Browsing by Author "Willis, John H"
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Item Open Access A widespread chromosomal inversion polymorphism contributes to a major life-history transition, local adaptation, and reproductive isolation.(PLoS Biol, 2010-09-28) Lowry, David B; Willis, John HThe role of chromosomal inversions in adaptation and speciation is controversial. Historically, inversions were thought to contribute to these processes either by directly causing hybrid sterility or by facilitating the maintenance of co-adapted gene complexes. Because inversions suppress recombination when heterozygous, a recently proposed local adaptation mechanism predicts that they will spread if they capture alleles at multiple loci involved in divergent adaptation to contrasting environments. Many empirical studies have found inversion polymorphisms linked to putatively adaptive phenotypes or distributed along environmental clines. However, direct involvement of an inversion in local adaptation and consequent ecological reproductive isolation has not to our knowledge been demonstrated in nature. In this study, we discovered that a chromosomal inversion polymorphism is geographically widespread, and we test the extent to which it contributes to adaptation and reproductive isolation under natural field conditions. Replicated crosses between the prezygotically reproductively isolated annual and perennial ecotypes of the yellow monkeyflower, Mimulus guttatus, revealed that alternative chromosomal inversion arrangements are associated with life-history divergence over thousands of kilometers across North America. The inversion polymorphism affected adaptive flowering time divergence and other morphological traits in all replicated crosses between four pairs of annual and perennial populations. To determine if the inversion contributes to adaptation and reproductive isolation in natural populations, we conducted a novel reciprocal transplant experiment involving outbred lines, where alternative arrangements of the inversion were reciprocally introgressed into the genetic backgrounds of each ecotype. Our results demonstrate for the first time in nature the contribution of an inversion to adaptation, an annual/perennial life-history shift, and multiple reproductive isolating barriers. These results are consistent with the local adaptation mechanism being responsible for the distribution of the two inversion arrangements across the geographic range of M. guttatus and that locally adaptive inversion effects contribute directly to reproductive isolation. Such a mechanism may be partially responsible for the observation that closely related species often differ by multiple chromosomal rearrangements.Item Open Access Evolution of Floral Color Patterning in Chilean Mimulus(2008-12-05) Cooley, Arielle MarieEvolution can be studied at many levels, from phenotypic to molecular, and from a variety of disciplines. An integrative approach can help provide a more complete understanding of the complexities of evolutionary change. This dissertation examines the ecology, genetics, and molecular mechanisms of the evolution of floral anthocyanin pigmentation in four species of Mimulus native to central Chile. Anthocyanins, which create red and purple colors in many plants, are a valuable model for studying evolutionary processes. They are ecologically important and highly variable both within and between species, and the underlying biosynthetic pathway is well characterized. The focus of this dissertation is dramatic diversification in anthocyanin coloration, in four taxa that are closely related to the genomic model system M. guttatus. I posed three primary questions: (1) Is floral diversification associated with pollinator divergence? (2) What is the genetic basis of the floral diversification? (3) What is the molecular mechanism of the increased production of anthocyanin pigment? The first question was addressed by evaluating patterns of pollinator visitation in natural populations of all four study taxa. The second question was explored using segregation analysis for a series of inter- and intraspecific crosses. One trait, increased petal anthocyanins in M. cupreus, was further dissected at the molecular level, using candidate gene testing and quantitative gene expression analysis. Pollinator studies showed little effect of flower color on pollinator behavior, implying that pollinator preference probably did not drive pigment evolution in this group. However, segregation analyses revealed that petal anthocyanin pigmentation has evolved three times independently in the study taxa, suggesting an adaptive origin. In addition to pollinator attraction, anthocyanins and their biochemical precursors protect against a variety of environmental stressors, and selection may have acted on these additional functions. Molecular analysis of petal anthocyanins in M. cupreus revealed that this single-locus trait maps to a transcription factor, McAn1, which is differentially expressed in high- versus low-pigmented flowers. Expression of the anthocyanin structural genes is tightly correlated with McAn1 expression. The results suggest that M. cupreus pigmentation evolved by a mutation cis to McAn1 that alters the intensity of anthocyanin biosynthesis.
Item Open Access Genetics Analysis of Standing Variation for Floral Morphology and Fitness Components in a Natural Population of Mimulus Guttatus (Common Monkeyflower)(2009) Lee, Young WhaAn unresolved problem in evolutionary biology is the nature of forces that maintain standing variation for quantitative traits. In this study we take advantage of newly developed genomic resources to understand how variation is maintained for flower size and fitness components in a natural population of annual Mimulus guttatus in the Oregon Cascades. Extensive inbreeding depression has been documented in this population for fertility and viability (Willis 1999 a,b), while previous biometric experiments have demonstrated that some of the floral variation in this site is due to common alleles perhaps maintained by balancing selection (Kelly and Willis 2001, Kelly 2003). Detailed comparison of the genetic architecture of these two categories of traits can clarify the relative contributions of mutation versus selection in maintaining trait variation within populations as well as the relevance of standing variation for trait diversification.
We present here the results from a large scale effort to dissect variation for flower size and a suite of genetically correlated traits. In 3 independent F2 mapping populations we mapped QTLs for floral morphology (flower width and length, pistil length, and stamen length), flowering time, and leaf size. We also mapped segregation distortion loci and QTLs for fertility components (pollen viability and seed set) that exhibit inbreeding depression. We compare the genetic architecture of these two sets of traits and find clear differences. Morphological traits and flowering time are polygenic and QTLs are generally additive. In contrast, deleterious QTLs associated with segregation distortion or fertility are partially recessive and include major QTLs. There is also little co-localization between morphological/flowering time and fertility QTLs. The analysis suggests that the genetic basis of segregating variation in morphology is fundamentally different from traits exhibiting inbreeding depression. Further, there is considerable variation in the extant of pleiotropy exhibited by QTLs for morphological traits as well as flowering time and we report that epistasis contributes to the standing variation for these traits. The analysis suggests that the standing variation is relevant for trait diversification and that the variation in floral allometry, plant form, and life history observed in the guttatus species complex could have readily evolved from the standing variation.
Item Open Access Integrating genetics, geography, and local adaptation to understand ecotype formation in the yellow monkeyflower, Mimulus guttatus(2010) Lowry, David BryantSpeciation is a constantly ongoing process whereby reproductive isolating baririer build up over time until groups of organisms can no longer exchange genes with each other. Adaptation is thought to play a major role in the formation of these barriers, although the genetic mechanisms and geographic mode underlying the spread of barriers due to adaptive evolution is poorly understood. Critically, speciation may occur in stages through the formation of intermediate partially reproductively isolated groups. The idea of such widespread ecotypes has been the subject of great controversy over the last century. Even so, we have relatively little understanding about whether widespread ecotypes exist, wheather they are reproductively isolated, and how adaptive alleles are distributed among partially isolated groups. In this dissertation, I examined these issues in widespread coastal perennial and inland annual ecotypes of the yellow monkeyflower, Mimulus guttatus. First, I determined that coastal and inland populations comprise distinct ecotypic groups. I then determined that these ecotypes are adapted to their respective habitats through genetically based flowering time and salt tolerance differences. I assessed the genetic architecture of these adaptations through quantitative trait loci (QTL) analysis and determined the geographic distribution of the underlying alleles through latitudinally replicated mapping populations. I quantified the contribution of these loci to adaptation in the field through the incorporation of advance generation hybrids in reciprocal transplant experiments. In the process, I discovered a widespread chromosomal inversion to be involved in the adaptive flowering time and annual/perennial life-history shift among the ecotypes. Overall, the results of this study suggest that widespread reproductively isolated ecotypes can form through the spread adaptive standing genetic variation between habitats and that chromosomal rearrangements can integral to this process.
Item Open Access Investigating the Genetic, Evolutionary, and Functional Mechanisms of Adaptations to Copper Mine Tailings in Mimulus guttatus(2017) Jeong, AnnieThe evolution of copper tolerance in the common yellow monkeyflower, Mimulus guttatus, is a classic example of rapid adaptation in plants; however, little is yet known about the genetic, functional, and evolutionary mechanisms involved. How does excess copper cause toxicity in M. guttatus, and how do tolerant plants avoid negative effects? What genes are involved in adaptations to copper mine tailings? How do they contribute to tolerance, and what do they teach us about how copper tolerance evolved? In my dissertation, I address these questions to gain a better understanding of this rapid local adaptation.
To better understand how copper affects M. guttatus, we used RNA-seq to find genes that are differentially expressed between hydroponically-grown tolerant and nontolerant lines of M. guttatus in excess copper. In addition, we used F1 hybrids to examine allele specific expression of candidate genes. We found that copper causes more differential gene expression and greater oxidative stress in the nontolerant genotype than in the tolerant genotype. Additionally, comparisons of differentially expressed genes between genotypes revealed that more genes are constitutively expressed than induced. We identified possible candidate genes and found that most of them are cis-regulated, while genes that were systemic or downstream responses to excess copper are more likely to be trans-regulated. Together, these patterns suggested that the tolerant genotype avoids oxidative stress by either excluding, sequestering, or pumping out copper ions from the cells.
To identify loci that contribute to adaptations to copper mine tailings, we looked for regions that directly contribute to survival in copper-contaminated soil. We first characterized two parental inbred lines to determine whether copy number and gene expression differences of candidate genes are consistent with previous results. We then mapped differential survival of F2s to find loci that correlated with survival and determine their effects on fitness. We compared a list of candidate genes to our results to see if any co-localized with survival. We looked for interactions between loci and tested how these genes contribute to copper tolerance. At least two loci on Scaffolds 4 and 9 contributed to survival on copper soil. Multi-copper oxidase (MCO) and copper ion ATPase transporter (COP) both co-localized with these loci and had large effects on fitness. The MCO locus was required and sufficient for survival, while the COP locus acted additively with MCO. We hypothesized that the causal gene at the MCO region was selected for first in the evolution of copper tolerance, and that these two genes work together to exclude Cu+ ions from the cell. Together, our findings improved our understanding of the genetic, functional, and evolutionary mechanisms of copper tolerance in M. guttatus and provide evidence for at least two genes that are involved in this common adaptation.
Item Open Access Is Rapid Adaptation to New Environments Fueled by Old Mutations? A Case Study of Copper Tolerance on Mimulus guttatus(2016-06-08) Williams, AnnaleseRapid adaptation and tolerance is a phenomenon experienced by a variety of organisms typically because of new and harsh environments. Mimulus guttatus, a plant commonly seen on the west coast of the United States, is a prime example as it has rapidly evolved to soil contamination by copper due to mining in California in the last 150 years. There have been two hypotheses posed by researchers as to the genetic basis of how organisms have evolved so quickly which I set out to study: 1) There is a low frequency of tolerant genotypes in the ancestral population otherwise known as standing variation or 2) new mutations occurred once exposed to a new environment. In the past, researchers found it difficult to distinguish between the two because they lacked the technology we have today for DNA analysis. I used four different populations of M. guttatus from varying locations in order to address which hypothesis was valid. I conducted both survival assays of these populations and DNA analysis of known tolerant and non-tolerant lines using a copper oxidase gene. I found that there was at least some degree of tolerance in all populations in the survival assays, supporting the hypothesis of standing variation. I also found patterns within DNA analysis suggesting the copper oxidase gene would be useful for further study to verify the standing variation hypothesis. The results from this experiment helps in understanding rapid evolution not just in the context of soil contamination by metals but also ties back to why an alarming number of species are not able to adapt to our constantly changing world.Item Open Access Mechanisms of Habitat Segregation Between Co-Occurring Monkeyflower Species(2017) Toll, KatherineClosely related, ecologically similar species are often separated at a small scale while being broadly sympatric. In Northern California’s coast range two monkeyflower species, Mimulus guttatus and Mimulus nudatus co-occur at the local scale but populations rarely overlap although they are often separated by less than a meter. In Chapter 1, I used a combination of reciprocal transplants, observational data and laboratory experiments to test a series of biotic and abiotic hypotheses for the observed pattern. M. guttatus naturally grows in wetter areas and is often submerged for up to four months of the year. A lab experiment found that M. nudatus was unable to survive submerged for more than a week, limiting its distribution in seasonal streams inundated for months and dominated by M. guttatus. Species transplanted into populations of heterospecific congeners produced large proportions (up to 80%) of inviable seeds due to hybrid inviability between these two species. Species differences in submergence tolerance establishes some degree of habitat association, then strong frequency-dependent selection against rare immigrants via hybrid seed inviability reduces the frequency of the less numerous species and maintains habitat segregation.
Resource or reproductive competition between ecologically similar co-occurring species can cause competitive exclusion or generate selection for character displacement. Hybrid seed lethality between two spatially segregated co-occurring monkeyflower species, Mimulus guttatus and M. nudatus, causes dramatic reductions in viable seed set when each species is a rare immigrant. In Chapter 2, to understand the mechanisms driving this pattern, I tested whether traits were associated with hybridization rate and whether selection differed between habitats in each species and F2 hybrids. To determine the genetic basis of species differences, I performed genetic mapping experiments in the greenhouse and in each habitat. I found mixed evidence for divergent selection between habitats for flowering time, flower size, and leaf area. However, flower size was the best predictor of hybridization rate in M. guttatus, suggesting the potential for selection for reproductive character displacement. Hybridization increased with decreasing flower size (increasing trait similarity) for M. guttatus in M. nudatus’ native habitat. Few quantitative trait loci contributed to flower size differences but were context dependent; different loci contributed in different habitats. At the individual QTL level, viability selection favored smaller flowers, whereas phenotypic selection analysis suggested that selection favored larger flowers in both habitats. Genotype frequencies deviated significantly from Mendelian expectations in the field, and all markers significantly differed between habitats suggesting that the difference in survival to flowering between habitats is highly polygenic. In sum, an ecologically important trait, flower size, contributes to habitat segregation through its effect on hybridization rate, and is controlled by few genetic loci in the lab and in the field.
Item Open Access Molecular phylogenetic studies in nyctaginaceae: patterns of diversification in arid North America(2007-05-04T17:36:36Z) Douglas, Norman AlanThe Four O'clock Family (Nyctaginaceae) has a number of genera with unusual morphological and ecological characters, several of which appear to have a "tendency" to evolve repeatedly in Nyctaginaceae. I present a molecular phylogeny for the Nyctaginaceae, consider taxonomic implications, biogeographic patterns, and the evolution of cleistogamy and gypsophily. These characters have each evolved multiple times in the xeric-adapted genera of the family. Further progress towards understanding these phenomena requires specific investigation of the ecology of pollination and gypsum tolerance. In the genus Boerhavia, an intensively sampled phylogeny based on internal transcribed spacer (ITS) and nitrate reductase (NIA) sequences provides new insights into relationships among species in the genus, and identifies a clade of annual species centered in the Sonoran Desert. Phylogeographic patterns are present in the genus that may reflect both relatively ancient vicariant events as well as the post-Pleistocene expansion of the Sonoran Desert. Many species in this group are found to be genetically cohesive, however two annual species complexes are found which species were nonmonophyletic. Since several mechanisms can potentially lead to the finding of nonmonophyletic species, Amplified Fragment Length Polymorphisms (AFLPs) were used to examine the structure of genetic variation in the two complexes. These data show that in these two groups, different evolutionary mechanisms are needed to explain the distribution of genetic diversity within and among populations. A complex comprised of Boerhavia spicata and B. xanti shows little evidence of genetic divergence between the species in Sonora, a pattern which may indicate recent contact between two very closely related forms. In contrast, high genetic structure between populations is found in the other complex, which contains the species with umbellate inflorescences. This complex includes several nominal species with highly restricted distributions, whose evolution may have been facilitated by low gene flow among populations. Little evidence was found for associations of inbreeding within populations, and floral traits which might be expected to influence outcrossing rates.Item Unknown One Gene or Many? Different Genetic Mechanisms Drive Convergent Evolution in Monkey Flowers(2016-04-24) Farnitano, MatthewEvolutionary history is riddled with examples of convergent evolution, in which the same adaptation appears independently across multiple populations as a result of similar selective pressures. Convergent evolution can proceed by identical, similar, or unrelated genetic mechanisms. The relative frequencies of these scenarios and the evolutionary constraints that produce them are poorly understood, partly due to a lack of diverse comparative models. One such promising model is repeated adaptation to serpentine soil, a soil environment characterized by abundant heavy metals, low nutrient content, and poor water retention. Many species of Mimulus monkey flowers have populations that can tolerate these soils, but most Mimulus populations cannot. I compared the genetic signatures of serpentine tolerance across the genomes of four tolerant Mimulus populations, in order to determine whether these different species employed similar genetic mechanisms. Previous work has identified a single locus strongly connected with serpentine tolerance in M. guttatus tolerant populations. I found that M. glaucescens also likely has a single or small number of loci responsible for this adaptation. However, serpentine tolerance in M. nudatus appears to be controlled by many genes of smaller effect, rather than a single locus. This vastly different genetic mechanism is surprising given the close evolutionary and ecological relationships of these species. The results of this study show that, even under similar circumstances, evolution can employ very different genetic strategies.Item Unknown Parental Conflict, Parent of Origin Effects, and the Evolution of Hybrid Seed Failure in Mimulus(2018) Coughlan, Jennifer M.The earth is home to roughly 9 million eukaryotic species. The formation and maintenance of this diversity requires the accumulation of barriers to reproduction. One of the most common post-zygotic barriers in plants is hybrid seed inviability (HSI). Despite its commonality, we know relatively little about the genetic mechanisms and evolutionary forces which are responsible for this barrier, particularly in naturally co-occurring species. Here I tested the role of parental conflict in HSI between co-occurring monkeyflowers in the M. guttatus species complex. I assessed the strength and directionality of HSI within and between phenotypically described perennial variants of the M. guttatus species complex. I find substantial HSI between two morphologically described variants, M. guttatus and M. decorus, amounting to ~30-50% reproductive isolation. Genetically distinct clades of M. decorus vary in their ability to cross with M. guttatus in both magnitude and direction of RI. Intriguingly, northern and southern clades of M. decorus are also incompatible with one another, showing strong, symmetric hybrid seed inviability. In all cases, HSI is accompanied by parent of origin effects on F1 seed size, consistent with a role of resource allocation to hybrid inviability. Parent of origin effects on reciprocal F1s were not limited to final size. I characterize the developmental trajectory of seeds between M. guttatus and both the northern and southern clades of M. decorus. Hybrid seeds show similar developmental trajectories depending on their end fate (i.e. viable vs inviable), despite differing in the maternal and paternal contributors in these crosses. Inviable seeds are characterized by patterns of paternal excess; chaotic and malformed endosperm. Viable hybrid seeds are characterized by maternal excess; limited, and precocious endosperm development. Relatively normal embryo development early on suggests that hybrid seed inviability stems, in part, from malformed endosperm. Lastly, I use a combination of modeling, next generation sequencing, and genotyping approaches to determine the genetic architecture and basis of HSI. I find that the genetic basis of HSI is complex, wherein several maternally and paternally inherited nuclear loci interact to cause HSI. In total, I show the presence of multiple perennial species in the M. guttatus species complex. These species show little phenotypic or obvious ecological differentiation, but are genetically unique and have substantial post-zygotic reproductive isolation, namely through the formation of inviable seeds. Patterns of seed development and final size are indicative of parent of origin effects on resource allocation to endosperm. Despite relatively low genetic differentiation for the group, the genetic basis of HSI is quite complex, involving multiple maternally and paternally interacting alleles. Future work will be needed to determine the identities of these genes, as well as patterns of repeatability across the complex.
Item Unknown The Effects of Seasonal Cues and Differential Gene Expression on the Developmental Switch of a Flower Polyphenism in Mimulus douglasii(2017) Baldridge, Laryssa LeighAngiosperms have evolved multiple mating systems that allow reproductive success under varied conditions. Striking among these are cleistogamous mating systems, where individuals can produce alternative flower types specialized for distinct mating strategies. Cleistogamy is thought to be environmentally-dependent, but little is known about environmental triggers that induce cleistogamous flower or the gene regulatory networks that determine the final floral phenotypes. If production of alternate flowers is environmentally induced, populations may evolve locally adapted responses. Mimulus douglasii, exhibits a cleistogamous mating system, and ranges across temperature and day length gradients, providing an ideal system to investigate environmental parameters that control cleistogamy and the gene regulatory networks responsible for the different floral forms. In these studies, we compared flowering responses across M. douglasii population accessions that produce phenotypically distinct outcrossing, and self-pollinating flower morphs. Under controlled conditions, we determined time to flower, and number and type of flowers produced under different temperatures and day lengths. We also compared gene expression profiles between chasmogamous and cleistogamous flowers using RNA-seq. We find that temperature and day length both effect onset of flowering. Long days shift flower type from predominantly chasmogamous to cleistogamous. The strength of the response to day length varies across accessions whether temperature varies or is held constant. We also find that gene expression patterns differ between the early development chasmogamous and cleistogamous flower buds. Cleistogamy is an environmentally sensitive polyphenism in Mimulus douglasii, allowing transition from one mating strategy to another. Longer days induce flowering and production of cleistogamous flowers. Shorter days induce chasmogamous flowers. Population origin has a small effect on response to environmental cues. Subtle shifts in the expression of cell division, cell expansion, and metabolic process related transcripts lead to the massive size difference observed between chasmogamous and cleistogamous flowers.
Item Unknown The Genetic Basis of Local Adaptation to Serpentine Soils in Mimulus guttatus(2014) Selby, JessicaWhile 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.
Item Unknown The Genetics of Adaptation to a Harsh Granite Outcrop Environment in Mimulus(2014) Ferris, Kathleen GrayClosely related populations or species often occupy ecologically disparate habitats. Adaptation to new habitats can maintain genetic variation within a species or eventually lead to speciation. Local adaptation to different environments has been repeatedly demonstrated in plants and animals, however the traits and genes that underlie this adaptation are poorly understood. This is because many traits differ between divergent populations and species. One way to solve this problem is to separate a trait from its genetic background through genetic manipulation and look for differences in fitness between genetically manipulated individuals.
My dissertation focuses on investigating the traits and genes that allow two species of Monkey flower, Mimulus laciniatus and Mimulus filicifolius, to survive in a unique habitat. Most closely related Mimulus species, such as M. guttatus, occur in streams and seeps, but M. laciniatus and M. filicifolius have each colonized a harsh granite outcrop environment. Another unique characteristic that both these species share is a lobed leaf shape. Because of the physiological properties of lobed leaves they should be adaptive in a dry, exposed granite outcrop. M. laciniatus also flowers earlier than nearby M. guttatus and is a small flowered self-fertilizing species while M. guttatus has large flowers and is highly outcrossing. Early flowering allows plants to escape the onset of seasonal drought while a self-fertilizing mating system and small flower size is often correlated with the occupation of harsh habitats.
In chapter one I describe a new granite outcrop endemic species of Mimulus, M. filicifolius based on morphological divergence from M. laciniatus. M. filicifolius was previously categorized as M. laciniatus but it is geographically disjunct and its leaves are more finely dissected (Sexton, Ferris, and Schoenig 2013). In the second chapter I explore whether M. filicifolius is genetically divergent and reproductively isolated from M. laciniatus using genetic sequence, microsattelite, and hybrid fertility data from four members of the M. guttatus species complex with highly overlapping geographic ranges: M. guttatus, M. nasutus, M. lacinaitus, and M. filicifolius. In the third chapter I investigate the genetic basis of leaf shape differences in three members of the M. guttatus species complex, M. laciniatus, M. nudatus, and M. guttatus using bulk segregant analysis to map quantitative trait loci. In the fourth and final chapter I examine the genetic basis of flowering time, floral size, and leaf shape divergence between sympatric M. guttatus and M. laciniatus populations in a common garden using quantitative trait locus (QTL) mapping, phenotypic selection on flowering time, flower size, and leaf shape in M. laciniatus x M. guttatus hybrids in a reciprocal transplant experiment in the field, and whether QTL's from my common garden experiment overlap fitness QTL's in the field by genotyping hybrid individuals that survived to flower in the field.
Item Unknown The Role of Polyploidy in Phenotypic and Genomic Evolution in the Shy Monkeyflower, Mimulus sookensis(2012) Modliszewski, Jennifer LouiseIn an ever-changing world, evolution is an essential process that may allow organisms to adapt to their environment through natural selection. All evolutionary processes act through a single fundamental medium: genetic variation. Polyploidy, or whole genome duplication, is a major mechanism for evolutionary change because it is both widespread across taxa and results in a proliferation of genetic material that evolution can act upon. The key questions addressed here are: (1) How does chromosome pairing during meiosis in allopolyploids affect the magnitude of genetic variation?, (2) How does the genome of polyploids evolve following formation, and what genetic mechanisms govern this evolution?, and (3) How does genetic and genomic evolution in polyploids affect phenotypic evolution? I use the shy monkeyflower, Mimulus sookensis, a tetraploid of hybrid origin between Mimulus guttatus and Mimulus nasutus, to address these focal questions. In order to develop a foundation to aid in interpretation of my findings, I first investigate the evolutionary history of M. sookensis. Chromosome counts establish that M. sookensis is indeed an allotetraploid, and a review of taxonomic literature reveals that this species is heretofore undescribed. By analysing the patterns of genetic variation at chloroplast and nuclear loci in M. guttatus, M. nasutus, and M. sookensis, I show that M. sookensis has recurrently formed from M. guttatus and M. nasutus. Crossing experiments within M. sookensis indicate that recurrent origins can contribute to genetic diversity without contributing to reproductive isolation among independently arisen polyploid lineages.
To address my focal questions, I take advantage of an intriguing and striking difference in flower size among M. sookensis, M. guttatus, and M. nasutus. The flowers of M. sookensis and M. nasutus are small and remarkably similar to one another, while the flowers of M. guttatus and diploid and tetraploid F1 hybrids between M. guttatus and M. nasutus are large and showy. This phenotypic divergence in flower size between M. sookensis and M. guttatus-like hybrids indicates that small flower size has evolved in M. sookensis. Using genetic marker data and phenotypic measurements from synthetic neoallotetraploid Mimulus, I demonstrate that there are low levels of fragment loss and phenotypic variation in neoallotetraploids; this suggests that homeologous pairing and recombination following polyploidization is not a major source of genetic variation or phenotypic evolution in M. sookensis. Analysis of the whole genome sequence of two M. sookensis lines reveals that M. sookensis is a fixed heterozygote throughout its entire genome, in that it has retained both a M. guttatus-like and M. nasutus-like subgenome, neither of which have been removed through homeologous recombination. These subgenomes have been homogenized by widespread gene conversion, and do not appear to have been differentially affected by deletions or deleterious mutations. Finally, to directly characterize the genetic architecture of flower size in M. sookensis, I cross a large-flowered synthetic neoallotetraploid Mimulus to small-flowered M. sookensis. I then employ a novel genotyping-by-sequencing approach to identify quantitative trait loci (QTL) associated with flower size. I find that there is one locus that accounts for a large proportion of phenotypic variation, and four other loci also contribute to flower size variation between the parental lines. Some of these loci co-localize with previously identified loci for flower size in diploid Mimulus, while others do not. Altogether, genetic marker data, phenotypic analysis of neoallotetraploids, whole genome sequence data, and QTL mapping data suggest that the genetic variation necessary for flower size evolution was likely caused by both gene conversion and new mutations, but not homeologous recombination. These results suggest that trait evolution in polyploids may be affected by the unique attributes of polyploids, but that new mutations are always an important source of genetic variation, regardless of ploidy level.
Item Unknown The selective and developmental maintenance of genetic variation in a natural population of Mimulus guttatus(2017) Troth, AshleyThe maintenance of genetic variation for quantitative traits has long puzzled evolutionary biologists. Previous studies have effectively interrogated large genomic regions both in the greenhouse and field to understand the selective forces maintaining variation. However, subtler points can be difficult to tease out from these genomic regions. Here, we take advantage of advances in sequencing technology to understand how variation for flowering time and size is maintained within a single population of Mimulus guttatus at the nucleotide level. By focusing on the nucleotide level, we directly address questions of allelic effect and frequency, and interrogate polymorphisms found to be significantly associated with traits in the greenhouse in other contexts to determine their contributions to growth and fitness.
Flowering time and flower size have been shown to be highly quantitative traits within the Iron Mountain population of M. guttatus, and it has been proposed that minor alleles are likely to increase trait values. We present here confirmation of this long-standing hypothesis. By creating a genome wide association (GWA) mapping panel, we have identified multiple significant site-trait associations within the IM population of M. guttatus, and found extensive evidence of pleiotropy and polygenic adaptation.
To understand how developmental processes might contribute to variation in flowering time and flower size, we next investigate genetic variation for circadian period length. The circadian clock is known to be upstream of floral induction pathways, and in Arabidopsis thaliana over one third of the genome is suspected to be under circadian regulation. We find extensive variation for endogenous period length, and genetic correlations between endogenous period length and days to germination, flower size measurements, height, and leaf size. Despite a small GWA analysis sample size, we find abundant evidence of overlap of sites found to be significant for growth and flowering traits and period length.
Finally, we investigate how genomic variants identified in the greenhouse contribute to variation in a natural context. By planting F1 crosses of the lines sequenced for the GWA mapping panel in the field, we are able to confirm significant impacts on field growth and fitness, and identify a genomic site significantly associated with survival to seed production. Taken together our results not only confirm previous quantitative trait locus work at the nucleotide level, but present a newly developed sequence resource for analysis of intra-population variation in M. guttatus.
Item Open Access Theoretical and Emperical Investigations into Adaptation(2010) Wright, Kevin MatthewThe problem is two fold: how does natural selection operate on systems of interacting genes and how does natural selection operate in natural populations. To address the first problem, I have conducted a theoretical investigation into the evolution of control and the distribution of mutations in a simple system of interacting genes, a linear metabolic pathway. I found that control is distributed unevenly between enzymes, with upstream enzymes possessing the greatest control and accumulating the most beneficial mutations during adaptive evolution. To address the second problem, I investigated the evolution of copper tolerance in the common yellow monkeyflower, Mimulus guttatus. I genetically mapped a major locus controlling copper tolerance, Tol1. A Dobzhansky-Muller incompatibility was hypothesized to also be controlled by Tol1, however, we have demonstrated that it maps to another, tightly linked locus, Nec1. Finally, we investigated the parallel evolution of copper tolerance in multiple new discovered mine populations. We found that copper tolerance has evolved in parallel multiple times via at least two distinct physiological mechanisms. In four mine populations, there was a strong signal of selection at markers linked to Tol1, implying that copper tolerance has evolved via the same genetic mechanisms in these populations.