Orientadores: Shirlei Maria Recco Pimentel, Ana Cristina Prado Veiga Menocello / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-12T03:22:49Z (GMT). No. of bitstreams: 1 Duarte_ThiagoCellin_M.pdf: 1944479 bytes, checksum: 814f8a0a8bd0078b0f432679c3115819 (MD5) Previous issue date: 2008 / Resumo: O gênero Pseudopaludicola, atualmente pertencente à família Leiuperidae, é formado por 12 espécies amplamente distribuídas pela América do Sul, com nove delas relatadas para o Brasil. Com base em dados morfológicos, as espécies do gênero foram alocadas em dois grupos: "pusilla" e "falcipes". Mudanças taxonômicas freqüentes foram relatadas para o gênero e análises recentes com base em dados moleculares mostraram que as relações intergenéricas de Pseudopaludicola também permanecem pouco esclarecidas. Devido à grande semelhança morfológica dos exemplares de Pseudopaludicola, há suspeita de confusões na identificação das espécies para algumas localidades e da existência de espécies novas. De modo geral, existem poucas informações citogenéticas para o gênero que, em sua maioria, se restringem à determinação do número de cromossomos e análise do cariótipo por método de coloração convencional. Considerando que a análise citogenética mais detalhada constitui uma ferramenta importante que pode contribuir para a diferenciação de espécies de Pseudopaludicola e para o entendimento da sistemática do gênero, no presente trabalho foram estudadas as espécies Pseudopaludicola mineira, P. canga e P. saltica, provenientes de suas localidades-tipo (Serra do Cipó, MG; Serra dos Carajás, PA; e Chapada dos Guimarães, MT, respectivamente), P. saltica de Uberlândia, MG, Pseudopaludicola aff. saltica de Rio Claro (SP), Pseudopaludicola aff. falcipes de Icém (SP), e outras três amostras de Pseudopaludicola sp. (1, 2 e 3) provenientes, respectivamente, de Andaraí (BA), Barreirinhas (MA) e Uberlândia (MG). As metáfases foram obtidas de suspensões de células de epitélio intestinal e de testículo, e coradas com Giemsa ou submetidas às técnicas impregnação por prata (Ag-NOR) para detecção de região organizadora de nucléolo (NOR) e de bandamento C, para a localização de heterocromatina. As espécies estudadas dividem-se em dois grupos quanto ao número de cromossomos, 2n=18 e 2n=22. As espécies P. mineira, Pseudopaludicola sp.1, P. saltica e Pseudopaludicola aff. saltica apresentam 2n=22 cromossomos. Pseudopaludicola mineira diferiu de Pseudopaludicola sp.1 pela morfologia dos pares 7, 8 e 11, posição da NOR no par 8 e pela distribuição de blocos heterocromáticos. As duas populações de P. saltica e a população de Pseudopaludicola aff. saltica apresentaram cromossomos com a mesma morfologia, exceto o par 8 que em P. saltica caracteriza cromossomos sexuais do tipo XX/XY, sendo o X telocêntrico e o Y submetacêntrico, ambos portadores da NOR, enquanto em Psedopaludicola aff. saltica o par 8 é telocêntrico, heteromórfico em tamanho, e apresenta marcação da NOR e banda heterocromática apenas no cromossomo maior do par. Os cariótipos de P. canga, Pseudopaludicola sp.2, Pseudopaludicola sp.3 e Pseudopaludicola aff. falcipes apresentaram cariótipos idênticos com 2n=18 cromossomos. Esses cariótipos diferem, no entanto, quanto à localização da NOR pericentromérica no braço curto do par 3 em P. canga e Pseudopaludicola sp.2 e telomérica no braço longo do par 9 em Pseudopaludicola sp.3 e Pseudopaludicola aff. falcipes. O padrão de bandamento C destas espécies mostrou-se bastante similar diferindo apenas pela presença de uma banda no braço longo do par 2 em P. canga e Pseudopaludicola sp.2 e ausente em Pseudopaludicola sp.3 e Pseudopaludicola aff. falcipes. Os dados citogenéticos permitiram diferenciar Pseudopaludicola sp.1 das demais espécies de 22 cromossomos já cariotipadas, sugerindo que possa se tratar de uma nova espécie. O sistema de determinação do sexo do tipo XX?/XY? detectado em P. saltica não foi relatado anteriormente para o gênero Pseudopaludicola, sendo esse o primeiro caso. A hipótese de fissão seguida de perda do braço menor em um dos homólogos de um par de cromossomos submetacêntricos é sugerida para explicar a origem do cromossomo X. O heteromorfismo do par 8 observado em Pseudopaludicola aff. saltica, pode ter ocorrido por mecanismo de crossing-over desigual. As espécies Pseudopaludicola canga e Pseudopaludicola sp.2 não puderam ser citogeneticamente diferenciadas, no entanto, não descartamos a possibilidade de serem táxons distintos. A grande similaridade dos cariótipos 2n=18 sugere que Pseudopaludicola sp.2, Pseudopaludicola sp.3 e Pseudopaludicola aff. falcipes possam também pertencer ao mesmo grupo em que se encontra P. canga, atualmente grupo "pusilla". Os dados sugerem ainda que Pseudopaludicola aff. falcipes (2n=18) seja proximamente relacionada à P. canga (2n=18) e não a P. falcipes (2n=22), apesar das semelhanças morfológicas entre seus exemplares. Os resultados obtidos no presente estudo reforçam a necessidade de uma extensa revisão taxonômica no gênero Pseudopaludicola. / Abstract: The genus Pseudopaludicola, of the family Leiuperidae, comprises 12 frog species and is widely distributed in South America. In Brazil, nine species have been described within this genus. As based on morphological data, the Pseudopaludicola species were classified in two groups named "pusilla" and "falcipes". Although this genus has undergone several taxonomic changes, recent molecular analyses revealed still unclear intergeneric relationships. The high morphological similarities among diverse species of Pseudopaludicola, associated to their sympatry in several localities, suggest taxonomic misidentification which had been based only in morphological characteristics. Besides, recent studies seem to indicate the existence of cryptic Pseudopaludicola species in several Brazilian localities. Cytogenetics of Pseudopaludicola has been scarce and restricted to the determination of chromosome number and morphology. Further cytogenetic analysis can contribute to differentiate the Pseudopaludicola species and, therefore, improve the sistematics of this genus. The objective of this work was to analyze the karyotypes of several Brazilian Pseudopaludicola species aiming at providing their characterization and further understanding of their systematic relationships. The analyzed species were the P. mineira, P. canga and P. saltica, from their type-localities (Serra do Cipó, MG; Serra dos Carajás, PA, and Chapada dos Guimarães, MT, respectively), P. saltica from Uberlândia, MG, Pseudopaludicola aff. saltica from Rio Claro (SP), Pseudopaludicola aff. falcipes from Icém (SP), and specimens of Pseudopaludicola sp. 1, 2 and 3, respectively from Andaraí (BA), Barreirinhas (MA) and Uberlândia (MG). Metaphases were obtained from intestinal epithelium and testicular cell suspensions, and stained with Giemsa or submitted to silver staining, in order to detect the nucleolus organizing regions (Ag-NOR), and to C-banding technique for heterochromatin localization. As based on chromosome number, there were two groups of karyotypes, with 2n=22 and 2n=18. The species P. mineira, Pseudopaludicola sp.1, P. saltica and Pseudopaludicola aff. saltica had a diploid number of 2n=22. Pseudopaludicola mineira and Pseudopaludicola sp.1 differed in the morphology of pairs 7, 8 and 11, in the NOR location in the pair 8 and in the heterochromatin distribution. The P. saltica and Pseudopaludicola aff. saltica populations showed very similar chromosomal morphology and identical heterochromatin pattern, except for the pair 8. In P. saltica, the pair 8 was characterized as sex chromosomes XX?/XY?, being the X classified as telocentric and Y submetacentric, whereas in Psedopaludicola aff. saltica, in both male and female specimens, the homologues of pair 8 are telocentrics, heteromorphic in size with the heterochromatin block present only in the longer homologue. The pair 8 is the NOR-bearing chromosome in both P. saltica and Psedopaludicola aff. saltica. High similarity was observed among the karyotypes of P. canga, Pseudopaludicola sp.2, Pseudopaludicola sp.3 and Pseudopaludicola aff. falcipes, all of them with 2n=18 chromosomes. However, these karyotypes differed in the NOR location, which was on pair 3 in P. canga and Pseudopaludicola sp.2, and on pair 9 in Pseudopaludicola sp.3 and Pseudopaludicola aff. falcipes. These species had similar heterochromatic blocks, except for one C-band on the long arm of pair 2 in P. canga and Pseudopaludicola sp.2, which was not observed in Pseudopaludicola sp.3 e Pseudopaludicola aff. falcipes). The cytogenetic data clearly distinguished Pseudopaludicola sp.1 from the other known species of this genus with 22 chromosomes, and suggested that this could be a not yet described species. The identification of sex chromosomes XX?/XY? in P. saltica, is the first case of sex chromosomes reported in the genus Pseudopaludicola. A mechanism of fission followed by loss of the short arm in one of homologues of a submetacentric pair could explain the origin of the X chromosome in P. saltica. The size heteromorphism in the homologues of the pair 8 of Pseudopaludicola aff. saltica, with the NOR site and heterochromatin present only in one of the homologues, could be explained by unequal crossing-over. The species Pseudopaludicola canga and Pseudopaludicola sp.2 could not be cytogenetically distinguished, suggesting that they belong to the same taxon. Since all the analyzed karyotypes of 2n=18 were very similar, we may suggest that Pseudopaludicola sp.2, Pseudopaludicola sp.3 e Pseudopaludicola aff. falcipes should be included in the same group of P. canga, which is currently allocated in the "pusilla" group. In addition, the results indicated that Pseudopaludicola aff. falcipes (2n=18) is more closely related to P. canga (2n=18) than to P. falcipes (2n=22), although the specimens are morphologically very similar and their identification is not unequivocal. Ultimately, the data presented herein reinforce the necessity of a taxonomic revision of the genus Pseudopaludicola. / Mestrado / Biologia Celular / Mestre em Biologia Celular e Estrutural

Orientadores: Luciana Bolsoni Lourenço, Carmen Silvia Busin / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-23T12:08:20Z (GMT). No. of bitstreams: 1 Gatto_KalebPretto_M.pdf: 33988822 bytes, checksum: 7e3f3565dac9a540ea7c353f51068d4f (MD5) Previous issue date: 2013 / Resumo: O resumo poderá ser visualizado no texto completo da tese digital / Abstract: The abstract is available with the full electronic document / Mestrado / Biologia Celular / Mestre em Biologia Celular e Estrutural

An excess of males among the mentally retarded has been noted in practically all surveys of a mentally retarded population. It has been hypothesized that X-linked genes may account for this excess. The main purpose of this study was to test the hypothesis using data on the mentally retarded in British Columbia. A second purpose was to calculate the frequency of non-specific X-linked mental retardation in the population. In addition, an attempt was made to delineate clinical types of X-linked mental retardation. Data on the mentally retarded in British Columbia were obtained from the B.C. Health Surveillance Registry. The Registry also provided information on sibships with two or more sibs affected with non-specific mental retardation. Family histories on sibships with two or more affected males were obtained from the Department of Medical Genetics, institutions for the mentally retarded, namely Woodlands School and Tranquille, and in some cases personal interviews. The number of mothers in British Columbia giving birth to two or more sons in a defined birth cohort was retrieved from the linked family records of the B.C. Record Linkage Project. Families with a pattern of X-linked inheritance for non-specific mental retardation were ascertained while family histories on sibships with two or more affected males were being recorded and by reviewing files of other non-specific mentally retarded males in the Department of Medical Genetics, Woodlands School and Tranquille. Clinical and psychological characteristics of the mental retardation in males from these families were obtained from medical files from the same sources. Among the mentally retarded in British Columbia, there is an overall 28.2% excess of males. The extent of this excess is similar to that observed in other studies. This excess of males is seen at all levels of retardation except at the profound level. Mental retardation of known causes does not significantly contribute to the excess, which is due primarily to nonspecific mental retardation. Non-specific mental retardation in two or more sibs may be genetic in origin. Data from sibships with both males and females affected do not support an hypothesis of multifactorial inheritance with specific sex thresholds accounting for the excess of mentally retarded males. A ratio of 3.1:1 of sibships with two or more affected males to sibships with two or more affected females suggests that X-linked inheritance may account for the excess of male affected sibships. Family history data on sibships with two or more affected males provide evidence that X-linked genes can account for the excess of male affected sibships. A minimum frequency of 1.83 per 1,000 males for X-linked mental retardation in the population of British Columbia was calculated using sibship data. This frequency can account for the entire excess of non-specific mentally retarded males in the province. Mental retardation inherited in an X-linked pattern may be due to either single genes on the X chromosome or autosomal dominant genes with sex-limited expression. Distinguishing between the two types of genes was not possible in the present study. Specific clinical subtypes of X-linked mental retardation could not be differentiated due to a large amount of variability which was found not only in the level of retardation but also in associated psychological, neurological and physical characteristics. Although further clinical, biochemical and cytogenetic investigations of affected males in families with X-linked mental retardation may elucidate subtypes of non-specific mental retardation, variabiliy in phenotypic expression has been identified as an important feature of X-linked mental retardation. / Medicine, Faculty of / Medical Genetics, Department of / Graduate

Orientadores: Andrea Trevas Maciel Guerra, Roberto Benedito de Paiva e Silva / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Ciências Médicas / Made available in DSpace on 2018-08-04T01:13:43Z (GMT). No. of bitstreams: 1 Suzigan_LigiaZuppiConceicao_M.pdf: 719674 bytes, checksum: 0fd7aced48effd8567e687fc3397c183 (MD5) Previous issue date: 2004 / Resumo: Objetivo: Identificar a percepção das pacientes com Síndrome de Turner (ST) a respeito de sua condição. Casuística e Método: Entrevistas individuais com 36 pacientes com ST entre 15 e 25 anos e mais de 2 anos de acompanhamento, abordando temas referentes ao impacto no momento do diagnóstico, compreensão a respeito da ST, seu impacto sobre a vida atual e expectativas de futuro. Resultados: Apenas 1/3 compreendeu o diagnóstico de ST imediatamente, e o sentimento associado a esse momento foi freqüentemente neutro (17) ou de preocupação (12). Cerca de 1/3 não soube explicar a etiologia da ST, não relacionou a ela os sintomas que apresenta e(ou) acredita haver cura. Em sua vida atual, embora a grande maioria declare que a ST não interfere em sua vida (2/3) e se considere feliz (3/4), em mais da metade dos casos há evidências de dificuldades de interação social e de relacionamento amoroso, baixa auto-estima, insatisfação com a aparência física, em particular a baixa estatura e sofrimento com a questão da esterilidade. Suas expectativas de futuro estão predominantemente ligadas a trabalho e estudo; mesmo estando com 19 anos, em média, uma em cada duas ainda espera crescer. Conclusão: Além da abordagem médica da ST, é fundamental que o conhecimento das pacientes a respeito dessa síndrome e as questões referentes a esterilidade, baixa estatura, auto-imagem e interações sociais sejam alvo de atenção especial e contínua a partir do momento do diagnóstico; a situação ideal seria a de atuação de um psicólogo juntamente com a equipe médica / Abstract: Objective: To identify the perception of patients with Turner syndrome (TS) about their condition. Methodology: Thirty-six women with TS, aged between 15 and 25 years and with over two years of medical follow-up, were individually interviewed about: the impact of TS at the moment of the diagnosis, their understanding of the syndrome, its effect in their current lives and their expectations for the future. Results: Only one third of the patients understood the diagnosis immediately and their feelings associated to that moment were neutral (17) or concerned (12). About one third of the interviewed women were unable to explain the etiology of TS, they have not related their symptoms with TS and/or believe there might be a cure for it. Although most say that the syndrome has no interference in their current lives (2/3) and that they consider themselves happy persons (3/4), in more than half of the interviews there are evidences of difficulties with social interactions and love relationships, low self-esteem, dissatisfaction with their physical appearances, mainly short stature, and worries about infertility. Their hopes for the future refer mainly to study and have a job; growing up expectation was mentioned by one in two of the women, in spite of their mean age of 19 years. Conclusion: Besides medical treatment, it is important that the knowledge of the patients about the syndrome and some issues as infertility, short stature, self-image and social interactions receive proper and continuous attention from the moment of the diagnosis. The ideal situation should be a joint-action of the psychologist and the medical team / Mestrado / Saude da Criança e do Adolescente / Mestre em Saude da Criança e do Adolescente

(English) Sex determination plays an important role in the viability of populations and species evolvability. This is one of the reasons why sex determination has become an important subject of many studies during more than the last 100 years. The thesis focuses on the evolution of sex determination systems in toxicoferan reptiles. Toxicofera is a group of squamate reptiles containing more than 6000 species. Their species richness is also reflected in the diversity of their sex determination systems. The presence of environmental sex determination (ESD) as well as genotypic sex determination (GSD) with either XX/XZ or ZZ/ZW sex chromosomes, was reported among the toxicoferan species; however, the current knowledge on sex determination in toxicoferan reptiles is not equally distributed across their lineages. The main aim of the theses is to expand our knowledge on sex chromosome evolution using cytogenetic methods in snakes, chameleons and anguimorphan lizards. The first part of the thesis deals with the sex chromosome evolution in caenophidian and henophidian snakes. It is focused mainly on the variability in the distribution of repetitive content as well as heterochromatinization of the W chromosome of caenophidian snakes. While the sex chromosomes of Caenophidia are cytogenetically quite well...

The present thesis deals with the phenomenon of additional sex chromosomes in Cimex lectularius (Hemiptera: Heteroptera: Cimicidae) using genome size analysis combined with the classical cytogenetic approach. Also, five other cimicid species and 12 species from the family Nabidae were analysed identically for comparative purposes. The thesis also pursues a description of methodical approaches of cytogenetics and flow cytometry in the study of C. lectularius. Recently analysed European specimens of C. lectularius from human host exhibited 12 distinct cytotypes, with a variable number of chromosomes X from two to 20 (2n♂ = 26+X1X2Y to 26+X1-20+Y). The fragmentation hypothesis of C. lectularius additional chromosomes X origin was established in the second half of the 20th century. However, the present genome size measurements suggest that various chromosomal rearrangements as duplication or deletion besides the fragmentation could occur. Males with basic cytotype 2n = 26+X1X2Y had average genome size of 2C = 1.94 pg, in contrast male with 2n = 26+X1-7+Y yielded 2C = 2.26 pg and also specimens with genome size decrease 2C = 1.69 pg appeared. The most informative turned up to be the relative genome size of sperm cells n = 13+X1X2 and n = 13+Y, where specimens with higher chromosome number showed...

Comprendre comment les espèces s'adaptent à leur environnement est un des buts majeurs de la biologie évolutive. Il s'agit d'identifier les gènes responsables des caractères adaptatifs, mais aussi de comprendre les mécanismes généraux de l'adaptation, et des phénomènes empêchant une adaptation optimale. Les régions non-recombinantes sont particulières pour ces aspects. En effet, elles peuvent protéger de la recombinaison des combinaisons d'allèles favorables, et inversement, la suppression de recombinaison peut entraîner une dégénérescence, comme une accumulation de mutations délétères ou des pertes de gènes. Même les organismes à reproduction sexuée possèdent cependant souvent de larges régions non-recombinantes, associées à la détermination du sexe génétique ou du type sexuel. Dans cette thèse, j’ai ainsi étudié les traces d’adaptation et de dégénérescence dans des génomes de champignons pathogènes de plantes. Les champignons du complexe d'espèces Microbotryum violaceum, qui causent la maladie du charbon des anthères chez les Caryophyllacées et comptent des dizaines d'espèces spécifiques d’hôtes différents, sont d'excellents modèles pour l'étude des processus génomiques de l'adaptation. Ils possèdent de plus des chromosomes de types sexuels non-recombinants sur une partie de leur longueur. Pour étudier l'évolution des chromosomes de types sexuels, la dégénérescence et l'adaptation à l'hôte dans le complexe M. violaceum, nous avons adopté diverses approches de génomique. En utilisant la technologie PacBio, nous avons obtenu un assemblage complet des chromosomes de types sexuels pour l'espèce M. lychnidis-dioicae. Nous avons montré que la région non-recombinante s'étend sur 90 % des chromosomes de types sexuels, présente un niveau de réarrangements exceptionnel entre les deux types sexuels, et que des centaines de gènes sont présents à l'état hémizygote et ont donc probablement été perdus dans un type sexuel. De plus, la comparaison des génomes d'une douzaine d'espèces de M. violaceum a montré une accumulation de mutations non-synonymes et d'éléments transposables dans les chromosomes de types sexuels. Nous avons aussi étudié la dégénérescence dans le contexte de l'exposition aux radiations ionisantes, en analysant des populations de M. lychnidis-dioicae exposées à différents niveaux de radiation dans la région de Tchernobyl. Nous n'avons pas détecté d'augmentation du taux de mutations non-synonymes par rapport au groupe témoin, ce qui suggère que le champignon est radio-résistant ou que la sélection est plus forte dans la région de Tchernobyl. Enfin, pour étudier l'adaptation à l’hôte, nous avons reséquencé des dizaines des génomes de deux espèces sœurs de M. violaceum. L'analyse du polymorphisme a révélé des balayages sélectifs tout le long des génomes et à des localisations différentes entre les deux espèces. Nous avons identifié un certain nombre de gènes candidats pour l'adaptation à l’hôte dans ces régions de balayages sélectifs, sur la base de leur expression in planta et de leurs annotations. Les gènes sur-exprimés dans la plante montraient d’autre part un taux de substitutions non-synonymes entre les deux espèces sœurs plus élevé que les autres gènes, ce qui suggère qu’une bonne partie pourrait être impliquée dans l'adaptation à l’hôte. Ces travaux ouvrent la voie à une comparaison des génomes de différentes espèces du complexe M. violaceum, d’une part pour reconstituer l'histoire de la suppression de recombinaison dans les chromosomes de types sexuels, et d’autre part pour étudier les bases génétiques de l'adaptation à différents hôtes dans un complexe d’espèces phylogénétiquement proches. / Understanding how species adapt to their environment is a major goal in evolutionary biology. Scientists aim to identity the genes underlying key adaptive traits, but also to understand more broadly adaptive processes and phenomena that allow or prevent optimal adaptation. Non-recombining regions are particular for these aspects. They can indeed protect adaptive combinations of alleles from recombination, and conversely, suppressed recombination can lead to degeneration, such as accumulation of deleterious mutations or genes losses. Even sexually-reproducing organisms often possess large non-recombining regions associated with sex ou mating-type determination. In this thesis, I therefore studied signatures of adaptation and degeneration in genomes of plant pathogenic fungi. Fungi of the species complex Microbotryum violaceum, with dozens of host-specific sibling species causing anther-smut disease in the Caryophyllaceae family, are particularly good models for addressing the question of the genomic processes involved in host adaptation. Moreover, they possess size-dimorphic, partly non-recombining mating-type chromosomes. To study the evolution of mating-type chromosomes, degeneration and host-adaptation in the M. violaceum species complex, we used a genomic approach. Using PacBio sequencing, we obtained a complete assembly of the mating-type chromosomes of the species M. lychnidis-dioicae. We showed that the non-recombining regions span 90 % of the mating-type chromosomes, exhibit an exceptional level of rearrangements between the two mating-types, and that hundreds of genes are in a hemizygous state and were therefore probably lost in one of the two mating-type chromosomes. Moreover, comparing a dozen of species of the M. violaceum complex revealed an accumulation of non-synonymous substitutions and of transposable elements in mating-type chromosomes. We also studied degeneration in the context of ionizing radiations, by analysing populations of M. lychnidis-dioicae exposed to different radiation levels in the Chernobyl area. We did not detect any increase in the rate of non-synonymous mutations compared to the control group or with radiation, which suggests that the fungi is radio-resistant or that selection is higher in the Chernobyl area. Lastly, we resequenced dozens of genomes of two sibling species of M. violaceum in order to study host adaptation. Analysing polymorphism patterns, we found several selective sweeps along the genome, at different locations in the two species. We identified candidate genes for host-adaptation in the regions of selective sweeps, based on their expression pattern and on their putative functions. In addition, genes up-regulated in planta exhibited a higher rate of non-synonymous substitutions than other genes, suggesting that many of them are likely involved in host adaptation. This work paves the way to a larger comparison of genomes of different species of the M. violaceum species complex, in order to reconstruct the history of recombination suppression on the mating-type chromosomes on the one hand, and to study the genetic bases of adaptation to different hosts in a complex of phylogenetically close species on the other hand.

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...

Snakes (Serpentes) are a group of squamate reptiles (Squamata) including more than 3600 species. The vast majority of snakes are from the group Caenophidia, which includes approximately 90% of all extant snake species and represents the most studied lineage. Squamate reptiles are variable in sex determination and genome organisation, however, caenophidian snakes are quite stable in these respects. The typical - and probably ancestral - snake karyotype is composed of 36 chromosomes with 16 macro- and 20 microchromosomes. In all snake species, genotypic sex determination (GSD) is expected and it was assumed until recently that all snakes possessed ZZ/ZW sex chromosomes. The main reason for this is that most of the studied snakes were from the group Caenophidia and in the rest of the snake lineages it was believed that their sex chromosomes were homologous. In fact, the sex chromosomes of non-caenophidian snakes have not yet been identified - with the single exception of Acrantophis dumerili. Nevertheless, a recent study showed that there was an independent evolution of XX/XY sex chromosomes in pythons and boas. Sex chromosomes of these snakes are homomorphic and so far they have not been detected by classical cytogenetic methods. In this context, the aim of this study is to explore whether it is...

Chez les organismes sexués, des suppressions de recombinaison peuvent évoluer dans certaines régions génomiques pour conserver des combinaisons d’allèles bénéfiques, ce qui aboutit à la transmission de plusieurs gènes en un seul locus, alors appelé « supergène ». Les supergènes déterminent des phénotypes complexes, comme l’identité sexuelle chez les organismes qui ont des chromosomes sexuels. Sur certains chromosomes sexuels, la région sans recombinaison s’est étendue plusieurs fois successivement, produisant des « strates évolutives ». Il est communément admis que ces strates évolutives sont issues de liaisons successives de gènes sexuellement antagonistes (qui ont des allèles bénéfiques à un sexe mais délétère à l’autre) à la région qui détermine le sexe, mais peu de preuves empiriques soutiennent cette hypothèse. Les champignons constituent des modèles intéressants pour étudier les causes évolutives des suppressions de recombinaison parce qu’ils peuvent avoir des chromosomes de types sexuels non recombinants sans être associés à des fonctions mâles ou femelles. Dans cette thèse, nous avons étudié l’évolution de la suppression de recombinaison sur les chromosomes de type sexuel chez les champignons castrateurs de plantes du genre Microbotryum. Chez les champignons Microbotryum, les croisements ne sont possibles qu’entre des gamètes qui ont des allèles distincts aux deux locus de types sexuels. Nous avons montré que les suppressions de recombinaison ont évolué plusieurs fois indépendamment pour lier les deux locus de types sexuels, depuis l’état ancestral avec les locus de types sexuels situés sur deux chromosomes différents. La suppression de recombinaison a soit lié les locus de types sexuels à leur centromère respectif, ou a lié les locus de types sexuels entre eux après que des réarrangements chromosomiques, différents dans les différentes espèces, les aient amenés sur le même chromosome. Les deux sortes de suppression de recombinaison sont bénéfiques sous le mode de reproduction par auto-fécondation intra-tétrade de Microbotryum, parce qu’ils augmentent le taux de compatibilité entre gamètes. Les suppressions de recombinaison ont donc évolué plusieurs fois indépendamment via des chemins évolutifs et des changements génomiques différents, ce qui renseigne sur la répétabilité de l’évolution. De plus, nous avons révélé l’existence de strates évolutives sur les chromosomes de type sexuels de plusieurs espèces de Microbotryum, ce qui remet en cause le rôle de l’antagonisme sexuel dans la formation de strates évolutives, les types sexuels n’étant pas associés à des fonctions mâles / femelles. Des études précédentes ont rapporté peu de différences phénotypiques associées aux types sexuels, ce qui rend peu probable qu’une sélection antagoniste existe entre types sexuels sur de nombreux gènes (l’existence de gènes avec des allèles bénéfiques à un type sexuel mais délétère à l’autre). Certains gènes situés dans les régions non-recombinantes des chromosomes de types sexuels étaient différentiellement exprimés entre types sexuels, mais nos analyses suggèrent qu’un tel différentiel d’expression peut être dû à la dégénérescence. En effet, des mutations délétères s’accumulent dans les régions non-recombinantes, ce qui peut modifier l’expression des gènes ou les séquences protéiques. Nous avons donc conclu que la sélection antagoniste ne peut pas expliquer la formation des strates évolutives chez les champignons Microbotryum. Par conséquent, des mécanismes alternatifs doivent être considérés pour expliquer l’extension progressive des régions non-recombinantes, et ces mécanismes pourraient aussi générer des strates évolutives sur les chromosomes sexuels. Ces travaux incitent de futures études à d’une part identifier d’autres strates évolutives qui ne sont pas associées à des fonctions mâles/femelles, et d’autre part à identifier leurs causes évolutives et leurs conséquences en termes de dégénérescence. / In sexual organisms, recombination suppression can evolve in specific genomic regions to protect beneficial allelic combinations, resulting in the transmission of multiple genes as a single locus, which is called a supergene. Supergenes determine complex phenotypes, such as gender in organisms with sex chromosomes. Some sex chromosomes display successive steps of recombination suppression known as “evolutionary strata”, which are commonly thought to result from the successive linkage of sexually antagonistic genes (i.e. alleles beneficial to one sex but detrimental to the other) to the sex-determining region. There has however been little empirical evidence supporting this hypothesis. Fungi constitute interesting models for studying the evolutionary causes of recombination suppression in sex-related chromosomes, as they can display non-recombining mating-type chromosomes not associated with male/female functions. Here, we studied the evolution of recombination suppression on mating-type chromosomes in the Microbotryum plant-castrating fungi using comparative genomic approaches. In Microbotryum fungi, mating occurs between gametes with distinct alleles at the two mating-type loci, as is typical of basidiomycete fungi. We showed that recombination suppression evolved multiple times independently to link the two mating-type loci from an ancestral state with mating-type loci on two distinct chromosomes. Recombination suppression either linked the mating-type genes to their respective centromere or linked mating-type loci after they were brought onto the same chromosome through genomic rearrangements that differed between species. Both types of linkage are beneficial under the intra-tetrad mating system of Microbotryum fungi as they increase the odds of gamete compatibility. Recombination suppression thus evolved multiple times through distinct evolutionary pathways and distinct genomic changes, which give insights about the repeatability and predictability of evolution. We also reported the existence of independent evolutionary strata on the mating-type chromosomes of several Microbotryum species, which questions the role of sexual antagonism in the stepwise extension of non-recombining regions because mating-types are not associated with male/female functions. Previous studies reported little phenotypic differences associated to mating-types, rending unlikely any antagonistic selection between mating types (i.e. “mating-type antagonism”, with genes having alleles beneficial to one mating-type but detrimental to the other). The genes located in non-recombining regions on the mating-type chromosomes can be differentially expressed between mating types, but our analyses indicated that such differential expression was more likely to result from genomic degeneration than from mating-type antagonism. Deleterious mutations are indeed known to accumulate in non-recombining regions resulting in modifications of gene expression or of protein sequence. We concluded that antagonistic selection cannot explain the formation of evolutionary strata in Microbotryum fungi. Alternative mechanisms must be therefore be considered to explain the stepwise expansion of non-recombining regions, and they could also be important on sex chromosomes. This work thus prompts for future studies to identify further evolutionary strata not associated with male/female functions as well as to elucidate their evolutionary causes and consequences in terms of genomic degeneration.