Ecology and Evolutionary Biology Commons^™

From Genes To Ecosystems: Resource Availability And Dna Methylation Drive The Diversity And Abundance Of Restriction Modification Systems In Prokaryotes, Spiridon E. Papoulis

Doctoral Dissertations

Together, prokaryotic hosts and their viruses numerically dominate the planet and are engaged in an eternal struggle of hosts evading viral predation and viruses overcoming defensive mechanisms employed by their hosts. Prokaryotic hosts have been found to carry several viral defense systems in recent years with Restriction Modification systems (RMs) were the first discovered in the 1950s. While we have biochemically elucidated many of these systems in the last 70 years, we still struggle to understand what drives their gain and loss in prokaryotic genomes. In this work, we take a computational approach to understand the underlying evolutionary drivers of …

Tetrameric Photosystem I: From Initial Discovery And Characterization In Chroococcidiopsis Sp. Ts-821 To Exploration Of Its Distribution And Understanding Of Its Significance In Cyanobacteria, Meng Li

Doctoral Dissertations

Photosystem I (PSI) forms trimeric complexes in most characterized cyanobacteria. We had reported the tetrameric form of PSI in the unicellular cyanobacterium, Chroococcidiopsis sp. TS-821 (TS-821). Using Cryo-EM, a 3D model of the PSI tetramer structure at 11.5 [Angstrom] resolution was obtained and a 2D map within the membrane plane of at 6.1 [Angstrom]. In contrast to the three-fold symmetry in trimeric PSI crystal structure from T. elongatus, two different inter-monomer interactions involving PsaLs are found in the PSI tetramer. Phylogenetic analysis based on PsaL protein sequences shows that TS-821 is closely related to heterocyst-forming cyanobacteria. Additionally, this tetrameric …

Computational Identification Of Terpene Synthase Genes And Their Evolutionary Analysis, Qidong Jia

Doctoral Dissertations

Terpenoids, the largest and most structurally and functionally diverse class of natural compounds on earth, are mostly synthesized by plants to be involved in various plant environment interactions. Some terpenoids are classified as primary metabolites essential for plant growth and development. Terpene synthases (TPSs), the key enzymes for terpenoid biosynthesis, are the major determinant of the tremendous diversity of terpenoid carbon skeletons. The TPS genes represent a mid-size family of about 30-100 functional genes in almost all major sequenced plant genomes. TPSs are also found in fungi and bacteria, but microbial TPS genes share low levels of sequence similarity and …

A New Adaptive Landscape: Urbanization As A Strong Evolutionary Force, Lauren Christie Breza

Masters Theses

Urbanization is rapidly increasing as human population growth steadily grows, but there is little consensus of the ecological consequence of this population shift and almost no information of the evolutionary consequences for local biodiversity. Nearly two-thirds of the world’s population will live in city centers by 2050 with profound impacts on landscapes that can act as important agents of selection. This study aims to identify 1) the net effect of urbanization on species richness, 2) how phylogenetic diversity varies between urban and rural sites, and 3) the strength of urbanization as a selection pressure. First, a meta-analysis was conducted in …

Belowground Interactions Shift The Relative Importance Of Direct And Indirect Genetic Effects, M A. Genung, J K. Bailey, J A. Schweitzer

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Intraspecific genetic variation can affect decomposition, nutrient cycling, and interactions between plants and their associated belowground communities. However, the effects of genetic variation on ecosystems can also be indirect, meaning that genes in a focal plant may affect ecosystems by altering the phenotype of interacting (i.e., neighboring) individuals. We manipulated genotype identity, species identity, and the possibility of belowground interactions between neighboring Solidago plants. We hypothesized that, because our plants were nitrogen (N) limited, the most important interactions between focal and neighbor plants would occur belowground. More specifically, we hypothesized that the genotypic identity of a plant's neighbor would have …

Improving Codon Evolution Models Using Complex Mutation Models, Preston Hewgley

Pursuit - The Journal of Undergraduate Research at The University of Tennessee

This paper discusses an improvement in a Stochastic Evolutionary Model of Protein Production Rate (SEMPPR) by revising the method by which it models mutation. SEMPPR previously assumed unbiased mutation, an assumption whose inaccuracy is made clear by observed codon counts of low-expression genes, where mutation determines equilibrium state. This paper presents a new, more complex model generalized on a per-codon basis and calculated from observed codon frequencies using a maximum likelihood framework. Results obtained from SEMPPR using the codon specific mutation model proved more accurate in predicting a protein’s production rate, reaffirming that complex mechanisms govern codon mutation rates.

Sharing And Re-Use Of Phylogenetic Trees (And Associated Data) To Facilitate Synthesis, Arlin Stoltzfus, Brian C. O'Meara, Jamie Whitacre, Ross Mounce, Emily L. Gillespie, Sudhir Kumar, Dan F. Rosauer, Rutger A. Vos

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Background

Recently, various evolution-related journals adopted policies to encourage or require archiving of phylogenetic trees and associated data. Such attention to practices that promote sharing of data reflects rapidly improving information technology, and rapidly expanding potential to use this technology to aggregate and link data from previously published research. Nevertheless, little is known about current practices, or best practices, for publishing trees and associated data so as to promote re-use.

Findings

Here we summarize results of an ongoing analysis of current practices for archiving phylogenetic trees and associated data, current practices of re-use, and current barriers to re-use. We find …