Zooarchaeological analysis of animal resources in the Upper Mun River Valley, Northeast Thailand

Recent research has made considerable progress towards our understanding of the origins of agriculture and the domestication of animals in prehistoric Southeast Asia. This thesis will contribute to this knowledge by investigating the faunal assemblage from archaeological sites in the Upper Mun River Valley, northeast Thailand. The major goal of this research is to address the hypothesis: Prehistoric communities in the Upper Mun River Valley became more reliant on domestic animals as part of their subsistence strategies over time, from the Neolithic to the Iron Age To address this hypothesis 22283 vertebrate animal remains from the prehistoric sites of Ban Non Wat, Ban Salao, and Nong Hua Raet were identified and analysed into 57 taxonomic groups. From this analysis, the subsistence strategies in these early communities were determined. Whether these strategies changed throughout time, due to social changes, was investigated. The zooarchaeological records from the three sites were compared to modern comparative studies from the Hmong and Lao-Isan cultures of Southeast Asia. The results show that the subsistence role of domestic animals in the Upper Mun River Valley changed from the Neolithic to the Iron Age. At Ban Non Wat, a site that encompasses a time span of 1650 BC to 500 AD, the volume (m3) of pig and bovid remains increased in the Bronze Age contexts, with bovid remains increasing again in Iron Age contexts. This illustrates the increasing importance of animal husbandry at this site. Wild resources such as deer, fish, and turtle/ tortoise remains were also identified in lower volumes in Iron Age contexts in comparison to Bronze Age and Neolithic at Ban Non Wat. At Ban Salao, an Iron Age site (500 BC to 500 AD), bovid remains made up the majority of the assemblage, with pig second highest. Only a small number of deer, fish, and turtle remains were identified. Likewise, at the Iron Age site of Nong Hua Raet (500 BC to 500 AD), bovid remains were found more often than pig remains and other animals, such as deer, fish, and turtle. The age at death estimates for pig, and the frequency of skeletal elements at Ban Salao and Nong Hua Raet, indicates that pigs may have been raised or butchered offsite. The lack of fish species related to rice agriculture, and low numbers of rats and mice, suggests that Ban Salao and Nong Hua Raet were not intensive rice farming sites. It is argued that these sites were seasonally occupied. If the Iron Age results are analysed as a community of sites, it demonstrates clustered groups specialising in one or two resources, with linear communities sharing resources. These findings demonstrate how the subsistence role of animals in early agricultural communities in the Upper Mun River Valley changed over time, with communities becoming more reliant on domestic animals from the Neolithic to the Iron Age. However, hunting and fishing remained an important part of subsistence strategies throughout all time periods at Ban Non Wat. The increased reliance on domestic animals confirms a socio-cultural change in subsistence towards the use of domestic animals as a food source, and provides evidence of an agricultural intensification of seasonal rice farming. The comparative studies from the Hmong and Lao-Isan cultures has led to the conclusion that the seasonal nature of intensive Iron Age agricultural may have had an influence on the season wild animals were hunted. The results of this thesis are inconclusive as to which current model of social change in Southeast Asia the data supports. This may relate to the overlap within the structure of the models themselves, or suggest that no model entirely encompasses social change that occurred in the prehistoric communities of the Upper Mun River Valley. This research contributes significantly to our understanding of changes to subsistence resources in agricultural communities of Upper Mun River Valley and the wider Southeast Asian region

Counting Bears, P’s And Q’s: An Efficient Sample Design for a Spatial Capture Recapture Hair Snag Study of Grizzly Bears

Accurate assessment of abundance can be expensive and managers often seek to minimize costs. Because spatial capture recapture (SCR) methods explicitly account for variation in trap effort in space and time and permit the use of covariates to explain abundance, substantial flexibility in design and thus reduction in costs may be possible. Estimates of grizzly bear (Usus arctos) densities and abundances in 4 management units in Alberta were very low  (superpopulation n =  47-133) in the latest studies occurring from 2004-2008. Since these first provincial population estimates were obtained, management, landscape, and habitat conditions have changed. Managers would like updated abundance information but also seek to reduce the costs of acquiring these data. We assessed 1) the behavior of SCR models across several general sample designs and 2) whether we could eliminate sampling in helicopter-access-only areas in the Yellowhead management unit while maintaining accurate estimates. We used a combination of retrospective subsampling of existing data from a 2004 sampling effort and simulations to evaluate several designs. Placing sampling arrays in areas with high densities of bears decreased variance, while the fine-scale configuration of traps did not greatly influence estimates. Simulations of designs for Alberta with more intensive sampling of only the areas accessible by road and no sampling of more expensive helicopter-access-only areas provided robust estimates with little loss in precision. We will describe the framework and assumptions of SCR models with covariates for abundance in comparison with traditional capture recapture models

Diet and Environment Shape Fecal Bacterial Microbiota Composition and Enteric Pathogen Load of Grizzly Bears

Background: Diet and environment impact the composition of mammalian intestinal microbiota; dietary or health disturbances trigger alterations in intestinal microbiota composition and render the host susceptible to enteric pathogens. To date no long term monitoring data exist on the fecal microbiota and pathogen load of carnivores either in natural environments or in captivity. This study investigates fecal microbiota composition and the presence of pathogenic Escherichia coli and toxigenic clostridia in wild and captive grizzly bears (Ursus arctos) and relates these to food resources consumed by bears. Methodology/Principal Findings: Feces were obtained from animals of two wild populations and from two captive animals during an active bear season. Wild animals consumed a diverse diet composed of plant material, animal prey and insects. Captive animals were fed a regular granulated diet with a supplement of fruits and vegetables. Bacterial populations were analyzed using quantitative PCR. Fecal microbiota composition fluctuated in wild and in captive animals. The abundance of Clostridium clusters I and XI, and of C. perfringens correlated to regular diet protein intake. Enteroaggregative E. coli were consistently present in all populations. The C. sordellii phospholipase C was identified in three samples of wild animals and for the first time in Ursids. Conclusion: This is the first longitudinal study monitoring the fecal microbiota of wild carnivores and comparing it to that o

Correcting for enzyme immunoassay changes in long term monitoring studies

Enzyme immunoassays (EIAs) are a common tool for measuring steroid hormones in wildlife due to their low cost, commercial availability, and rapid results. Testing technologies improve continuously, sometimes requiring changes in protocols or crucial assay components. Antibody replacement between EIA kits can cause differences in EIA sensitivity, which can hinder monitoring hormone concentration over time. The antibody in a common cortisol EIA kit used for long-term monitoring of stress in wildlife was replaced in 2014, causing differences in cross reactivity and standard curve concentrations. Therefore, the objective of this study was to develop a method to standardize results following changes in EIA sensitivity. We validated this method using cortisol concentrations measured in the hair of brown bears (Ursus arctos). • We used a simple linear regression to model the relationship between cortisol concentrations using kit 1 and kit 2. • We found a linear relationship between the two kits (R2 = 0.85) and used the regression equation (kit2 = (0.98 × kit1) + 1.65) to predict cortisol concentrations in re-measured samples. • Mean predicted percent error was 16% and 72% of samples had a predicted percent error <20%, suggesting that this method is well-suited for correcting changes in EIA sensitivity.publishedVersio

Using digital time-lapse cameras to monitor species-specific understorey and overstorey phenology in support of wildlife habitat assessment

Critical to habitat management is the understanding of not only the location of animal food resources, but also the timing of their availability. Grizzly bear (Ursus arctos) diets, for example, shift seasonally as different vegetation species enter key phenological phases. In this paper, we describe the use of a network of seven ground-based digital camera systems to monitor understorey and overstorey vegetation within species-specific regions of interest. Established across an elevation gradient in western Alberta, Canada, the cameras collected true-colour (RGB) images daily from 13 April 2009 to 27 October 2009. Fourth-order polynomials were fit to an RGB-derived index, which was then compared to field-based observations of phenological phases. Using linear regression to statistically relate the camera and field data, results indicated that 61% (r 2?= 0.61, df = 1, F?= 14.3, p?= 0.0043) of the variance observed in the field phenological phase data is captured by the cameras for the start of the growing season and 72% (r 2?= 0.72, df = 1, F?= 23.09, p?= 0.0009) of the variance in length of growing season. Based on the linear regression models, the mean absolute differences in residuals between predicted and observed start of growing season and length of growing season were 4 and 6 days, respectively. This work extends upon previous research by demonstrating that specific understorey and overstorey species can be targeted for phenological monitoring in a forested environment, using readily available digital camera technology and RGB-based vegetation indices

The bear circadian clock doesn’t ‘sleep’ during winter dormancy

Most biological functions are synchronized to the environmental light:dark cycle via a circadian timekeeping system. Bears exhibit shallow torpor combined with metabolic suppression during winter dormancy. We sought to confirm that free-running circadian rhythms of body temperature (Tb) and activity were expressed in torpid grizzly (brown) bears and that they were functionally responsive to environmental light. We also measured activity and ambient light exposures in denning wild bears to determine if rhythms were evident and what the photic conditions of their natural dens were. Lastly, we used cultured skin fibroblasts obtained from captive torpid bears to assess molecular clock operation in peripheral tissues. Circadian parameters were estimated using robust wavelet transforms and maximum entropy spectral analyses

Y-chromosomal testing of brown bears (Ursus arctos): Validation of a multiplex PCR-approach for nine STRs suitable for fecal and hair samples

High-resolution Y-chromosomal markers have been applied to humans and other primates to study population genetics, migration, social structures and reproduction. Y-linked markers allow the direct assessment of the genetic structure and gene flow of uniquely male inherited lineages and may also be useful for wildlife conservation and forensics, but have so far been available only for few wild species. Thus, we have developed two multiplex PCR reactions encompassing nine Y-STR markers identified from the brown bear (Ursus arctos) and tested them on hair, fecal and tissue samples. The multiplex PCR approach was optimized and analyzed for species specificity, sensitivity and stutter-peak ratios. The nine Y-STRs also showed specific STR-fragments for male black bears and male polar bears, while none of the nine markers produced any PCR products when using DNA from female bears or males from 12 other mammals. The multiplex PCR approach in two PCR reactions could be amplified with as low as 0.2 ng template input. Precision was high in DNA templates from hairs, fecal scats and tissues, with standard deviations less than 0.14 and median stutter ratios from 0.04 to 0.63. Among the eight di- and one tetra-nucleotide repeat markers, we detected simple repeat structures in seven of the nine markers with 9–25 repeat units. Allelic variation was found for eight of the nine Y-STRs, with 2–9 alleles for each marker and a total of 36 alleles among 453 male brown bears sampled mainly from Northern Europe. We conclude that the multiplex PCR approach with these nine Y-STRs would provide male bear Y-chromosomal specificity and evidence suited for samples from conservation and wildlife forensics

Report from UCSF.

Table S1. Body weights (kg) of captive bears just prior to entering winter dormancy. (PDF 630 kb

Long-Term Persistence of Functional Thymic Epithelial Progenitor Cells In Vivo under Conditions of Low FOXN1 Expression

Normal thymus function reflects interactions between developing T-cells and several thymic stroma cell types. Within the stroma, key functions reside in the distinct cortical and medullary thymic epithelial cell (TEC) types. It has been demonstrated that, during organogenesis, all TECs can be derived from a common thymic epithelial progenitor cell (TEPC). The properties of this common progenitor are thus of interest. Differentiation of both cTEC and mTEC depends on the epithelial-specific transcription factor FOXN1, although formation of the common TEPC from which the TEC lineage originates does not require FOXN1. Here, we have used a revertible severely hypomorphic allele of Foxn1, Foxn1R, to test the stability of the common TEPC in vivo. By reactivating Foxn1 expression postnatally in Foxn1R/- mice we demonstrate that functional TEPCs can persist in the thymic rudiment until at least 6 months of age, and retain the potential to give rise to both cortical and medullary thymic epithelial cells (cTECs and mTECs). These data demonstrate that the TEPC-state is remarkably stable in vivo under conditions of low Foxn1 expression, suggesting that manipulation of FOXN1 activity may prove a valuable method for long term maintenance of TEPC in vitro