Explaining the origin and maintenance of biodiversity is a central goal in ecology and evolutionary biology. Some of the most important, theoretical explanations for this diversity centre on the evolution of life histories. Comparative studies on life history evolution, have received significant attention in the zoological literature, but have lagged in plants. Recent developments, however, have emphasised the value of comparative analysis of data for many species to test existing theories of life history evolution, as well as to provide the basis for developing additional or alternative theories. The primary goal of this study was to explore existing theories of life history evolution using a dataset of demographic information in the form of matrix population models for a large number of plant species. By projecting average matrix population models for 207 plant species, life tables and fecundity schedules were obtained and, in turn, were used to estimate relevant life history parameters. These parameters were then used to explore the i) lability of life history traits in plants ii) their continuum of life history variation, iii) the evolution of senescence and iv) the significance of demographic entropy in population ecology. Elasticities and sensitivities of life history traits showed significant phylogenetic signal compared to other life history traits, although, all the values of phylogenetic signal observed were < 1 indicating that life history traits are generally labile. Eighty one percent of species in the datset had mortality curves that increased with age compared to one hundred percent of species that showed a reproductive value curve that decreases with age at the end of life. In particular, the parameters that measured pace and duration were inversely related suggesting in general, the presence of senescence in our data set. Finally, the tenets of the directionality theory based on demographic entropy were generally not confirmed. This study provides an important contribution to the life history evolution of iteroparous perennial plants and confirms existing theories on life history evolution.

Long non-protein coding RNAs (lncRNAs) represent a diverse and enigmatic classification of RNA. With roles associated with development and stress responses, these non-coding gene regulators are essential, and yet remain understudied in plants. Thus far, of just over 430 experimentally validated lncRNAs, only 13 are derived from plant systems and many of which do not meet the classic criteria of the RNA class. Without a solid definition of what makes a lncRNA, and few empirically validated transcripts, methods currently available for prediction fall short. To address this deficiency in lncRNA research, we constructed and applied a machine learning-based lncRNA prediction protocol that does not impose predefined rules, and utilises only experimentally confirmed lncRNAs in its training datasets. Through model evaluation, we found that our novel lncRNA prediction tool had an estimated accuracy of over 96%. In a study that predicted lncRNAs from transcriptomes of evolutionary diverse plant species, we determined that molecular features of lncRNAs display different phylogenetic signal patterns compared to protein-coding genes. Additionally, our analyses suggested that stress-resistant species express fewer lncRNAs than more stress sensitive species. To expand on these results, we used the prediction tool in concert with a transcriptomic study of two natural accessions of the drought tolerant species Eutrema salsugineum. Previously reported to show little physiological differences in a first drought, but differ significantly in a second, we instead demonstrated that the two ecotypes displayed vastly different transcriptomic responses, including the expression of lncRNAs, to a first and second drought treatment. In conclusion, the prediction tool can be applied to studies to further our knowledge of lncRNA evolution and as an additional tool in classic transcriptomic studies. The suggested importance of lncRNAs in drought resistance, and evidence of expression in two natural E. salsugineum accessions, merits further studies on the molecular and evolutionary mechanisms of these putatively regulatory transcripts. / Thesis / Doctor of Philosophy (PhD)

This diploma thesis has focused on the diversity and biogeography of Asterochloris photobionts. Since no study so far has been published on the biogeography of symbiotic microorganisms, the presented thesis is the first attemp to trace the biogeographic distribution and endemism of symbionts. By gathering 121 Asterochloris sequences obtained from lichen thalli sampled outside Europe and America, the diversity within the genus increased dramatically. The phylogenetic analysis based on the concatenated alignment of ITS rDNA and actin sequences obtained from Cladonia and Stereocaulon photobionts revealed 28 differently supported clades. Of them, eight lineages were newly discovered. Three environmental factors explaining the best the distribution pattern of Asterochloris photobionts were selected according to the statistical tests of the phylogenetic signal: two different types of biogeographical ecoregions and the substrate type. In general, the genus Asterochloris is distributed cosmopolitally, with a very low rate of endemism. Newly obtained data indicate that the restricted distribution of any photobiont clade is not caused by either historic or biological factors, but more likely by specific climatic or habitat preferences.

Humans are generally having a strong, widespread, and negative impact on nature. Given the many ways we are impacting nature and the many ways nature is responding, it is useful to study responses in an integrative context. My thesis is focused largely (two out of the three data chapters) on butterfly species’ range shifts consistent with modern climate change in Canada. I employed a macroecological approach to my research, drawing on methods and findings from evolutionary biology, phylogenetics, conservation biology, and natural history. I answered three main research questions. First, is there a trade-off between population growth rate (rmax) and carrying capacity (K) at the mutation scale (Chapter 2)? I found rmax and K to not trade off, but in fact to positively co-vary at the mutation scale. This suggests trade-offs between these traits only emerge after selection removes mutants with low resource acquisition rates (i.e., unhealthy genotypes), revealing trade-offs between remaining genotypes with varied resource allocation strategies. Second, did butterfly species shift their northern range boundaries northward over the 1900s, consistent with climate warming (Chapter 3)? Leading a team of collaborators, we found that most butterfly species’ northern range boundaries did indeed shift northward over the 1900s. But range shift rates were slower than those documented in the literature for more recent time periods, likely reflecting the weaker warming experienced in the time period of my study. Third, were species’ rates of range shift related to their phylogeny (Chapter 3) or traits (Chapter 4)? I found no compelling relationships between rates of range shift and phylogeny or traits. If certain traits make some species more successful at northern boundary range expansion than others, their effect was not strong enough to emerge from the background noise inherent in the broad scale data set I used.

Humans are generally having a strong, widespread, and negative impact on nature. Given the many ways we are impacting nature and the many ways nature is responding, it is useful to study responses in an integrative context. My thesis is focused largely (two out of the three data chapters) on butterfly species’ range shifts consistent with modern climate change in Canada. I employed a macroecological approach to my research, drawing on methods and findings from evolutionary biology, phylogenetics, conservation biology, and natural history. I answered three main research questions. First, is there a trade-off between population growth rate (rmax) and carrying capacity (K) at the mutation scale (Chapter 2)? I found rmax and K to not trade off, but in fact to positively co-vary at the mutation scale. This suggests trade-offs between these traits only emerge after selection removes mutants with low resource acquisition rates (i.e., unhealthy genotypes), revealing trade-offs between remaining genotypes with varied resource allocation strategies. Second, did butterfly species shift their northern range boundaries northward over the 1900s, consistent with climate warming (Chapter 3)? Leading a team of collaborators, we found that most butterfly species’ northern range boundaries did indeed shift northward over the 1900s. But range shift rates were slower than those documented in the literature for more recent time periods, likely reflecting the weaker warming experienced in the time period of my study. Third, were species’ rates of range shift related to their phylogeny (Chapter 3) or traits (Chapter 4)? I found no compelling relationships between rates of range shift and phylogeny or traits. If certain traits make some species more successful at northern boundary range expansion than others, their effect was not strong enough to emerge from the background noise inherent in the broad scale data set I used.

Os processos de dispersão, sobrevivência da prole e os períodos fenológicos das espécies vegetais, são o resultado tanto de sua história evolutiva quanto de suas adaptações ao ambiente. Para analisar o padrão evolutivo destes processos, foi testada a hipótese de que a similaridade entre espécies aparentadas em relação aos seus atributos reprodutivos (frutos, sementes e a fenologia da floração e frutificação) é maior do que o esperado por mero acaso (alto sinal filogenético), através de testes de Mantel parcial controlando o efeito da forma de vida das espécies. Os resultados revelaram que a maioria dos atributos de sementes, dois atributos dos diásporos (display das cores e a porcentagem de polpa) e o tempo de desenvolvimento dos diásporos, apresentaram um moderado sinal filogenético. Isto sugere que a conservação de atributos de sementes para sobrevivência da prole e a labilidade dos atributos de diásporos buscando dispersões mais efetivas, afetam significativamente o fitness das espécies, além de indicar uma influência do tempo de desenvolvimento dos diásporos nos picos de frutificação. / The processes of dispersal, offspring survival and phenological periods of plant species result both from their evolutionary history and adaptations to the environment. To analyze the evolutionary pattern of these processes, the hypothesis that the similarity among related species in relation to their reproductive traits (fruits, seeds and the phenology of flowering and fruiting) is higher than expected by chance (high phylogenetic signal) was tested through partial Mantel tests, controlling for the effect of species life form. The results revealed that most seed traits, two diaspores traits (color display and pulp percentage) and the time of diaspore development, show moderate phylogenetic signal. This suggests that the conservation of seed traits for offspring survival and the lability of diaspore traits seeking more effective dispersions, significantly affect the species fitness, and it also indicates the influence of the time of diaspore development on the fruiting peaks.

Em ecologia de comunidades buscam-se padrões reproduzíveis, dentre os quais se destaca a busca por regras de montagem ou padrões de organização de comunidades. Diante disso propomos a avaliação desses padrões, com base em convergência e divergência de atributos (TCAP – trait convergence assembly patterns e TDAP – trait divergence assembly patterns, respectivamente), e da influência filogenética na organização de assembléias de espécies lenhosas em florestas. As comunidades foram descritas a partir de atributos funcionais de espécies vegetais, considerando um gradiente sucessional de Floresta Ombrófila Mista, entre áreas que sofreram supressão total da vegetação (denominadas comunidades iniciais) e áreas que não sofreram intervenções expressivas (comunidades avançadas). Para tal, as espécies amostradas, tanto para o estrato superior (indivíduos com DAP ≥ 10 cm), quanto para o estrato inferior (indivíduos com altura > 0,10 m e até 1 cm de DAP), que apresentaram frequência superior a 10%, considerando a amostragem total, foram descritas a partir de 17 atributos funcionais e por relações filogenéticas. Os dados foram analisados a partir de algoritmos baseados em multiplicação e correlações parciais entre diferentes matrizes, que possibilitam discriminar a relevância de TCAP, TDAP e do sinal filogenético para os padrões. Os resultados indicaram que está ocorrendo estruturação das comunidades vegetais a partir dos padrões avaliados, seja convergência ou divergência, relacionados, também, com a filogenia. Diante disso, avaliamos fatores abióticos (filtros ambientais) e bióticos (filtros bióticos) exercem efeitos distintos em comunidades ao longo de um gradiente sucessional, sendo possível observar, também, o sinal filogenético nessas. / In community ecology reproducible patterns are sought, among which stands out the search for assembly rules or assembly patterns. Considering this we propose to evaluate these patterns, based on convergence and divergence of attributes (TCAP – trait convergence assembly patterns and TDAP – trait divergence assembly patterns, respectively) and the phylogenetic influence in the organization of assemblages of woody species in forests. The communities were described from functional traits of plant species, considering a successional gradient of Araucaria Forest, among areas subjected to total removal of vegetation (called initial communities) and areas that haven’t suffered significant interventions (advanced communities). To this end, the species sampled for both the upper stratum (individuals with DBH ≥ 10 cm), and for the lower stratum (individuals with height > 0.10 m and until 1 cm DBH), which had a frequency exceeding 10%, considering the total sampling, were described from 17 functional attributes and phylogenetic relationships. Data were analyzed using algorithms based on multiplication and partial correlations between different matrixes, which permit to discriminate the relevance of TCAP, TDAP and phylogenetic signal to the patterns. The results indicated that is occurring organization of plant communities from the patterns assessed, either convergence or divergence, related also with the phylogeny. Given this, we conclude that abiotic (environmental filters) and biotic (biotic filters) factors exert distinct effects on communities along a successional gradient, and it was possible to observe also the phylogenetic signal in these.

Os processos de dispersão, sobrevivência da prole e os períodos fenológicos das espécies vegetais, são o resultado tanto de sua história evolutiva quanto de suas adaptações ao ambiente. Para analisar o padrão evolutivo destes processos, foi testada a hipótese de que a similaridade entre espécies aparentadas em relação aos seus atributos reprodutivos (frutos, sementes e a fenologia da floração e frutificação) é maior do que o esperado por mero acaso (alto sinal filogenético), através de testes de Mantel parcial controlando o efeito da forma de vida das espécies. Os resultados revelaram que a maioria dos atributos de sementes, dois atributos dos diásporos (display das cores e a porcentagem de polpa) e o tempo de desenvolvimento dos diásporos, apresentaram um moderado sinal filogenético. Isto sugere que a conservação de atributos de sementes para sobrevivência da prole e a labilidade dos atributos de diásporos buscando dispersões mais efetivas, afetam significativamente o fitness das espécies, além de indicar uma influência do tempo de desenvolvimento dos diásporos nos picos de frutificação. / The processes of dispersal, offspring survival and phenological periods of plant species result both from their evolutionary history and adaptations to the environment. To analyze the evolutionary pattern of these processes, the hypothesis that the similarity among related species in relation to their reproductive traits (fruits, seeds and the phenology of flowering and fruiting) is higher than expected by chance (high phylogenetic signal) was tested through partial Mantel tests, controlling for the effect of species life form. The results revealed that most seed traits, two diaspores traits (color display and pulp percentage) and the time of diaspore development, show moderate phylogenetic signal. This suggests that the conservation of seed traits for offspring survival and the lability of diaspore traits seeking more effective dispersions, significantly affect the species fitness, and it also indicates the influence of the time of diaspore development on the fruiting peaks.

Em ecologia de comunidades buscam-se padrões reproduzíveis, dentre os quais se destaca a busca por regras de montagem ou padrões de organização de comunidades. Diante disso propomos a avaliação desses padrões, com base em convergência e divergência de atributos (TCAP – trait convergence assembly patterns e TDAP – trait divergence assembly patterns, respectivamente), e da influência filogenética na organização de assembléias de espécies lenhosas em florestas. As comunidades foram descritas a partir de atributos funcionais de espécies vegetais, considerando um gradiente sucessional de Floresta Ombrófila Mista, entre áreas que sofreram supressão total da vegetação (denominadas comunidades iniciais) e áreas que não sofreram intervenções expressivas (comunidades avançadas). Para tal, as espécies amostradas, tanto para o estrato superior (indivíduos com DAP ≥ 10 cm), quanto para o estrato inferior (indivíduos com altura > 0,10 m e até 1 cm de DAP), que apresentaram frequência superior a 10%, considerando a amostragem total, foram descritas a partir de 17 atributos funcionais e por relações filogenéticas. Os dados foram analisados a partir de algoritmos baseados em multiplicação e correlações parciais entre diferentes matrizes, que possibilitam discriminar a relevância de TCAP, TDAP e do sinal filogenético para os padrões. Os resultados indicaram que está ocorrendo estruturação das comunidades vegetais a partir dos padrões avaliados, seja convergência ou divergência, relacionados, também, com a filogenia. Diante disso, avaliamos fatores abióticos (filtros ambientais) e bióticos (filtros bióticos) exercem efeitos distintos em comunidades ao longo de um gradiente sucessional, sendo possível observar, também, o sinal filogenético nessas. / In community ecology reproducible patterns are sought, among which stands out the search for assembly rules or assembly patterns. Considering this we propose to evaluate these patterns, based on convergence and divergence of attributes (TCAP – trait convergence assembly patterns and TDAP – trait divergence assembly patterns, respectively) and the phylogenetic influence in the organization of assemblages of woody species in forests. The communities were described from functional traits of plant species, considering a successional gradient of Araucaria Forest, among areas subjected to total removal of vegetation (called initial communities) and areas that haven’t suffered significant interventions (advanced communities). To this end, the species sampled for both the upper stratum (individuals with DBH ≥ 10 cm), and for the lower stratum (individuals with height > 0.10 m and until 1 cm DBH), which had a frequency exceeding 10%, considering the total sampling, were described from 17 functional attributes and phylogenetic relationships. Data were analyzed using algorithms based on multiplication and partial correlations between different matrixes, which permit to discriminate the relevance of TCAP, TDAP and phylogenetic signal to the patterns. The results indicated that is occurring organization of plant communities from the patterns assessed, either convergence or divergence, related also with the phylogeny. Given this, we conclude that abiotic (environmental filters) and biotic (biotic filters) factors exert distinct effects on communities along a successional gradient, and it was possible to observe also the phylogenetic signal in these.

Os processos de dispersão, sobrevivência da prole e os períodos fenológicos das espécies vegetais, são o resultado tanto de sua história evolutiva quanto de suas adaptações ao ambiente. Para analisar o padrão evolutivo destes processos, foi testada a hipótese de que a similaridade entre espécies aparentadas em relação aos seus atributos reprodutivos (frutos, sementes e a fenologia da floração e frutificação) é maior do que o esperado por mero acaso (alto sinal filogenético), através de testes de Mantel parcial controlando o efeito da forma de vida das espécies. Os resultados revelaram que a maioria dos atributos de sementes, dois atributos dos diásporos (display das cores e a porcentagem de polpa) e o tempo de desenvolvimento dos diásporos, apresentaram um moderado sinal filogenético. Isto sugere que a conservação de atributos de sementes para sobrevivência da prole e a labilidade dos atributos de diásporos buscando dispersões mais efetivas, afetam significativamente o fitness das espécies, além de indicar uma influência do tempo de desenvolvimento dos diásporos nos picos de frutificação. / The processes of dispersal, offspring survival and phenological periods of plant species result both from their evolutionary history and adaptations to the environment. To analyze the evolutionary pattern of these processes, the hypothesis that the similarity among related species in relation to their reproductive traits (fruits, seeds and the phenology of flowering and fruiting) is higher than expected by chance (high phylogenetic signal) was tested through partial Mantel tests, controlling for the effect of species life form. The results revealed that most seed traits, two diaspores traits (color display and pulp percentage) and the time of diaspore development, show moderate phylogenetic signal. This suggests that the conservation of seed traits for offspring survival and the lability of diaspore traits seeking more effective dispersions, significantly affect the species fitness, and it also indicates the influence of the time of diaspore development on the fruiting peaks.