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.

<p>While local adaptation has been frequently demonstrated via reciprocal transplant experiments, our understanding of the genetic basis of it remains minimal. There is a notable lack of studies that identify naturally segregating variants, determine the traits controlled by these variants and characterize their fitness effects in the field. Such studies are critical for understanding how spatially varying selective pressures can drive population divergence and maintain genetic variation. The experiments presented here aim to characterize the genetic basis of local adaptation to serpentine soils in Mimulus guttatus. First, I show that serpentine and non-serpentine populations of M. guttatus are locally adapted to soil habitat wherein non-serpentine plants are unable to survive on serpentine soils. Serpentine tolerance appears to come at a cost as serpentine plants are smaller in the juvenile stage than non-serpentine plants when grown at non-serpentine field sites. These size differences may limit the competitive ability of serpentine tolerant plants in non-serpentine habitats which tend to be more heavily vegetated than serpentine habitats. Next I identify environmental variables that are important selective agents in the serpentine habitat. Using hydroponic assays to isolate an individual chemical variable of serpentine soils - low calcium levels to high magnesium levels (low Ca:Mg ratio) - I show that serpentine and non-serpentine populations of M. guttatus have significant differences in tolerance to low Ca:Mg. I then characterize the genetic basis of these ecotypic differences in survival and tolerance using quantitative trait locus (QTL) mapping. I identify a single, major QTL that controls both the ability to survive on serpentine soils and tolerance to low Ca:Mg ratio which suggests that M. guttatus populations have adapted to serpentine soils through an ability to tolerate the low levels of Ca while simultaneously not suffering from Mg toxicity. Furthermore, I show that this same QTL controls ability to survive on serpentine soils in a second, geographically distant population. However, preliminary work suggests that the two populations are not equally tolerant to each other's soils indicating that either other loci also contribute to serpentine tolerance and these are not shared between the two serpentine populations or that there are different serpentine tolerance alleles at the major QTL are not functionally equivalent. This work addresses long-standing questions in evolutionary biology regarding the number and effect size of loci that underlie adaptive traits by identifying a large effect locus that contributes to adaptive differences between M. guttatus populations.</p> / Dissertation

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

Master of Science / Biology / Michael Tobler / Environmental variation can shape phenotypic variation in organisms. Most evidence for trait differentiation along environmental gradients comes from analyses of dichotomous habitat types that differ in only one or few environmental factors. In reality, however, environmental variation is often more subtle, gradual, and multifarious. I investigated geographic variation in body shape, trophic resource use, and individual diet specialization in two species of darters (Etheostoma spectabile and E. flabellare; Percidae) that occur along river gradients. I explicitly tested how abiotic and biotic environmental factors shape trait variation within and between species. Results indicated significant among population variation in the body shape of both species. Population differences in body shape were correlated with variation in substrate composition. Although body shape analyses revealed a small but significant signal of convergent evolution of body shape when both species occur in sympatry, E. spectabile and E. flabellare mostly exhibited unique responses to shared sources of selection. The analyses of darter trophic resource use uncovered significant resource partitioning between the two species and geographic variation in diets that is likely driven by differences in resource availability. Furthermore, the majority of populations exhibited significant individual specialization. Variation in individual specialization in populations of E. flabellare was related to invertebrate density and competitor richness, and in E. spectabile to the combined effects of invertebrate density and invertebrate diversity. My results indicate substantial variation in trophic resource use among individuals, populations, and species of small-bodied fishes that are typically assumed to be generalist insectivores. Variation in diet specialization may be more widespread than previously considered, and ecological opportunity is an important factor in shaping trophic resource use of individuals and populations. Overall, the results indicate that even subtle and gradual environmental variation can induce substantial variation in phenotypes on a relatively small spatial scale.

In my thesis I present data collected from a long-term selection experiment using the freshwater model organism Chlamydomonas reinhardtii. The selection experiment was designed to disentangle the effects of the number of multiple environmental drivers (MEDs) and the identity of those environmental drivers including high CO2, high temperature, general nutrient depletion, reduced light intensity, reduced phosphate availability, the addition of a herbicide, UV radiation and reduced pH. Using up to eight environmental drivers, I show how simple organisms such as C. reinhardtii evolve in response to MEDs. The first step in this investigation is to examine the short-term response of MEDs. Data collected at the beginning of the selection experiment will provide insight into the early stages of microevolution by investigating key differences in the short-term (plastic) responses to few vs. many MEDs. Here, I focus on how the data collected from the responses to single environmental drivers can help us predict the responses to MEDs by using ecological models (additive, comparative, multiplicative). I show that the short-term plastic responses to single environmental drivers can predict the effect of MEDs using the comparative model because the response is largely driven by the single dominant driver present. I also demonstrate the importance of the number of environmental drivers (NED) for making predictions from the single environmental drivers and show that predictions become more reliable as the NED increases. The results gathered from short-term responses provide evidence that single environmental driver studies are useful for predicting the effect of MEDs. After evolution, I found that the strength of selection varies with NED in a predictable way, which connects the NED to the evolutionary response (size of the direct response) through the strength of selection. Here, I used statistical models to quantify the effect of NED on the evolutionary response to MEDs and then interpreted this by considering the possible genetic constraints on adaptation to MEDs. A subset of populations evolved in environments with five environmental drivers and all populations evolved in the single environmental driver environments are used to examine how adapting to single vs. many environmental drivers affect local adaptation. I examine how populations selected in environments with one environmental driver, five environmental drivers and the evolved control, differ in their response to new environments with the same NED, environments with different NED, and a novel environment. I found that there is a relationship between local adaptation and the strength of selection in the local environment and patterns of local adaptation are affected by the NED of new environments. Lastly, I present the phenotypic consequences of evolution under MEDs. I found that before evolution, measures of chlorophyll content and cell size decline with increasing NED. However, after evolution the relationship between chlorophyll content and cell size with NED is weaker because populations converge on the same phenotypes as they evolve. I also present a case-study of how mass spectrometry methods can be used to better understand underlying molecular mechanisms of two phenotypes (chlorophyll positive and chlorophyll negative cells). This selection experiment is a good example of how laboratory investigations and model organisms can be used to design experiments with enough replication to have high statistical power in order to make more accurate predictions on the short- long-term effects of MEDs. Whilst there have been some studies on the effects of MEDs, these studies rarely have more than three environmental drivers (sometimes 5 environmental drivers) and there are only a handful of long-term MED studies. This study can be used to develop a priori hypotheses for investigating how environmental change will shape natural microbial communities, and is especially useful for organisms where long-term studies with multiple environmental drivers are unfeasible.

A distribuição e riqueza de espécies ao redor do globo intriga o ser humano desde os tempos antigos. Algumas teorias para explicar tais padrões se baseiam no conceito de adaptação local, procurando avaliar o desempenho relativo dos indivíduos nativos de uma dada localidade perante ao desempenho de indivíduos imigrantes. Este desempenho diferenciado ocorreria devido à heterogeneidade espacial encontrada no ambiente, gerando gradientes de seleção natural. Estas pressões de seleção levariam a adaptação às condições locais dos indivíduos das espécies. No caso de gradientes altitudinais, vários fatores ambientais estão correlacionados com a elevação, caracterizando pressões seletivas diferenciadas e espacialmente distribuídas. Para organismos que ocorrem nestes gradientes, os limites de distribuição geográfica pode estar ligada a variação nas condições ambientais. Neste estudo escolhemos um par de espécies irmãs de Rhipsalis (R. crispata e R. oblonga - Rhipsalideae, Cactaceae) que se distribui ao longo de um gradiente altitudinal na Mata Atlântica brasileira, R. oblonga até 1000m de altitude e R. crispata até 700m de altitude, para verificar a capacidade adaptativa das espécies às mudanças de algumas condições ambientais associadas a variação altitudinal. Para verificar a capacidade adaptativa das espécies, realizamos experimentos de transplante, com mais de 4000 plantas para áreas de diferentes altitudes. As estações experimentais foram montadas em três altitudes (50m, 100m e 825m), replicadas duas vezes em pontos distintos da serra do mar, onde havia variação natural das condições de microhabitat em cada altitude. Nós esperávamos que R. oblonga apresentasse desempenho biológico, avaliado pelos dados de crescimento e sobrevivência, superior que o de R. crispata com o aumento da altitude, e que R. crispata apresentasse seu melhor desempenho nas áreas de baixa altitude. Nossos resultados indicaram que R. oblonga apresenta melhor desempenho que R. crispata na maioria dos ambientes e que o melhor crescimento de R. crispata ocorreu em áreas baixa costeiras. R. oblonga apresenta uma distribuição geográfica mais ampla, assim também é mais tolerante à mudanças ambientais. Enquanto que R. crispata, por apresentar distribuição geográfica menor, também é menos tolerante a mudanças ambientais, o que fica claro ao observar as respostas das espécies, segundo as variação nas condições de microhabitat. Nossos resultados indicam que distribuição altitudinal das espécies pode ser explicada por diferenças na capacidade adaptativa das espécies / Old and relevant questions exist in relation to species distribution and richness in the earth planet. Some theories to explain these patterns are based on the concept of local adaptation, i.e., difference on the performance of individuals due to environment spatial heterogeneity related to gradients of natural selection. Selective pressures could lead to adaptation to local conditions by populations of a given species. In altitudinal gradients, various environmental factors change according to the changes in elevation. In this study we selected a pair of Rhipsalis\' sister species (R. crispata and R. oblonga - Rhipsalideae, Cactaceae), distributed across altitudinal gradient in the Brazilian Atlantic Forest to verify, by transplant experiments, the species adaptive capacity to environmental conditions associated with elevation.. The experimental stations were set up in three altitudes levels (50m, 100m and 825m), replicated twice in Serra do Mar. We expected that R. crispata presents a better biological performance (growth and survival) than R. oblonga in lower elevation, and vice versa.. Our results indicated that R. oblonga exceeds R. crispata in most environments, but R. crispata was better than R. oblonga in the low coastal altitude sites. Rhipsalis oblonga presents broad geographic distributions, so it is more tolerant to environmental changes and R. crispata, due to its less widely geographic distribution, is less tolerant to environmental changes. Our results indicate that altitudinal species distribution could be explained by differences in species adaptive capacity

Cette thèse utilise des approches de génétique des populations et de statistique pour étudier des événements anciens de démographie humaine, inférer de l’adaptation locale dans diverses populations et étudier le déterminisme du goût. En utilisant une approche bayésienne, j’évalue les preuves génétiques d’une réduction de population entre 190 000 et 130 000 ans avant notre ère. Je trouve que les données sont en faveur d’un modèle sans goulot d’étranglement durant cette période. Dans le second article, je développe une méthode destinée à la détection d’adaptation locale basée sur l’étude des haplotypes privés. Appliquée à des données de génotypage, cette méthode permet de détecter des signaux d’adaptation connus chez l’Homme mais aussi d’étendre nos connaissances en matière d’adaptation. J’étudie ensuite les signaux d’adaptation dans des données de génomes entiers de plusieurs populations et montre que le régime alimentaire et les pathogènes ont une influence majeure sur la variabilité adaptative des populations prises en compte. J’étudie dans un dernier article les perceptions gustatives de populations ayant différents modes de vie. Je présente les résultats phénotypiques de perception des goûts, et les associe à des données de génotypage. Je montre que les gènes impliqués dans la perception des goûts ont évolué avec le mode de vie. En effectuant une étude d’association, je montre aussi que les variations dans la perception des goûts impliquent plus de gènes que les seuls gènes codant pour les récepteurs gustatifs. Mes résultats montrent l’utilité des données génétiques denses pour mieux comprendre l’évolution humaine. / This thesis uses population genetics and statistical approaches to investigate early human demography, infer local adaptation in diverse sets of populations, and study the genetic basis for taste perception. Using a Bayesian approach, I evaluate the genetic evidence of a bottleneck between 190,000 and 130,000 years ago and find that the data is in favor of a model without bottleneck at this time point. I further develop a method to detect local adaptation based on frequencies of private haplotypes. Applied to large-scale human genotype data, this method detects known signals of positive selection but also permits to improve knowledge on potential adaptation events in humans. I further investigate patterns of adaptation in whole genome data based on a diverse set of African populations. The results from the regions potentially selected show that diet and pathogens are the common driving forces of adaptation in all studied populations. I last study taste perception in populations differing on lifestyle (hunter-gatherers, farmers and nomad herders). I present taste perception phenotypes for all tastes (sweet, bitter, sour, salty and umami) and relate them to high density genotype data. I show that taste and taste-involved genes have evolved with lifestyle. By performing an association study, I also show that variation in taste perception involves more genes than only the taste receptors genes.I covered several topics of human ancient demography and adaptation and show the utility of using large-scale genetic data to better understand human history.

Understanding the strategies that plant populations implement to increase evolutionary responsiveness to better survive environmental changes induced by climate change is a critical challenge for ecology and evolutionary studies. This dissertation investigates the role of hybridization, local adaptation, and phenotypic plasticity in plant population responses to environmental change. Specifically, I utilized meta-analysis techniques to investigate the prevalence of local adaptation and phenotypic plasticity as the two main mechanisms used to adapt to heterogeneous environments, and experimentally explored the genetic pathway of plasticity in phenology traits such as bolting time in Arabidopsis thaliana under high temperatures. Furthermore, A. thaliana was used to create artificial hybrids to test if novel trait combinations allow hybrids to outperform their parental source in novel and stressful environments. In the second chapter, I included reciprocal transplant plant studies and found that local adaptation is more common than adaptive plasticity as an evolutionary response to environmental heterogeneity. Although local adaptation was more common, plastic responses have been reported as a mechanism to tolerate increases in global temperature; however, the underlying genetic and developmental mechanisms are only starting to be elucidated. To address this, the third chapter determined whether alternative splicing of the ambient temperature flowering pathway gene FLOWERING LOCUS-M (FLM), and expression of SHORT VEGETATIVE PHASE (SVP), can explain flowering time plasticity in ecotypes of A. thaliana under 18°C and 26°C. Although the expression of SVP and FLM-β tracks reaction norms, I failed to find evidence that alternative FLM splicing plays a role in phenotypic plasticity in intraspecific flowering time variation. Intraspecific hybridization (admixture) disrupts divergent genetic architectures between populations to generate phenotypic novelty and raw material for environmental selection to act upon. In order to understand the effect of this disruption to local adaptation of A. thaliana ecotypes separated along geographic and locally adaptive genetic distances, the fourth chapter used experimentally created F1-hybrids between geographically distant ecotypes, and used single nucleotide polymorphism (SNP) data to estimate (putatively neutral) background and adaptive genetic distances. My results suggest that disruption of locally adaptive genomic loci decreases the performance of offspring between distantly related parents, but that crosses between very closely related parents also reduce performance, suggesting that during admixture selection may have to balance the consequences of disrupting local adaption while also avoiding inbreeding depression. Lastly, I examined the effect of recombination events under limiting and novel growing conditions (i.e. drought, high temperatures, and freezing field over-wintering conditions) in A. thaliana F2-hybrids. I provide empirical data for the effect of limiting growing environment on phenology, growth, and fitness traits on the admixed and parental ecotypes. I found that recombination events generate novel phenotypes. Generally, offspring phenotypic variation increases and shifts from the parental ecotype phenotypes, and in some cases, offspring display transgressive segregation, heterosis, or outbreeding depression. This work provides a novel contribution towards understanding mechanisms that plant implement to deal with rapid environmental changes. Specifically, plastic responses and hybridization events may interplay to maintain and increase genotypic diversity.

Patterns of woody-plant mortality have been linked to global-scale environmental changes, such as extreme drought, heat stress, more frequent and intense fires, and episodic outbreaks of insects and pathogens. Although many studies have focussed on survival and mortality in response to specific physiological stresses, little attention has been paid to the role of genetic heritability of traits and local adaptation in influencing patterns of plant mortality, especially in non-native species. Tamarix spp. is a dominant, non-native riparian tree in western North America that is experiencing dieback in some areas of its range due to episodic herbivory by the recently introduced northern tamarisk leaf beetle (Diorhabda carinulata). We propose that genotype x environment interactions largely underpin current and future patterns of Tamarix mortality. We anticipate that (i) despite its recent introduction, and the potential for significant gene flow, Tamarix in western North America is generally adapted to local environmental conditions across its current range in part due to hybridization of two species; (ii) local adaptation to specific climate, soil and resource availability will yield predictable responses to episodic herbivory; and (iii) the ability to cope with a combination of episodic herbivory and increased aridity associated with climate change will be largely based on functional tradeoffs in resource allocation. This review focusses on the potential heritability of plant carbon allocation patterns in Tamarix, focussing on the relative contribution of acquired carbon to non-structural carbohydrate (NSC) pools versus other sinks as the basis for surviving episodic disturbance. Where high aridity and/or poor edaphic position lead to chronic stress, NSC pools may fall below a minimum threshold because of an imbalance between the supply of carbon and its demand by various sinks. Identifying patterns of local adaptation of traits related to resource allocation will improve forecasting of Tamarix population susceptibility to episodic herbivory.

京都大学 / 0048 / 新制・課程博士 / 博士(人間・環境学) / 甲第22791号 / 人博第962号 / 新制||人||228(附属図書館) / 2020||人博||962(吉田南総合図書館) / 京都大学大学院人間・環境学研究科相関環境学専攻 / (主査)教授 瀬戸口 浩彰, 教授 市岡 孝朗, 教授 宮下 英明 / 学位規則第4条第1項該当 / Doctor of Human and Environmental Studies / Kyoto University / DFAM