Browsing by Subject "Natural selection"
- Results Per Page
- Sort Options
Item Open Access Ancestry-based Methods for Characterizing the Evolutionary History of Admixed Populations(2022) Hamid, ImanAdmixture occurs when previously isolated populations come together to form a new population with genetic ancestry from those sources. Admixture is ubiquitous across the tree of life, including humans, and is often associated with migration and exposure to new environments and selective pressures. Admixed populations provide a unique opportunity to study adaptation on short timescales by introducing beneficial alleles at high frequency. However, admixed populations are often excluded from genomic studies due to lack of applicable methodology. Instead of relying on classical methods confounded by the process of admixture itself, we can detect changes in patterns of genetics ancestry that are informative about selection in admixed populations and at the short timescales often relevant for post-admixture selection. However, we lack theoretical expectations and methods to detect and characterize ancestry-based genomic signals indicative of post-admixture selection and adaptation. Common ancestry outlier approaches discard information about the surrounding genomic context and are prone to false positives due to drift and demography. Here, I present three studies which leverage patterns of genetic ancestry to investigate the evolutionary history of admixed populations. First, I develop a suite of ancestry-based summary statistics and computational methods to detect post-admixture adaptation, and demonstrate their application in a case study of human adaptation to malaria. In particular, these summary statistics incorporate patterns of ancestry beyond the site under selection, such as the length of contiguous ancestry tracts surrounding the locus, and are informative about the strength and timing of selection in admixed populations. I observe one of the strongest signals of recent selection in humans at the malaria protective Duffy-null allele, and show that this mode of strong single-locus selection over 20 generations has impacted genome-wide patterns of ancestry. Next, I move beyond summary statistics to develop a deep learning strategy for localizing regions of the genome under selection. This method takes images of chromosomes painted by ancestry as input to avoid the loss of information and bias that can occur when relying on user-defined summary statistics. I demonstrate this approach on simulated admixture scenarios and find that the method successfully localizes variants under selection 95% percent of the time, outperforms the common ancestry outlier approach, and is robust to demographic misspecification. Lastly, I present the first Illyrian genome sequences available from the Iron Age in a study of the ancestry and genetic relationships of five neonates buried in Korčula, Croatia. I find genetic support for classifying these individuals as Illyrian, and show that patterns of ancestry and genetic variation are consistent with their geographic location between Italy and the mainland Balkans. In the combined work presented here, I advance our ability to study the evolutionary history of admixed populations, which has implications for our understanding of phenotypic variation, disease risk, and conservation genetics across many study systems. Further, these methods tailored to the mosaic ancestry of admixed populations is a step towards expanding the diversity of populations, especially humans, who benefit from discoveries and advancement in genomic research.
Item Open Access From Genes to Traits and Ecosystems: Evolutionary Ecology of Sphagnum (Peat Moss)(2020) Piatkowski, Bryan ThomasPlants in the genus Sphagnum (peat moss) are the dominant biotic features of boreal peatlands that store nearly one-third of Earth’s terrestrial carbon. Peat mosses are ecosystem engineers and create the peatlands that they inhabit through the accumulation of peat, or partially decayed biomass, and the functional traits underlying this extended phenotype. Interspecific functional trait variation is hypothesized to promote niche differentiation through the creation and maintenance of ecological gradients along which species sort within communities. One prominent gradient relates to height-above-water-table wherein some species produce hummocks raised up to a meter above the water table, while others live in hollows at or near the water table. However, it is unclear how these traits evolved during Sphagnum diversification, to what extent natural selection produced functional trait variation, and which genes might contribute to such phenotypes.
In Chapter 2, a meta-analysis of data from recent studies is used to relate patterns of functional trait variation to the phylogeny of Sphagnum. The results suggest that interspecific variation in various measures of growth, decomposability, and litter biochemistry is phylogenetically conserved in Sphagnum, meaning that closely related species tend to be more similar in trait values than species selected at random from the phylogeny. Furthermore, these results suggest that patterns of trait covariation might represent adaptive syndromes related to niche. This is the first study to formally relate functional trait variation in Sphagnum to its evolutionary history.
In Chapter 3, a field experiment and phylogenetic comparative methods are used to show that natural selection is responsible for shaping interspecific variation in Sphagnum decomposability and its coevolution with niche. In the largest experiment of its kind to date, litter decomposability was measured for over 50 species of Sphagnum under natural conditions. Models of trait evolution were competed against one another to determine which best explained the evolution of this important functional trait. The best model was a multiple-peak Ornstein-Uhlenbeck process wherein the predominantly hummock and hollow clades of Sphagnum possess separate adaptive optima towards which trait values are pulled. Furthermore, the results suggest that shifts in trait optima occurred concomitantly with shifts in realized niche along the hummock-hollow gradient.
In Chapter 4, comparative genomics is used to identify genes involved in the biosynthesis of an ecologically-important class of secondary metabolites, the anthocyanins, and determine when this biosynthetic pathway first evolved in embryophyte land plants. In Sphagnum, complex phenolic molecules embedded in the cell walls influence litter decomposability and, in turn, the rate of peat accumulation. One group of such phenolics, the sphagnorubins, confer red-violet pigmentation to some species of Sphagnum. Sphagnorubins are thought to be homologous to anthocyanin pigments, known best from flowering plants, that have numerous roles including mitigation of abiotic stress. Phylogenetic analyses using full genome sequences representing nearly all major green plant lineages show that the entire anthocyanin biosynthetic pathway was not intact until the most recent common ancestor of seed plants. Furthermore, orthologs of many downstream enzymes in the pathway are absent from seedless plants including mosses, liverworts, and ferns. These results suggest that the production of red-violet flavonoid pigments in seedless plants, including sphagnorubins, requires the activity of novel enzymes and represents convergent evolution of red-violet coloration across land plants.
In Chapter 5, comparative genomics is used to test for molecular adaptation in Sphagnum genomes. Two reference-quality peat moss genomes were compared to those from other plants to identify genes bearing signatures of positive selection and gene families marked by significant rates of expansion in the Sphagnum lineage. Gene Ontology enrichment analyses were then used to identify over-represented classes of genes that might have been particularly important during the evolution of peat mosses. The results suggest adaptive evolution largely occurred in genes and gene families related to epigenetic regulation, secondary metabolism, stress response, and transmembrane transport. Together, these data suggest that selection favored changes to genes involved in response to environmental stress and provide candidate loci that might underlie adaptation to the harsh conditions of boreal peatlands.
Item Open Access Population Genetics, Natural Selection and Genetic Architecture of the Selfing Syndrome in the Morning Glory Ipomoea lacunosa(2017) Rifkin, JoannaThe evolutionary transition from outcrossing to self-pollination occurs frequently in flowering plants and has direct and indirect effects on genomics, life history and floral morphology. The life history and floral traits common to selfing plants are collectively called the "selfing syndrome." This dissertation uses the highly selfing morning glory Ipomoea lacunosa to address three major questions in the evolution of highly selfing plants: what are the genomic consequences of selfing, do the morphological changes associated with the transition to self-pollination result from natural selection or genetic drift, and how does the genetic architecture of those morphological traits affect their evolution? In the first chapter, we analyze genetic data from I. lacunosa and its outcrossing sister species I. cordatotriloba to compare the genomic consequences of selfing in I. lacunosa to theoretical predictions. We find that the reduction in genetic diversity is greater than that predicted by theory, suggesting a population bottleneck in I. lacunosa's history. There is also evidence for the relaxation of natural selection. The second chapter combines these genetic data with phenotypic measurements in a Qst-Fst comparison to determine whether natural selection is responsible for life history and floral morphology differences between I. lacunosa and its outcrossing relative I. cordatotriloba. Our analyses reveal that several component traits in the selfing syndrome diverged in response to natural selection. Chapter Three uses a quantitative trait locus (QTL) mapping approach to characterize the genetic architecture of the selfing syndrome and investigate how genetic correlations between traits affected its evolution. We find generally lower levels of genetic correlation between selfing syndrome traits than previous QTL studies of the selfing syndrome. The low level of genetic correlation indicates that independent selection on selfing syndrome traits is responsible for the evolution of the syndrome as a whole.
Item Open Access Selection and Constraint: Population Genetic Approaches to Understanding the Evolution of Sea Urchin Development(2011) Garfield, DavidChanges in the expression and function of genes active during metazoan development have played a critical role in the evolution of morphological differences between species and phyla, yet the origins of these changes remain poorly understood. What roles do positive and negative selection play in the evolution of development? How do evolutionary changes accumulate given the degree to which organisms are able to buffer the effects of environmental and genetic perturbations during development? The crucial insight of the Modern Evolutionary Synthesis was that divergence between species arises from variation within populations. Following this principle, I have made use of tools from quantitative and population genetics to investigate three central questions: 1) How much genetic variation is there in the networks of genes that underlie metazoan development? 2) What affect does developmental buffering have on the accumulation of selectable genetic variation? 3) To what extent does selection act to shape patterns of genetic variation among different kinds of genes and at different stages of development? I show that developmental systems can harbor extensive levels of genetic variation, and that the amount of genetic variation in individual genes at different stages of development is related to the extent to which variation in those genes is buffered by genetic interactions. I also show that while selection plays an active role in shaping genetic variation in development, the extent to which variation in a gene is visible to selection depends in predictable ways on a) the biological function of that gene and b) whether the mutations in question influence gene expression or protein function. My results as a whole demonstrate the utility of population level approaches to the study of the evolution of development, and provide key insights into the role that selection plays in generating developmental variation.
Item Open Access The Mating System Evolution of Ipomoea lacunosa(2013) Duncan, Tanya MarieThe evolution of selfing from outcrossing is one of the most frequent mating system transitions in angiosperms. Plants that are highly selfing typically exhibit a suite of morphological traits termed a "selfing syndrome," including reduced corollas and reproductive structures, loss of corolla pigmentation, little anther-stigma separation, and a low pollen/ovule ratio. The overall consensus among scientist is that the morphological changes that accompany the transition to selfing are adaptive and thus a product of natural selection. Few attempts, however, have been made to determine whether traits of the selfing syndrome are truly an operation of natural selection or if genetic drift could be the acting force. My dissertation examines the roles that natural selection and genetic drift played in the evolution of the selfing syndrome in Ipomoea lacunosa. With the use of field observations, crossing data, and molecular analyses, I show that I. lacunosa has evolved increased selfing ability, decreased anther-stigma distance and smaller, white flowers, compared to its closest relative I. cordatotriloba. Furthermore, using a standard QST - FST comparison, I evaluated the relative importance of selection and drift in the evolution of the selfing syndrome in I. lacunosa. I also identified the genetic basis of flower color divergence between I. lacunosa (white) and I. cordatotriloba (purple) and examined patterns of variation to determine if selection or genetic drift caused the divergence. Analyses revealed that the traits of I. lacunosa characteristic of the selfing syndrome have evolved as a product of natural selection, not genetic drift.
Item Open Access Using Landscape Genomics to Conserve Adaptive Capacity: A Case Study with a Southern Appalachian Salamander(2017) Forester, BrennaLandscape genomics is an emerging field that investigates how environmental features drive patterns of neutral and adaptive genetic variation across landscapes. Importantly, landscape genomics can provide insight into the adaptive potential of wild populations of non-model species, since these analyses do not require prior genomic information or the use of manipulative experiments such as reciprocal transplants. However, a fundamental challenge in landscape genomics is detecting genetic markers under selection from large genomic data sets. This analytical step is particularly important since partitioning these data into neutral and adaptive components of genetic diversity provides the information upon which management decisions are based.
Difficulties with the partitioning step include distinguishing neutral demographic signals from signals of selection, detecting selection across heterogeneous landscapes, and detecting signals of selection that are derived from multilocus adaptive processes. To address these issues, I used two different sets of landscape genetic simulations to test a suite of genotype-environment association (GEA) analyses across a range of landscape heterogeneities, selection strengths, dispersal abilities, demographic histories, sample sizes, sampling designs, and genetic architectures. I found that multivariate GEA methods showed a superior combination of low false positive and high true positive rates across simulation scenarios, providing a powerful tool for investigating the genetic basis of local adaptation and improving management actions.
I then applied a multivariate GEA approach to a reduced representation genomic data set for Weller's salamander (Plethodon welleri). This endemic, fully terrestrial, forest-dwelling salamander is a species of conservation concern across its small range in the Southern Appalachian Mountains. Its restriction to mountaintop habitats makes it particularly vulnerable to ongoing habitat fragmentation and climate change. I developed and illustrated the use of an “adaptive dissimilarity” index to characterize the scope of adaptive variation across the Weller’s salamander range. In combination with other metrics including neutral genetic variation, population differentiation, and effective population size, I addressed a series of conservation scenarios that were improved by the explicit consideration of differences in adaptive genetic variation among populations. These scenarios included: (1) site prioritization to ensure evolutionary resiliency across the species range; (2) genetic rescue to increase genetic diversity and population fitness while minimizing the risk of outbreeding depression; and (3) assisted gene flow to maximize adaptive potential in response to rapid climate change. These analyses are helping us better understand the capacity of species to adapt to changing conditions and what management actions will be most effective to conserve biodiversity under global change. These efforts must be part of the broader effort to stem the biodiversity crisis by conserving not just genetic diversity, but also the ecological and evolutionary processes that sustain it.