The taxonomic status of the 16 nominal species of the genus Trinectes (Pleuronectiformes: Achiridae) Rafinesque 1832 was revised based on a morphological study of 647 type and non-type specimens. Nine species were recognized as valid Trinectes inscriptus, T. maculatus, T. microphthalmus, and T. paulistanus are found in the Atlantic Ocean, from the Northern United States to Southern Brazil, whereas T. fimbriatus, T. fluviatilis, T. fonsecensis, T. opercularis, and T. xanthurus are found in the Pacific Ocean, from Mexico to Peru. An identification key to species is provided. The phylogenetic relationships of the species recognized were hypothesized based on a cladistic analysis of 22 morphological, meristic, and osteological characters. The analysis resulted in one most parsimonious tree with a length of 39 steps (CI = 0.69; RI = 0.79). The tree showed that Trinectes is monophyletic on the basis of two synapomorphies: an unpierced interbranchial septum, and seven to nine pterygiophores anterior to the neural spine of the third precaudal vertebra. Trinectes inscriptus is the most plesiomorphic species of the genus, and all other species form a monophyletic group subdivided into two clades. The first contains (from most plesiomorphic to recent): T. paulistanus, T. fonsecensis, and the T. fluviatilis-T. xanthurus clade. The second clade includes (from most plesiomorphic to recent): T. maculatus, T. opercularis, and the T. fimbriatus- T. microphthalmus clade. The resulting cladogram depicts a sequence of speciation events and provides an opportunity to propose a biogeographical hypothesis on the evolution of Trinectes.

<p> Species interactions can regulate a population&rsquo;s density and therefore can act as a selective force on that population. Such evolutionary responses have the potential to feedback and change ecological interactions between species. For species that compete for resources, the interaction between ecological and evolutionary dynamics will regulate the stability of the species interactions, determining whether competing species can coexist. The outcome of competition between species is determined by two factors: (1) niche overlap, or the similarity in how species use resources and are affected by their environment, and (2) fitness differences, or differences in how efficiently each species uses resources in their environment. Decreasing niche overlap will decrease competitive interactions, thereby stabilizing coexistence. Decreasing fitness differences makes species more equal in their competitive abilities, facilitating coexistence. In the absence of evolutionary constraints, both niche overlap and fitness differences among species are subject to change as a consequence of evolution among competitors, and thus ecological dynamics between two species will also change. In this dissertation, I develop a broader understanding of (1) how niche overlap and fitness differences between species change after evolution in response to competition, (2) how changes in niche overlap and fitness differences are mediated through changes in resource use of protists, and (3) what role evolutionary history plays in shaping ecological and evolutionary dynamics. </p><p> I address these goals with a suite of approaches including theoretical models, an experimental lab system, and comparative methods. I constructed a quantitative genetic model of trait evolution, where the trait of a species determined its resource use, and found that species are prone to change in their niche overlap as well as their fitness differences as a result of trait evolution. However, the magnitude of changes in niche overlap and fitness differences were determined by the resource availability within the environments. When resources were broadly available, species changed more in their niche overlap, whereas when resources were narrowly available, species changed more in their fitness difference. To test these predictions, I developed a system in the laboratory where protists competed for a bacterial resource. Species were allowed to evolve in either monoculture or a two-species mixture; the effects of evolution on competition, niche overlap and fitness differences were quantified using parameterized models. In general I found that species tended to converge in their niche as a result of evolution, however, changes in fitness differences between species were larger and more influential on coexistence than changes in niche differences. Both increases in niche overlap, and increases in fitness differences decreased coexistence among species pairs. By describing the bacterial communities associated with these protists before and after selection I determined that protists tended to converge or not change in which bacteria they were consuming as a result of selection. Additionally, for eleven protist species, I determined whether traits or relatedness predicted competitive ability by placing species on a molecular phylogeny and conducting pairwise competition experiments for all pairs. I found no correlations, suggesting neither traits, nor evolutionary history was informative for explaining current ecological and evolutionary interactions in this deeply divergent clade. </p><p> There are two major conclusions from this dissertation: (1) when species evolve in response to competition, changes in fitness differences may often be more important than changes in niche overlap, (2) evolution can, and may be likely to, decrease the ability of species to coexist through increases in niche overlap and increases in fitness differences. This work suggests that one must simultaneously consider the role of evolutionary and ecological processes to understand community processes. Specifically, when researchers are attempting to explain mechanisms of coexistence between species, they must consider how evolutionary dynamics may change the ecological interactions within communities of competitors.</p><p>

<p> Biological sex estimation has been a central tenant in physical anthropology and bioarchaeology since the foundation of the fields. Traditionally, sex estimation techniques have centered on pelvic morphology but features of the pelvis are often poorly preserved in forensic and archaeological contexts. However, teeth have very high preservation potential. Because the crown is susceptible to ante- and postmortem damage, the cementoenamel junction (CEJ) provides a more often preserved portion of the tooth. Several studies have shown the potential use of measurements of the CEJ in biological sex estimation; however, these studies have been limited in their scope, samples sizes, and materials utilized. Additionally, the role of biological affinity in the estimation of biological sex from measurements of the CEJ have not been fully explored. Three main goals of the present study are: 1) to assess the ability to estimate biological sex from measurements of the cementoenamel junction across populations; 2) to assess the role of biological affinity in sex estimation based on the measurements of the cementoenamel junction across populations; and 3) to examine the relationship between dental arcade size and biological sex within and between populations. </p><p> A total of 737 dentitions (7,369 teeth) from American and South African Whites and Blacks were measured based on buccal-lingual and mesial-distal CEJ measurements defined by Hillson and colleagues (2005). Percent dimorphism was calculated for buccal-lingual, mesial-distal and geometric mean measurements for each tooth. Percent dimorphism was highest in the canines for all groups. Discriminant function and logistic regression analyses were run to assess the ability of the measurements to correctly classify biological sex within and between populations and groups. Correct classification ranged from 84.1% to 90.7%. Within group comparisons (i.e., American females, South African males, etc.) highlighted that molars, premolars, and incisors have the greatest weight in the discriminant function in classifying differences between ancestral groups.</p><p> Finally, a total of 162 dental arcades (maxillary and mandibular) were measured from photographs using <i>ImageJ</i> software to assess differences in dental arcade size and to assess the relationship between mesial-distal measurements of the CEJ and the length of the dental arcade. Statistically significant differences in mean arcade size were found for all groups except South African Whites and South African Blacks (mandible only). Pearson&rsquo;s correlation coefficient tests were used to test if a correlation existed between the sum of the mesial-distal CEJ measurements and the total arc length. A significant correlation was found in all groups except American Whites, South African Whites, and All Whites combined (mandible only). In summary, the buccal-lingual and mesial-distal measurements of the CEJ can be used to estimate biological sex with a high degree of correct classification. Canines, specifically the lower canine, shows the highest percent of sexual size dimorphism for all groups. Lower overall sexual size dimorphism is noted in the South African groups, especially South African Whites, when compared with their American contemporaries. Results indicate that the size (and possibly the shape) of molars, premolars and incisors have the most influence on differences seen between ancestral groups.</p><p>

The adaptive landscape heuristic can be used to answer the question "how predictable is evolution?" because its topology will impact the repeatability of evolution. In my Masters research I addressed this question in two ways: (1) I reviewed empirical adaptive landscape studies in the fields of directed protein evolution and microbial experimental evolution and (2) I performed a selection experiment to characterize adaptive landscape topology by measuring variance in fitness and metabolic phenotype within and among genetically distinct Pseudomonas fluorescens strains in two environments. Empirical studies have found that protein level landscapes are generally smooth, however, population level landscapes are rugged even in simple environments. Experimentally I found that the pattern of variance in fitness and metabolic phenotype was unique to the selection environment. The response to selection was highly repeatable at the level of fitness, but the underlying genetic routes taken were different for each environment and more variable in xylose than in glucose, suggesting a more rugged underlying landscape. More generally, my research suggests that making statements about the predictability of adaptive evolution at the population level may be challenging and wi11likely depend on the specifics of the environment in which selection occurs.

Experimental evolution was used to independently evolve 12 replicate populations of Drosophila melanogaster for 34+ generations in one of three treatment environments of varying PO2: hypoxia (5.0-10.1 kPa), normoxia (21.3 kPa), and hyperoxia (40.5 kPa). Several traits related to whole animal performance and metabolism were monitored during experimental evolution and several common garden assays were performed at various stages to directly compare evolved and acclimatory differences between treatments. Results clearly demonstrate the evolution of increased anoxia tolerance in hypoxia-evolved populations, suggesting adaptation to this environment. This was correlated with an increase in citrate synthase activity compared to normoxic (control) populations, suggesting an increase in mitochondrial density in these populations. In contrast, no direct evidence of increased performance of the hyperoxia-evolved populations was detected, although an evolutionary cost was observed as a substantial decline in anoxia tolerance. Changes in performance did not result in an increase in any of the fitness components measured, including productivity and longevity, suggesting that these assays failed to capture the components of fitness relevant to adaptation.

Aspects of the behavioral ecology of bird song learning are examined in three parts. First, an approach from image analysis is extended to allow rapid, quantitative description of animal sounds. In this approach, sounds are summarized as sets of time-frequency-amplitude landmarks. Second, the role of dawn song in tree swallow (Tachycineta bicolor) breeding biology is examined. Song syllable sharing among tree swallows was found to be high among birds nesting at the same site, but sharing was lower between birds nesting at different sites. When birds nested at different sites, the distance between those sites was not related to the amount of difference between the birds' syllable repertoire compositions. All tree swallow song repertoires did not remain constant during the breeding season; some individuals added new syllable types, others modified existing types. Singing performance was correlated with reproductive success in tree swallows: males that sang more precise repetitions of their syllable types attracted more extra-pair mates. Furthermore, pairwise comparisons between the social and genetic fathers of extra-pair young found that the genetic fathers averaged higher syllable consistency than the cuckolded males. Third, a comparative study of the phylogenetic distribution of vocal mimicry examined the evolutionary history of song learning in oscine passerines. Vocal mimicry, defined as the habitual incorporation of heterospecific sounds into song displays, was found in twenty-eight separate clades of oscines. These clades were found in every major oscine superfamily, but made up a higher proportion of daughter groups within the most ancient superfamilies of oscines. The most plesiomorphic lineages of oscines were found to contain many highly-skilled mimics. These observations support the hypothesis that the course of song learning in oscines has run repeatedly from permissive learning rules that permit mimicry to restrictive learning rules that limit mimicry.

Under the Dobzhansky-Muller model, postzygotic isolation results from incompatibility between interacting genes. Evidence points to regulatory networks as a rich source of incompatibilities that impact hybrid fitness. Pleiotropy is a natural feature of regulatory networks because regulatory elements generally have multiple targets. Both pleiotropy and hybrid incompatibility arise due to genetic interactions; therefore we can expect an intimate association between them. In the following chapters, I investigate the relationship between pleiotropy and hybrid incompatibility in the context of regulatory networks. In chapter one, I extend a general network-based study of hybrid incompatibility by incorporating a sequence-based thermodynamic model of transcriptional regulation. In the absence of pleiotropy, hybrid misregulation of a positively selected trait evolves quickly as a consequence of non-recognition or spurious binding in regulatory interactions across species boundaries. In a conserved trait, hybrid incompatibility evolves much slower as a product of compensatory drift. In chapter two, I show that pleiotropy can promote or constrain the evolution of hybrid incompatibility in a regulatory network depending on its fitness landscape, which emerges from the thermodynamic properties of molecular binding. Pleiotropy may promote hybrid incompatibility in accordance with the "selection, pleiotropy, and compensation model" of evolution, in which compensation for the pleiotropic side-effects of adaptation accelerates incompatibility in conserved traits. Pleiotropy can limit the evolution of hybrid incompatibility by constraining change in trans-acting regulatory elements in favor of adaptation at less pleiotropic downstream cis-regulatory targets. Without change in both interactors, incompatibility does not occur under the Dobzhansky-Muller model. In chapter three, I evaluate the hypothesis that pleiotropy facilitates the onset of hybrid incompatibility under antagonistic coevolution, an ubiquitous and persistent source of natural selection. When infectivity and resistance in a host-parasite system are determined epistatically by network interactions, reciprocal selective pressure results in a genotypic chase. This causes pleiotropic mutations to accumulate and be compensated over time, producing intrinsic hybrid incompatibility in both species independent of local adaptation. Thus, cyclical antagonistic coevolution eventually overcomes constraint on pleiotropic loci, facilitating the evolution of regulatory incompatibilities commonly observed in hybrids.

The carotenoid tradeoff hypothesis states that diet-derived carotenoids are traded-off among competing physiological demands, but this statement is rarely tested in ornamented females. The following dissertation tests the carotenoid tradeoff hypothesis in reverse sexually dimorphic convict cichlids (Amantitlania siquia) using carotenoid-supplemented diet treatments and a field-based study of carotenoid intake. Spectral, microscopic, and chemical analysis determined how females allocated the pigments to tissues and how those decisions affected their ventral patch coloration. The results presented in the current study show that carotenoids enhance offspring growth and survival, lower oxidative stress, and reduce the time to clear a parasite. The two final chapters suggest that carotenoid limitation and absorption may not explain carotenoid allocation dynamics in A. siquia. The final chapter proposes an alternative to the carotenoid tradeoff hypothesis as a mechanism to explain the relationship among color, parasites, and oxidative stress.

Morphology can play a major role in ecological diversification and adaptive radiation when it consistently enhances performance and behavior. Here I investigate how cranial and dental morphology, feeding performance and behavior relate to one another and to the dietary radiation in Neotropical leaf-nosed bats (Family Phyllostomidae). First, I build a 3D biomechanical model to investigate the mechanism connecting cranial morphology and bite performance (bite force) and how bats with different diets vary in biomechanical parameters predicting bite force. The model demonstrates that cranial morphology is a strong predictor of bite force variation, and that bats differ in biomechanical predictors of bite force when they are classified according to dietary hardness. Second, I investigate the relationship between biting behavior and bite force across phyllostomids. My results indicate that bats modulate their performance by changing their biting behaviors to maximize bite force when feeding on hard foods. Using phylogenetic correlations and ancestral state reconstructions, I provide evidence for correlated evolution of behavior and performance, and rapid evolution in these traits that coincided with the use of plant resources. Third, I investigate the trends in molar complexity, chewing behavior and efficiency in breaking down prey across phyllostomids with different diets. My results illustrate that frugivores exhibit a higher dental complexity than insectivores and omnivores, and that the latter groups achieve higher performance in insect breakdown through higher molar complexity and chewing behavior. Finally, I investigate if other behavioral traits relevant to fitness have shaped the evolution of the skull morphology, using roost excavation in Lophostoma silvicolum as a model system. Through finite element analysis, I provide support for the prediction that the skull of L. silvicolum presents adaptations for roost excavation, in the form of a stronger skull. When all my findings are considered there is evidence that, although morphology can strongly predict performance, behavior plays an important role in modulating performance, and selection on this ability could have contributed to the ecological diversification of phyllostomids. Overall, the dietary radiation of phyllostomids, in particular the use of plant resources, was associated with dramatic changes in cranial and dental morphology, feeding performance and behavior.

abstract: Transgenic experiments in Drosophila have proven to be a useful tool aiding in the determination of mammalian protein function. A CNS specific protein, dCORL is a member of the Sno/Ski family. Sno acts as a switch between Dpp/dActivin signaling. dCORL is involved in Dpp and dActivin signaling, but the two homologous mCORL protein functions are unknown. Conducting transgenic experiments in the adult wings, and third instar larval brains using mCORL1, mCORL2 and dCORL are used to provide insight into the function of these proteins. These experiments show mCORL1 has a different function from mCORL2 and dCORL when expressed in Drosophila. mCORL2 and dCORL have functional similarities that are likely conserved. Six amino acid substitutions between mCORL1 and mCORL2/dCORL may be the reason for the functional difference. The evolutionary implications of this research suggest the conservation of a switch between Dpp/dActivin signaling that predates the divergence of arthropods and vertebrates. / Dissertation/Thesis / Masters Thesis Biology 2019