Humans show such strong sensitivity to whether resources are distributed fairly that they sacrifice personal gain to avoid distributional inequity. This inequity aversion plays an important role in guiding human social decision-making and appears to be ubiquitous across human populations. However, we currently do not understand whether or how inequity aversion evolved over the course of human evolution or how it develops in children. / Human Evolutionary Biology

At broad scales, community ecologists study how biogeographic factors like environmental dissimilarity and geographic distance influence community assembly and composition. At small scales, community ecologists study how one or several species interact to determine habitat partitioning and coexistence. In this dissertation, I present studies at both scales. Chapter One investigates community assembly across the Caribbean, Central, and South American radiations of Anolis lizards and Eleutherodactylid frogs to test whether oceanic islands are unique in their assembly processes. Such uniqueness is suggested by high levels of endemism on islands; however, comparable levels of endemism can be found in mainland communities. I modeled the rate of species turnover between mainland communities, with respect to geographic distance and environmental dissimilarity, and then used the mainland model to predict turnover among islands. Turnover among island communities was significantly higher than predicted from the mainland model, confirming the long-held but untested assumption that island assemblages accumulate biodiversity differently than their mainland counterparts. Chapter Two reviews the evidence for ecological character displacement (ECD), an evolutionary process whereby two resource competitors diverge from one another in phenotype and resource use, facilitating coexistence in a community. I find that, despite current scientific opinion, the evidence for ECD is equivocal; most cases of ECD pattern fail to rule out processes alternative to resource competition that could create the same pattern. I conclude that better evidence may come from real time tests of ECD. Chapters Three and Four describe just such a test in small island populations of Anolis carolinensis. In Chapter Three, I find that small island populations of A. carolinensis that have come into sympatry with a novel competitor, the invasive A. sagrei, shift their habitat use to become more arboreal, compared to allopatric populations. Consistent with prediction, individuals from sympatric populations have larger toepads with additional adhesive scales - a common adaptation to arboreality in Anolis. In Chapter Four, I describe a common garden experiment that finds that the observed toepad divergence is an evolved response, suggesting rates of divergence for toepad area and scale number on par with well known examples of contemporary evolution.

Epistasis describes non-additive interactions which affect gene expression and phenotype. It can happen on multiple levels, including on a genomic level with interactions between genes or even chromosomes affecting global patterns of gene expression. It can also happen within a gene itself, with epistatic interactions between amino acids affecting gene expression and resultant phenotypes. I present three studies in two organisms to study this phenomenon on a global-genomic scale, and also on a local-genic scale.

A long-standing question in evolutionary biology is whether adaptation will typically proceed through a few mutations with large selective effects or many mutations with small effects. Many studies have implicated few loci of major effect, but it has been predicted that small-effect mutations should exist and contribute to adaptation. However, such mutations have not been found in many studies, either because they do not exist or because the experimental design limited their detection. To determine the effects and types of mutations contributing to adaptation, I studied laboratory and wild populations of bacteria. I characterized the distribution of the effect sizes in laboratory populations of an aerobic bacterium, Methylobacterium extorquens, and studied the types of genetic changes associated with adaptation to a novel host in wild populations of Mycoplasma gallisepticum.

With an estimated 8,000-20,000 species, bivalves represent the second largest living class of molluscs (Bieler et al. 2013). Revived interest in molluscan phylogeny has resulted in a torrent of molecular sequence data from phylogenetic, mitogenomic, and phylogenomic studies. Despite recent progress, basal relationships of the class Bivalvia remain contentious, owing to conflicting hypotheses often between morphology and molecules.

The malaria parasite, Plasmodium falciparum, has a demonstrated history of adaptation to antimalarials and host immune pressure. This ability unraveled global eradication programs fifty years ago and seriously threatens renewed efforts today. Despite the magnitude of the global health problem, little is known about the genetic mechanisms by which the parasite evades control efforts. Population genomic methods provide a new way to identify the mutations and genes responsible for drug resistance and other clinically important traits.

Bacteria evolve during the colonization of human hosts, yet little is known about the selective pressures and evolutionary forces that shape this evolution. Illumination of these processes may inspire new therapeutic directions for combating bacterial infections and promoting healthy bacteria-host interactions. The advent of high-throughput sequencing has enabled the identification of mutations that occur within the human host, and various tools from computational and evolutionary biology can aid in creating biological understanding from these mutations. Chapter 1 describes recent progress in understanding within-patient bacterial adaption, focusing on insights made from genomic studies.

This dissertation investigates the embryonic specification of a specific group of cells: the germ cells. Germ cells, which give rise to sperm and egg, are the only cells in sexually-reproducing animals that directly contribute hereditary information to the next generation. Germ cells are therefore a universal cell type across animals, and represent a profound novelty that likely arose near the base of the animal phylogeny. Yet despite their conserved, essential function in all animals, there is surprising diversity in the mechanisms that specify these cells during embryonic development. In this dissertation, I address the diversity of germ cell specification mechanisms in insects. I focus on two species, the milkweed bug Oncopeltus fasciatus (Hemiptera) and the cricket Gryllus bimaculatus (Orthoptera), which both branch basally to the Holometabola (those insects which undergo metamorphosis, including the well-studied fruit fly Drosophila melanogaster), and thus provide important phylogenetic breadth to our understanding of germ cell specification across insects. Using functional genetic approaches, I show that germ cell specification in both Oncopeltus and Gryllus differs fundamentally from germ cell specification in Drosophila. Specifically, I provide evidence that germ cells arise via inductive cell signaling during mid-embryogenesis, rather than via maternally-supplied cytoplasmic determinants localized in the oocyte, as is the case for Drosophila. These data suggest that Drosophila employs an evolutionarily derived mode of germ cell specification. In further support of this hypothesis, I show that several of the genes required for Drosophila germ cell specification perform other functions in both Oncopeltus and Gryllus. I demonstrate that one of these genes, oskar, which is the only gene both necessary and sufficient for germ cell specification in Drosophila, instead functions in nervous system of the cricket, both during embryonic development and in the adult brain. I suggest that the evolution of the derived mode of germ cell specification seen in Drosophila may have involved co-opting oskar into the germ cell specification pathway from an ancestral role in the nervous system.

Abstract: Archosauria, the "ruling reptiles," characterized along their stem by relatively large, macrocarnivorous animals, are today represented by two enormously successful but divergent extant clades: Aves, the birds, and Crocodylia, the crocodiles and alligators. This thesis seeks to characterize major transformations in the cranial region of archosaurs, a prominent theme in their evolution.

Sexual imprinting, the process of learning mate preferences at a young age, could promote speciation by reducing attraction to individuals from divergent populations or species, consequently creating or maintaining reproductive isolation. Yet, despite the documentation of sexual imprinting in many taxa, its connection to speciation has been understudied. I chose to explore the potential link between sexual imprinting and reproductive isolation and in two North American rodents--the white-footed mouse (Peromyscus leucopus) and its sister species, the cotton mouse (Peromyscus gossypinus). These species have overlapping distributions in nature, possibly allowing interbreeding and admixture. In Chapter 1, I used double-digest restriction-associated DNA sequencing to test for hybridization in sympatric natural populations and found that 1.5% of sampled individuals showed evidence of admixture yet the species have maintained genetic distinctness in sympatry. In the lab, the species hybridize when given no choice of mates but mate more readily with conspecifics, suggesting that mating preferences may prevent hybridization in the wild. In Chapter 2, I tested whether mating preferences create significant reproductive isolation. I measured mating preferences in controlled laboratory conditions and found that both species and sexes preferred conspecific to heterospecific mates in 85% of trials. I then raised offspring with foster parents of the opposite species and found that P. leucopus has a genetically-determined preference while P. gossypinus learns its preference. In Chapter 3, I tested whether sexual imprinting on parental diet could generate assortative mating within a species. I tested this hypothesis by feeding P. gossypinus parents either orange- or garlic-flavored water, thereby exposing their offspring to these flavors through their parents until weaning. I tested the preferences of these offspring as adults and found that P. gossypinus, especially females, had strong assortative mating preferences. This implies that at least females learn parental dietary information and that assortative mating could evolve within a single generation. Together, my results confirm that sexual imprinting on parental traits--possibly mediated through dietary differences--can create assortative mating capable of generating sexual isolation and reducing gene flow between species. My research supports the importance of mating preferences and learning in speciation.