Studying Evolutionary Change: Transdisciplinary Advances in Understanding and Measuring Evolution

Evolutionary processes can be found in almost any historical, i.e. evolving, system that erroneously copies from the past. Well studied examples do not only originate in evolutionary biology but also in historical linguistics. Yet an approach that would bind together studies of such evolving systems is still elusive. This thesis is an attempt to narrowing down this gap to some extend. An evolving system can be described using characters that identify their changing features. While the problem of a proper choice of characters is beyond the scope of this thesis and remains in the hands of experts we concern ourselves with some theoretical as well data driven approaches. Having a well chosen set of characters describing a system of different entities such as homologous genes, i.e. genes of same origin in different species, we can build a phylogenetic tree. Consider the special case of gene clusters containing paralogous genes, i.e. genes of same origin within a species usually located closely, such as the well known HOX cluster. These are formed by step- wise duplication of its members, often involving unequal crossing over forming hybrid genes. Gene conversion and possibly other mechanisms of concerted evolution further obfuscate phylogenetic relationships. Hence, it is very difficult or even impossible to disentangle the detailed history of gene duplications in gene clusters. Expanding gene clusters that use unequal crossing over as proposed by Walter Gehring leads to distinctive patterns of genetic distances. We show that this special class of distances helps in extracting phylogenetic information from the data still. Disregarding genome rearrangements, we find that the shortest Hamiltonian path then coincides with the ordering of paralogous genes in a cluster. This observation can be used to detect ancient genomic rearrangements of gene clus- ters and to distinguish gene clusters whose evolution was dominated by unequal crossing over within genes from those that expanded through other mechanisms. While the evolution of DNA or protein sequences is well studied and can be formally described, we find that this does not hold for other systems such as language evolution. This is due to a lack of detectable mechanisms that drive the evolutionary processes in other fields. Hence, it is hard to quantify distances between entities, e.g. languages, and therefore the characters describing them. Starting out with distortions of distances, we first see that poor choices of the distance measure can lead to incorrect phylogenies. Given that phylogenetic inference requires additive metrics we can infer the correct phylogeny from a distance matrix D if there is a monotonic, subadditive function ζ such that ζ^−1(D) is additive. We compute the metric-preserving transformation ζ as the solution of an optimization problem. This result shows that the problem of phylogeny reconstruction is well defined even if a detailed mechanistic model of the evolutionary process is missing. Yet, this does not hinder studies of language evolution using automated tools. As the amount of available and large digital corpora increased so did the possibilities to study them automatically. The obvious parallels between historical linguistics and phylogenetics lead to many studies adapting bioinformatics tools to fit linguistics means. Here, we use jAlign to calculate bigram alignments, i.e. an alignment algorithm that operates with regard to adjacency of letters. Its performance is tested in different cognate recognition tasks. Using pairwise alignments one major obstacle is the systematic errors they make such as underestimation of gaps and their misplacement. Applying multiple sequence alignments instead of a pairwise algorithm implicitly includes more evolutionary information and thus can overcome the problem of correct gap placement. They can be seen as a generalization of the string-to-string edit problem to more than two strings. With the steady increase in computational power, exact, dynamic programming solutions have become feasible in practice also for 3- and 4-way alignments. For the pairwise (2-way) case, there is a clear distinction between local and global alignments. As more sequences are consid- ered, this distinction, which can in fact be made independently for both ends of each sequence, gives rise to a rich set of partially local alignment problems. So far these have remained largely unexplored. Thus, a general formal frame- work that gives raise to a classification of partially local alignment problems is introduced. It leads to a generic scheme that guides the principled design of exact dynamic programming solutions for particular partially local alignment problems

A mechanism for excitation and inhibition of the Mauthner's cells in teleost: A histological and neurophysiological study

No Abstract.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/49969/1/901070203_ftp.pd

Belfast Maine: Irish Identity and Acceptance In a Small City On Penobscot Bay

Retzlaff’s article examines how stereotypes were applied to Irish newcomers in early Belfast, Maine, even by “old-timers,” who also descended from Irish immigrants. Neither shared ancestry nor shared religion removed the stigma of these stereotypes, which complicated Irish identity in Belfast during the eighteenth and nineteenth centuries as Protestant and Catholic newcomers alike sought to benefit from their ties to the Irish community while separating themselves from their Irish tropes. Kay Retzlaff is a professor of English at the University of Maine at Augusta. She earned her PhD from the University of Maine. Her MA and BA are from the University of Nebraska–Lincoln. She has taught at the University of Kentucky and the American University. She is writing the history of the Irish community in Belfast, Main

EC80-873 Economic Analysis of Chemical, Ecofallow and Conventional Tillage System Wheat-Fallow Rotations

Extension circular 80-873 is about economic analysis of chemical, ecofalloe and conventional tillage system wheat- fallow rotations

Constraining cosmological models with cluster power spectra

Using extensive N-body simulations we estimate redshift space power spectra of clusters of galaxies for different cosmological models (SCDM, TCDM, CHDM, Lambda-CDM, OCDM, BSI, tau-CDM) and compare the results with observational data for Abell-ACO clusters. Our mock samples of galaxy clusters have the same geometry and selection functions as the observational sample which contains 417 clusters of galaxies in a double cone of galactic latitude |b| > 30 degrees up to a depth of 240 Mpc/h. The power spectrum has been estimated for wave numbers k in the range 0.03 < k k_max ~ 0.05 h/Mpc the power spectrum of the Abell-ACO clusters has a power-law shape, P(k)\propto k^n, with n ~ -1.9, while it changes sharply to a positive slope at k < k_max. By comparison with the mock catalogues SCDM, TCDM (n=0.9), and also OCDM with Omega_0 = 0.35 are rejected. Better agreement with observation can be found for the Lambda-CDM model with Omega_0 = 0.35 and h = 0.7 and the CHDM model with two degenerate neutrinos and Omega_HDM = 0.2 as well as for a CDM model with broken scale invariance (BSI) and the tau-CDM model. As for the peak in the Abell-ACO cluster power spectrum, we find that it does not represent a very unusual finding within the set of mock samples extracted from our simulations.Comment: LaTeX, 27 pages, 8 figures (EPS). Revised version (title changed, CHDM model added, discussion expanded). Accepted by New

A Translational Evaluation of Potential Iatrogenic Effects of Single and Combined Contingencies during Functional Analyses of Target Responses

The interview informed synthesized contingency analysis (IISCA) is controversial, with some extolling its benefits relative to traditional functional analysis (FA; e.g., efficiency; Slaton, Hanley, & Raftery, 2017) and others focusing on its shortcomings (e.g., false-positive outcomes; Fisher, Greer, Romani, Zangrillo, & Owen, 2016). One limitation of prior comparisons is investigators could not ascertain with surety the true function(s) of the participants’ problem behavior for use as the criterion variable. In Chapter 1, we developed a translational study to circumvent this limitation by training a specific function for a surrogate destructive behavior prior to conducting an FA and synthesized contingency analysis (SCA) of this response. In Chapter 2, we used single-subject experimental designs to evaluate iatrogenic effects during FA and SCA. The FA correctly identified the function of the target response in all six cases and produced no iatrogenic effects. The SCA produced differentiated results in all cases, and produced iatrogenic effects in three of six cases. Finally, in Chapter 3 we discuss these finding in terms the mechanisms that may promote iatrogenic effects