This is my actual updated thesis. Please disregard the other one submitted on Dec, 30. Thank you and I apologize for this confusion. / Microbialites are sedimentary structures built by microorganisms through trapping and binding sediment and/or biological-mediated carbonate precipitation. Carbonate structures from four different locations in the Yucatan Peninsula have been documented and analyzed to determine origins and relationships with current and past hydrochemistry. Cenote Fatima had three carbonate structures: two at -13 m depth (CF1A, CF2A) and one at -27 m depth (CF3A) and they were in sheltered light conditions. Two samples were from La Concha (LC1A, LC2A) with a similar depth at -12 m and two more samples were at Hoyo Negro at -18 m (HN1A), and at -45 m (HN2A) which were in dark conditions. Samples from Xul Ha (XH1A and XH2A) next to Laguna Bacalar which has some of the largest freshwater microbialite formations in the world and both these locations were in full light conditions. S/Ca ratios in Xul Ha samples show a hydrogeochemical origin linked to the dissolution of gypsum from underground karst. Xul Ha had the highest recorded S and Sr levels and our results match previous geochemical research on stromatolites and thrombolites. Samples from Cenote Fatima had radiocarbon ages that matched past water levels that have been recorded in Hoyo Negro and Hells Bells showing a drop in δ 13C of ≈3.5‰ between ≈7600 – ≈9000 cal. yr. BP. Cenote Fatima also shows a narrow growth window in the sunlit upper water column (3-4m) indicating a biogenically influenced origin. Hoyo Negro samples were shown to match the geochemistry of Holocene aquifer based on calcite raft core records and were deemed to be more abiotic based on prior research on Hells Bells in Cenote Zapote. Based on radiocarbon ages they thought to have formed during Stage 5e (125,000 yr. BP). / Thesis / Master of Science (MSc) / This research aims to help our understanding in the role microbialites play in origins of life and biosignatures on exoplanets by looking at element geochemistry and isotopic differences within the structures. This study also examines ability of microbialites to store past and present records of hydrochemistry data.

Four sediment cores and ten sediment trap samples were collected from Yax Chen cave, part of the Ox Bel Ha cave system on the Yucatan Peninsula in Mexico, for microfossil and micro-XRF geochemical analysis. In cores, Cl ̄trends (measuring salinity changes in meteoric water mass) show a direct relationship with microfossil (specifically the foraminifer Elphidium spp.) and weathering proxies (K, Ti, and Fe) used for measuring wet/dry conditions. Micro-XRF measurements of Cl ̄are derived from pore water in the cores, allowing for a more accurate observation of change in the cave system. Conversely, weathering proxies are measured from transported sediments. All four cores show a general decrease in groundwater salinity up core. Two of the cores, which were collected above the present halocline (~11m), show salinity changes in the meteoric water mass. One core was collected at the halocline and measures its movement in response to precipitation and Holocene sea-level rise. These findings are in agreement with other studies from the Yucatan coast (e.g. cenotes Aktun Ha and Sac Actum) as well as other paleoclimate records in the region. Additionally, these findings correlate with archaeological evidence, revealing several droughts that occurred throughout late Pre-Classic to late Classical Maya. High resolution analysis of Cl ̄offers new insights on how coastal aquifers respond to climate change and may have implications for regional archaeology. The use of micro-XRF geochemical analysis is an effective tool which can be used to understand the spatial and temporal complexities of Yucatan coastal aquifers. / Thesis / Master of Science (MSc)

Yucatan minipigs have become increasingly common animal models in neuroscience where recent studies, investigating blast-induced traumatic brain injury, stroke, and glioblastoma, aim to uncover brain injury mechanisms [1-3]. Magnetic Resonance Imaging (MRI) has the potential to validate and optimize unknown parameters in controlled populations. The key to group-level MRI analysis within a species is to align (or register) subject scans to the same volumetric space using a brain template. However, large animal brain templates are lacking, which limits the use of MRI as an effective research tool to study group effects. The objective of this study was to create an MRI-based Yucatan minipig brain template allowing for uniform group-level analysis of this animal model in a standard volumetric space to characterize brain mechanisms. To do this, 5-7 month old, male Yucatan minipigs were scanned using a 3 Tesla whole-body scanner (Siemens AG, Erlangen) in accordance with IACUC. T1-weighted anatomical volumes (resolution = 1×1×1 mm3; TR = 2300 ms; TE= 2.89 ms; TI = 900 ms; FOV = 256 mm2 ; FA = 8 deg) were collected with a three-dimensional magnetization prepared rapid acquisition gradient echo (MPRAGE) pulse sequence [4]. The volumes were preprocessed, co-registered, and averaged using both linear and non-linear registration algorithms in AFNI [5] to create four templates (n=58): linear brain, non-linear brain, linear head, and non-linear head. To validate the templates, tissue probability maps (TPMs) and variance maps were created, and landmark variation was measured. TPMs computed in FSL [6] and AFNI show enhanced tissue probability and contrast in the non-linear template. Additionally, variance maps showed a more uniform spatial variance in the non-linear template compared to the linear. Registration variation within the brain template was within 1.5 mm and displayed improved landmark variation in the non-linear brain template. External evaluation subjects (n=12), not included in the template, were registered to the four templates to assess functionality. The results indicate that the developed templates provide acceptable registration accuracy to enable population comparisons. With these templates, researchers will be able to use MRI as a tool to further neurological discovery and collaborate in a uniform space. / M.S. / Magnetic resonance imaging (MRI) is commonly used in neuroscience as a non-invasive diagnostic tool with the potential to reveal unknown brain injury mechanisms. MRI is particularly useful in large animal models to validate and optimize unknown parameters in controlled populations. The key to group-level MRI analysis within a species is to align (or register) subject scans to the same volumetric space using a brain template. However, large animal brain templates are lacking, which limits the use of MRI as an effective research tool to study group effects. The objective of this study was to create an MRI-based Yucatan minipig brain template allowing for uniform group-level analysis of this animal model in a standard volumetric space to better characterize brain mechanisms. The neuroanatomy of the Yucatan minipig, which is characterized by an increased brain size and gyrencephalic intricacies similar to humans, has made it an increasingly common animal model in neuroscience. Linear and non-linear registration methods were performed in Analysis of Functional NeuroImages (AFNI) software to create both brain and head templates for 5-7 month old, male Yucatan minipigs (n=58). This study was validated looking at template variance, tissue probability maps (TPMs) of segmented grey matter, white matter, and cerebrospinal fluid, and landmark variation. The results indicate that the developed templates provide acceptable registration accuracy to enable population comparisons. With these templates, researchers will be able to use MRI as a tool to further neurological discovery and collaborate in a uniform space.

The suitability of aquaculture for inland water bodies in the State of Yucatan, a karstic area of southeast Mexico was investigated. Five types of water bodies distinct in morphometric and hydrological characteristics were identified through land-based surveys. Representative sites for each were selected for further study: a sinkhole, a permanent aguada (clogged sinkhole), a rain-filled seasonal pond, a small <1 ha) gravel quarry and a large (>9 ha) gravel quarry. The water quality in all of the sites had a high pH (range 7.2-9.4) alkalinity (range 130-840 mg/l CaC03) and hardness (range 198-998mg CaC03). Their nutrient status varied from the permanently stratified and hypereutrophic conditions in the permanent aguada, to oligotrophic conditions in gravel quarries. In general, the water quality resulted adequate for fish culture in the gravel quarries, the sinkhole and in the seasonal pond, but ecological considerations prevented sinkholes for aquaculture development. Aquaculture trials involving the stocking of fry of the native cichlid Cichlasoma urophthalmus and O. niloticus in seasonal ponds and a small gravel quarry demonstrated the feasibility of neglected water bodies for small-scale aquaculture. A net yield of 180 Kg/ha/6 months was obtained from a gravel quarry fertilised with grass Panicum virgatum and stocked with C. urophthalmus. Yields from seasonal ponds were 157Kg/ha of O. niloticus from a small (0.010 ha), and 30 kg/ha of C. urophthalmus from a large (1.11 ha) seasonal pond (no fertilisation or feeding. An environmental impact assessment was carried out at an experimental cage site in gravel quarry. An estimated 0.02 kg of phosphorus was wasted per kg fish produced. A socioeconomic survey on attitudes towards aquaculture adoption was carried out in four agricultural villages and a fishing port. This led to the construction and operation of a small pond demonstration unit. Results suggest that farmers are receptive and adoption of aquaculture as a complementary activity may be feasible and beneficial to rural development, especially in areas with existing water bodies. Economic modelling of the different production units involved showed returns to labour higher than the average agricultural wage. A computer-based Geographical Information System identified areas suitable for aquacultural development. Two major areas were identified: the northern Karst plains where gravel quarries are abundant and suitable for intensive cage-culture; and the southern hilly region where small-scale seasonal aquaculture could be developed.

Understanding the mechanisms that control sedimentation in the anchialine caves of the Yucatan Peninsula, Mexico is vital for interpreting the sedimentary deposits therein. External forcing mechanisms of varying scales, such as eustatic sea-level rise and large storm events, can have a significant influence on the rate and composition of sediment transported and deposited in the cave. Using sediment cores, high resolution radiocarbon dating, cave mapping and continuous aquifer attribute data, it was shown that sedimentation patterns in the cave were not controlled by sea-level rise/fall alone. Overlying vegetation and cave physiography were controlling factors which resulted in sedimentation in the cave being transient in time and space. The coastal aquifer responded to seasonal variations in precipitation but also showed a broad regional response to intense rainfall associated with Hurricane Ingrid in 2013. Due to the extensive hydraulic conductivity of the aquifer, the hydrologic response to Hurricane Ingrid was shorted lived (weeks) while its effect on sedimentation in the cave lasted for months. Sedimentation rates in the cave did not respond to elevated precipitation alone but showed a link with overlying vegetation. In regions of the cave with overlying mangrove forest, sedimentation was significantly higher than areas with tropical forest coverage. Mangrove forests baffled sediment creating an aquitard which resulted in the ponding of meteoric waters and subsequent enrichment in nutrients. Nutrient rich meteoric waters were funneled into cenotes increasing primary productivity for organic matter sediment production. Sedimentary deposits in anchialine caves are subject to punctuated sedimentation as a result of external forcing mechanisms or triggers. In the case of Yax Chen the trigger for sedimentation was not contemporaneous with Holocene sea-level rise. This has important implications for the use of cave sediments as proxies for sea-level research and paleo hurricane studies. / Thesis / Candidate in Philosophy

BACKGROUND: Ethnobotanical knowledge continues to be important for treating illness in many rural communities, despite access to health care clinics and pharmaceuticals. However, access to health care clinics and other modern services can have an impact on the distribution of medical ethnobotanical knowledge. Many factors have been shown to be associated with distributions in this type of knowledge. The goal of the sub-analyses reported in this paper was to better understand the relationship between herbal remedy knowledge, and two such factors, age and social network position, among the Yucatec Maya in Tabi, Yucatan. METHODS: The sample consisted of 116 Yucatec Maya adults. Cultural consensus analysis was used to measure variation in herbal remedy knowledge using competence scores, which is a measure of participant agreement within a domain. Social network analysis was used to measure individual position within a network using in-degree scores, based on the number of people who asked an individual about herbal remedies. Surveys were used to capture relevant personal attributes, including age. RESULTS: Analysis revealed a significant positive correlation between age and the herbal medicine competence score for individuals 45 and under, and no relationship for individuals over 45. There was an insignificant relationship between in-degree and competence scores for individuals 50 and under and a significant positive correlation for those over 50. CONCLUSIONS: There are two possible mechanisms that could account for the differences between cohorts: 1) knowledge accumulation over time; and/or 2) the stunting of knowledge acquisition through delayed acquisition, competing treatment options, and changes in values. Primary ethnographic evidence suggests that both mechanisms may be at play in Tabi. Future studies using longitudinal or cross-site comparisons are necessary to determine the whether and how the second mechanism is influencing the different cohorts.

UA Open Access Publishing Fund / Background: Ethnobotanical knowledge continues to be important for treating illness in many rural communities, despite access to health care clinics and pharmaceuticals. However, access to health care clinics and other modern services can have an impact on the distribution of medical ethnobotanical knowledge. Many factors have been shown to be associated with distributions in this type of knowledge. The goal of the sub-analyses reported in this paper was to better understand the relationship between herbal remedy knowledge, and two such factors, age and social network position, among the Yucatec Maya in Tabi, Yucatan. Methods: The sample consisted of 116 Yucatec Maya adults. Cultural consensus analysis was used to measure variation in herbal remedy knowledge using competence scores, which is a measure of participant agreement within a domain. Social network analysis was used to measure individual position within a network using in-degree scores, based on the number of people who asked an individual about herbal remedies. Surveys were used to capture relevant personal attributes, including age. Results: Analysis revealed a significant positive correlation between age and the herbal medicine competence score for individuals 45 and under, and no relationship for individuals over 45. There was an insignificant relationship between in-degree and competence scores for individuals 50 and under and a significant positive correlation for those over 50. Conclusions: There are two possible mechanisms that could account for the differences between cohorts: 1) knowledge accumulation over time; and/or 2) the stunting of knowledge acquisition through delayed acquisition, competing treatment options, and changes in values. Primary ethnographic evidence suggests that both mechanisms may be at play in Tabi. Future studies using longitudinal or cross-site comparisons are necessary to determine the whether and how the second mechanism is influencing the different cohorts.

The archaeological remains at Hacienda Tabi provide an opportunity to study the effects of large-scale societal changes on the lives of the Maya who worked on the hacienda. The households, represented by the ruins of the worker’s village surrounding the main hacienda grounds, were at the core of late colonial/independence era Maya life. These households were subject to the forces of acculturation that accompanied the rise and supremacy of the hacienda system during the late eighteenth century. Archaeological excavations at Hacienda Tabi have revealed a re-orientation of social organization during this period. Prior to the formation of the hacienda system, domestic and social organization focused on kinship and extended family subsistence organization. Social status, wealth, and power in pre-hacienda communities were predicated on issues of age, sex, and familial rank within both the extended family and community. The hacienda system brought about fundamental changes in the organization and relations of production. These changes, e.g. the separation of producer from the means of production and commodity based production versus subsistence based production, changed the basis and therefore the form of Yucatecan social organization. Under the new system, the nuclear family rather than the extended family or community became the prime unit of social organization. In the hacienda community status was based on occupation and one’s place within the newly established labor hierarchy. The changing realities of social organization found under the hacienda system are reflected in the settlement patterns and material remains of the workers’ village at Hacienda Tabi. The material culture and types of housing excavated and recorded at Tabi underscore the inequalities engendered within the hacienda system of production. The research conducted at Hacienda Tabi has illuminated the changes associated with Yucatan’s articulation into the greater world system.

Thesis (Ph. D.)--University of Wisconsin--Madison, 1975. / Vita. Typescript. eContent provider-neutral record in process. Description based on print version record. Includes bibliographical references.

Mayan peoples of the Yucatán peninsula were colonized subjects of the Spanish empire from 1546 until 1821. Often, the events of nearly three centuries are viewed as a singular struggle between European hegemonies and a monolithic indigenous community that oscillated between passivity and rebellion. This dissertation shows that responses to colonial circumstances can be best understood by paying particular attention to the scale of interpretation. Analysis of extensive and intensive archaeological survey data from Beneficios Altos, a frontier Spanish colonial province, reveals the effects of colonial policy on nearly every segment of society. Archaeological materials are complemented by an interrogation of geographically relevant documents collected from Mexican archives. These two lines of information combine to suggest that investigation of the colonial process benefits from a microhistorical perspective that focuses on the roles of individuals and communities surviving colonial circumstances. This dissertation focuses on one element of the colonial relationship: the negotiation of alienating pressures from a hegemonic authority that sought to define every aspect of daily life and interaction. Negotiation took place not between idealized collective Spaniard and Maya entities, but rather between persons seeking to improve their personal circumstances either as agents of the colonizers or as members of the colonized--often a fluid distinction. Individual negotiation and alienating pressures are presented in this dissertation as they were materialized upon Beneficios Altos landscapes. Employing a microhistorical focus but heeding macrohistorical trends, this study examines negotiated survival through the following watershed events and processes: sixteenth century battles of the conquest period; rapid redefinition of the physical and spiritual layout of the region by the Catholic Church; establishment of foundational politics and economic policies of colonialism; world events that inspired a dramatic reversal of demographic trends within this frontier region; nineteenth century eruption and chaos of a violent military conflict known as the Caste War; and the identities of those who resettled the fractured landscape during the twentieth century. This dissertation focuses on individual interactions and highlights the importance of frontier areas and archaeological landscapes in crafting a new perspective on the nature of colonialism.