Dinoflagellate Genomic Organization and Phylogenetic Marker Discovery Utilizing Deep Sequencing Data

Dinoflagellates possess large genomes in which most genes are present in many copies. This has made studies of their genomic organization and phylogenetics challenging. Recent advances in sequencing technology have made deep sequencing of dinoflagellate transcriptomes feasible. This dissertation investigates the genomic organization of dinoflagellates to better understand the challenges of assembling dinoflagellate transcriptomic and genomic data from short read sequencing methods, and develops new techniques that utilize deep sequencing data to identify orthologous genes across a diverse set of taxa. To better understand the genomic organization of dinoflagellates, a genomic cosmid clone of the tandemly repeated gene Alchohol Dehydrogenase (AHD) was sequenced and analyzed. The organization of this clone was found to be counter to prevailing hypotheses of genomic organization in dinoflagellates. Further, a new non-canonical splicing motif was described that could greatly improve the automated modeling and annotation of genomic data. A custom phylogenetic marker discovery pipeline, incorporating methods that leverage the statistical power of large data sets was written. A case study on Stramenopiles was undertaken to test the utility in resolving relationships between known groups as well as the phylogenetic affinity of seven unknown taxa. The pipeline generated a set of 373 genes useful as phylogenetic markers that successfully resolved relationships among the major groups of Stramenopiles, and placed all unknown taxa on the tree with strong bootstrap support. This pipeline was then used to discover 668 genes useful as phylogenetic markers in dinoflagellates. Phylogenetic analysis of 58 dinoflagellates, using this set of markers, produced a phylogeny with good support of all branches. The Suessiales were found to be sister to the Peridinales. The Prorocentrales formed a monophyletic group with the Dinophysiales that was sister to the Gonyaulacales. The Gymnodinales was found to be paraphyletic, forming three monophyletic groups. While this pipeline was used to find phylogenetic markers, it will likely also be useful for finding orthologs of interest for other purposes, for the discovery of horizontally transferred genes, and for the separation of sequences in metagenomic data sets.

Afro-Cuban Bata Drum Aesthetics: Developing Individual and Group Technique, Sound and Identity

The Lucumi religion (also Santeria and Regla de Ocha) developed in 19th-century colonial Cuba, by syncretizing elements of Catholicism with the Yoruba worship of orisha. When fully initiated, santeros (priests) actively participate in religious ceremonies by periodically being possessed or "mounted" by a patron saint or orisha, usually within the context of a drumming ritual, known as a toque de santo, bembe, or tambor. Within these rituals, there is a clearly defined goal of trance possession, though its manifestation is not the sole measure of success or failure. Rather than focusing on the fleeting, exciting moments that immediately precede the arrival of an orisha in the form of a possession trance, this thesis investigates the entire four- to six-hour musical performance that is central to the ceremony. It examines the brief pauses, the moments of reduced intensity, the slow but deliberate build-ups of energy and excitement, and even the periods when novices are invited to perform the sacred bata drums, and places these moments on an equal footing with the more dynamic periods where possession is imminent or in progress. This document approaches Lucumi ritual from the viewpoint of bata drummers, ritual specialists who, during the course of a toque de santo, exercise wide latitude in determining the shape of the event. Known as omo Ana (children of the orisha Ana who is manifest in drums and rhythms), bata drummers comprise a fraternity that is accessible only through ritual initiation. Though they are sensitive to the desires of the many participants during a toque de santo, and indeed make their living by satisfying the expectations of their hosts, many of the drummers' activities are inwardly focused on the cultivation and preservation of this fraternity. Occasionally interfering with spirit possession, and other expectations of the participants, these aberrant activities include teaching and learning, developing group identity or signature sound, and achieving a state of intimacy among the musicians known as "communitas."