Understanding the maintenance of phenotypic variation within populations has long been a puzzle in evolutionary biology. Many models ignore that fact that animals are not living alone; instead social factors have the potential to alter the development and fitness consequences of alternative phenotypes to promote variation in many systems. Furthermore, while there is empirical evidence that individuals alter phenotypes in response to social cues, it is unclear under what conditions socially-cued plasticity will evolve and be adaptive. My dissertation research combines theory with developmental experiments in sailfin mollies (Poecilia latipinna) to understand if and how individuals alter phenotypes in response to social cues. The first chapter of my dissertation uses an individual-based modelling approach to determine if and when individuals should evolve a strategy that uses social cues during development to alter the expression of alternative phenotypes. We found that socially-cued plasticity evolves under limited conditions where selection acts on survival differences between alternative phenotypes and the expression of socially-cued plasticity is costly. Socially-cued plasticity was not adaptive when selection acted on fecundity. Because costs facilitated the evolution of adaptive socially-cued plasticity, our results suggest that socially-cued plasticity is a special case of plasticity where general models do not hold. Furthermore, we found that socially-cued plasticity is a self-limiting strategy; using social cues to alter phenotypes in adulthood was most likely to evolve when the majority of the population was not using socially-cued plasticity; this scenario allowed social cues to be reliable predictors of environmental conditions. In the second and third chapter of my dissertation, I used sailfin mollies to determine how species with alternative reproductive phenotypes (ARPs) alter their life history and mating behavior in response to social cues during development. Sailfin mollies are a livebearing fish that exhibit extensive variation in body size and correlated traits including age at maturity, morphology and mating behavior, both within and between populations. Together these traits make up a male's ARP. Smalls males mature quickly (50-60 days) and use their disproportionally longer intromittent organ in sneaking behavior. Large males take longer to mature (130-150 days) and use their disproportionally larger dorsal fins in courtship displays to entice female cooperation in mating. Intermediate-sized males, which are intermediate in morphology and time to maturity, switch between courting and thrusting depending on the social context. Previous studies have examined the role of abiotic environmental factors on male ARP in mollies, but found that these factors cannot account for the observed inter- and intra-population variation. Since mollies are gregarious and social environment has been shown to influence adult male behavior, we hypothesize that variability in social conditions can influence the relationships between genotype and phenotype to produce ARP variation. My second chapter describes an experimental study where we examined the relationship between genotype and phenotype by determining how the variation in social environment during development influenced sex-specific differences in life history phenotypes. We found that both variation in the social environment influences life history development in both males and females, but there were sex-specific differences in how social environment modulated the genotype-phenotype relationship. These results suggest that social environment is an important driver of life history differences in sailfin mollies. My final experiment tested the hypothesis that social environment during development affects male alternative mating behaviors. We found that courtship and sneaking behaviors were affected by variation in the social environment, but these effects manifested in complex interactions between experimental treatments. For example, the relationship between body size and courtship displays was affected by a genotype by social environment interaction, and there was a three-way interaction between genotype, developmental stage, and the male’s own body size. In addition,. These results implicated alternative reproductive morph, social environment during development, stage, and body size as non-independent factors in the expression of male ARPs. Results from my dissertation demonstrate that conditions for adaptive evolution of socially-cued plasticity are limited, but despite this, variation in social cues elicited substantial variation in life history and behavior, in ways not accounted for by current life history or sexual selection theory. These seemingly paradoxical results may be resolved by considering the natural history of mollies. Sailfin molly males of different ARPs have differences in survival and therefore results from the modelling chapter suggest mollies may be a system where socially-cued plasticity would evolve. To determine if the patterns observed in this dissertation are adaptive, or are accounted for by gene flow, by exposing animals to social environments they would not typically encounter in nature, or by other non-adaptive processes, future studies should assess mortality in different social environments and reproductive success to determine how social environment affects fitness. Taken together, my dissertation provides a better understanding of how phenotypic plasticity evolves and how social environment affects life history and mating behaviors. / A Dissertation submitted to the Department of Biological Science in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / 2019 / November 7, 2019. / alternative reproductive phenotypes, life history, Poecilia latipinna, social environment, socially-cued anticipatory plasticity, theory / Includes bibliographical references. / Kimberly A. Hughes, Professor Directing Dissertation; Elaine Hull, University Representative; Joseph Travis, Committee Member; Emily DuVal, Committee Member; Don Levitan, Committee Member.

Thesis (Ph. D.)--Ohio State University, 2003. / Title from first page of PDF file. Document formatted into pages; contains xiv, 131 p.; also includes graphics. Includes abstract and vita. Advisor: David L. Haury, College of Education. Includes bibliographical references (p. 97-104).

Thesis (M.S.)--Michigan State University. Interdepartmental Biological Sciences, 2008. / Title from PDF t.p. (viewed on Aug. 3, 2009) Includes bibliographical references (p.166-168). Also issued in print.

Thesis (Ph. D.)--University of Texas at Austin, 2007. / Vita. Includes bibliographical references.

Next generation sequencing can rapidly analyze entire genomes in just hours. However, due to the nature of the sequencing process, errors may arise which limit the accuracy of the reads obtained. Luckily, modern sequencing technologies associate with their reads, a quality score, derived from the sequencing procedures, which represents our confidence in each nucleotide in the sequence. Currently, these quality scores are used as a criteria for the removal or modification of reads in the data set. These methods result in the loss of information contained in those sequences and rely on parameters that are somewhat arbitrary; this may lead to a biased sample and inaccurate analyses. I propose an alternative method for incorporating the error of the sequences without discarding poor quality reads by including the error probabilities of the reads in the likelihood calculations used for sequence analysis. It was found that, despite introducing variability, using the error-informed likelihood method improved analyses compared with those which ignored the error altogether. While this method will likely result in analyses with less definite results compared with those in which the data was treated with a preprocessing technique, these results will utilize all of the provided data and will be more grounded in reality as we take into account the uncertainty that we have in our sequenced samples. / A Thesis submitted to the Department of Scientific Computing in partial fulfillment of the requirements for the degree of Master of Science. / Fall Semester 2015. / November 6, 2015. / error, likelihood, ngs, sequencing / Includes bibliographical references. / Peter Beerli, Professor Directing Thesis; Anke Meyer-Baese, Committee Member; Alan Lemmon, Committee Member.

In species across virtually every vertebrate taxonomic division, vocal signals play key roles in predator avoidance, reproduction, competition, and mediating social interactions. Understanding signaling systems, and the various selection factors relating to their evolution and maintenance, therefore provides unique insight into species' behavior, social dynamics, and evolution. Decades of research has greatly improved knowledge of animal signals and how they are used, yet understanding of the mechanisms by which entire communication systems operate and evolve remains incomplete. The research presented in this dissertation examined the vocal repertoire of adult male blue monkeys (Cercopithecus mitis stuhlmanni). Specifically, I examined three elements of vocal signals - acoustic structure, signal content, and adaptive function - across the entire male repertoire, and used results to infer mechanisms of selection on signal usage and divergence. During 12 months of fieldwork in the Kakamega Forest, Kenya, assisted by a team of trained research assistants, I used a combination of natural observation, playback experiments, and digital audio recordings to examine vocal behavior of 32 adult males and responses to their calls by males and 62 adult females from 12 social groups and the surrounding area. Analyses of digital recordings identified six distinct call types used by adult males: ant, boom, ka, katrain, nasal scream, and pyow. The repertoire is best described as discrete, though some gradation occurs between pyows and ants. To identify signal content - attributes of signalers reliably indicated by features of signals - I investigated each call types' relationship to callers' identity, social status, body size, and attention to external variables (e.g. predators). Results showed that at least three call types (boom, katrain, pyow) were reliable indicators of identity, and features of at least one call type (pyow) were correlated with body size. Resident males used all call types whereas "bachelors" used only nasal screams, indicating social status is content in all calls except nasal screams. Two calls (ka, katrain) were strongly associated with and essentially exclusive to aerial predators, and ants had a similar relationship to terrestrial predators. The pyow and boom were each associated with multiple external variables, demonstrating that these two calls do not include any specific external stimulus in content. Lastly, the content of nasal screams, used exclusively during aggression with other males, included presence of another male. I tested four separate, non-exclusive functional hypotheses for each call type, using predictions relating to receiver response to hearing calls, as well as variation in temporal, demographic, and contextual patterns of usage. The ka, katrain, and ant each clearly functions in predator avoidance, with the first two relating specifically to aerial predators and the latter specifically to terrestrial threats such as snakes and dogs. Notably, the katrain also caused rival males to move away from callers, consistent with a mate defense function. The pyow, best described as a general alerting signal, demonstrated a clear role in repelling rival males, yet also functioned in facilitating within-group cohesion. The boom showed a clear role in affiliative interactions between callers and females in their groups, possibly functioning as a signal of benign intent, and was the only call type associated with proceptive interactions and an increase in number of estrous females, indicating a function in mating. Like pyows and katrains, booms also have a secondary function of repelling rival males.

The Andes, along with the Amazon and Atlantic forests, harbor the richest avifauna in the world with roughly one third of all the world's species of birds. Many biogeographical studies have sought to explain the origin and diversification of Andean taxa. However, because of the Andes' extensive latitudinal span and complexity, there is no one single cause of origin or of diversification that can explain the diversity found in them. Along the Andes, multiple biogeographic patterns of disjunction between highland and lowland sister-groups have been linked to Andean uplift. For example, Ribas et al. (2007) provided evidence that the spatio-temporal diversification in the monophyletic parrot genus Pionus is causally linked to Andean tectonic and palaeoclimate change through vicariance. Thus, if the Andes uplift is responsible for some of the patterns of montane-lowland disjunctions, it may be one of the mechanisms underlying the taxonomic assembly of the Andean montane avifauna. In this dissertation I explored whether the origin and diversification of three groups of Andean birds--the exclusively Andean parrot genera Hapalopsittaca, the subclade of mangoes containing Doryfera, Schistes, and Colibri, and the ovenbirds of the tribe Thripophagini--can be linked to Earth history. The results show that the origin of these Andean taxa can be explained through vicariance from their lowland sister-groups, mediated by the uplift of the Andes. Thus, this thesis proposes that geological events are directly responsible for originating diversity throughout montane environments. Once in the Andes, the diversification of these montane taxa can be explained by events such as the tectonic evolution of the Andes--which created canyons and valleys that may have caused the vicariance of continuous populations--as well as by the climatic oscillation of the Pleistocene, which caused altitudinal shifts, expansion, and contraction of the montane vegetation belts during the climatic oscillations of the Pleistocene.

Thesis (Ph. D.)--University of Chicago, Committee on Evolutionary Biology, 2002. / Includes bibliographical references. Also available on the Internet.

Thesis (Ph.D.)--University of Texas at Arlington, 2009.

Thesis (Ph. D.)--University of Chicago, Committee on Evolutionary Biology, June 2001. / Includes bibliographical references. Also available on the Internet.