Finding the genes that underlie variation in production and developmental traits has important economic applications. Incubation behaviour represents a loss of production in conventional breeds of chicken adapted to local conditions and was what motivated this thesis. The Mendelian traits of comb type, crest, Silkie and normal feathers, feathered leg, fibromelanosis, comb colour, skin and shank colour, feather colour and patterns are of interest because of the insight they give to genes and development and were also investigated in the thesis. We used White Leghorn and Silkie lines of chicken to detect the genetic loci controlling incubation behaviour and Mendelian traits using linkage based analysis in an F2 cross. The evidence for QTL affecting incubation status over the whole period on chromosome 5 was strong (P<0.05). After the addition of 218 new informative SNP markers across the genome including chromosome 5 the 95% confidence interval spanned a region around 45 cM having previously been 95 cM. Three other suggestive QTL for incubation status were found after the addition of SNP markers on chromosome 1, 18, 19, E22C19W28 at 70, 0, 1 and 13cM respectively. The mode of action of the incubation status QTL indicates that the White Leghorn allele was either promoting incubation behaviour or that heterozygotes have performance that exceeds the homozygotes except the QTL on chromosome 1 where the Silkie allele is promoting incubation behaviour as might be expected. A highly significant QTL (P<0.01) for early incubation behaviour (25-30 weeks) was found on chromosome 8 at 18 cM. This QTL has an additive effect with the possession of a Silkie allele increasing the likelihood of incubation behaviour. Other suggestive QTL for early incubation behaviour were found on chromosome 26 and 1 at 0 and 66cM respectively. For Mendelian traits, genome wide significant (P<0.01) genetic loci for comb type, crest type and feather type was found on chromosome 7 at 77cM, linkage group E22C19W28 at 7cM and on chromosome 3 at 169cM respectively. Significant genetic loci (P<0.01) for leg colour and skin colour were found on chromosome 20 at 56cM and 60cM respectively. In the present study, loci for all feather patterns were found on E22C19W28 even after removing animals carrying the dominant white alleles, suggesting dominant white or another allele at the locus was still influential. Comb type and incubation behaviour were investigated at the gene level. Thyroid stimulating hormone receptor (TSHR) is believed to be involved in the process of domestication and was found at the peak position of the most significant QTL on chromosome 5 for incubation behaviour. Functional exploration of Wnt genes as a candidate gene for comb type was investigated by in-situ hybridization in Silkie and White Leghorn embryos. The Wnt6 gene showed expression in the region of the presumptive comb development of embryos. In conclusion, for the first time genetic loci that explain maternal behaviour have been described. The coincidence of the incubation behaviour locus on chromosome 5 with the site of the strongest selective sweep in poultry, the TSHR, and the coincidence of QTL on chromosome 1 and 8 with thyroid hormone activity it would appear that the thyrotrophic axis may be critical to the loss of incubation behaviour and improved reproductive performance with domestication. Further analysis of these loci should be able to produce markers that can reduce the propensity for birds to incubate. Comb type marker might allow introgression of this trait to prevent comb damage in commercial hens.

The aim of this thesis is to analyse the relation between morphological awareness and morphologically based spellings, in Portuguese (European Variant). Two situations where the spelling is determined by morphology are examined: when the spelling flouts letter-sound correspondence rules (consistency in the spelling of stems in base and in derived forms), and when there is more than one spelling for the same sound (discrimination in the spelling of homophone suffixes). The studies used cross-sectional (studies 1, 2 and 6) and longitudinal (studies 3, 4 and 5) designs. Study 1 examines when children from grades 1 to 4 (6- to 9-year-olds; N = 805) can take advantage of morphological information that is made available to them, implicitly, through morphological priming. The primes are base forms that share the same stem with the targets and contain well articulated, stressed vowels. The target words and pseudo-words are derived forms that contain non-stressed schwa vowels. Although differently pronounced the latter vowels are spelled consistently with those in the stems of the base forms. Primes were either oral or oral plus written. Priming effects were assessed by comparison with a non-primed condition. No priming effects were detected in 6- and 7-year-old children. Both priming conditions produced a significantly higher level of correct spelling in children 8 and 9 years of age. Oral plus written primes allowed older children to use morphological spellings in both words and pseudo-words. These results suggest that older children can use implicit morphological information to spell schwa vowels morphologically. Study 2 examined the concurrent relations between morphological awareness and morphologically based spellings. Two issues were considered: consistency in the spelling of stems in base and derived (or pseudo-derived) forms and discrimination in the spelling of words and pseudo-words ending in homophone suffixes. Children from grades 1 to 3 (6 to 8-year-olds; N = 184) participated in the study. It was found that there was a significant relation between morphological awareness and consistency in the spelling of stems in Base - Pseudo-derived stimuli, after controlling for differences in grade and IQ. Mixed results were found for the spelling of homophone suffixes. The only significant prediction obtained was between morphological awareness and discrimination in the spelling of the words ending in the homophone suffixes '-esa'/ '-eza'. In Study 3, the relation between morphological awareness and consistency in the spelling of stems is analysed, longitudinally. Children from grades 1 to 4 (6- to 9-year-olds; N = 184) were assessed in three sessions (A, B and C) each separated by six months. The results showed that some of the measures of morphological awareness could predict consistency in the spelling of stems over periods of six and of twelve months, after controlling for shared variance with Grade and IQ. This is indicative of a strong link between morphological awareness and consistency in the spelling of stems. In study 4, the relation between morphological awareness and discrimination in the spelling of words and pseudo-words ending in the homophone suffixes '-esa'/ '-eza' is analysed. The suffix '-esa' forms nouns that indicate origin or provenance. The homophone '-eza' forms abstract nouns. The participants and design were the same as in the previous study. It was found that the younger children tended to use one spelling for the two suffixes. Then, when alternative spellings were used, their assignment was unsystematic. Systematic assignment was rare even in the older children. Some measures of morphological awareness in session B, accounted for unique variance in the discrimination scores measured in session C, after controlling for differences explained by grade and IQ. In study 5, the relation between morphological awareness and discrimination in the spelling of words and pseudo-words ending in the homophone suffixes '-ice'/ '-isse' is analysed. The suffix '-ice' forms abstract nouns. The homophone '-isse' is used in the subjunctive of some verbs. The participants and design were the same as before. Correct assignment of suffixes followed the same pattern of spelling phases as described in the previous study. Significant predictions were found between sessions A and B, B and C and A and C. Some of the morphological awareness measures strongly predicted discrimination scores, after controlling for the effects of grade and IQ. Study 6 examines the spelling of older children (Grades 5, 7 and 9) and adults (student-teachers and in-service-teachers (N total = 107). The aim was to find out when consistency in the spelling of stems and discrimination of homophone suffixes were eventually achieved and whether the adult participants were aware of the morphological rules that make discrimination predictable. Consistency in the spelling of stems was only systematic in grade nine. Discrimination of the homophone suffixes '-esa'/ '-eza' was not completely systematic after sixteen years of instruction (student teachers) Discrimination of words ending in the homophone suffixes '-ice'/ '-isse' was systematic by student teachers. Discrimination in the spelling of pseudo-words was not achieved. Spelling justifications were asked from teachers. These revealed that the knowledge of morphological rules was scarce, in complete or absent. This thesis provides first evidence that older children can use morphological information that is provided, implicitly, through priming. It also shows that achieving consistency in the spelling of morphologically related stems is a long process. Systematic discrimination of homophone suffixes is even harder. However, morphological awareness was generally found to contribute strongly to the spelling, and to predict spelling outcomes, even after stringent controls for grade and IQ. Further research is necessary to examine how children develop morphologically based spellings that cannot be anchored first, in a stable phonological matrix. These results also suggest that instruction with a strong morphological rationale might significantly enhance spelling development.

This study tests the hypothesis that Khoe speaking herders from northern Botswana brought pottery to the southern tip of Africa. Stylistically in terms of lip types, rim orientations, vessel size, shape and decoration no homogeneity was noted between and within samples from several sites in Southern Africa thus refuting the idea that these vessels were made by the same population. Noted was the fact that during the LSA the technology behind the manufacturing pots and probably the idea of using these pots was the same but each group decorated their variously shaped pots according to their own choices influenced probably by their cultural beliefs. This study argues for a need to shift the mindset that for every new tradition in the southern African archaeological record appearing it has to involve massive movement of people introducing it. Therefore this study brings forth the idea that pottery probably reached the tip of Africa by diffusion.

Hierarchically ordered porous oxides have garnered much interest because of the numerous applications that can be developed from these materials. The catalytic properties, separation ability, and ion exchangeability of these materials, specifically zeolites, make them great candidates for applications. One area which has not been heavily studied is ways to control the morphology and particle size of these materials through soft chemistry approaches. This dissertation looks at two methodologies which can be used to alter zeolitic particle morphology. The first is a dual templating approach which attempts to incorporate microporous walls within a mesoporous structure. The zeolitic material, silicalite-1, is used as a siliceous precursor for the formation of the mesoporous SBA-15 material. A battery of characterization techniques were used to identify the structural properties of the material, including porosimetry, diffraction, microscopy, and spectroscopy. The overall conclusion was that a material with different properties than the parent SBA-15 were obtained, but that no characterization technique could be used to show the definitive presence of the zeolite in the walls. Another technique studied is the growth of zeolitic materials within the water domains of microemulsions. The concept of a reverse microemulsion, a confined water droplet in a continuous oil phase makes it an interesting system for morphological control. The zeolitic materials should only be able to grow within the water domain, and the reactive materials should be less available as they are trapped in separate micelles. Zeolite A (LTA) and zeolite L (LTL), two technologically important zeolites, were studied. Enhanced growth, larger particles, and unique material aggregates are just a few of the observations made for the two systems. The development of these materials should facilitate the application of zeolite in emerging technologies. In particular, preliminary work has been done on the development of large zeolite crystals with tuned orientations and particle sizes. This research shows multiple ways in which particle size and morphology can be tuned simply by altering the chemistry and reaction conditions of the system. This research has led to unique findings dealing with large zeolite crystals, and should open the door for continued research in this area.

This study examines the effects of morphological awareness and reading ability on the accuracy and speed of reading multi-morphemic words. Test of word reading ability and morphological awareness were given to 134 Grade 5 students. They also completed a test of their ability to read morphologically complex words, in which accuracy and response times were recorded. Two sets of response time scores were calculated – the first taking into account only the accurately pronounced words, and the second taking into account both the accurately and the inaccurately pronounced words. These words varied in surface frequency, base frequency, and transparency. Analysis of variances indicated that multi-morphemic word reading accuracy and speed were positively related to reading ability, morphological awareness, surface and base frequencies, and transparency. Significant interactions showed that (a) high base frequency increased reading accuracy and speed for words with low surface frequency, particularly for the less able students, and (b) the combination of high base frequency and transparency increased reading accuracy and speed for words with low surface frequency. Findings were similar for accuracy and both sets of response time scores. These results imply that morphological knowledge is involved in the reading of multi-morphemic words, suggesting that investigation of instruction that targets the morphological characteristics of words is warranted. / Thesis (Master, Education) -- Queen's University, 2010-04-19 18:50:46.661

With the advent of automated sequencing, sequence data are now available to help us understand the functioning of our genome, as well as its history. To date,powerful methods such as maximum likelihood have been used to estimate its mode and tempo of evolution and its branching pattern. However, these methods appear to have some limitations. The purpose of this thesis is to examine these issues in light of Bayesian modelling, taking advantage of some recent advances in Bayesian computation. Firstly, Bayesian methods to estimate divergence dates when rates of evolution vary from lineage to lineages are extended and compared. The power of the technique is demonstrated by analysing twenty-two genes sampled across the metazoans to test the Cambrian explosion hypothesis. While the molecular clock gives divergence dates at least twice as old as those indicated by the fossil records, it is shown (i) that modelling rate change gives results consistent with the fossils, (ii) that this improves dramatically the fit to the data and (iii) that these results are not dependent on the choice of a specific model of rate change.Results from this analysis support a molecular explosion of the metazoans about 600 million years (MY) ago, i.e. only some 50 MY before the morphological Cambrian explosion. Secondly, two new Bayesian tests of phylogenetic trees are developed. The first aims at selecting the correct tree, while the second constructs confidence sets of trees. Two other tests are also developed, in the frequentist framework. Based on p-values adjusted for multiple comparisons,they are built to match their Bayesian counterparts. These four new tests are compared with previous tests. Their sensitivity to model misspecification and the problem of regions is discussed. Finally, some extensions to the models examined are made to estimate divergence dates from data of multiple genes, and to detect positive selection.

A integração morfológica refere-se à organização modular das relações e conexões entre os caracteres, a qual influencia a direção e velocidade da mudança evolutiva, seja restringindo ou facilitando esta ao longo das diferentes direções do morfoespaço. Desta forma, a descrição de padrões e magnitudes de integração e a análise de suas conseqüências evolutivas são aspectos centrais do estudo da evolução de morfologias complexas. Aqui analisamos a integração morfológica no crânio de diferentes famílias de mamíferos, abordando as seguintes questões. Existem padrões de integração comuns a todos os grupos? Seriam esses padrões compatíveis com hipóteses a priori baseadas em ontogenia e função compartilhadas? Que tipos de respostas evolutivas á seleção poderiam ser produzidas por estes padrões? Para isso, digitalizamos representantes de 20 ordens e 40 famílias de mamíferos e então estimamos as matrizes de correlação e variância/covariância correspondentes, comparando-as entre si. Também comparamos cada um dos padrões de integração estimados a hipóteses a priori baseadas em ontogenia e função compartilhadas. Por fim, analisamos as repostas de cada uma das matrizes V/CV a vetores de seleção simulados. Nossos resultados apontam para um padrão de integração amplamente compartilhado entre todas as famílias, indicando que a diversidade morfológica deste grupo foi produzida usando uma estrutura de covariação compartilhada, a qual se manteve similar durante pelo menos 65 milhões de anos. Comparações com uma matriz V/CV genética de roedores sugerem que esta similaridade se estende aos fatores genéticos subjacentes à variação fenotípica. Diversos módulos funcionais/ontogenéticos foram detectados nos táxons amostrados. A principal diferença entre os grupos foram observadas nas magnitudes de integração: as famílias de metatérios e duas das famílias de roedores apresentaram alto nível de integração geral e módulos pouco distintos, enquanto as famílias de primatas e quirópteros apresentaram o padrão de inverso. Nossos dados fornecem evidência de que a evolução da morfologia craniana em mamíferos pode ser vista como marcada por alterações no nível de integração entre caracteres, na qual os módulos ficaram mais evidentes. A consequência evolutiva retirada destas observações foi a de que as linhagens e famílias com menor integração são menos restritas, do ponto de vista evolutivo, e capazes de lidar com pressões seletivas com maior flexibilidade. / Morphological integration refers to the modular structuring of intertrait relationships in an organism, which could bias the direction and rate of morphological change, either constraining or facilitating evolution along certain dimensions of the morphospace. Therefore, the description of morphological integration patterns and its magnitude and the analysis of their evolutionary consequences are central to understand the evolution of complex traits. Here we analyze morphological integration in the skull of several mammalian orders, addressing the following questions: are there common patterns of inter-trait relationships? Are these patterns compatible with hypotheses based on shared development and function? What kind of responses to evolutionary forces could be generated by these patterns? We digitized more than 2000 specimens in 20 mammalian orders and 40 families. We then estimated the correspondent correlation and covariance matrices among traits and compared those matrices among the families. We also compared observed patterns of integration to theoretical expectations based on common development and function. Finally, we analyzed the responses of each covariance matrix to simulated selection vectors. Our results pointed to a largely shared pattern of inter-trait correlations, implying that mammalian skull diversity has been produced using a common covariance structure that remained similar for at least 65 million years. Comparisons with a rodent genetic variance/covariance matrix suggest that this broad similarity extends also to the genetic factors underlying phenotypic variation. Several morphological modules expected from shared development and function were detected in the mammalian taxa studied. The main differences among groups were found for the magnitudes of integration: metatherians and two rodent families presented higher overall levels of integration and reduced modular distinctiveness ,while primates and chiropterans exhibited the opposite pattern. Our data constitute evidence that the broad picture of mammalian skull evolution could be regarded as a history of inter-module disintegration, while the modules themselves became more clearly marked. The evolutionary implication of these findings is that groups with lower overall integration are less evolutionarily constrained, and are able to cope with selection with more flexibility.

The plant family Gesneriaceae is represented in Sri Lanka by six genera: Aeschynanthus, Epithema, Championia, Henckelia, Rhynchoglossum and Rhynchotechum, with 13 species (plus one subspecies/variety) of which ten are endemic including the monotypic genus Championia, according to the last revision in 1981. They are exclusively distributed in undisturbed habitats, and some have high ornamental value. The species are morphologically diverse, but face a problem of taxonomic delineation, which is further complicated by the presence of putative hybrids. Sri Lanka and Indian Peninsula, represent the Deccan plate of the ancient Gondwanan supercontinent. The presence of a relict flora may indicate the significance of the geological history of the Deccan plate for the evolution of angiosperms. The high degree of endemism here, along with their affinities to the global angiosperm flora paints a complex picture, but its biogeographic history is still unclear. The pantropical family Gesneriaceae distributed in Sri Lanka and South India is therefore an appropriate study group in this context. Besides, the family itself has a complex but largely unresolved biogeographical history especially concerning the origin and diversification of Old World Gesneriaceae. Modern approaches for the taxonomic studies were applied, integrating morphological and molecular data. Multiple samples were collected for each species across their geographical distribution. Nuclear ITS and chloroplast trnL-F sequences for the taxa from Sri Lanka were used to generate regional genus phylogenies of all six genera, using maximum parsimony. The rate of evolution of the nuclear ITS region versus chloroplast trnL-F was varied greatly across the six genera studied. Molecular delimitations were mostly congruent with the classical taxonomy. Over 65 taxonomic characters were studied in detail to recognize synapomorphies for clades and taxa. A complete taxonomic revision of Gesneriaceae in Sri Lanka, including lectotypification, was conducted based on both, the molecular and morphological data. This resulted in the recognition of 14 species in the six genera, including one newly described species H. wijesundarae Ranasinghe and Mich. Möller. Henckelia communis and H. angusta were not supported molecularly as two separate entities but are recognized as two species because of consistent morphological differences between them. Henckelia humboldtiana is proposed to represent a species complex due to its highly variable and inconsistent molecular and morphological diversity and overlap with H. incana and H. floccosa; more research is needed here. National conservation assessments were conducted, and all 14 species were recognized as threatened. Biogeographic affinities of Sri Lankan Gesneriaceae were elucidated, generating a dated phylogeny using an existing matrix of four plastid gene regions; trnL-F, matK, rps16 and ndhF, amended by sequences generated in this study. The final combined matrix included 175 taxa including newly generated sequences for the 13 Sri Lankan taxa. Phylogenetic trees were generated using parsimony, maximum likelihood and Bayesian inference. Molecular dating was carried out using BEAST and ancestral area reconstruction using BioGeoBears. These analyses indicated that the six genera of Gesneriaceae arrived in Sri Lanka separately and sometimes different time periods. One lineage dated back to the early diversification of the subfamily Didymocarpoideae (generally regarded as the Old World Gesneriaceae), which occurred around the KT boundary, before the Deccan plate was connected to Asia.

A integração morfológica refere-se à organização modular das relações e conexões entre os caracteres, a qual influencia a direção e velocidade da mudança evolutiva, seja restringindo ou facilitando esta ao longo das diferentes direções do morfoespaço. Desta forma, a descrição de padrões e magnitudes de integração e a análise de suas conseqüências evolutivas são aspectos centrais do estudo da evolução de morfologias complexas. Aqui analisamos a integração morfológica no crânio de diferentes famílias de mamíferos, abordando as seguintes questões. Existem padrões de integração comuns a todos os grupos? Seriam esses padrões compatíveis com hipóteses a priori baseadas em ontogenia e função compartilhadas? Que tipos de respostas evolutivas á seleção poderiam ser produzidas por estes padrões? Para isso, digitalizamos representantes de 20 ordens e 40 famílias de mamíferos e então estimamos as matrizes de correlação e variância/covariância correspondentes, comparando-as entre si. Também comparamos cada um dos padrões de integração estimados a hipóteses a priori baseadas em ontogenia e função compartilhadas. Por fim, analisamos as repostas de cada uma das matrizes V/CV a vetores de seleção simulados. Nossos resultados apontam para um padrão de integração amplamente compartilhado entre todas as famílias, indicando que a diversidade morfológica deste grupo foi produzida usando uma estrutura de covariação compartilhada, a qual se manteve similar durante pelo menos 65 milhões de anos. Comparações com uma matriz V/CV genética de roedores sugerem que esta similaridade se estende aos fatores genéticos subjacentes à variação fenotípica. Diversos módulos funcionais/ontogenéticos foram detectados nos táxons amostrados. A principal diferença entre os grupos foram observadas nas magnitudes de integração: as famílias de metatérios e duas das famílias de roedores apresentaram alto nível de integração geral e módulos pouco distintos, enquanto as famílias de primatas e quirópteros apresentaram o padrão de inverso. Nossos dados fornecem evidência de que a evolução da morfologia craniana em mamíferos pode ser vista como marcada por alterações no nível de integração entre caracteres, na qual os módulos ficaram mais evidentes. A consequência evolutiva retirada destas observações foi a de que as linhagens e famílias com menor integração são menos restritas, do ponto de vista evolutivo, e capazes de lidar com pressões seletivas com maior flexibilidade. / Morphological integration refers to the modular structuring of intertrait relationships in an organism, which could bias the direction and rate of morphological change, either constraining or facilitating evolution along certain dimensions of the morphospace. Therefore, the description of morphological integration patterns and its magnitude and the analysis of their evolutionary consequences are central to understand the evolution of complex traits. Here we analyze morphological integration in the skull of several mammalian orders, addressing the following questions: are there common patterns of inter-trait relationships? Are these patterns compatible with hypotheses based on shared development and function? What kind of responses to evolutionary forces could be generated by these patterns? We digitized more than 2000 specimens in 20 mammalian orders and 40 families. We then estimated the correspondent correlation and covariance matrices among traits and compared those matrices among the families. We also compared observed patterns of integration to theoretical expectations based on common development and function. Finally, we analyzed the responses of each covariance matrix to simulated selection vectors. Our results pointed to a largely shared pattern of inter-trait correlations, implying that mammalian skull diversity has been produced using a common covariance structure that remained similar for at least 65 million years. Comparisons with a rodent genetic variance/covariance matrix suggest that this broad similarity extends also to the genetic factors underlying phenotypic variation. Several morphological modules expected from shared development and function were detected in the mammalian taxa studied. The main differences among groups were found for the magnitudes of integration: metatherians and two rodent families presented higher overall levels of integration and reduced modular distinctiveness ,while primates and chiropterans exhibited the opposite pattern. Our data constitute evidence that the broad picture of mammalian skull evolution could be regarded as a history of inter-module disintegration, while the modules themselves became more clearly marked. The evolutionary implication of these findings is that groups with lower overall integration are less evolutionarily constrained, and are able to cope with selection with more flexibility.

No description available.