thaliana, j’ai identifié deux mutants d’insertion de T-DNA par génotypage et complémenté ces mutants avec le gène natif. La perte de fonction de CYP715A1 n’a pas d’impact sur la croissance et la fertilité de la plante en conditions de laboratoire. Cependant, une analyse par microscopie électronique en transmission montre un phénotype d’intine ondulée. La perte de fonction du gène CYP715A1 a également entraîné une réduction de la taille des pétales et un défaut d’anthèse. [...] / Plants produce a remarkable diversity of secondary metabolites to face continually challenging and fluctuating environmental constraints. However, how plants have reached such a high degree of metabolic complexity and what are the evolutionary forces responsible for this chemodiversity still remain largely unclarified. Gene evolution based on gene birth and extinction has been reported to nicely reflect the natural evolution. Without horizontal gene transfer, young genes are often restricted to a few species and have undergone rapid evolution, whereas old genes can be broadly distributed and are always indicative of essential housekeeping functions. It is thus of interest to study plant adaptation with parallel focus on both taxonomically widespread and lineage-specific genes. P450s are one of the largest protein families in plants, featuring both conserved and branched phylogenies. Examples of P450 properties reflecting metabolic versatility, chemodiversity and thus plant adaptation have been reported. To illustrate evolution of P450 functions in plant metabolism, we selected two P450 genes, one evolutionary conserved CYP715A1 and the second a recently specialized lineage-specific gene CYP98A9 in Arabidopsis thaliana.CYP715s evolved before the divergence between gymnosperms and angiosperms and are present in single copy in most sequenced plant genomes, suggesting an essential housekeeping function highly conserved across seed plants. Based on transcriptome analysis and promoter-driven GUS expression, CYP715A1 is selectively expressed in tapetal cells of young buds and filaments of open flowers during flower development. In addition, CYP715A1 is highly induced in the pericycle cells of the root elongation zone upon salt stress. The salt induction relies on the 2-3kb region of CYP715A1 promoter, suggesting some salt-response elements may exist in this area. To characterize the function of CYP715A1 in Arabidopsis, I identified two T-DNA insertion mutants by genotyping and confirmed by complementation with native CYP715A1 gene. Loss of function of CYP715A1 has no impact on plant growth and fertility in laboratory conditions. However, transmission electron microscopy (TEM) analysis has shown constant undulated intine phenotype in two knockout mutants and also the petal growth is significantly inhibited. These two phenotypes nicely match the native expression pattern of CYP715A1. Gene co-expression analysis suggests involvement of CYP715A1 in gibberellin (GA) metabolism under salt treatment. GAs profiling on mutant flowers also indicates reduced accumulation specific GAs. Unfortunately, no significant phenotype either related to root growth or root architecture under salt treatment can be observed. Recombinant expression of the CYP715A1 enzyme in yeast so far does not allow confirming GAmetabolism. However, metabolic profiling of inflorescences in mutants and over-expression lines, together with transcriptome analysis of the loss of function cyp715a1 mutants strongly support a CYP715A1 role in signaling, hormone homeostasis and volatile emission in agreement with the purifying selection leading to gene conservation observed in spermatophytes.[...]