Thesis (M.Sc. (Zoology) --University of Limpopo, 2014 / Refer to the document / The Department of Biodiversity at the University of Limpopo, and the National Research Foundation (NRF)

A major challenge in the post-genomic era is to understand how genome sequence variants (genotype) give rise to the enormous diversity observed in terms of morphology, physiology and behavior (phenotype) among living organisms. Domestic animals—with their tremendous phenotypic variation—are excellent model organisms for determining the relationships between genotype and phenotype. In this thesis, I describe the utilization of the chicken, in combination with modern genetic and genomic approaches, in developing our understanding of the genetic mechanisms underlying phenotypic variation. These studies provide novel information on the genetics behind variation in carotenoid- and melanin-based pigmentation—observed in many organisms—and also cast light on the genetic basis of chicken domestication. In paper I, we report that the yellow skin phenotype—observed in most commercial chickens—is caused by one or several tissue-specific mutations altering the expression of beta-carotene oxygenase 2 (BCO2 or BCDO2) in skin. In addition, we present the first conclusive evidence of a hybrid origin of the domestic chicken, since the allele causing yellow skin most likely originates from the grey jungle fowl (Gallus sonneratii) and not from the previously described sole ancestor, the red jungle fowl (Gallus gallus). In paper II, we detect a number of loci that were likely important during the domestication process of chicken and the later specialization into meat (broiler) and egg (layer) producing lines. One of the major findings was that worldwide, almost all domestic chickens carry a missense mutation in TSHR (thyroid stimulating hormone receptor) in a position that is completely conserved amongst vertebrates. We speculate that this “domestication-mutation” has played an important role in the transformation of the wild red jungle fowl ancestor into the modern domestic chicken. In paper III, we demonstrate that the dilution of red (pheomelanin) pigmentation—observed in the plumage of the Inhibitor of Gold chicken—is caused by a frame-shift mutation in the catechol-O-methyltransferase domain containing 1 (COMTD1) gene. The production and regulation of pheomelanin is poorly understood and this discovery advances our current knowledge of this pathway.

L'objectif de cette thèse est d'étudier la croissance et le développement du manguier (Mangifera indica L.) en lien avec un facteur exogène, la température, et plusieurs facteurs endogènes architecturaux de type structurel (topologie) et temporel. Les études sont menées à l'échelle de l'organe (l'axe végétatif, ses feuilles et l'axe florifère) et de la succession des axes (végétatifs ou florifères) sur plusieurs cycles de croissance. À la première échelle, l'étude met en évidence une relation allométrique négative entre la vitesse relative de croissance, positivement reliée à la température, et la durée de croissance de l'organe. Cette relation est commune entre les trois organes et les deux cultivars étudiés. Par ailleurs, des modèles de segmentation montrent que les stades phénologiques classiquement admis sont caractérisés par des vitesses absolues de croissance contrastées. Cette approche met en évidence des asynchronismes entre l'axe végétatif et ses feuilles. À la seconde échelle, l'effet des facteurs architecturaux sur le développement est analysé pour quatre cultivars. Nos résultats montrent de fortes interactions entre certains facteurs structurels (ex. position de l'axe, apicale vs. latérale) ou temporels (ex. date d'apparition), et des caractéristiques développementales qualitatives (ex. occurrence de la floraison), quantitatives (ex. nombre d'inflorescences) ou temporelles (ex. date de floraison). Ces résultats font ressortir une « mémoire de l'effet architectural » qui se propage d'un cycle de croissance aux suivants. Nos études multi-échelles permettent de quantifier les parts respectives des facteurs endogènes et exogènes contribuant aux variations phénotypiques (incluant la plasticité) du manguier. / The aim of this work is to study mango (Mangifera indica L.) growth and development in relation to an exogenous factor, temperature, and to endogenous factors, whether structural (topology) or temporal. The study is carried out at two scales: the organ (vegetative axis, its leaves, and reproductive axis) and the succession of axes (vegetative or reproductive). At the first scale, there was a common negative allometric relationship between the relative growth rate, positively related to temperature, and the duration of growth of the organ. This relationship is common between the three organs and the two studied cultivars. Otherwise, segmentation models reveal that the phenological stages classically studied are characterized by contrasted values of absolute growth rate. This approach shows asynchronisms between the axis and its leaves. At the second scale, the effect of endogenous factors on mango development is investigated for four cultivars. Our results reveal strong interplays between some structural (e.g. axis position, apical vs. lateral) or temporal (e.g. date of burst) factors, and qualitative (e.g. occurrence of flowering), quantitative (e.g. number of inflorescences) or temporal (e.g. date of flowering) developmental traits. These results highlight a “memory of the architectural effect” which spreads from one growing cycle to the followings. Our multiscale study enables to quantify the respective contributions of endogenous and exogenous factors to the phenotypic variations (including plasticity) of mango.

Population divergence shaped by natural selection is central to evolutionary ecology research and has been in focus since Darwin formulated “The origin of species”. Still, the process of adaptive divergence among sympatric populations is poorly understood. In this thesis I studied patterns of adaptive divergence among subpopulations of pike (Esox lucius) that are sympatric in the Baltic Sea but become short-term allopatric during spawning and initial juvenile growth in freshwater streams. I also examined causes and consequences of phenotypic variation among individuals within subpopulations to evaluate the contribution of natural selection to population divergence.   I first investigated homing behaviour and population structures of pike to assess the potential for adaptive divergence among sympatric pike that migrate to spawn in different streams. Mark-recapture data suggested that migrating pike displayed homing behaviour and repeatedly returned to the same stream. Analyses of microsatellite data revealed partial reproductive isolation among subpopulations spawning in different streams. These subpopulations, however, were truly sympatric during the life-stage spent in the Baltic Sea.   To address whether short-term allopatry has resulted in adaptive divergence among sympatric subpopulations I combined observational, experimental and molecular approaches. Observational data showed that subpopulations differed in morphological and life-history traits and common-garden experiments suggested that differences were, at least in part, genetically based. Moreover, QST-FST comparisons indicated that genetically based phenotypic differences has been driven by divergent selection, and a reciprocal translocation experiment showed that phenotypic variation represented local adaptations to spawning habitats. Finally, longitudinal and cross-sectional comparisons among individuals revealed associations between phenotypes, performance and fitness components.   In conclusion, my thesis illustrates how short-term allopatry due to migratory behaviour can result in adaptive divergence among sympatric subpopulations. These findings advance the understanding of evolutionary processes at the finest spatiotemporal scale and illustrate that local adaptations can arise in environments with high connectivity.  The results also emphasise that fine spatial scale population structures must be taken into consideration in management and conservation of biodiversity in the Baltic Sea.

Submitted by Luciana Ferreira (lucgeral@gmail.com) on 2017-06-12T12:08:08Z No. of bitstreams: 2 Dissertação - Elias Emanuel Silva Mota - 2013.pdf: 4153662 bytes, checksum: e76c4d102d7d03a072c342e97b447eeb (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2017-06-12T12:08:39Z (GMT) No. of bitstreams: 2 Dissertação - Elias Emanuel Silva Mota - 2013.pdf: 4153662 bytes, checksum: e76c4d102d7d03a072c342e97b447eeb (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2017-06-12T12:08:39Z (GMT). No. of bitstreams: 2 Dissertação - Elias Emanuel Silva Mota - 2013.pdf: 4153662 bytes, checksum: e76c4d102d7d03a072c342e97b447eeb (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2013-03-27 / The Cerrado biome is the second largest in Brazil, occupying 23% of the national territory, has several vegetation types, and has the richest flora among the world's savannas. The baru tree, due to its wide geographic distribution, is a species with the ability to display high levels of genetic diversity, thus providing the ability to occupy different habitats. The species in question has a multitude of uses, constituting a key species for studying domestication and cultivation. This study aimed to obtain information about the patterns of phenotypic variation for some traits of fruits, seeds and seedlings of baru and to estimate the genotic variability among and within 25 natural subpopulations of Dipteryx alata Vog., based on quantitative data. Fruits were collected from plants of 25 regions in the Cerrado biome, sampling six plants per subpopulation and, at least, 25 fruits per plant. The data were submitted to descriptive analysis, analysis of variance and correlation between traits. There was significant variation for all variables at all levels evaluated; among fruits within plants, among plants within subpopulations and among subpopulations for the fruits and seed traits evaluated. There was variation among progeny within subpopulations and among subpopulations for initial and final height, number of leaves, total leaf size, number of internodes and root length of seedlings. A greater proportion of variability was observed between plants within subpopulations. Correlation analysis demonstrated significant correlations for most pairs of characters of fruit evaluated at different hierarchical levels. The heritability found for final height, fresh weight and dry weight of shoots indicates possibility of gains from selection for these characters. / O Cerrado é o segundo maior bioma do país, ocupando 23% do território nacional, apresenta uma vegetação com diversas fitofisionomias e possui a mais rica flora dentre as savanas do mundo. O barueiro devido a sua ampla distribuição geográfica é uma espécie com a possibilidade de apresentar altos níveis de diversidade genética, conferindo assim capacidade de ocupar diferentes hábitats. A espécie em questão apresenta uma multiplicidade de usos, constituindo-se em espécie chave para estudos de domesticação e cultivo. O presente trabalho objetivou obter informações sobre os padrões de variação fenotípica para algumas características de frutos, sementes e mudas de baru e estimar a variabilidade genotípica existente entre e dentro de 25 subpopulações naturais de Dipteryx alata Vog. com base em dados quantitativos, contribuindo para medidas de conservação e auxílio em futuros programas de melhoramento genético da espécie. Foram coletados frutos de plantas de barueiro de 25 regiões, em seis estados, amostrando seis matrizes por subpopulação, com coleta de, pelo menos, 25 frutos por matriz. Os dados de caracteres físicos de frutos e sementes foram submetidos à análise descritiva, análise de variância e correlação entre caracteres. Houve variação significativa para todas as variáveis avaliadas, em todos os níveis hierárquicos avaliados; entre frutos dentro de matrizes, entre matrizes dentro de subpopulações e entre subpopulações para os caracteres de frutos e sementes avaliados. Houve variação entre progênies dentro de subpopulações e entre subpopulações para altura inicial e final, número de folíolos, tamanho total da folha, número de internódios e comprimento da parte aérea das plântulas. A maior proporção da variabilidade foi observada entre matrizes dentro de subpopulações. A análise de correlação demonstrou a existência de correlações significativas para a maioria dos pares de caracteres de frutos avaliados nos diferentes níveis hierárquicos. A herdabilidade encontrada para a altura final de mudas, a massa fresca e a massa seca da parte aérea indica possibilidade de ganhos por seleção para estes caracteres.

Orientador: Luís Felipe de Toledo Ramos Pereira / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-25T14:12:31Z (GMT). No. of bitstreams: 1 Lambertini_Carolina_M.pdf: 6513639 bytes, checksum: 76f60b46e28d803521c2f06db67818b3 (MD5) Previous issue date: 2014 / Resumo: Os anfíbios são os animais mais ameaçados do planeta, tendo como fatores mais impactantes a perda de habitat e a quitridiomicose. Esta doença em anuros é causada pelo fungo Batrachochytrium dendrobatidis (Bd), que já foi registrado em todos os continentes e no Brasil estende-se por toda a Mata Atlântica, e já foi encontrado no Cerrado e na Amazônia. Existem diversos fatores que podem influenciar a dinâmica de infecção na natureza, e como fatores intrínsecos ao Bd podemos citar a variação genotípica, morfológica, variação na virulência e taxas de crescimento. Com isso, o presente estudo teve como objetivos realizar a caracterização genotípica e fenotípica de cepas de Bd provenientes de um gradiente de elevação na Mata Atlântica, e verificar se existem associações entre o tamanho dos zoósporos e zoosporângios das cepas isoladas com dados de prevalência e intensidade de infecção e taxa de crescimento do Bd. Adicionalmente, foi analisado se as taxas de infecção aumentam conforme o aumento da elevação. Para tanto, foram isoladas e genotipadas cinco cepas de Bd. Foi realizado o diagnóstico e quantificação da doença, assim como a confecção de suas curvas de crescimento. Com base nos resultados foram desenvolvidos dois índices relacionados à variação em tamanho e dados de prevalência e intensidade de infecção. Todas as cepas isoladas pertencem à linhagem Bd-GPL2. Foi detectada variação fenotípica entre as cepas e associações entre tamanho das cepas com prevalência e intensidade de infecção, e não houve associação com as taxas de crescimento. A prevalência e intensidade de infecção não aumentaram com a altitude. Os índices de tamanho e infecção também foram associados. Com isso, a variação fenotípica pode ser considerada preditora da dinâmica de infecção do Bd na natureza. Isto poderá ser utilizado como eficiente ferramenta de baixo custo para estudos que busquem reconhecer áreas nas quais o fungo pode ser mais prevalente e apresentar maior intensidade de infecção. Estes fatores podem ser cruciais para determinar populações de anfíbios ameaçadas / Abstract: Amphibians are the most threatened animals of the world. Habitat loss and chytridiomicosys are considered the main causes for their declines. Chytridiomycosis is a disease caused in anurans by the fungus Batrachochytrium dendrobatidis (Bd), detected worldwide. In Brazil it was registered all over the Atlantic rainforest and in some localities of the Cerrado and Amazonia. Several factors influence this disease dynamics, such as intrinsic factors related to Bd: different lineages, morphology, virulence, and growth rate. Given these factors, the present study aimed to genotype and analyze Bd strain¿s size from an elevational range, and verify if these factors were correlated to Bd size, prevalence, infection load, growth rate, and elevation. We isolated and genotyped five strains, and quantified growth rates. We developed two indexes related to Bd size, prevalence, and infection load. The five strains were Bd-GPL2. We found size variation and correlations between Bd size, prevalence, and infection load, but not with growth rate. Prevalence and infection load did not increase with elevation. The size and infection indexes were correlated. The phenotypic variation can be considered as a predictor to disease dynamics on environment. It can be used in other studies as a tool to efficiently (cheap and fast) identify areas where the fungus can develop faster and be more deleterious to amphibian populations / Mestrado / Biodiversidade Animal / Mestra em Biologia Animal

The threespine stickleback (Gasterosteus aculeatus) is an important model for studying evolution. Sticklebacks are widely distributed in the northern hemisphere and inhabit freshwater, brackish, and marine waters. Anadromous and marine populations (hereafter marine) are assumed to be homogenous in space and invariant in time in their phenotypic characteristics, despite marine environments varying on regional and local scales. Recent studies suggest there is in fact genetic and phenotypic structure in marine sticklebacks, yet the ecological causes remain unclear. My goal was to assess trait variation in marine stickleback populations around Southern coastal British Columbia (BC), and to determine whether or not oceanographic and habitat characteristics explained this variation. The area around Vancouver Island was ideal because four distinct oceanographic regions surround the island with varying coastal habitat types. Between May-July 2019, I sampled ~600 sticklebacks from 15 sites. I then characterized trait variation using two-dimensional (2D) geometric morphometric analysis to compare individuals between oceanographic regions and coastal habitats. I focused on five traits: armour phenotype, head size, body size, head shape, and body shape. I chose these traits because they are ecologically important and well-studied in freshwater populations, where their ecological drivers are known. I found that marine sticklebacks did vary morphologically among and between regions and habitats, but the variation was not immediately related to environmental variation, nor obviously comparable to variation in freshwater populations. Sexual dimorphism was the largest source of variation in the data, a well-established finding. But oceanographic and habitat variables influenced differences between males and females. I concluded that marine sticklebacks offer abundant opportunities for expanding our knowledge of drivers of morphology in nature. / Graduate / 2022-04-11

Because of growing concern of habitat fragmentation and its adverse effects on salamander communities in Appalachian region, sympatric populations of ambystomatid salamanders A. opacum and A. maculatum were studied in Northeast Tennessee to address a number of questions: i) the extent of sexual size dimorphism (SSD) in both species, ii) what traits influence the dorsal skin pigmentation and how, iii) whether gender differences in developmental stability occur, and iv) the extent of phenotypic variation within each species. The findings of this study revealed SSD in both species of salamanders. The most parsimonious statistical model was developed that explained the influence of body mass, dorsal body area, and sex on development of dorsal white pigmentation in marbled salamanders. Data on asymmetry indicate that females are under more stress than males in marbled salamanders, while for spotted salamanders nonsignificant asymmetry is indicative of similar level of stress in both sexes. Data on coefficient of variation (CV) suggest stabilizing selection on optimal body size and mass in female marbled salamanders compared to males; however, for spotted salamanders CV indicates relatively similar selection pressure for body size and mass for both sexes.

Pseudomonas brassicacearum a la particularité de générer une diversité intraclonale aussi bien in vitro qu'en conditions naturelles dans la rhizosphère de plantes. Ce phénomène de variation phénotypique commun chez les bactéries est un processus d'adaptation aux environnements changeants. Des données de transcriptomique issues de puces à ADN, contenant aussi bien des séquences codantes que non codantes, nous ont permis d'identifier les gènes dont l'expression est altérée et surtout de relier ce phénomène à l'expression d'ARN non codants régulateurs (ARNnc) de type Rsm qui sont sous le contrôle du système à deux composants GacS/GacA. Nous avons montré que des mutations ponctuelles dans les gènes gacS ou gacA sont à l'origine de cette variation phénotypique et que l'expression de l'un des trois gènes rsmX, rsmY ou rsmZ permet de restaurer le phénotype de la souche sauvage. L'importance de ces ARNnc dans la survie de la bactérie aux fluctuations de son environnement est dénotée par la duplication de rsmX en un gène que nous avons nommé rsmX-2, dont la fonction a été validée. Nos données suggèrent une activation exclusive des gènes rsmX-1 et rsmX-2 par GacA et l'intervention de régulateurs additionnels dans le cas de rsmY et rsmZ. Au vu de la redondance fonctionnelle de ces quatre ARNnc, nous avons investigué leur niveau d'expression et leur stabilité dans différentes conditions de culture et montré des différences pour les quatre ARNnc. En réponse à une carence en nutriments, l'expression des ARNnc Rsm est fortement activée et atteint son maximum quand le ppGpp est détecté dans le milieu, suggérant un lien entre le système Gac/Rsm et la réponse « stringente ». / The plant-beneficial bacterium Pseudomonas brassicacearum forms phenotypic variants in vitro as well as in planta during root colonisation under natural conditions. Transcriptome analysis of typical phenotypic variants using microarrays containing coding as well as non-coding DNA fragments showed differential expression of several genes relevant to secondary metabolism and of the small non-coding RNA (ncRNA) genes rsmX, rsmY and rsmZ, which was characterized by down-regulation. Naturally occurring mutations in the GacS/GacA two-component system accounted for phenotypic switching. The importance of these ncRNAs in the survival of the bacteria to changing environments is denoted by the duplication of rsmX gene, which we called rsmX-2 and whose function has been validated. Our data suggest an exclusive activation of rsmX-1 and rsmX-2 genes by GacA and the involvement of additional regulators in the case of rsmY and rsmZ. Given the functional redundancy of these ncRNAs, we investigated their expression level and stability in different culture conditions and showed differences for the four ncRNAs. In response to nutrient depletion, the four ncRNAs expression is strongly activated and reaches its maximum when the ppGpp is detected in bacterial cells, suggesting a link between the Gac/Rsm system and the "stringent" response. Determining the level of each Rsm ncRNA, which is defined by a balance between synthesis and degradation of each transcript, shows the maintenance of a very important pool of RsmZ compared to other ncRNAs.

We investigated the population dynamics of the giant water bug, Belostoma angustum, across highland sin the Pampas of southern Brazil. We evaluated genetic and morphological variation, as well as the demographic history of 18 populations. The overall range includes two highlands and a lowland between them, overall exceeding 400 kilometers along the longitudinal gradient. Genetic variation was assessed from mitochondrial and nuclear markers. The morphological variation was estimated using linear measurements of males and females, and from male genitalic structures using geometric morphometrics approaches. We evaluated the effect of the highland topography, drainage basins, and past climate changes on the population structure. Our results from multiple analyses of molecular variance (AMOVA) show that Belostoma angustum structures as a large panmictic population across the Pampas highlands range. Every most frequent haplotype is shared by individuals from all three sampled areas in genetic markers from the mitochondrial as well as from the nuclear locus. Differentiation among haplotypes was very low, not greater than two mutation steps. The congruent phylogeographical pattern in both markers indicate absent sex-biased migration rates. Furthermore, there was no evidence for isolation-by-distance (IBD) based on the mitochondrial data. The pairwise st was low and not significant, indicating historical gene flow among populations of the giant water bug studied throughout Pampas highlands. Our findings about the demographic history of panmictic population throughout Pampas highlands suggest it experienced recent and rapid population expansion that started in the Late Pleistocene period, approximately 15,000 years old after Last Glacial Maximum. The recent marked demographic expansion could explain the high percentage of the exclusive haplotypes and the very low mutational steps among them. We did not find morphological variation among populations of B. angustum throughout Pampas highlands reflected, except for some body dimensions. The overall phenotypic uniformity among populations becomes more likely if gene flow is hypothesized to homogenize populations. However, in the body size, specially, there was variation among populations potentially explained by phenotypic plasticity, thereby generating phenotypic diversity without genetic differentiation. Our genetic findings suggest indirectly that individuals of B. angustum are strong fliers able to overcome the topographical barriers of the sampled area. / Neste trabalho, investigamos a dinâmica populacional de uma barata d\' água, Belostoma angustum, ao longo do Pampa no sul do Brasil. Foram avaliadas a variação genética, morfológica e a história demográfica de 18 populações. A área total amostrada inclui duas serranias e uma planície entre elas, excedendo 400 quilômetros ao longo de um gradiente longitudinal. A variação genética foi avaliada a partir de marcadores mitocondriais e nucleares. A variação morfológica foi avaliada utilizando medidas lineares de machos e fêmeas, e de estruturas genitais masculinas usando abordagens de morfometria geométrica. Testamos o efeito da topografia das serranias, das bacias de drenagem e das mudanças climáticas passadas sobre a estrutura das populações. Os resultados de múltiplas análises de variância molecular (AMOVA) mostram que Belostoma angustum forma uma grande população panmítica ao longo das serranias do Pampa. Todos os haplótipos mais frequentes são compartilhados por indivíduos de todas as três grandes áreas amostradas em marcadores genéticos dos loci mitocondrial e nuclear. A diferenciação entre haplótipos foi muito baixa, não excedendo dois passos mutacionais. O padrão filogeográfico congruente em ambos os marcadores indica taxas de migração não enviesada para um dos sexos. Além disso, não encontramos evidência de isolamento por distância (IBD) com base nos dados mitocondriais. Os valores de st par a par foram baixos e não significativos, indicando fluxo gênico histórico entre as populações da barata d\'água estudada ao longo das serranias Pampianas. Os resultados sobre a história demográfica da população panmítica ao longo do planalto do Pampa sugerem que essa população experimentou uma expansão populacional recente e rápida que teve início no fim do período Pleistoceno (há aproximadamente 15.000 anos), após a última máxima glacial. A expansão demográfica recente e acentuada poderia explicar a alta porcentagem de haplótipos exclusivos e o número reduzido de passos mutacionais entre eles. Não encontramos variação morfológica entre as populações de B. angustum amostradas ao longo das serranias do Pampa, exceto em algumas dimensões corporais. A uniformidade fenotípica entre as populações torna-se mais provável na medida em que o fluxo de genes atue homogeneizando as populações. Entretanto, no caso do tamanho do corpo, especialmente, há variação entre populações potencialmente explicada por plasticidade fenotípica, gerando assim diferenciação fenotípica sem diferenciação genética. Nossos resultados genéticos sugerem indiretamente que os indivíduos de B. angustum possuem capacidade de voo suficiente para transpor as barreiras topográficas na área amostrada.