Browsing by Subject "Ancient DNA"

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    Microbial Communities Associated with Phosphoclast-bearing Sediments of the Benguela Upwelling Zone
    (2016-09) Zoss, Roman
    Phosphorus is a limiting nutrient in the environment and is an important component of many biological molecules. Calcium phosphate mineral deposits, known as phosphorites, are also the primary source of P for agriculture. Understanding phosphorite formation may improve management of P resources. However, the processes that mediate calcium phosphate mineral precipitation in certain marine pore waters remain poorly understood. Phosphogenesis occurs in sediments beneath some oceanic upwelling zones that harbor polyphosphate-accumulating giant sulfur bacteria (GSB). These bacteria may concentrate phosphate in sediment pore waters, creating supersaturated conditions with respect to apatite. However, the relationship between microbes and phosphogenesis is not fully resolved. To further study this relationship, we examined microbial communities from two sources: sediment cores recovered from the shelf of the Benguela region, and DNA extracted from washed phosphoclasts recovered from those same sediments. We used iTag and clone library sequencing of the 16S rRNA gene to examine the microbial communities and their relationship with the environment. We found that many of our sediments shared large numbers of phylotypes with one another, and that the same metabolic guilds were represented at localities across the shelf. Sulfur-reducing bacteria and sulfur-oxidizing bacteria were abundant in our datasets. Phylotypes that are known to carry out nitrification and/or anammox (anaerobic ammonia oxidation) were also well-represented. Our phosphoclast extraction, however, contained a distinct microbial community from those observed in the modern sediments. We observed both an enrichment of certain common microbial classes and a complete absence of others. These results could represent an ancient microbial assemblage that was present when the apatite precipitated. While these taxa may or may not have contributed to apatite precipitation, several groups represented in the phosphoclast dataset have the genetic potential, as determined through the analysis of published genomes, to synthesize, and perhaps accumulate, polyphosphate.
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    Multivariate DNA taphonomy: evaluating the effects of environmental context, specimen properties, and laboratory strategies on the preservation and detection of DNA in ancient and challenging specimens.
    (2012-05) Alveshere, Andrea Joanna
    Within their diminutive structures, DNA molecules hold tantalizing potential to address myriad questions about human history, prehistory, and the evolution and dispersal of all forms of life. When accessible and accurate, DNA from ancient and degraded specimens can elucidate many topics of interest to researchers in a variety of fields including archaeology, biological anthropology, forensics, conservation and evolutionary biology, agronomy, and medicine. Despite the great informational potential of genetic studies, the high cost and destructive nature of DNA analyses discourage many researchers from submitting archaeological specimens for testing. A diversity of DNA detection protocols, the limited scope of individual research projects, and a bias toward publishing successful results make it difficult to evaluate the comparative influence of different preservation factors, field methods, and laboratory strategies on the recovery of useful genetic information from ancient and degraded specimens. The work presented in this manuscript is predicated upon the contention that the opportunity to conduct ancient DNA research entails an obligation to make the most of every specimen fragment consumed, every data point collected, and every funding dollar spent. The scope of this project is to develop a system for evaluating whether DNA testing might be appropriate for a given specimen; for determining which steps can be taken to increase the chances of recovering useful data; and for maximizing the contribution of individual research projects, conducted across disparate fields, to the greater body of knowledge on DNA preservation and detection. This endeavor involved: (1) inventorying variables having potential to influence DNA preservation and/or detection; (2) investigating subsets of the candidate variables through case studies of archaeological materials from Kromdraai, Wonderwerk Cave, and Border Cave, South Africa, Silvernale Village, Minnesota, and UV-irradiated forensic-type samples; and (3) the development and validation (via case study data) of the Biomolecular Preservation and Detection Information System (BIOPADIS™), a standardized system for synthesis, management, and analysis of biomolecular taphonomy data. BIOPADIS™ (\bī-’op-ad-is\) comprises a relational database that accommodates all manner of relevant data, a querying capability that makes these data accessible, and a set of statistical approaches appropriate for identifying and evaluating correlations within these multivariate, multi-study data.