Dissertations / Theses on the topic 'Cryptic sex'

Bibliography: pages 163-179.
Spirostreptida millipedes comprise three families, the Harpagophoridae, Spirostreptidae and Odontopygidae. They are polygynandrous. Males transfer sperm via species-specific accessory genitalia called gonopods, that comprise three components, two of which, the emote and telopodite, are involved in processes of sperm transfer. The emotes function to translocate ejaculates from the penes to the vulvae, where they are stored. A delay between insemination and fertilisation provides an arena for syn- and postcopulatory sexual competition. These operate at the gametic level via sperm competition and cryptic female choice. By combining studies of genital form and function with single and double mating experiments, this study elucidates these processes in some southern African Spirostreptida millipedes.

Sexual reproduction entails complex co-evolution between the sexes, necessary for successful fertilization, ensuring individual and population-level fitness. Interfertility is the main criterion for species definition and understanding speciation requires detailed studies of reproductive barriers. However, many studies on reproductive barriers are constrained to infer evolutionary processes from patterns. In this thesis, I focus on a hybrid zone between collared and pied flycatchers (Ficedula albicollis and hypoleuca) on the island of Öland, and a trait that is essential for fertilization: sperm. Long-term monitoring of these species, combined with recent advances in molecular tools, allow me to study how complex on-going intersexual and interspecific interactions influence reproductive isolation in this young hybrid zone. I start by exploring the links between pre- and postmating sexual selection within collared flycatchers (paper I and II). I show that secondary sexual characters and indirect mate-choice benefits are tightly linked to physiology (paper I), and that a male’s attractiveness and dominance status dictate which sperm traits are optimal, as a male’s fertilization success depends on an interaction between sperm and display traits (paper II). I then report a source of strong postzygotic isolation between recently diverged collared and pied flycatchers: impaired spermatogenesis resulting in absence of mature sperm cells in hybrid males (paper III). I show however that pied flycatcher females, who are most exposed to hybridization, can mitigate these costs through mechanisms of cryptic female choice impairing heterospecific sperm performance, allowing them to bias paternity towards pure-species offspring (paper IV). Finally, by exploring the testes transcriptomes and sperm proteomes of both species, I highlight the importance of gene and protein regulation mechanisms in facilitating phenotypic divergence between these species (paper V). Thus, my thesis reveals complex interactions between primary and secondary sexual characters in a wild bird and suggests that mechanisms of sexual selection are tightly linked to essential physiological functions. I also show that genetic incompatibilities can evolve rapidly despite low genome-wide levels of divergence but that divergence in regulatory regions and proteins potentially allows fast evolution of molecular mechanisms impairing or preventing costly heterospecific fertilization.

La majorité des espèces parthénogétiques sont souvent perçues comme clonales. La clonalité est coûteuse à long terme, car elle peut entraîner l'accumulation de mutations délétères et une moins bonne capacité d’adaptation. Cependant, les cas d’espèces asexuées non clonales s'accumulent. L’asexualité non-clonale génère des conséquences génomiques et de fitness très différentes de la clonalité, et pourraient représenter une étape-clé dans la transition du sexe vers l’asexualité. De plus, l’asexualité peut être souvent non-obligatoire, avec des événements de sexe cryptiques. Ces évènements peuvent aussi façonner le génome et l'évolution des lignées asexuées. Dans cette thèse, j'ai étudié le mode de reproduction d'Artemia parthenogenetica, et son rôle dans la transition du sexe vers l'asexualité et l'évolution des lignées asexuées. En particulier, j'ai utilisé la capacité des mâles produits par voie asexuée (“mâles rares”) à se croiser avec des femelles sexuées et à transmettre l’asexualité à leurs descendants (asexualité contagieuse), pour générer expérimentalement de nouvelles lignées. J’ai montré que les Artemia asexués diploïdes ont un mode de reproduction non-clonal, dans lequel la recombinaison entraîne une perte d'hétérozygotie (LOH, pour “loss of heterozygosity”) chez les descendants. Le LOH est coûteux car il peut révéler des mutations délétères récessives. Peut-être en raison de la sélection causée par les conséquences délétères du LOH, le taux de recombinaison chez les Artemia asexués était plus faible que chez une espèce sexuée apparentée. J'ai également constaté que les hybrides sexués avaient une reproduction mixte sexuée et asexuée, et que les femelles asexuées issues de populations naturelles étaient capables de sexe rare. Cela signifie que des événements rares de sexe chez les Artemia asexués pourraient se produire entre un mâle rare et une femelle asexuée se reproduisant sexuellement. En effectuant une revue de la façon don t les modes de reproduction asexués sont identifiés dans la littérature, j'ai constaté que l'identification et la perception générale des asexués étaient biaisées en faveur de la clonalité, car une grande partie des espèces asexuées examinées étaient en fait non-clonales, et les preuves de la clonalité étaient souvent insuffisantes. En outre, la majorité des asexués non-clonaux avaient des modes de reproduction qui entraînaient de faibles taux de LOH. Cela suggère que les asexués non-clonaux évoluent souvent secondairement vers une reproduction plus clonale. Ainsi, même les espèces clonales pourraient ne pas avoir été clonales au cours de leur histoire évolutive. Enfin, avec une analyse génomique sur de nouvelles lignées générées par contagion, j'ai démontré que chez Artemia, les mâles rares sont produits asexuellement par recombinaison et donc LOH sur les chromosomes sexuels ZW. Nous savons que l'asexualité contagieuse, et peut-être des croisements entre lignées, ont eu lieu au cou rs de l'histoire évolutive d'A. parthenogenetica. L'asexualité contagieuse et/ou des événements sexuels chez les asexués constituent peut-être des opportunités pour que le(s) gène(s) contrôlant l'asexualité s'échappe(nt) des lignées en déclin vers de nouvelles lignées. Dans ce cas, l'asexualité contagieuse par le biais de mâles rares pourrait être la raison pour laquelle la recombinaison persiste chez les Artemia asexués. Chez de nombreuses espèces, l’identification de l’asexualité non clonale et des événements de sexe n'est toujours pas claire et nécessite une étude approfondie. Théoriquement, il y a un fort besoin de modèles prenant en compte les conséquences génomiques de l'asexualité non-clonale et non-obligatoire, et leur rôle dans la transition du sexe vers l'asexualité et la maintenance du sexe
The majority of parthenogenetic species are often thought to be clonal. Clonality is costly in the long term, as it can result in accumulation of deleterious mutations and lower adaptability. However, cases reporting non-clonal asexuals are accumulating. Non-clonal asexuality has very different genomic and fitness consequences compared to clonality, and may be a key intermediate step in the transition from sex to asexuality. Additionally, asexuality may be often non-obligate, with events of cryptic sex. These events may also shape the genome and evolution of asexual lineages. In this PhD, I investigated the reproductive mode of Artemia parthenogenetica and its role in the transition from sex to asexuality and the evolution of asexual lineages. Specifically, I used the capacity of asexually produced males (“rare males”) to cross with sexual females and transmit asexuality to their offspring (contagious asexuality), to experimentally generate new lineages. I showed that diploid asexual Artemia have a non-clonal reproductive mode, in which recombination results in loss of heterozygosity (LOH) in the offspring. LOH is costly as it can reveal recessive deleterious mutations. Perhaps due to selection caused by the deleterious consequences of LOH, the recombination rate in these asexuals was lower than in a closely related sexual species. I also found that sex-asex hybrids had a mixed sexual and asexual reproduction, and that asexual females from natural populations were capable of rare sex. This means that rare events of sex in asexual Artemia could occur between a rare male and an asexual female reproducing sexually. In a review of how asexual reproductive modes were identified in the literature, I found that there was a bias in the identification and general perception of asexuals toward clonality, as an important part of the asexual species reviewed were in fact non-clonal, and evidence for clonality was often missing. Furthermore, the maj ority of non-clonal asexuals had reproductive modes that resulted in low LOH. This suggests that non-clonal asexuals often evolve secondarily toward a more clonal-like reproduction, so that even clonal species may not have been clonal throughout their evolutionary history. Finally, using genomics on contagion-generated lineages, I found that in Artemia, rare males are produced asexually through recombination and thus LOH on the ZW sex chromosomes. We know that contagious asexuality, and possibly between-lineages crosses, occurred in the evolutionary history of A. parthenogenetica. Perhaps, contagious asexuality and/or within asexual sex events provide opportunities for the gene(s) controlling asexuality to escape declining lineages into new ones. In this case, contagious asexuality through rare males may be the reason why recombination persists in asexual Artemia. Whether non-clonal asexuality and sex events occur in many parthenogenetic species is still unclear, and requires thorou gh investigation. Theoretically, there is a strong need for models taking into account the genomic consequences of non-clonal and non-obligate asexuality, and their role in the transition from sex to asexuality and the maintenance of sex

[ES] El género de copépodos Tigriopus Norman, 1869 se distribuye en todo el mundo en piscinas costeras de rocas y actualmente se considera que incluye 15 especies válidas. Tigriopus fulvus (Fischer, 1860), con su subespecie Tigriopus fulvus adriaticus Van Douwe 1913 y Tigriopus fulvus algiricus Monard 1935, actualmente se informa que ocurren en el área mediterránea, pero actualmente se desconoce la diversidad real del género. Nuestro objetivo fue evaluar la identidad real de las poblaciones mediterráneas de Tigriopus y dilucidar su taxonomía y patrón de diversidad genética. Para alcanzar estos objetivos, utilizamos dos enfoques diferentes. El primero, basado en la morfología, donde las posibles diferencias morfológicas entre muestras topotípicas de Tigriopus fulvus s.s. y muestras topotípicas de las dos subespecies fueron investigadas. Un segundo, sobre una base molecular, donde se secuenciaron fragmentos de dos genes de ADN mitocondrial (subunidad I de citocromo c oxidasa, COI y subunidad de ARN ribosómico pequeño, 12S) y un gen de ADN nuclear (28S) para ser usados como marcador de referencia. En este marco, se utilizaron enfoques taxonómicos moleculares, como el descubrimiento automático de brechas de código de barras (ABGD), bPTP (procesos de árbol de Poisson bayesianos) y la relación K / ¿, para investigar la existencia de las supuestas subespecies de Tigriopus a través de la identificación de Operacional Unidades Taxonómicas (OTU). Nuestros datos sugieren la presencia de una sola especie caracterizada por una notable estructura genética basada en la geografía en toda el área de estudio. El patrón de diversidad observado se atribuye tentativamente aquí a una fuerte monopolización de los estanques de rocas por parte de los primeros inmigrantes que los alcanzan. Sin embargo, tal monopolización se ve interrumpida periódicamente por los eventos de extinción locales, que son frecuentes en los hábitats intrínsecamente inestables de las piscinas de rocas Aquí proponemos para este patrón el nombre de "monopolización periódica" ("Clockwork monopolization").
[CA] El género de copépodos Tigriopus Norman, 1869 se distribuix en tot el mon en piscines costeres de roques i actualment se considera que inclou 15 especies valides. Tigriopus fulvus (Fischer, 1860), en la seua subespecie Tigriopus fulvus adriaticus Van Douwe 1913 i Tigriopus fulvus algiricus Monard 1935, actualment s'informa que ocorren en l'area mediterranea, pero actualment se desconeix la diversitat real del género. Nostre objectiu fon evaluar l'identitat real de les poblacions mediterranees de Tigriopus i dilucidar la seua taxonomia i patrón de diversitat genetica. Per a alcançar estos objectius, utilisem dos enfocaments diferents. El primer, basat en la morfologia, a on les possibles diferencies morfologiques entre mostres topotípicas de Tigriopus fulvus s.s. i mostres topotípicas dels dos subespecies foren investigades. Un segon, sobre una base molecular, a on se secuenciaron fragments de dos gens d'adn mitocondrial (subunidad i de citocromo c oxidasa, coi i subunidad d'arn ribosómico menut, 12s) i un gen d'adn nuclear (28s) per a ser amprats com marcador de referencia. En este marc, s'utilisaren enfocaments taxonomics moleculars, com el descobriment automatic de breches de codic de barres (ABGD), bPTP (processos d'arbre de poisson bayesianos) i la relacio K/¿, per a investigar l'existencia de les supostes subespecies de Tigriopus a través de l'identificacio d'operacional unitats taxonomiques (OTU). Nostres senyes sugerixen la presencia d'una sola especie caracterisada per una notable estructura genetica basada en la geografia en tota l'area d'estudi. El patrón de diversitat observat s'atribuix tentativament aci a una forta monopolisacio dels safarejos de roques per part dels primers immigrants que els alcancen. No obstant, tal monopolisacio se veu interrompuda periodicament pels events d'extincio locals, que son freqüents en els hábitats intrinsecament inestables de les piscines de roques aci proponem per a este patrón el nom de "Monopolisacio Periodica" ("Clockwork Monopolization").
[EN] The copepod genus Tigriopus Norman, 1869 is distributed worldwide in coastal rock-pools and it is currently considered to include 15 valid species. Tigriopus fulvus (Fischer, 1860), with its subspecies Tigriopus fulvus adriaticus Van Douwe, 1913 and Tigriopus fulvus algiricus Monard, 1935, are currently reported to occur in the Mediterranean area, but the actual diversity of the genus is currently unknown. We aimed to assess the actual identity of Mediterranean Tigriopus populations and to elucidate their taxonomy and pattern of genetic diversity. In order to reach these goals, we use two different approaches. The first, based on morphology, where the possible morphological differences among topotypical samples of Tigriopus fulvus s.s. and topotypical samples of the two subspecies were investigated. A second, on a molecular basis, where fragments of two mitochondrial DNA genes (cytochrome c oxidase subunit I, COI and small ribosomal RNA subunit, 12S) and a nuclear DNA gene (28S) were sequenced to be used as a reference marker. In this frame, molecular taxonomical approaches, such as Automatic Barcode Gap Discovery (ABGD), bPTP (bayesian Poisson Tree Processes) and K/¿ ratio, were used in order to investigate the existences of the alleged subspecies of Tigriopus through the identification of Operational Taxonomic Units (OTUs). Our data suggest the presence of a single species characterized by a noteworthy geographically-based genetic structure in the whole study area. The observed diversity pattern is tentatively ascribed here to a strong monopolization of the rock pools by the first immigrants that reach them. However, such a monopolization is periodically disrupted by local extinction events, which are frequent in the intrinsically unstable rock pool habitats. We propose the name "clockwork monopolization" for this pattern.
Vecchioni, L. (2020). Systematics and phylogeography of the genus Tigriopus (Copepoda, Harpacticoida, Harpacticidae) in the basin of the Mediterranean Sea [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/144122
TESIS

The upland (Pseudacris feriarum) and midland (P. triseriata) chorus frogs are closely related cryptic species that are best distinguished genetically. The distribution of these species within the Commonwealth of Kentucky has previously been defined by only a handful of genetic samples, making delineation of range limits for each species difficult. Accurate understanding of species distributions, and the genetic structure within them, are vitally important for conservation management of amphibian species. In this study, I have collected genetic samples from across the putative ranges of P. triseriata and P. feriarum in Kentucky and used next-generation sequencing technology to generate more fine-scale estimates of species ranges. The genetic data generated in this study support the delineation of two species in Kentucky, and the species assignments of all individuals and populations are in general concordance with the previously hypothesized species distributions. However, I have identified two previously unrecognized contact zones for these species and revealed areas of hybridization. By delineating species distributions and identifying potentially important regions of genetic admixture, this study will be informative to future conservation management and conservation genetic research of chorus frogs in Kentucky.

Money laundering is a non-violent crime, however when successfully executed it has a negative impact on society, as it tends to support other illicit activities, including terrorism. As was the case for other financial crimes, the internet opened the door for new tools that enable criminals to launder their illicit profits. One of these tools is cryptocurrency.This paper takes the form of a literature review, in order to find the most relevant and important work within the research topic, and to identify central issues associated with laundering money through cryptocurrencies. It aims to explain the crypto-laundering process, methods and features that make cryptocurrencies tempting to criminals when searching tools to launder their illicit profits.The findings of this literature review demonstrate that cryptocurrencies have more characteristics that appeal to launderers than deters them. The results also show the existence of different methods that are employed in crypto-laundering and how it mirrors traditional money laundering stages, making evident that crypto-laundering is a real threat. Due to these results, it is essential that the criminological community delve into financial crimes perpetrated in the online environment.

Up until now, Bitcoin as a marketing tool to leverage the brand image of an e-retailer has only been researched scarcely. This paper contributes to filling this gap by looking at Bitcoin’s suitability as primarily a cognition-based trust-building tool in the context of online sex shops. Online sex shops in which affective-based trust is taken as a use-case to exemplarily assess whether far associations customers have with Bitcoin can be transferred unto their brand image, assessing its effectiveness. Moreover, as Bitcoin is a payment method, this study feels the pulse in how far trust is established with the general public to assess chances of success when introducing it as an option to existing alternatives. Trust is considered important in the transaction and decision-making processes of a customer as much as it is in building and fostering brand image. Two expert interviews and one survey make up the data source for this research to gain a holistic view from the customer’s, the retailer’s and the industry expert’s perspective. Findings from the different sources were first in-case analyzed before cross-comparing them. The study highlighted the fact that Bitcoin as a marketing tool is highly case-sensitive, cognition-based, and risky in both - financial and marketing terms. It is best used as part of a long-term strategy and in cases in which the brand image of a brand is as similar to that of Bitcoin as possible. Additionally, Bitcoin disposes of many of the same qualities as other payment methods do and although trust in it is still limited, it is competitive in terms of factors like transaction speed and cost. There is no uniform bundle of associations and a positive or negative evaluation thereof to be connected to it, however, factors like gender, financial education, and trust in one’s own abilities are all found to influence trust and usage intention. The study finds potential for both – Bitcoin as a marketing tool and payment method.

L’originalité du golfe de Gabès (Sud de la Tunisie) a été reconnue par les malacologistes depuis le19ème siècle mais reste mal définie. Les espèces de cette région présentent des caractères morphologiques qui ont conduit à l’établissement de variétés, sous-espèces et espèces faiblement caractérisées. Certains auteurs les traitent comme des taxons endémiques tandis que d'autres les considèrent comme de simples variants locaux d'espèces à large répartition méditerranéenne. Le manque d’information concernant la valeur taxonomique de ces caractères morphologiques ne permet pas de traiter de façon robuste la question de l’endémisme dans le golfe de Gabès. Le premier objectif est de réviser le statut taxonomique des mollusques du golfe de Gabès en s’appuyant sur une approche de taxonomie moléculaire. La confrontation des différents caractères a permis d’identifier ceux qui discriminent correctement les individus en espèces, d’éliminer à l’inverse ceux qui ne remplissent pas cette fonction et d’en redéfinir de nouveaux. Le deuxième objectif est de relier les particularités faunistiques du Golfe à ses caractéristiques océanographiques et de discuter les phénomènes de spéciation qui pourraient être à l’origine de l’endémisme. Nos analyses ont porté sur six genres: Jujubinus (Trochidae), Diodora (Fissurellidae), Ocinebrina, Muricopsis (Muricidae), Aplus (Buccinidae) et Tritia (Nassariidae). L’approche intégrative utilisée a permis de proposer des hypothèses de délimitation d’espèces que nous avons ensuite confrontées aux données morphologiques et géographiques. Au final, l’endémisme est confirmé dans certains cas mais l’hypothèse qu’une partie des espèces décrites du golfe de Gabès ne sont que des variétés éco phénotypiques est également attestée. Notre approche moléculaire a mis aussi en évidence l’existencede nouvelles espèces et d’espèces cryptiques insoupçonnées dans la Méditerranée. Finalement l’hypothèse que le golfe de Gabès est un centre de spéciation est retenue. Plus de données moléculaires (reliées à des données fossiles) d’autres groupes provenant de différentes localités (spécialement du golfe de Syrte) apparaissent toutefois nécessaires
The present Mediterranean marine fauna is the result of a history going back to the Messinian Salinity Crisis, with current biogeographical patterns mostly reflecting Quaternary to modern oceanographic conditions. The Gulf of Gabès, in southern Tunisia, is remarkable for its extreme ecological characteristics that distinguish it from "ambiant" Mediterranean conditions. Starting with the work of malacologists at the turn of the 19th-20th centuries, the molluscs of the Gulf of Gabès have been recognized as exhibiting morphological characters that set them apart from more typical forms that occur in the rest of the Mediterranean. At present, 6% of the species of the overall Gulf of Gabès mollusc fauna are treated as valid local endemics. Using an integrative taxonomy approach, combining molecular and morphological data, the objective of the study is to re-evaluate the status of these Gulf of Gabès local forms: are they valid, endemic species or do they represent ecophenotypic variation? Given the young geological age (6-8 ka) of the Gulf, where would local endemics have originated? The gastropod genera Jujubinus (Trochidae), Diodora (Fissurellidae), Tritia (Nassariidae) Ocinebrina (Muricidae), Muricopsis (Muricidae) and Aplus (Buccinidae) all have in common non-planktotrophic larval development. Our integrative approach confirms the validity of some of the endemic taxa, but also infirm that others are not valid species; molecular data also reveal unsuspected cryptic lineages both within and outside the Gulf. Regarding the question of the origin of the endemic species, various hypotheses have been proposed, one of them being that the Gulf of Gabès is a “speciation factory”. To formally test this hypothesis, more molecular data (coupled with fossil record data) are needed from other species groups and from other localities in the Mediterranean (specifically the Gulf of Syrte)

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES
In Portugal and in Spain, for a very long time a belief was cultivated about the Jews, that when being expelled from the Iberian Peninsula, at the beginning of the Modern Age, hid in certain places treasures to be rescued in posterity. Despite this account being cloaked in an atmosphere of mystery and distorted by imagination, in the hope that many nurture of finding riches in gold and jewels, there is evidence that these hidden riches consisted of censored books since, fleeing to other christian countries, they couldn’t take it with them. So in 1992, to corroborate this account, when in the modest Spanish village of Barracota a house was being remodeled, a “kept treasure”, hid by screens in a space between walls, was found. It was a heterogeneous set of 10 prints, a manuscript and a nômina. From those surprising finding its unveiled by extremeño Professor Fernando Serrano Mangas, that the set of clandestine books was hidden around 1557 by Crypto-jew Doctor Francisco Peñaranda. Therefore, this dissertation seeks to illustrate, starting from the analysis of the works “Alborayque” and “A muito devota oração da emparedada”, the mystic crypto-jewish universe and its paths in the 16th century’s contour. Working in this perspective according to the evidentiary method, proposed by Carlo Ginzburg, to highlight fundamental elements from the world vision of this minority that was the object of persecution by the Modern Inquisition.
Durante muito tempo, em Portugal e na Espanha, se cultivou a crença de que os judeus ao serem expulsos da Península Ibérica, no início da Idade Moderna, esconderam tesouros em determinados locais para serem resgatados na posteridade. Apesar desse relato está envolto em um clima de mistérios e também ser distorcido pela imaginação popular, na esperança que muitos acariciam de encontrar riquezas em joias e metais preciosos, existem indícios de que essas riquezas encobertas eram constituídas por livros censurados uma vez que, em sua fuga para outros países cristãos, eles não poderiam levá-los consigo. Assim, para corroborar com esse relato, em 1992 quando era realizada a reforma de uma secular residência na pacata vila de Barcarrota, na Espanha, foi encontrado um “tesouro oculto” escondido por tapumes num espaço vazio existente entre as paredes. Tratava-se de um conjunto heterogêneo de dez impressos, um manuscrito e uma nômina. A partir dessa surpreendente descoberta é desvelado, pelo historiador e professor extremeño Fernando Serrano Mangas, que esse conjunto de livros clandestinos foi ocultado pelo médico criptojudeu Francisco de Peñaranda, por volta de 1557. Portanto, essa dissertação procura ilustrar, a partir da análise das obras “Alborayque” e “A muito devota oração da emparedada”, o universo místico criptojudaico e seus meandros no contorno do século XVI. Nessa perspectiva, trabalhamos segundo o método indiciário, proposto por Carlo Ginzburg, para destacar elementos fundamentais da cosmovisão dessa minoria que foi objeto de perseguição pela Inquisição Moderna.
São Cristóvão, SE

Dictyostelium discoideum serves as an ideal system to study social evolution because of the social stage of its lifecycle, where individuals aggregate to build a multicellular structure. However, much of its basic biology remains unknown and this limits its utility. I used three separate projects to fill these gaps. In my first project, I examined how speciation and genetic diversity affects kin discrimination using a related dictyostelid, Polysphondylium violaceum . I sequenced the ribosomal DNA of 90 clones of P. violaceum and found that P. violaceum is split into several morphologically identical groups. When allowed to cooperate in pairwise mixes, I found that some clones cooperated with others in their group, but in mixes between groups, clones did not cooperate. For my second project, I looked at whether D. discoideum has sex in natural populations. While sex has been observed in laboratory clones of D. discoideum , it is unclear whether sex occurs in natural populations, and sex can influence the evolution of traits. I used a dataset of microsatellites in 24 clones of D. discoideum to look for a decrease in linkage disequilibrium as a molecular sign of sex. Linkage disequilibrium is higher between physically close loci than between loci on different chromosomes. From this, I conclude that D. discoideum undergoes recombination in nature. Lastly, I used the genome sequence of D. discoideum to look at large scale patterns of evolution. Mutations tend to be biased towards A/T from G/C so, on average, mutations should lower the nucleotide content of sequences. The removal of these mutations, purifying selection, should preserve nucleotide content. I used the genomes of D. discoideum and Plasmodium falciparum identify classes of sequences that should be under different amounts of purifying selection and compared their nucleotide contents. In all cases, those sequences under more purifying selection had higher GC contents than sequences under less purifying selection. Looking at relative nucleotide content may thus serve as an indicator purifying selection. These three studies add insight on how cooperation works in dictyostelids as well as adding an understanding of how traits, social and otherwise, would evolve in this system.

Postcopulatory sexual selection—sperm competition and cryptic female choice—has become a major area of research over the past 40 years. Within this field there are many outstanding questions at every level of analysis, from proximate to ultimate. The fitness consequences for both sexes in the period after copulation and before fertilization are considerable, but are obscured within the female reproductive tract. Our understanding of postcopulatory mechanisms is especially sparse in taxa other than birds and insects. Nearly nothing is known in reptiles except that multiple paternity is common and widespread, and often results from long-term sperm storage across breeding seasons. We present some of the very first data on the determinants of fertilization success in the context of sperm competition in reptiles, a group that accounts for 30% of terrestrial vertebrates. In the first chapter, "Asymmetric gametic isolation between two populations of red-sided garter snakes", we discuss the use of between-population crosses to reveal gametic isolation. The effect of population density and operational sex ratios on mating systems and the speciation process has fueled theoretical debate. We attempted to address these issues using two populations of red-sided garter snakes (Thamnophis sirtalis parietalis) from Manitoba, Canada. Our study populations differ markedly in their density mating aggregations, with a 10-fold difference between them. Using microsatellite markers for paternity analysis of litters produced from within and between population crosses. We found that the population with highest aggregation density, and presumably with the highest level of sexual conflict (i.e., when the evolutionary interests of the sexes differ) over mating, was also the population that exhibited homotypic sperm precedence. The less dense population showed a distinct postcopulatory male-size advantage. We also demonstrated that sperm stored within the female over hibernation can father 20-30% of offspring in a litter. In the second chapter, "Sperm competition and mate-order effects in red-sided garter snakes", we test whether females use mate-order effects to ensure that a larger (fitter) male will sire her offspring. Does that second male should have precedence in sperm competition? We tested for second-male precedence using singly-mated females that mated with a second male. Average proportion of paternity was shared equally among the first (P₁, i.e., proportion of offspring from a litter fathered by the first male to mate) and second males (P₂) to mate, and stored sperm (P[subscript ss]). This may be a case where last male precedence breaks down with more than two males. All females were spring virgins (they had not mated that spring, but may have stored sperm from fall matings); thus sperm stored presumably from fall matings is important in this system. As the interval between matings increased P₁ increased at the expense of P[subscript ss]. As the second male to mate's copulation duration increased, P₁ also increased at the expense of P₂. This last result may indicate female influence over sperm transfer during coerced matings. Copulatory plugs (CPs) are found in many taxa, but the functional significance is debated. Male garter snakes produce a gelatinous copulatory plug during mating that occludes the opening of the female reproductive tract for approximately two days. In chapter three, "Not just a chastity belt: the role of mating plugs in red-sided garter snakes revisited", we experimentally tested the role of the CPs. In snakes, sperm are produced in the testes and delivered through the ductus deferens, and the copulatory plug is thought to be produced by the sexual segment of the kidney and conveyed through the ureter. We manipulated the delivery of the two fluids separately by ligating the ducts. We confirmed that the CP is not formed in ureter-ligated males and that sperm leaks out immediately after copulation. The CP is analogous to a spermatophore. The protein matrix contains most of the sperm which are liberated as the plug dissolves within the female's vaginal pouch. One of the fundamental principles in sperm competition is that increased sperm numbers increase the odds of winning in competitions for fertilization success and males will adjust their ejaculate relative to competition and the quality of his mate. In chapter four, "Sperm depleted males and the unfortunate females who mate with them", we detect significant among-male variation in the number of sperm ejaculated, and that male mate-order reduces sperm numbers. Male sperm numbers drop significantly from one mating to the next, and this has implications for sperm competiveness, as Thamnophis sirtalis exhibits a disassociated reproductive tactic, in that sperm stores are produced outside the breeding season, and thus cannot be replenished after mating. Interestingly, however, the on average the mobility of the sperm increased for a male's second mating. Therefore, increased sperm quality may compensate for reduced numbers in a competitive context. Further, females increase their remating rate when mating with males that are unable to deliver sperm. In chapter five, "Sexual conflict during mating in red-sided garter snakes as evidenced by genital manipulation", we revisited the CP in the context of sexual conflict. Sex-differences in optimal copulation duration can be a source of conflict, as increased copulation duration may be advantageous for males as it delays female remating. Males of many species actively guard females to prevent them from remating, and in some cases males produce copulatory plugs to prevent remating. If precopulatory choice is limited at the time of her first mating, conflict may be especially onerous to a female. The size of the plug is influenced by the copulation duration. We experimentally tested the contribution of male and female control over copulation duration. We ablated the largest basal spine on the male's hemipene and found a reduction in copulation duration and an increase in the variation of plug mass. Further, we anesthetized the female's cloaca and found copulation duration increased, which suggests that males benefit from increased copulation duration while females actively try to reduce copulation duration. Therefore, sexual conflict is manifest in divergent copulation duration optima for males and females.
Graduation date: 2013

It has been estimated that coral reefs shelter 830 000 species. Well-studied biodiversity patterns provide tools for better representation of species in marine protected areas. A cross-shelf gradient in biodiversity exists for fishes, corals, and macroalgae. Here, an inshore to offshore gradient in biodiversity on the Saudi Arabian coast of the Red Sea was sampled using Autonomous Reef Monitoring Structures (ARMS) with barcoding and metabarcoding techniques. It was hypothesized that differences in community structure would be driven by an increase in habitat area. The difference was attributed to the greater accumulation of sediments close to shore that increases the area habitable for sediment dwelling organisms and favors macroalgal cover. Macroalgae are inhabited by a greater number of species than live coral. Only 10% of the sequences of the barcoded fraction and <1% of the metabarcoded fraction had a BLAST hit on the NCBI database with a previously identified species sequence. In addition, the rarefaction curves for all fractions did not plateau. The ARMS community composition changed from inshore to offshore and was significantly correlated with the percentage of algal and bryozoan plate cover. The differences in community composition were related to changes in habitat but not to sediments retrieved from the ARMS.

Les expériences de séquençage à haut débit ont permis de démontrer que la transcription ne se limite pas aux régions codantes et qu’une grande partie du génome est transcrite en ARN non-codants (ARNnc). Parmi eux, les transcrits cryptiques sont initiés à l’intérieur des régions codantes. Des études faites chez la levure Saccharomyces cerevisiae, ont pu identifier plusieurs facteurs qui répriment la transcription cryptique. Un de ces facteurs est Spt6, une chaperonne d’histones requise pour le maintien d’un bon niveau de nucléosomes le long des gènes transcrits. Lorsque Spt6 est muté, on observe une déplétion des nucléosomes conduisant à l’activation des promoteurs cryptiques. Cependant, le mécanisme par lequel ces transcrits cryptiques sont régulés n’est pas encore clair. Dans ce mémoire, nous présentons un travail dans lequel nous avons développé une méthode probabiliste dans le but de caractériser les transcrits cryptiques à partir de données de RNA-Seq. Cette méthode est basée sur une cumulation des données et permet de tenir compte des variations dans l’expression et dans la longueur des gènes, grâce à une étape de randomisation des données. Les résultats démontrent que notre méthode est au moins aussi efficace que les méthodes précédemment décrites dans la littérature et offre un bon compromis entre le taux de faux positifs et de faux négatifs. Enfin, le plus important est que cette méthode permet de prédire les régions génomiques où les transcrits cryptiques sont initiés. Nous avons mis en évidence la présence de transcrits cryptiques sur les brins sens et antisens par rapport au gène. Nous avons également montré que les promoteurs cryptiques sens et antisens sont enrichis en motif TATA et que les transcrits cryptiques sont polyadénylés, ce qui suggère qu’ils peuvent être régulés par les mêmes mécanismes qui régulent les gènes. Alors que les transcrits cryptiques sur le brin sens se terminent à la même position que les gènes dont ils sont issus, les transcrits cryptiques sur le brin antisens terminent préférablement aux extrémités 3’ des gènes situés en amont. Nous proposons donc que les terminateurs chez S. cerevisiae ont évolué pour terminer la transcription de manière bidirectionnelle afin d’empêcher une transcription aberrante qui pourrait envahir les gènes voisins.
High throughout sequencing experiments have shown that transcription in not limited to coding regions and that most of the genome is transcribed into non-coding RNA (ncRNA). Among them, cryptic transcripts are aberrantly initiated from within the coding regions. Several studies in Saccharomyces cerevisiae have identified many factors that suppress cryptic transcription. One such factor is Spt6, a histone chaperone required for maintaining appropriate nucleosome levels on transcribed genes. In Spt6 mutant cells, nucleosomes are depleted, leading to activation of cryptic promoters. However, the mechanism by which these cryptic transcripts are regulated remains unclear. In this thesis, we present the development of a probabilistic method for the characterization of cryptic transcripts from RNA-Seq data. The method is used to characterize cryptic transcription in spt6-1004 cells. The method is based on a cumulative distribution function, thus taking into account variations in gene expression and gene length thanks to a data randomization step. Results show that our method is at least as good as previously published methods and provides a good compromise between false positives and false negatives. Importantly, this method allows for the prediction of genomic regions where cryptic transcripts are initiated. We have demonstrated the presence of cryptic transcripts running on the sense and antisense strands relative to genes. We also showed that, both sense and antisense cryptic promoters are enriched for TATA-like sequences and that cryptic transcripts are polyadenylated, suggesting that they may be regulated by the same mechanism that occurs on genes. While the cryptic transcripts on the sense strand terminate at the same position as the genes from which they are derived, cryptic transcripts on the antisense strand preferentially terminate at the 3’-end of upstream genes. We therefore propose that S. cerevisiae terminators have evolved to terminate transcription bidirectionally in order to prevent an aberrant transcription that could invade neighboring genes.

The thesis deals with phylogeny, taxonomy and nomenclature of selected groups of the lichen genus Caloplaca. Particularly, the C. cerina group was closely investigated using molecular methods (ITS sequences), morphology and chemistry, based on material from Europe, and to some extent also from North America and western Asia. This approach resulted in the description of three new species (C. sterilis, C. subalpina, C. thracopontica), and detected an unexpected richness of lineages. Nomenclature, taxonomy, morphology and ecology of C. aurantia and C. flavescens from the C. aurantia group were studied in detail, including selection of the neotype of the former species. Their distribution was reviewed for the territory of the Czech Republic. Poorly known taxon C. aurantiomurorum from Algeria was lectotypified and synonymized with C. aurantia. Apart from the two groups, C. phlogina and C. scythica, differing partly in thallus colour and distinctly in distribution, were examined using both molecular (ITS sequences) and phenotypic data and found to be conspecific.