Seleção balanceadora é definida como aquela que aumenta a variabilidade genética de populações em relação ao esperado sob neutralidade. Uma expectativa sobre seus efeitos é a redução da diferenciação populacional nos genes onde atua. Contudo, regimes que mantêm conjuntos distintos de alelos em diferentes populações poderiam resultar em aumento de diferenciação populacional. Com o objetivo de compreender melhor os efeitos da seleção balanceadora sobre a distribuição da variação genética entre populações, investigamos a diferenciação populacional em genes dos Antígenos Leucocitários Humanos (HLA, do inglês, Human Leukocyte Antigen), que são os genes mais polimórficos do genoma humano e o exemplo mais clássico de seleção balanceadora em humanos. As proteínas HLA são responsáveis pela apresentação de peptídeos aos linfócitos T, mediando uma etapa crítica da resposta imune. A vantagem da manutenção de variação nesses genes está possivelmente associada à capacidade de resposta a uma maior diversidade de patógenos. Neste estudo, analisamos dados do projeto 1000 Genomas (1000G), que sequenciou indivíduos de diferentes populações usando sequenciamento de nova geração (NGS, do inglês, Next Generation Sequencing). Essa técnica de sequenciamento é conhecidamente problemática quando aplicada a regiões altamente polimórficas, como os genes HLA. Por isso, avaliamos a confiabilidade dos genótipos e frequências alélicas estimados a partir dos dados do 1000G nos genes HLA, utilizando como padrão ouro dados de sequenciamento Sanger de 930 das 1092 amostras do 1000G. Encontramos um viés de superestimativa da frequência do alelo referência em alguns polimorfismos de nucleotídeo único (SNPs, do inglês, Single Nucleotide Polimorphisms), indicando que viés de mapeamento é uma causa importante de erros nos dados do 1000G. Esses resultados são relevantes para a compreensão dos desafios do uso de dados de NGS em outras regiões de alta diversidade. Usando os resultados dessa análise, excluímos de nosso estudo de diferenciação populacional sítios com estimativas de frequências alélicas pouco confiáveis nos dados do 1000G. Em uma segunda etapa de controle metodológico, demonstramos o efeito do uso de dados ricos em variantes raras em estudos de diferenciação populacional. Controlando para esse efeito, e usando apenas sítios que demonstramos ser confiáveis em nossos dados, descobrimos que a diferenciação populacional de SNPs nos genes HLA é menor que a diferenciação de SNPs em outras regiões do genoma. Esse resultado aponta para um papel predominante de pressões seletivas globais na distribuição da variação genética de HLA entre populações. Contudo, apresentamos também evidências de que a diferenciação populacional de haplótipos nos genes HLA pode ser maior do que a observada no nível dos SNPs, sugerindo que pressões locais podem influenciar a distribuição de haplótipos entre populações. Nossos achados indicam que é possível reconciliar baixa diferenciação populacional em SNPs com maior diferenciação em haplótipos, possivelmente sujeitos a pressões seletivas locais. / Balancing selection is defined as any kind of selective regime that increases genetic variability in populations relative to what is expected under neutrality. Theory predicts that balancing selection reduces population differentiation. However, balancing selection regimes in which different sets of alleles are maintained in different populations could increase population differentiation. To better understand the effects of balancing selection on the distribution of genetic variation among populations, we investigated population differentiation at the Human Leukocyte Antigen (HLA) genes, which are the most polymorphic genes in the human genome, and constitute the most striking example of balancing selection in humans. The HLA molecules are responsible for the presentation of peptides to T cells, thus mediating a critical step of the immune response. The advantage of maintaining variation in those genes through balancing selection is possibly related to the increased ability of the immune system to respond to a wider variety of pathogens. In this study, we analysed the public dataset of the 1000 Genomes project (1000G), which sequenced 1092 individuals from different populations using Next Generation Sequencing (NGS) technologies. These sequencing techniques are known to be problematic when applied to highly polymorphic genomic regions, such as the HLA genes. Therefore, we evaluated the reliability of genotype calls and allele frequency estimates of the SNPs reported by 1000G at HLA genes, using Sanger sequencing data of 930 of the 1092 1000G samples as a gold standard. We found a bias towards overestimation of reference allele frequency for some single nucleotide polymorphisms (SNPs), indicating mapping bias is an important cause of error in frequency estimation in the 1000G data. These results provide insights into the challenges of using of NGS data at other genomic regions of high diversity. Using the results of this analysis, we selected a list of sites that have reliable allele frequency estimates in the 1000G data to be used in our population differentiation study. In another methodological control, we demonstrate the effect of using a dataset rich in rare variants in population differentiation studies. Controlling for this effect, and using only the sites which we demonstrated that were reliable, we found that population differentiation of single nucleotide polymorphisms (SNPs) at the HLA genes is lower than that of SNPs in other genomic regions. This suggests a predominant role of global selective pressures in shaping the distribution of variation at the HLA genes among populations. However, we also show evidence that population differentiation of HLA haplotypes may be higher than what we observe at the SNP level, suggesting that local selective pressures may influence the distribution of haplotypes among populations. Altogether, our results indicate that it is possible to reconcile low population differentiation at the SNP level - as predicted by theory - to higher differentiation at haplotypes, which are possibly under local selective pressures.

Successful preservation of Earth’s biodiversity requires an understanding of the processes that generate new species. The generation of species without gene exchange is considered predominant; however, a growing body of evidence indicates that populations can diverge while exchanging genes, and that this may be common. Previous research hypothesized that blue-footed (Sula nebouxii) and Peruvian (S. variegata) boobies diverged from their common ancestor while exchanging genes. Here, I combine ecological and genetic perspectives to thoroughly evaluate this hypothesis. Using a panel of eight molecular markers, I estimate population differentiation for each species. I find evidence of weak population differentiation for both species, an uncommon pattern in seabirds, and argue that specialization to an unpredictable food resource has shaped contemporary population differentiation. Next, I use molecular markers and morphology to evaluate the hybrid status of five morphologically aberrant individuals. I report that all are likely F1 (first generation) hybrids, and are the product of crosses between female Peruvian boobies and male blue-footed boobies. Sex biases in pairing may occur because of an underlying preference for elaborate courtship displays. I then expand the dataset to 19 loci and use cline theory and Bayesian assignment tests to characterize the hybrid zone, to examine introgression, and to evaluate the hybrid status of the aberrant individuals. The hybrid zone is most likely maintained by strong endogenous and exogenous selection against hybrids and dispersal of parentals into the hybrid zone (a tension zone), and introgression is low for nuclear loci and absent for mitochondrial loci. Finally, I test the hypothesis that this species pair diverged from their common ancestor with gene flow using recently developed analyses and multiple loci. Divergence without gene flow is rejected and unidirectional introgression of sex-linked loci during divergence is reported. The results of this study support the hypotheses that: 1) populations can diverge while exchanging genes; 2) the Z chromosome may play a role in avian speciation; and 3) organisms specialized to variable foraging environments should exhibit low population differentiation. This study adds to our understanding of both population differentiation and speciation in seabirds, and the generation of new species more generally. / Thesis (Ph.D, Biology) -- Queen's University, 2011-04-06 13:55:32.151

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<p>A central goal of evolutionary biology is to understand the processes responsible for morphological, genetic and behavioural differentiation between sexes and among geographically distinct populations. Perhaps the most significant processes are genetic drift, natural selection, phenotypic plasticity and sexual selection. The main aim of this thesis was to investigate differentiation among individuals and populations of the sex-role reversed pipefish (<i>Syngnathus typhle</i>) and, consequently, determine which processes may be responsible for emerging patterns. This unique species is characterised by males predominately choosing amongst displaying females.</p><p>In this thesis I revealed, on a microgeographic scale, morphological differentiation without genetic divergence among populations. Interestingly, females differed in size whereas the males did not. For females in this sex-role reversed species, the costs of expressing a plastic phenotype may be outweighed by the potential gains from greater survivorship, higher fecundity or increased mating success. Thus, females gain the ability to make themselves as conspicuous and attractive to males as possible in the specific environment they are living. Moreover, behavioural experiments, which focussed on describing “personalities”, reproductive investment strategies, and mate-sampling tactics, also indicated that males as well as females had the behavioural plasticity required to adjust to the environment in which they live. To this end, using video playbacks as experimental stimuli may be especially rewarding in this species.</p><p>Overall, the studies in this thesis acknowledge the ability of species to fine-tune their phenotype to maximise fitness and, therefore, highlight the importance of considering patterns of differentiation in an environment-specific context. </p>

A central goal of evolutionary biology is to understand the processes responsible for morphological, genetic and behavioural differentiation between sexes and among geographically distinct populations. Perhaps the most significant processes are genetic drift, natural selection, phenotypic plasticity and sexual selection. The main aim of this thesis was to investigate differentiation among individuals and populations of the sex-role reversed pipefish (Syngnathus typhle) and, consequently, determine which processes may be responsible for emerging patterns. This unique species is characterised by males predominately choosing amongst displaying females. In this thesis I revealed, on a microgeographic scale, morphological differentiation without genetic divergence among populations. Interestingly, females differed in size whereas the males did not. For females in this sex-role reversed species, the costs of expressing a plastic phenotype may be outweighed by the potential gains from greater survivorship, higher fecundity or increased mating success. Thus, females gain the ability to make themselves as conspicuous and attractive to males as possible in the specific environment they are living. Moreover, behavioural experiments, which focussed on describing “personalities”, reproductive investment strategies, and mate-sampling tactics, also indicated that males as well as females had the behavioural plasticity required to adjust to the environment in which they live. To this end, using video playbacks as experimental stimuli may be especially rewarding in this species. Overall, the studies in this thesis acknowledge the ability of species to fine-tune their phenotype to maximise fitness and, therefore, highlight the importance of considering patterns of differentiation in an environment-specific context.

Abstract Sequence variation of the atpB-rbcL noncoding spacer region of the chloroplast DNA was used to reconstruct the phylogeography of Tetraena mongolica.T. mongolica (Zogophylaceae) is a relict species of a monotypic genus of in Inner Mongolia of China. It has been listed as seriously endangered plants that only distributed on the Ordos plateau of Inner Mongolic. The area is a refuge of many relict Asian Plants. Reproduction of T. mongolica is mainly by seed but a reproduction is anther way under the stress. A total of 880 bp of the atpB-rbcL spacer of cpDNA was sequenced from 8 populations of T. Mongolic. According to the cpDNA data, the level of gene flow (Nm:0.04-2.01), and population differentiation (Fst:0.199-0.895) were indicated, and the ¡§isolation by distance¡¨ model was not supported (R2 =0.0024). Based on minimum spanning network and nested clade analysis, the past fragmentation is the main phylogeographic factor affecting the population structure of T. mongolica .We suggested the deluges of Yellow River and isolation of Gianlishan Mountain cased the population fragmentation of T. mongolica. Keywords: phylogeography, Tetraena mongolica, gene flow, population differentiation, nested clade analysis, past fragmentation

Speciation is an important process that is responsible for the generation of biodiversity on Earth. The importance of gene flow during speciation is hotly debated; however, it can be investigated by studying the process of intraspecific population differentiation. Here, I investigate the mechanisms that influence population differentiation and gene flow in brown (Sula leucogaster) and red-footed boobies (S. sula). These species are congeneric, broadly sympatric, and ecologically similar; however, they differ in their marine habitat preference (inshore vs. pelagic). I hypothesized that: (i) gene flow is restricted by major physical barriers in both species, and (ii) gene flow in the absence of physical barriers is more prevalent in red-footed boobies due to their pelagic marine habitat preference. First, I characterized the structure and function of the booby mitochondrial genome. Using extensive DNA sequencing and phylogenetic methods, I found that boobies have tandemly duplicated mitochondrial control regions that evolve in concert. I suggest that concerted evolution of duplicated control region may be common in seabirds. To quantify matrilineal population genetic structure and gene flow, I sequenced one control region in 513 brown and red-footed boobies. Both species exhibited strong population genetic structure that was attributable to continental barriers to gene flow such as the Isthmus of Panama. In the absence of physical barriers, gene flow was more prevalent in red-footed boobies. I also used microsatellite and nuclear intron loci to perform multilocus phylogeographic analyses of brown and red-footed boobies. Individuals of both species could be grouped into four genetic populations that corresponded to oceanographic regions. In red-footed boobies, gene flow following secondary contact of previously isolated lineages was common, perhaps due to a pelagic habitat preference. In brown boobies, major genetic populations apparently diverged in the absence of gene flow. Despite this, Isla San Benedicto in the Eastern Pacific is a site of secondary contact between brown booby lineages that diverged approximately one million years ago, and hybrids are apparently fertile. These findings suggest that gene flow following secondary contact may be an important, but overlooked, component of speciation. / Thesis (Ph.D, Biology) -- Queen's University, 2012-04-28 17:28:53.302

In this thesis, I combine molecular analyses, common-garden and field experiments to examine how evolutionary and ecological processes influence patterns of genetic variation among and within populations of the declining, insect-pollinated, self-incompatible, perennial herb Primula farinosa. More specifically I examined 1) whether genetic diversity at neutral marker loci was related to habitat fragmentation and habitat stability, 2) whether floral display and flowering time were more strongly differentiated among populations than were putatively neutral marker loci, 3) whether adaptive population differentiation could be detected on a local spatial scale, and 4) whether floral display differentially affected male and female reproductive success. Genetic diversity at neutral marker loci was lower within fragmented populations on the Swedish mainland than within the more densely occurring populations on the island Öland, SE Sweden. On Öland, fluctuations in population size were more pronounced on thin than on deep soils, but genetic diversity was not related to soil depth. Among-population genetic differentiation in scape length and flowering time was stronger than that of neutral marker loci, which is consistent with divergent selection acting on these traits. Water availability should influence the length of the growing season and thus the time available for fruit maturation, but flowering time in a common-garden experiment was not related to estimates of water availability at sites of origin. In a reciprocal transplant experiment conducted among four populations separated by up to a few kilometres and growing in environment differing in water availability and grazing intensity, no evidence of local adaption was observed. Finally, in a field experiment, interactions with pollinators and antagonists differentially affected selection on floral display through male and female function. Taken together, the results indicate that habitat connectivity and environmental heterogeneity contribute to high neutral and adaptive genetic variation in Primula farinosa on the island Öland, SE Sweden, and illustrate that effects on both male and female reproductive success need to be considered to understand fully the evolution of floral display.

Sarus cranes (Grus antigone) are the tallest members of the crane family, Gruidae. They are found in four geographically distinct regions: northwest India (Indian Sarus- Grus antigone antigone), southeast Asia (Burmese Sarus- Grus antigone sharpei) and northern Australia (Australian Sarus- Grus antigone gillae). Although the three subspecies are morphologically distinct, their genetic distinctness is unclear. In this study, I focused on control region sequences of mitochondrial DNA (mtDNA) to assess the genetic and phylogeographic distinctness of Sarus subspecies. I used samples from four fragmented populations, seven from India, 16 from southeast Asia, five from Myanmar and eight from Australia. Phylogenetic trees were estimated using two Brolga crane sequences (G. rubicunda) as outgroups. All phylogenetic trees had low resolution, but AMOVA showed that all four Sarus populations are differentiated from each other. Nested clade phylogenetic analysis showed that most of the southeast Asian haplotypes are found at the center, suggesting that the Thai population includes the maximum number of ancestral haplotypes. Sarus cranes probably originated in southeast Asia and migrated both north towards India and south towards Australia during the last glacial maximum.

Local adaptation to climate in temperate forest trees involves the integration of multiple physiological, morphological, and phenological traits. Latitudinal clines for the relevant component traits are frequently observed for species that have a north-south distribution, but these relationships do not account for climatic variation within a given latitudinal band, which may be reflected in adaptive traits. We used black cottonwood (Populus trichocarpa) as a model to characterize the interplay between geography, climate, and adaptation to abiotic factors. Twelve traits (height, diameter, volume index, crown diameter, number of branches, number of sylleptic branches, relative number of branches, Relative canopy depth, Bud set, Bud flush, cold index of injury, carbon isotope ratio) were measured in a range-wide sample of 124 P. trichocarpa genotypes grown in a common garden. Heritability's were moderate to high (0.24 to 0.55) and significant population differentiation (QST > 0.3) suggested adaptive divergence. When climate variables were taken as predictors and the 12 traits as response variables in a multivariate regression tree analysis, aridity (Eref) explained the most variation, with subsequent splits grouping individuals according to mean temperature of the warmest month, frost-free period (FFP), and mean annual precipitation (MAP). This grouping matches relatively well the splits using geographic variables as predictors: the northernmost groups (short FFP and low Eref) had the lowest growth performance, and the highest cold hardiness. The groups spanning the south of British Columbia (low Eref and intermediate temperatures) displayed an average growth and cold hardiness. The group from the coast of California and Oregon (high Eref and FFP) had the best growth performance and the lowest cold hardiness. The southernmost and high-elevated group (with High Eref and low FFP) performed poorly, had a low cold hardiness and a significantly lower WUE. / Master of Science