Browsing by Subject "Mimulus guttatus"
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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 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.