<p>In this thesis, I combined comparative and experimental approaches to examine selection on reproductive traits, and population differentiation in the insect-pollinated, outcrossing, perennial herb <i>Arabidopsis lyrata</i>. More specifically, I (1) determined whether selection on flowering phenology and floral display can be attributed to interactions with pollinators and herbivores, (2) examined whether population differentiation in flowering phenology and floral display is correlated with current selection on these traits, and (3) tested for local adaptation from contrasting environments in Europe.</p><p>A field experiment conducted in a Swedish population demonstrated, that interactions with pollinators may markedly affect selection on both floral display and phenology of flowering. In an alpine population in Norway, grazing damage to inflorescences strongly influenced selection on floral display. The results suggest that variation in the abundance of pollinators and herbivores should contribute to spatio-temporal variation in selection on flowering phenology and floral display in <i>A. lyrata</i>. </p><p>A common-garden experiment showed that flowering phenology and floral display vary among Scandinavian populations of <i>A. lyrata</i>. For some traits patterns of population differentiation were consistent with differences in the direction and strength of phenotypic selection determined in comparisons (a) between an alpine population in Norway and a coastal population in Sweden, and (b) among coastal populations in Sweden. This suggests that current selection contributes to the maintenance of genetic differentiation in these traits.</p><p>Adaptive differentiation among populations was examined in a reciprocal transplant experiment that included populations from three contrasting environments, alpine Norway, coastal Sweden and lowland, continental Germany. The experiment provided evidence for local adaptation, and indicated that populations have diverged in traits affecting plant establishment and early growth.</p>

In this thesis, quantitative genetic approaches, common-garden experiments, and field studies were combined to examine patterns of population differentiation and the genetic architecture of characters of putative adaptive significance in the widely distributed perennial herb Lythrum salicaria. In this work, I (1) documented patterns of population differentiation in phenology, life-history, and morphology along latitudinal gradients at different geographical scales, (2) investigated the genetic architecture of phenology, flower morphology, and inflorescence size, and (3) combined estimates of phenotypic selection in the field with information on the genetic variance-covariance matrix (G) to examine potential constraints to adaptive evolution. A common-garden experiment demonstrated latitudinal variation in life-history, and phenology of growth and reproduction among L. salicaria populations sampled across Sweden. Flower morphology varied significantly among populations, but was, with the exception of calyx length, not related to latitude of origin. A second experiment, which included two Swedish, two Dutch, and two Spanish populations, indicated that the latitudinal gradient in reproductive and vegetative phenology might extend throughout Europe. A quantitative-genetic study of two Swedish populations revealed significant additive genetic variation for all phenological and morphological traits investigated. The G matrices of the populations differed significantly according to common principal component analysis, and genetic correlations within the study populations did not strictly correspond to trait correlations observed among populations. In a field study, I detected directional selection through female function for larger inflorescences in two consecutive years. Relative fitness increased disproportionately with inflorescence size in the year when supplemental hand-pollination indicated that pollen limitation was severe. Genetic correlations with inflorescence size considerably influenced predicted response to selection in other characters. Taken together, the results suggest that among-population differences in phenology and life-history in L. salicaria have evolved in response to latitudinal variation in length of the growing season. They demonstrate that the evolutionary potential of local populations may be considerable. The genetic covariance structure substantially influences predicted short-term evolutionary trajectories. However, the weak correspondence between genetic correlations documented within populations and trait correlations among populations, suggest that the G matrix has not imposed strict constraints on patterns of among-population differentiation.

In this thesis, I combined comparative and experimental approaches to examine selection on reproductive traits, and population differentiation in the insect-pollinated, outcrossing, perennial herb Arabidopsis lyrata. More specifically, I (1) determined whether selection on flowering phenology and floral display can be attributed to interactions with pollinators and herbivores, (2) examined whether population differentiation in flowering phenology and floral display is correlated with current selection on these traits, and (3) tested for local adaptation from contrasting environments in Europe. A field experiment conducted in a Swedish population demonstrated, that interactions with pollinators may markedly affect selection on both floral display and phenology of flowering. In an alpine population in Norway, grazing damage to inflorescences strongly influenced selection on floral display. The results suggest that variation in the abundance of pollinators and herbivores should contribute to spatio-temporal variation in selection on flowering phenology and floral display in A. lyrata. A common-garden experiment showed that flowering phenology and floral display vary among Scandinavian populations of A. lyrata. For some traits patterns of population differentiation were consistent with differences in the direction and strength of phenotypic selection determined in comparisons (a) between an alpine population in Norway and a coastal population in Sweden, and (b) among coastal populations in Sweden. This suggests that current selection contributes to the maintenance of genetic differentiation in these traits. Adaptive differentiation among populations was examined in a reciprocal transplant experiment that included populations from three contrasting environments, alpine Norway, coastal Sweden and lowland, continental Germany. The experiment provided evidence for local adaptation, and indicated that populations have diverged in traits affecting plant establishment and early growth.

The distribution of the expressed genotype is moved around in the population over time byevolution. Natural selection is one of the forces that act on the phenotype to change the patterns ofnucleotide variation underlying those distributions. How the phenotype changes over aheterogeneous environment describes the type of evolutionary force acting on this trait and thisshould be reflected in the variation at loci underlying this trait. While the variation in phenotypesand at the nucleotide level in a population indicates the same evolutionary force, it does notnecessarily mean that they are connected. In natural populations the continuous shifting of geneticmaterial through recombination events break down possible associations between loci facilitates theexamination of possible causal loci to single base pair differences in DNA-sequences. Connecting thegenotype and the phenotype thus provides an important step in the understanding the geneticarchitecture of complex traits and the forces that shape the observed patterns.This thesis examines the European aspen, Populus tremula, sampled from subpopulations overan extensive latitudinal gradient covering most of Sweden. Results show a clear geneticdifferentiation in the timing of bud set, a measure of the autumnal cessation of growth, betweendifferent parts of Sweden pointing at local adaptation. In the search for candidate genes thatunderlie the local adaptation found, most genes (25) in the photoperiodic gene network wereexamined for signals of selection. Genes in the photoperiodic network show an increase in theheterogeneity of differentiation between sampled subpopulations in Sweden. Almost half (12) of theexamined genes are under some form of selection. Eight of these genes show positive directionalselection on protein evolution and the gene that code for a photoreceptor, responsible for mediatingchanging light conditions to downstream targets in the network, has the hallmarks of a selectivesweep. The negative correlation between positive directional selection and synonymous diversityindicates that the majority of the photoperiod gene network has undergone recurrent selectivesweeps. A phenomenon that likely has occurred when P. tremula has readapted to the northern lightregimes during population expansion following retracting ice between periods of glaciations. Two ofthe genes under selection also have single nucleotide polymorphisms (SNP) that associate with budset, two in the PHYB2 gene and one in the LHY2 gene. Furthermore, there is an additional SNP inLHY1 that explain part of the variation in timing of bud set, despite the lack of a signal of selection atthe LHY1 gene. Together these SNPs explain 10-15% of the variation in the timing of bud set and 20-30% more if accounting for the positive co-variances between SNPs. There is thus rather extensiveevidence that genes in the photoperiod gene network control the timing of bud set, and reflect localadaptation in this trait.

The human colonization of worldwide landmasses occurred through complex patterns of dispersal and admixture. At the same time, the survival in the different areas of the world depended on the adaptation to new habitats that imposed novel selective challenges. With the advent of high-throughput genotyping technologies and dense catalogues of human genetic variation, the demographic history of many human populations has been unraveled from genomic data, with important implications in medical genetics. However, several human groups are yet to be genetically characterized. These incomplete past histories include the determination of ancestries of the current Cuban population, as well as the origins and dispersal of European Romani, whose demographic history is aimed to be reconstructed in this work. Finally, the present study also aims to describe the genetic basis and evolution of one of the most striking human phenotypes, the African Pygmy height. / La colonización humana de las diferentes masas continentales se produjo mediante complejos patrones de dispersión y mezcla. La supervivencia en las diversas regiones del planeta ha dependido de la adaptación a las presiones selectivas impuestas por los nuevos hábitats. Con el desarrollo de tecnologías de genotipado masivo y las bases de datos de la diversidad genética humana, la historia demográfica de muchas poblaciones humanas, y sus implicaciones médicas, han sido descritas. Sin embargo, algunas poblaciones todavía no han sido caracterizadas genéticamente. Por ejemplo, tanto la descomposición de la ancestría genética de la población cubana actual como los orígenes y la dispersión de los gitanos europeos siguen siendo historias incompletas que se han reconstruido en esta tesis. Finalmente, este estudio también tiene como objetivo describir la evolución y las bases genéticas de uno de los fenotipos humanos más llamativos, la altura de los pigmeos africanos.

My dissertation research investigates the genetic architecture and evolutionary significance of physiological variation in two wildflower species, Ipomopsis aggregata and Arabidopsis thaliana. In particular, my work focuses on water use efficiency (WUE), a critical physiological trait that dictates plant growth and performance in resource-limited environments. I used a combination of quantitative trait loci (QTL) mapping, field selection experiments, and classic quantitative genetics to investigate 1) the genetic architecture of water use efficiency and flowering time, 2) patterns of natural selection on water use efficiency, flowering time, and other ecological traits in I. aggregata, and 3) additive genetic variation, genetic correlations, and selection on water use efficiency, flowering time, and plasticity to drought in Arabidopsis thaliana. Using an Ipomopsis aggregata genetic mapping population, I identified four QTL underlying WUE, three QTL-QTL epistatic interactions, and evidence for a possible QTL x cytoplasmic interaction affecting WUE. I found a similar genetic architecture underlying flowering time, with four main effect QTLs that all adjacently localized to the same linkage groups as WUE, and three QTL-QTL epistatic interactions, which occur between the same chromosome pairs as the WUE interactions. The combined main and interactive effects explain 35% and 40% of the phenotypic variation in WUE and flowering time, respectively. The adjacent localization suggests a possible role for the evolution of co-inheritance or, if the true QTL positions actually overlap, a possible role for pleiotropy underlying the phenotypic correlation between WUE and flowering time. Additionally, these results suggest epistasis is a significant factor affecting phenotypic variation in nature. In a reciprocal transplant and water addition experiment, I demonstrated variable natural selection on WUE, flowering time, and nectar production in I. aggregata across elevation/habitat and differential water availability. At low elevation in the water addition treatment, natural selection favors early flowering and greater nectar sugar concentration, while dry conditions favor high WUE and early flowering time. At high elevation, where the growing season is shorter and drier, selection favors early flowering regardless of water addition. These results suggest natural selection on ecophysiological and floral traits varies with resource availability (e.g. water availability and pollinator visitation). Using data from a glasshouse experiment involving a global panel of accessions of Arabidopsis thaliana, I demonstrated strong positive genetic correlation between WUE and flowering time, as well as selection for low WUE and early flowering under experimental season-ending drought. Finally, I found significant genetic variation in plasticity as well as selection favoring greater WUE plasticity under drought, indicating plasticity to drought is adaptive in A. thaliana. / text

Many organisms are sexually dimorphic for ecologically and socially important traits. One of the major foci of biology is to understand the evolution of such sexually dimorphic traits. Here I present my work on the evolution of a dimorphic trait, female-limited Batesian mimicry, in Papilio swallowtail butterflies. I begin by developing a character state path network to study the diversity of mimicry types and directionality of trait change during the evolution of female-limited mimicry. My phylogenetic analysis showed that female-limited mimicry has evolved independently in several groups of swallowtails, mainly via single-step character changes from monomorphic non-mimetic ancestors to female-limited mimetic descendents. Mimetic polymorphism has evolved in tandem with female-limited mimicry, the two being tightly correlated among mimetic species. Most traditional explanations of female-limited mimicry and mimetic polymorphism invoke sexual selection. In reviewing these hypotheses, I show that their key assumptions and predictions remain untested, and that sexual selection cannot maintain female polymorphism under some conditions. Sexual selection hypotheses are also unable to explain community ecological aspects of mimicry rings. Hence, I developed a novel model of female-limited mimicry based on sex-specific, frequency- and density-dependent advantages of mimicry. This model shows that both-sex mimicry, female-limited mimicry and mimetic polymorphism are favored along a gradient of relative mimic frequency. My ecological data from south Indian mimicry rings support a key prediction of this model. Finally, I employ the patterns of female-limited mimicry among swallowtail butterflies to highlight the contrast between Darwin’s sexual selection model and Wallace’s natural selection model of sexual dimorphism. I show that most of the sexual dimorphism in swallowtail wing color patterns is a product of natural selection for protective female coloration, predominantly in the form of female-limited mimicry. Thus, swallowtails support Wallace’s model of sexual dimorphism, underlining the importance of natural selection. / text

Flamboyant colors are widespread throughout the animal kingdom. While many of these traits arise through sexual selection, bright coloration can also evolve through natural selection. Many aposematic species, for example, use conspicuous warning coloration to communicate their noxiousness to predators. Recent research suggests these signals can also function in the context of mate choice. Studies of warning color evolution can therefore provide new insights into how the interplay of natural and sexual selection impact the trajectory of conspicuous signal evolution. For my dissertation, I investigated the potential for male-male competition to impact the warning color evolution of a species of poison frog. I focused my work on an exceptionally bright and toxic population of the strawberry poison frog (Oophaga pumilio) where males are brighter than females, a classic signature of sexual selection. In Chapter 1, I used theoretical models of predator and frog visual systems to determine which can see the variation in bright warning coloration within this population. I found that birds, the presumed major predator, likely cannot see this variation, indicating that sexual selection can work under the radar of predators in this species. In Chapter 2, I tested the aggressive responses of males using a two-way choice paradigm that manipulated the perceived brightness of stimulus males. I found that males directed more of their behaviors to bright stimulus frogs, and brighter focal frogs more readily approached stimuli and directed more of their attention to the brighter rival. In Chapter 3, I tested the outcomes of dyadic interactions between males of varying brightness and observed male reactions to simulated intruders in their territories. I found that brighter males initiated aggressive interactions with rivals more readily, and brightness asymmetries between males settled interactions in a way that is consistent with classic hypotheses about male sexual signals. In Chapter 4 I sought to describe physiological correlates of male warning color brightness. While male brightness did not co-vary with classic measures of body condition (circulating testosterone and skin carotenoids), it did correlate with toxins sequestered from the diet and thus appears to be a reliable signal of toxicity in this population. / text

Rhodopsin, a visual pigment protein found in retinal photoreceptors, mediates vision at low-light levels. Recent studies focusing primarily in human and mouse have challenged the assumption of neutral evolution of synonymous substitutions in mammals. Using recently developed likelihood-based codon models accounting for mutational bias and selection, we find significant evidence for selective constraint on synonymous substitutions in mammalian rhodopsins, and a preference for cytosine at 3rd codon positions. A second project investigated adaptive evolution in rhodopsin, in view of theories of nocturnality in early mammals. We detected a significant acceleration of non-synonymous substitution rates at the origins of therian mammals, and a tendency of synonymous substitutions towards C-ending codons prior to that. These findings suggest an evolutionary scenario in which synonymous substitutions that increase mRNA stability and/or translation efficiency may have preceded adaptive non-synonymous evolution in early mammalian rhodopsins. These findings have important implications for theories of early mammalian nocturnality.

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