A quick visual survey of the animal world around us reveals a wide array of morphological diversity, yet it is currently not known how such great diversity may have arisen in evolution. The recent emergence of molecular and developmental data from the field of developmental genetics, including genes, gene expression patterns, and most recently entire genomes, have provided a new set of characters to add in the analysis of animal evolution. One morphological character that displays a wide range of diversity is the appendage. Within the arthropods in particular, limbs vary in their size, shape and number along the body axis, providing an excellent experimental model to study how these changes have come about in evolution. The work in this dissertation uses comparative gene expression patterns to address how an arthropod limb patterning network has been modified to produce different limb morphologies. Over the past several decades, data from the field of Drosophila developmental genetics have aided our understanding of how the fly limb is patterned. Yet, Drosophila is a highly derived insect with an unbranched limb that undergoes a complete metamorphosis. I was interested in learning whether other arthropods displaying different modes of development as well as branched limbs use a similar molecular mechanism to Drosophila in the development and patterning of their limbs. The first arthropod examined was Triops, a branchiopod crustacean with a highly branched and fused limb type. Although some of the genes in the Drosophila limb patterning network appear to be conserved in this animal, the space and time in which they are expressed are different from what we observe in Drosophila. In the second species examined, the grasshopper, Schistocerca americana, again the components of the limb patterning gene network are conserved but the expression patterns are different. It appears that in the grasshopper, downstream genes involved in patterning the P/D axis are conserved in expression and perhaps function, but early in development, there is a dramatic change in the expression of one of the more upstream, dorsal components, a gene called decapentaplegic ( dpp), and it is correlated with the absence of imaginal discs. (Abstract shortened by UMI.)

A complete understanding of the speciation process requires elucidation of the underlying genetic details. Considerable empirical and theoretical research has revealed two important patterns that characterize the genetic basis of reproductive isolation. First, reproductive isolation is usually caused by incompatible substitutions at different, interacting loci. Second, the locations of genes contributing to reproductive isolation are biased toward the X chromosome. These observations suggest that reproductive barriers between young species are frequently due to disrupted interactions involving genes on the X chromosome. This idea motivates a detailed study of introgression for X-linked loci across a European hybrid zone between two species of house mice, Mus domesticus and M. musculus (Appendix A). Allele frequency patterns at 13 molecular markers with known chromosomal positions identify one region with clearly reduced introgression. This piece of the X chromosome may contain genes that confer reproductive barriers between M. domesticus and M. musculus. Expected patterns of hybrid zone introgression for incompatible substitutions between the X chromosome and the autosomes are also investigated using computer simulations (Appendix B). The results indicate that both the locations and shapes of allele frequency clines are distorted by selection against hybrids, with effects related to the dominance of the interacting alleles and inheritance patterns of the X chromosome (hemizygosity). Additionally, loci closely linked to the targets of selection show only weak reductions in introgression, suggesting that neutral gene flow is not strongly impeded by selection against hybrids. Finally, the mouse genome sequence is used to compare patterns of hybrid zone introgression to several genomic attributes (Appendix C). No clear correlates of introgression emerge, suggesting that reproductive isolation between M. domesticus and M. musculus may involve a small number of genes with large effects. Using location in the X-linked region of reduced introgression, a high rate of protein evolution, and restricted expression in the male germ line as criteria, seven candidate genes for reproductive isolation are identified. These results underscore the value of studying natural patterns of introgression in model genetic organisms for understanding the genetic basis of speciation.

The composition of the body in relation to the distribution of skin, muscle, bone and other tissues is directly related to the activities the individual is capable of performing throughout its life stages. The infant squirrel monkey is born with 20.658 TBW devoted to muscle, 24.65% TBW in bone, 24.15% TBW in skin, and 24.7% TBW in other supporting tissues. The adult squirrel monkey tissue distribution changes to 41.0% TBW in muscle, 17.2% TBW in bone, 17.5% TBW in skin, and 24.6% TBW in other supporting tissues. Consistently the adult demonstrates a tissue distribution and size that is compatible to living in the trees, moving through areas to forage, and the ability to escape predators that enter their preferred habitat. The infant demonstrates a body composition and size consistent with limited mobility and dependence on its mother for nutrients. The trend in the change of tissue distribution through growth and maturation from infant to adult is demonstrated and explained in relation to activities at the various life stages of the squirrel monkey.

Two zoologists with considerable experience in the Canadian Arctic suggested to the writer that the “Gammarus Problem” would be an extremely interesting subject for investigation, and one which has several advantages, for material is relatively easy to obtain, and there are a number of species available. The precise studies on the species and sub-species of this amphipod genus in British estuaries are well known, and have been cited as examples in discussions on speciation and “new systematics”. In North America such studies are lacking and the time seemed opportune to try to elucidate the relationships between some of the forms living on these shores. In particular the species from northern waters were of interest. Dr. E.L. Bousfield (1958) has described the fresh-water amphipods of North America, and is currently preparing an account of the systematics of coastal species. This account provided material for the present discussion on the general relationships of North American species, but as it has not yet been published the reference “personal communication” or “pers. comm.” is used throughout the discussion. [...]

In the field of helminthology, the life cycle of an organism not only brings to light the ontogeny of the individual, but also indicates its phylogenetic relationship in the general scheme of taxonomy. By means of the work presented in this thesis leading to the completion of the life history of Monoecocestus sigmodontis, it is hoped that some further contribution has been made to our knowledge of the Anoplocephalidae and their host-parasite relationship. In addition to developmental studies of this tapeworm, we have endeavored to uncover evidence of resistance to infection with this parasite on the part of the definitive host, the cotton rat, Sigmodon hispidus.

The theory of kin selection is central to the understanding of social evolution. Recent theoretical work suggests a limitation on the action of kin selection in structured populations. The first such limit involves a specialized population structure, termed "budding viscosity," common to social insects, in which new groups are formed by fission with no individual dispersal. An argument based on the separation of kin selection dynamics into among and within group components suggests that kin selection cannot operate in this structure. However, stochastic computer simulations show that random variation among daughter groups can supply the needed among-groups variation and allow kin selection to proceed. The second limit on kin selection involves simple population viscosity, in which individuals disperse limited distances and so are related to their neighbors. Altruism toward neighbors, favored by kin selection, is opposed by local competition. Computer simulation confirms this limitation and shows that some form of specific kin recognition is required to favor the evolution of altruism by kin selection. All applications of kin selection require a measure of genetic relatedness; a computer program for calculating this statistic from genetic data on natural populations is described.

Kin-selection theory states that individuals can increase their total fitness both through direct reproduction and through reproduction of relatives. The recently developed social contract theory asserts that dominant females should yield some direct reproduction to the subordinates in order to keep them in the colony. The theory predicts that a dominant will cede more reproduction to an unrelated subordinate than to a related subordinate since it will take more to keep her. I found that the social wasp, Polistes dominulus, is unusual in that foundresses regularly nest with non-relatives, even when relatives are available on other nests. This offers the opportunity to test one of the basic predictions of social contract theory, that reproductive skew increases as relatedness among co-foundresses increases. Subordinates of the collected colonies did get a small fraction of direct reproduction, but there was no difference in skew among colonies with different co-foundress relatednesses, contrary to skew theory predictions. Subordinates's relatedness to the queen does not affect colony efficiency. This study found no sign of either higher cooperation in colonies with more related females or greater conflicts in colonies founded by unrelated females.

<p> The main goal of this study was to determine the thermal ecology of the small tree lizard <i>Urosaurus ornatus</i> in a Chihuahuan Desert landscape. The study site was located at Indio Mountains Research Station (IMRS), Hudspeth County, Texas. We obtained body temperature (Tb) data on 385 lizards collected from April 2007 to June 2014 during the active period using a cloacal thermometer. Additionally, we recorded air temperature (Ta) and substrate temperature (Ts) of lizard microhabitats at the time of capture, and the operative temperature of lizard models left in the sun and shade from May to September 2014. My results showed that the mean Tb for all adult lizards was 33.6 &plusmn; 2.8&deg;C, with a range of 24.0 to 40.2&deg;C. This average Tb was similar but lower than those found in other populations in Southwestern United States. The results indicated that <i>U. ornatus </i> at IMRS displays mostly a thigmothermic behavior. Thermoregulatory behavior of these individuals showed that <i>U. ornatus</i> is a thermoconformer on IMRS. There was no statistical difference in mean Tb between males and females or between non-gravid females. However, there was a significant difference between lizards found in the sun and lizards found in the shade. It is expected that rising global temperatures will influence this region and therefore will have an impact on the population of <i>U. ornatus </i> too; possibly affecting aspects such as time for feeding, reproducing, and of course thermoregulating. Thus, it is important for us to understand the thermoregulatory needs of ectothermic organisms as they are dependent on the direct environmental temperatures for survival, especially since many recognize that rapid global warming has already been activated by human misuse of natural resources.</p>

<p> Seabirds are ecosystem engineers with two major impacts on island ecosystems: they bring large quantities of marine nutrients to the terrestrial environment in the form of guano, carcasses, feathers, eggs, and spilled food, and they disturb the soil surface. Burrowing seabirds can denude the soil surface of all seedlings and leaf litter, plowing them under and loosening the soil. However, seabirds are colonial, and burrows are not even spaced over the surface of an island, producing spatial variability within a single island that might reveal how seabird activities control island ecosystem function. </p><p> In this dissertation I review seabird island ecology in general, focusing on how introduced predators have reduced seabird populations, interrupting seabird activities and altering island ecology. I then describe three studies designed to quantify the effects of seabirds on soil and plant properties within individual islands and compare these patterns across islands varying in seabird density, especially where seabirds have declined because of invasive rats (<i>Rattus</i> spp.). </p><p> I used geostatistics to quantify the spatial variance in seabird burrows and various soil and plant properties (including soil and leaf N) within six islands of low, intermediate, and high burrow density. I found that burrow density was not a good predictor at within-island scales, and though the variance of some soil properties (pH, soil &delta;¹⁵N, and soil compaction) peaked on intermediate islands as expected, variables reflecting the soil N cycle (net ammonification and net nitrification potential, NH₄⁺ and NO₃^-) continued to increase in variability on very high-density seabird islands. Ecosystem properties clearly responded to seabirds at different spatial scales, possibly because seabirds deposit guano at different spatial scales than they dig. </p><p> Using data within three rat-invaded and three rat-free islands, I used structural equation models to examine seabird influences on N cycling. I found some mechanisms that were constant across islands, such seabird-related decreases in soil water and pH, but other mechanisms differed between invaded and uninvaded islands, suggesting that rats manifest an alternative state for island N cycles, which may or may not be reversible. </p><p> Finally, I investigated whether plants can use ammonia (NH₃ gas) volatilized from seabird islands, measuring NH₃ concentrations across 10 islands and within a single island where I also experimentally manipulated plant N demand. Both rat-invaded and rat-free islands produced meaningful concentrations of NH₃ gas, and multiple plant species including <i> Melicytus ramiflorus</i> and <i>Coprosma macrocarpa</i> used it for up to 20% and 30% (respectively) of their total leaf N. Plant N demand modified NH₃ uptake, suggesting that plants located not on seabird colonies, but downwind, may benefit the most from this gaseous N source. </p><p> I suggest that future studies attempt to estimate thresholds of burrow density at which seabird-controlled ecosystem properties can recover from rat invasion.</p>

<p> The integration of advances in computing technology with major innovations in sequence data collection and phylogenetic inference has revolutionized evolutionary biology in the 21^st century. In particular, the continual development of both theory and software that allow for more flexibility in utilizing molecular clock methods has radically transformed our understanding of the mode and tempo of diversification across the Tree of Life. Over the course of five chapters, this dissertation explores methodological challenges to phylogenetic inference with the aim of better understanding the evolutionary history of the Holocentridae (squirrelfishes and soldierfishes). </p><p> Chapter 1 begins by focusing on the problem of accommodating clade specific rate heterogeneity in molecular clock analyses. While various nucleotide substitution models have been developed to accommodate among lineage rate heterogeneity, recently developed "uncorrelated relaxed clock" and "random local clock" models are predicted to perform better in the presence of lineage specific rate heterogeneity as these models relax assumptions of inheritance of nucleotide substitution rates between descendant lineages. Using simulations and two cetacean (whale and dolphin) datasets as a case study, we demonstrate abrupt changes in rate isolated to one or a few lineages in the phylogeny can mislead rate and age estimation, even when the node of interest is calibrated; and provide suggestions for diagnosing extreme clade specific rate heterogeneity.</p><p> Homoplasy is another important, yet often overlooked, source of error in phylogenetic studies. Chapters 2 and 3 utilize phylogenetic informative approaches to screen nucleotide sequence data for homoplasious site patterns. Using phylogenetic informativeness profiles, chapter 2 reconciles two competing hypotheses of ray-finned fish divergence times by highlighting that mitogenomic based Jurassic and Triassic divergence time estimates for most major lineages of spiny-rayed (acanthomorph) fishes were an artifact of tree extension. Evolutionary relationships of early diverging acanthomorph fishes are also contentious, with molecular data supporting either holocentrids or a clade comprised of holocentrids and primarily deep-sea fishes as the sister lineage to the species-rich percomorpha. Chapter 3 reveals this conflict to also be largely driven by homoplasy and reconciles results based on previously published data with a 132 gene next-generation sequence dataset to identify the sister lineage of percomorph and the phylogenetic placement of holocentrid fishes.</p><p> Chapter 4 continues to explore holocentrid evolutionary relationships. Using a multi-locus dataset that includes all but one holocentrid genus, this chapter provides the first molecular phylogeny of the group. The systematics of holocentrid fishes has unstable for over 100 years. We demonstrate several of the key synapomorphies for holocentrid genera are in fact homoplasious. Likewise, several genera of holocentrine (squirrelfish) are rendered consistently paraphyletic by a series of maximum-likelihood and Bayesian analyses and we propose taxonomic revisions to reflect shared ancestry.</p><p> Chapter 5 further investigates the temporal history of holocentrid evolution. Contemporary holocentrid species richness is concentrated in the Indo-Australian Archipelago (IAA), yet these fishes also represent some of the most numerous fossil taxa in deposits of the Eocene West Tethyan biodiversity hotspot. Using likelihood-based methods integrated with a molecular timetree that incorporates fossils as tip taxa, we reconstruct the history of range evolution for these fishes. Following the collapse of the West Tethys, holocentrids exhibit a signature of increased range fragmentation, becoming isolated between the Atlantic and Indo-Pacific Ocean basins. However, rather than originating within the emerging IAA hotspot, the IAA appears to have acted as a reservoir for holocentrid diversity that originated in adjacent regions over deep evolutionary timescales. By integrating extinct lineages, these results provide a necessary historic perspective on the formation and maintenance of global marine biodiversity. </p>