Browsing by Subject "Genetic variation"
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Item Patterns of ancestry and genetic diversity in reintroduced populations of the slimy sculpin: implications for conservation(2010-02-11) Huff, David, D.; Miller, Loren, M.; Vondracek, BruceReintroductions are a common approach for preserving intraspecific biodiversity in fragmented landscapes. However, they may exacerbate the reduction in genetic diversity initially caused by population fragmentation because the effective population size of reintroduced populations is often smaller and reintroduced populations also tend to be more geographically isolated than native populations. Mixing genetically divergent sources for reintroduction purposes is a practice intended to increase genetic diversity. We documented the outcome of reintroductions from three mixed sources on the ancestral composition and genetic variation of a North American fish, the slimy sculpin (Cottus cognatus). We used microsatellite markers to evaluate allelic richness and heterozygosity in the reintroduced populations relative to computer simulated expectations. Sculpins in reintroduced populations exhibited higher levels of heterozygosity and allelic richness than any single source, but only slightly higher than the single most genetically diverse source population. Simulations intended to mimic an ideal scenario for maximizing genetic variation in the reintroduced populations also predicted increases, but they were only moderately greater than the most variable source population. We found that a single source contributed more than the other two sources at most reintroduction sites. We urge caution when choosing whether to mix source populations in reintroduction programs. Genetic characteristics of candidate source populations should be evaluated prior to reintroduction if feasible. When combined with knowledge of the degree of genetic distinction among sources, simulations may allow the genetic diversity benefits of mixing populations to be weighed against the risks of outbreeding depression in reintroduced and nearby populations.Item The Road From Variants To Traits: How Regulatory Variants Affect Gene Expression & Organismal Phenotypes(2024-03) Renganaath, KaushikNature hosts an incredible amount of diversity and beneath such diversity lies fascinating genetics that we have spent years trying to decode. Differences in our DNA sequences lead to variation in organismal traits. Most of these variants have been found to reside in noncoding portions of the genome, implying that a lot of organismal trait variation arises from variation in gene expression levels. Advances in sequencing technology have over the years allowed us to map hundreds of genomic loci underlying gene expression variation, and these loci are called expression quantitative trait loci (eQTLs). These eQTLs are of two types, local and trans, depending on their proximity to the genes they regulate. Local eQTLs regulate expression of genes in close genomic proximity while trans eQTLs regulate distant genes. Today, we possess a vast catalog of eQTLs across multiple taxa. Yet, we don’t fully understand the mechanisms by which eQTLs affect organismal traits. In this dissertation, I computationally dissect the mechanisms connecting genetic variation, gene expression and organismal traits in yeast Saccharomyces cerevisiae. As the first eukaryotic organism to have its genome fully sequenced, S.cerevisiae has over the years been a workhorse for understanding the genetics underlying complex traits. We today have comprehensive sets of QTLs underlying traits like gene expression and growth in yeast that account for most of heritable variation in these traits, allowing us to investigate the mechanisms by which eQTLs lead to organismal trait variation. In this dissertation, I characterize causal variants underlying local eQTLs in yeast (Chapter II) and the mechanisms by which eQTLs influence growth in different conditions (Chapter III). My work unravels fundamental principles by which eQTLs influence complex organismal traits.