Browsing by Subject "Adaptation"

This dissertation examines the adaptability of civic cults during the Hellenistic period. Faced with shifting populations, increasing social tensions, economic changes, and political pressures, Hellenistic communities devised a number of strategies aimed at negotiating the tension between maintenance of traditional religious practices and adaptive, context-specific change. Through the lens of inscribed Greek sacred laws we see communities balancing the twin requirements of innovation and tradition. The epigraphic record shows significant changes to the choreography of religious experience in response to demographic change; experimentation in funding mechanisms, in what appear to be responses to economic and cultural changes; ambitious attempts to redefine the configuration of sacred space both inside the city and out; savvy rhetorical and ritual framing of innovation in the face of cults that had had failed or else were on the brink of doing so.

Through a series of case studies I elucidate the legislative strategies with which communities dealt with these challenges. In chapter 1, I investigate legal strategies aimed at maintaining traditional oracular procedures as more visitors were coming to iatromantic shrines. I focus on the shrine of Apollo Coropeius in Thessaly where the civic authority at Demetrias passed a law reevaluating the administrative and ritual procedures for consultation. In chapter 2, I analyze the changing obligations of sacred personnel to perform rites in the city at large, i.e. before festivals, in the face of shifting socioeconomic norms. Communities frequently experimented with alternative mechanisms to fund religious activities. A sacred law from Halicarnassus forms the backbone of this analysis. I argue that cultural pressures may have helped shape these mechanisms. Chapter 3 concerns legislative strategies for the reconfiguration of sacred space, particularly the moving or refactoring of sanctuaries. Here I analyze a third-century decree from Tanagra that regulates the transfer of a sanctuary of Demeter and Kore. Other laws, particularly from Anaphe and Peparethus, provide crucial details for the rearrangement of important cult structures. In these cases, we see the concerted efforts to provide for private and public and sacred and secular interests in order to ensure the perpetuation of traditional religious practices. The fourth chapter investigates the reinvention of cult caused by political and ideological interests. Communities employed rhetorical strategies to justify or mask the reinvention or renewal of traditional rites that had lapsed or were on the brink of doing so. I focus on two case studies that illustrate the complexities of legislating ritual reinvention. A second-century Athenian law details the rites for the revived Thargelia whereas a decree from Magnesia-on-the-Maeander details the expansion of the cult of Artemis Leukophryene with a new festival commemorating the goddess' new temple. In both cases, we can see rhetorical strategies of augmentation and renewal reflected in the writings of Anaximines of Lampsacus. The concluding chapter provides a view of the other side of the coin: what happens when communities fail to adapt to the challenges that threatened their cults? Polybius, Pausanias, and Plutarch shed much light on our most pressing questions. For instance, what did failed cults look like? How did Greeks envisage dilapidated sanctuaries and defunct cults? Overall, the case studies based on sacred laws present a Greek view of religious change that finds strength in change, continuity in adaptation, commonality in variation, stability in the shifting sands of historical change. The portrait of Greek religion that emerges from this study is one in which tradition and innovation form two sides of the same coin, rather than opposing forces

Background: The Cataldo Cancer Stigma Scale (CASS) was developed to measure patient experienced and perceived stigma and was further modified for use in the pediatric patient population. This study aimed to adapt and translate a Swahili version of the CASS for use in the Tanzanian pediatric patient population to measure cancer stigma and identify the types of stigma pediatric cancer patients face. Methods: Approximately 40 items were extracted from two prior developmental and validation studies of the CASS that assessed stigma in adult patients and non-patient cohorts. The survey items, developed initially in English, underwent translation into Swahili, back-translated, reconciled, and screened for duplications. The translated items were refined using concurrent cognitive interviewing. Results: After three rounds of cognitive interviews with 15 respondents, comprehension of the survey questions was assessed and improved with all items reaching at least 80% comprehension. Additional reviews included grammar and specific Swahili word selection changes to clarify the question’s meaning. Duplications or repetition of sentences were also considered to remove questions from the survey. The final survey comprised 25 survey items with 7 stigma sub-categories. Conclusions: This study sheds light on the complex nature of cancer-related stigma in pediatric patients. For future purposes, research is needed to validate the CASS survey with a larger sample of the population, including a comparison stigma assessment to establish validity.

According to IPCC estimates, sea levels will rise between .18 and .6 meters by 2100. More recent estimates indicate that actual amounts of sea level rise may be much more, and that 1 meter of sea level rise by 2100 is likely a conservative estimate. These rising sea levels will result not only in more flooding during storm events, but also increased erosion and gradual inundation of coastal property. At the same time, coastal populations in the United States continue to increase rapidly: over half of all Americans live in coastal counties, and at least 25 million more people are expected to move to the coast by 2015. The end result is that human populations, coastal infrastructure, and coastal ecosystems will become increasingly vulnerable to the impacts of climate change. This study examines the political and legal constraints to and opportunities for adaptation to rising sea levels. Using legal and policy analysis and case studies from California, North Carolina and Texas, this study explores the ability of governments to use market tools, land use regulations, and property acquisition to promote adaptation to rising sea levels. Because of market dynamics and political factors including flaws in public risk perception, I conclude that governments who wish to avoid extensive coastal engineering, , can address coastal community vulnerability through a combination of regulations and incentives that spur state and local governments to engage in forward land use planning and other measures to reduce their exposure to sea level rise impacts.

Admixture 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.

Bayesian methods offer adaptive inference via hierarchical extensions and uncertaintyquantification automatically with corresponding posterior distribution. Frequentist evaluation of Bayesian methods becomes a fundamental and necessary step in Bayesian analysis.

Bayesian nonparametric regression under a rescaled Gaussian process prior offers smoothness-adaptive function estimation with near minimax-optimal error rates. Hierarchical extensions of this approach, equipped with stochastic variable selection, are known to also adapt to the unknown intrinsic dimension of a sparse true regression function. But it remains unclear if such extensions offer variable selection consistency, i.e., if the true subset of important variables could be consistently learned from the data. It is shown here that variable consistency may indeed be achieved with such models at least when the true regression function has finite smoothness to induce a polynomially larger penalty on inclusion of false positive predictors. Our result covers the high dimensional asymptotic setting where the predictor dimension is allowed to grow with the sample size.

Stochastic Block Models (SBMs) are a fundamental tool for community detection in network analysis. But little theoretical work exists on the statistical performance of Bayesian SBMs, especially when the number of communities is unknown. This project studies weakly assortative SBMs whose members of the same community are more likely to connect with one another than with members from other communities. The weak assortativity constraint is embedded within an otherwise weak prior, and, under mild regularity conditions, the resulting posterior distribution is shown to concentrate on the true number of communities and membership allocation as the network size grows to infinity. A reversible-jump Markov Chain Monte Carlo posterior computation strategy is developed by adapting the allocation sampler. Finite sample properties are examined via simulation studies in which the proposed method offers competitive estimation accuracy relative to existing methods under a variety of challenging scenarios.

Tail index estimation has been well studied in the frequentist literature. However, few asymptotic studies on Bayesian tail index estimation are available. This paper works with a transformation based semi-parametric density model by non-parametrically transforming a parametric CDF. The semiparametric density model offers both accurate density estimation and tail index estimation. Compared with frequentist methods, it avoids choosing a high quantile to threshold the data. We provide sufficient conditions on the parametric family and the logistic Gaussian process priors, such that posterior contraction rate of tail index can be established. Limitations of the semiparametric density model are also discussed.

An 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.