The main aim of this thesis is to understand the extent to which intraspecific variation in developmental event timing might provide the raw material from which heterochronies may originate. To this end I studied the timing of a suite of both morphological and physiological events in the embryonic development of Radix balthica, a species of aquatic snail known to exhibit event timing variation during the embryonic period (Tills et al. 2010; Rundle et al. 2011) and that sits within an evolutionary clade, in which extensive heterochrony has been documented (Smirthwaite et al. 2007). I found that variation in embryonic developmental event timing within R. balthica is pervasive (Chapters 2 - 5) and distributed primarily at low (inter-individual and egg mass), rather than high (population) biological levels (Chapter 3). This variation also appears to have a genetic basis (Chapter 2) and to be heritable (Chapters 4 and 5). Examination of the development of function in the cardiovascular (CV) system in Chapter 5 also revealed extensive variation, including differences between egg masses in the timing of aspects of this development, and differences between populations in the rates of change in heart rate during different phases of ontogeny. Variation in CV development also had effects on life history, which suggest that altered embryonic development might have implications for Darwinian fitness (Chapter 5). This thesis demonstrates that intraspecific variation in developmental event timing represents a fundamental link between ontogeny and phylogeny and that study of altered timing at the inter-individual level provides the opportunity to address questions concerning its evolvability and implications.

With the contribution of intraspecific trait variation (ITV) to ecological processes being increasingly appreciated, its role in defining niche characteristics arises as a topic of interest. I hypothesised that species with a high magnitude of ITV would occupy a larger climate niche breadth than species with little ITV. Trait and occurrence data for 211 angiosperm tree species across Puerto Rico was used to investigate this hypothesis. Multiple indices for climate niche breadth (NB) and intraspecific variation were calculated, after which regression tests were performed to identify and characterise any relationships between NB and ITV. I found consistent positive correlations between niche breadth and intraspecific variation values (a single negative result was present), supporting the hypothesis that ITV of functional traits has a positive influence on climate niche breadth. These results highlight the contribution of ITV to species distribution, though the mechanisms behind this relationship are unclear and present a question for future study.

The mountain pine beetle is associated with a diverse array of fungi. Grosmannia clavigera is the most pathogenic of these fungi. A comparison was made between two methods that have been used to assess fungal pathogenicity. Results were similar for older trees inoculated with G. clavigera using either the alternating flap technique or cork borer method. Using the cork borer method, younger lodgepole pine trees were inoculated with five different isolates of G. clavigera. After a 48 week incubation period, isolates ATCC 18086, B5 and H55 had induced stronger pathogenic indicators compared to isolates KW 1407 and B20. After a 7 week incubation period, only isolate ATCC 18086 had induced stronger pathogenic indicators. Usually, this isolate grew faster at lower temperatures and in a low oxygen environment. Isolate KW 1407 consistently produced milder pathogenic indicators during both incubation periods. Among the non-pathogenic fungal associates of the mountain pine beetle, Ceratocystiopsis minuta may be considered the most important because it is the type species for the genus Ceratocystiopsis. The history of this genus is complicated because no physical specimen exists for C. minuta. The phylogeny of the genus Ceratocystiopsis was evaluated. Many isolates of C. minuta were assessed as potential epitypes. Several isolates of C. minuta from previous work were shown to be misidentified. C. minuta isolate CBS 116796 is recommended for future genetic work within the genus Ceratocystiopsis. For morphological work, using measurements from the literature is recommended since CBS 116796 did not produce fruiting bodies.

The mountain pine beetle is associated with a diverse array of fungi. Grosmannia clavigera is the most pathogenic of these fungi. A comparison was made between two methods that have been used to assess fungal pathogenicity. Results were similar for older trees inoculated with G. clavigera using either the alternating flap technique or cork borer method. Using the cork borer method, younger lodgepole pine trees were inoculated with five different isolates of G. clavigera. After a 48 week incubation period, isolates ATCC 18086, B5 and H55 had induced stronger pathogenic indicators compared to isolates KW 1407 and B20. After a 7 week incubation period, only isolate ATCC 18086 had induced stronger pathogenic indicators. Usually, this isolate grew faster at lower temperatures and in a low oxygen environment. Isolate KW 1407 consistently produced milder pathogenic indicators during both incubation periods. Among the non-pathogenic fungal associates of the mountain pine beetle, Ceratocystiopsis minuta may be considered the most important because it is the type species for the genus Ceratocystiopsis. The history of this genus is complicated because no physical specimen exists for C. minuta. The phylogeny of the genus Ceratocystiopsis was evaluated. Many isolates of C. minuta were assessed as potential epitypes. Several isolates of C. minuta from previous work were shown to be misidentified. C. minuta isolate CBS 116796 is recommended for future genetic work within the genus Ceratocystiopsis. For morphological work, using measurements from the literature is recommended since CBS 116796 did not produce fruiting bodies.

The mountain pine beetle is associated with a diverse array of fungi. Grosmannia clavigera is the most pathogenic of these fungi. A comparison was made between two methods that have been used to assess fungal pathogenicity. Results were similar for older trees inoculated with G. clavigera using either the alternating flap technique or cork borer method. Using the cork borer method, younger lodgepole pine trees were inoculated with five different isolates of G. clavigera. After a 48 week incubation period, isolates ATCC 18086, B5 and H55 had induced stronger pathogenic indicators compared to isolates KW 1407 and B20. After a 7 week incubation period, only isolate ATCC 18086 had induced stronger pathogenic indicators. Usually, this isolate grew faster at lower temperatures and in a low oxygen environment. Isolate KW 1407 consistently produced milder pathogenic indicators during both incubation periods. Among the non-pathogenic fungal associates of the mountain pine beetle, Ceratocystiopsis minuta may be considered the most important because it is the type species for the genus Ceratocystiopsis. The history of this genus is complicated because no physical specimen exists for C. minuta. The phylogeny of the genus Ceratocystiopsis was evaluated. Many isolates of C. minuta were assessed as potential epitypes. Several isolates of C. minuta from previous work were shown to be misidentified. C. minuta isolate CBS 116796 is recommended for future genetic work within the genus Ceratocystiopsis. For morphological work, using measurements from the literature is recommended since CBS 116796 did not produce fruiting bodies. / Forestry, Faculty of / Graduate

Witsenia is a monospecific genus of the putatively basal group, the woody Iridaceae. This upright iris has extremely long black and yellow flowers ( see fig. 1) that are thought to have been pollinated by an extinct Sunbird. The role of the unusual black floral colouration is investigated as this colour is seldom associated with bird pollination. This plant typically exists in discreet and restricted populations in wet habitats in the South Western Cape (South Africa). The restricted nature of the plant is peculiar as it occurs in either low or high altitudes, yet appears to be extremely sensitive to altitude. Popular belief suggests that Witsenia maura occurs in the Peninsula only, and results from this study show the Peninsula population to be genetically separate from other populations, reflecting a long term separation. Samples from nine populations are sequenced to investigate haplotypic variation within the species, and dispersal of ancestral populations. This thesis investigates the current knowledge of Witsenia, its ecology, history and distribution. An examination of flowers under UV light reveals the first evidence of UV nectar guides in an ornithophilous flower. Conservation issues are also addressed, and it is established that although small and apparently shrinking due to global warming, populations are nonetheless viable if managed properly. A molecular study of the species and examinination of its variation revealed exceptional haplotype diversity. This diversity can best be explained by swamps acting as refugia during interglacial periods.

As espécies do gênero Leishmania parasitam mamíferos do Novo e Velho Mundo e possuem ciclos de vida com alternância entre vertebrados e invertebrados. A maioria das espécies se desenvolve em artrópodes hematófagos, que podem pertencer a diversas ordens e famílias. A Leishmaniose visceral é uma importante zoonose e possui canídeos silvestres e domésticos como importantes reservatórios conhecidos na diversidade genética de Leishmania infantum chagasi no Brasil ainda não é conhecida. Leishmaniose é uma doença severa com ampla distribuição geográfica com uma incidência de dois milhões de casos por ano e 350 milhões de pessoas em áreas de risco de infecção. O objetivo deste projeto foi avaliar a variação intraespecífica e biogeografia de isolados brasileiros de Leishmania infatum chagasi baseados em genes nucleares e mitocondriais. Os marcadores SSUrDNA, gGAPDH, Citocromo b, Hsp 70, Quitinase e ITS1rDNA foram amplificados, sequenciados e comparados filogeneticamente pelos métodos de parcimônia e bayesiana através de análises concatenadas. As sequencias obtidas apresentaram variabilidade entre 0 e 1% e a topologia gerada não evidenciou diferenças intraespecíficas entre os isolados brasileiros de Leishmania infantum chagasi e consequentemente padrões biogeográficos. Apesar dos resultados obtidos não refletirem a variabilidade esperada, as diversas sequencias obtidas darão subsídios para a determinação e padronização de novos testes diagnósticos da Leishmaniose visceral canina. / The Leishmania species parasite mammals in the New World and have life cycles with alternating between vertebrates and invertebrates. Most species develops in blood-sucking arthropods, which may belong to different orders and families. Visceral leishmaniasis is an important zoonosis and has wild and domestic canids as important known reservoirs and genetic diversity of Leishmania infantum chagasi in Brazil is not yet known. Leishmaniasis is a severe disease with wide geographical distribution with an incidence of two million cases per year and 350 million people at risk in endemic areas. The aim of this study was to evaluate the intraspecific variation and biogeography based on nuclear and mitochondrial genes. The SSUrDNA markers, gGAPDH, cytochrome b, hsp 70, chitinase and ITS1rDNA were amplified, sequenced and compared phylogenetically by maximum parsimony and Bayesian methods in concatenated analysis. The variability of sequences was 0 to 1%, and the topology generated showed no intraspecific differences between Brazilian strains of Leishmania infantum chagasi and consequently biogeographic patterns. Although the results do not reflect the expected variability, the various sequences obtained will provide subsidies for the establishment and standardization of new diagnostic tests of canine visceral leishmaniasis.

O presente trabalho avalia a variação não-geográfica de Necromys lasiurus (Lund, 1840) dentro do território brasileiro, utilizando a morfometria craniana. Os dados foram obtidos a partir de 20 medidas craniodentárias tomadas de 1.572 indivíduos depositados em diversas coleções brasileiras. Foram descritas classes etárias baseadas exclusivamente no desgaste dos molares superiores e as mesmas foram utilizadas como índices etários para a avaliação da variação etária. Foram realizadas análises uni e multivariadas para descrever a variação sexual e etária de N. lasiurus considerando primeiramente toda a amostra e, em seguida, separadamente para cada localidade ou agrupamento cujo número amostral se mostrou suficiente para a condução dos testes estatísticos. N. lasiurus revelou dimorfismo relacionado às classes etárias intermediárias tanto na amostra total quanto nas amostras locais. No entanto, a ocorrência de dimorfismo sexual não se repetiu em todas as localidades avaliadas. A análise da variação etária com a amostra total revelou importantes padrões de variação craniana, como o rápido desenvolvimento da região orofacial em relação a outras regiões do crânio. No entanto, a avaliação da ontogenia nas amostras locais revelou diversos padrões ontogenéticos distintos. Além disso, as análises multivariadas apontam para a existência de uma estruturação geográfica da variação, corroborando estudos anteriores com a espécie. Os resultados obtidos indicam que futuras análises de cunho geográfico e taxonômico sobre N. lasiurus devem abordar os sexos de maneira separada e as classes etárias podem ser homogeneizadas para a formação de amostras com indivíduos suficientes para permitir a realização de análises estatísticas. / The present study assess the non-geographic variation of Necromys lasiurus (Lund, 1840) in Brazil, using skull morphometrics. A total of 20 craniometric measurements were taken from 1,572 specimens deposited in many Brazilian zoological collections. Age classes were described based on the wear stage of the superior molars and used as index to asses the variation due to age. Uni and multivariate analyses were used in order to describe the sexual and ontogenetic variation of N. lasiurus, first using the total sample and then using geographic samples that contained sufficient individuals for the application of the statistical tests. N. lasiurus presented sexual dimorphism related to intemediate age classes in total and in some local samples. The age assessment revealed important ontogenetic patterns of the skull development, like the rapid growth of orofacial region compared to other parts. The local analyses revealed individual patterns of variation for each sample. Besides, the multivariate approach showed geographic patterns of variation, just like previous studies said. The results of this study indicate that future geographic and taxonomic investigations on N. lasiurus should keep both sexes separated and the age classes could be homogenized in order do form adequate samples that allow the application of statistical tests.

As espécies do gênero Leishmania parasitam mamíferos do Novo e Velho Mundo e possuem ciclos de vida com alternância entre vertebrados e invertebrados. A maioria das espécies se desenvolve em artrópodes hematófagos, que podem pertencer a diversas ordens e famílias. A Leishmaniose visceral é uma importante zoonose e possui canídeos silvestres e domésticos como importantes reservatórios conhecidos na diversidade genética de Leishmania infantum chagasi no Brasil ainda não é conhecida. Leishmaniose é uma doença severa com ampla distribuição geográfica com uma incidência de dois milhões de casos por ano e 350 milhões de pessoas em áreas de risco de infecção. O objetivo deste projeto foi avaliar a variação intraespecífica e biogeografia de isolados brasileiros de Leishmania infatum chagasi baseados em genes nucleares e mitocondriais. Os marcadores SSUrDNA, gGAPDH, Citocromo b, Hsp 70, Quitinase e ITS1rDNA foram amplificados, sequenciados e comparados filogeneticamente pelos métodos de parcimônia e bayesiana através de análises concatenadas. As sequencias obtidas apresentaram variabilidade entre 0 e 1% e a topologia gerada não evidenciou diferenças intraespecíficas entre os isolados brasileiros de Leishmania infantum chagasi e consequentemente padrões biogeográficos. Apesar dos resultados obtidos não refletirem a variabilidade esperada, as diversas sequencias obtidas darão subsídios para a determinação e padronização de novos testes diagnósticos da Leishmaniose visceral canina. / The Leishmania species parasite mammals in the New World and have life cycles with alternating between vertebrates and invertebrates. Most species develops in blood-sucking arthropods, which may belong to different orders and families. Visceral leishmaniasis is an important zoonosis and has wild and domestic canids as important known reservoirs and genetic diversity of Leishmania infantum chagasi in Brazil is not yet known. Leishmaniasis is a severe disease with wide geographical distribution with an incidence of two million cases per year and 350 million people at risk in endemic areas. The aim of this study was to evaluate the intraspecific variation and biogeography based on nuclear and mitochondrial genes. The SSUrDNA markers, gGAPDH, cytochrome b, hsp 70, chitinase and ITS1rDNA were amplified, sequenced and compared phylogenetically by maximum parsimony and Bayesian methods in concatenated analysis. The variability of sequences was 0 to 1%, and the topology generated showed no intraspecific differences between Brazilian strains of Leishmania infantum chagasi and consequently biogeographic patterns. Although the results do not reflect the expected variability, the various sequences obtained will provide subsidies for the establishment and standardization of new diagnostic tests of canine visceral leishmaniasis.

Native plant materials are often seeded to restore biodiversity and ecosystem function in areas overtaken by exotic weeds. Plant materials are evaluated on intraspecific differences in productivity and expression of traits advantageous to establishment (e.g., phenology, seed mass, and growth rate); some investigations also consider population-level adaptation to exotic species. However, there is a lack of studies that broadly evaluate response to competition from exotic species at multiple scales within a species. In a greenhouse experiment, we used analysis of variance to assess the growth response of a perennial grass native to the Intermountain West, (Elymus elymoides), to competition from a common invasive species, (Bromus tectorum), at three levels of intraspecific differentiation: subspecies, lineage (wild vs. domestic germplasm), and population. We used regression analysis to assess whether E. elymoides populations from highly invaded areas were less affected by B. tectorum competition. Finally, we explored the relationship between growth traits and competitive response using random forest regression. We found significant differences among E. elymoides subspecies in their response to B. tectorum competition, no difference between wild and domestic lineages, and no population-level differentiation within subspecies. Field abundance of B. tectorum had a significant positive relationship with E. elymoides biomass, but not competitive response, suggesting that E. elymoides has not adapted to the invader. Elymus elymoides plants which were less affected by competition were smaller, allocated more biomass to leaves, and had fewer fine roots, suggesting that light interception and tissue retention were prioritized by seedlings in this competitive greenhouse environment.