<p> Adaptive radiations offer unique insight into how diversification is initiated in novel or changing environments but the value of such studies is often limited by incomplete or lacking information on the ancestral species. The threespine stickleback species complex is proving to be particularly valuable in enhancing our understanding of evolutionary processes because there is reason to believe a surrogate for the ancestral group is extant and representative of the oceanic form that gave rise to most post-glacial freshwater populations during the last ~12,000 years. If we are to maximize the value of this radiation a thorough understanding of the putative ancestor group is needed. This dissertation explores the degree of phenotypic variation in oceanic stickleback in Cook Inlet, AK as well as the relative contributions of genetic and plastic aspects shaping the phenotypic variation revealed.</p><p> Geometric morphometrics were used to describe shape differences in two oceanic forms of stickleback, anadromous and fully marine. These groups differ in shape along the same benthic-limnetic axis described within the freshwater derived populations in the same region. A common-garden rearing study revealed high levels of body shape plasticity in both groups as well as likely genetic influences maintaining important aspects of shape differences between their stocks of origin. Interestingly, plasticity related to the salinity of early rearing environment differed across types suggesting that there may be a flexible dual stem in the threespine stickleback radiation, a surprising result that has not been considered to date in any system to my knowledge.</p><p> Additionally, because life-history traits are intimately linked to reproductive success and thus fitness, differences in life-history strategies between these two oceanic types should reflect meaningful adaptive variation, whether plastic or strictly genetic based. Established methodologies in stickleback life-history studies were employed to assess phenotypic variation across populations, types, and years in many important traits (e.g., egg and clutch size, reproductive effort, allometric relationships between reproductive effort and female body size). Life-history strategies differed significantly across type and year. Generally, marine females exhibit greater reproductive investment and have larger and more numerous eggs per clutch. Anadromous populations experience an apparent reproductive cost to the migration to freshwater relative to their fully-marine counterpart. It&rsquo;s unclear from these studies then where the fitness advantage to anadromy lies in the primitively oceanic species complex. However, important differences in mortality on the breeding grounds for adults and young as well as a possibly faster clutch production frequency in the anadromous lifestyle explains the apparent paradox in these data.</p><p> The finding of differences in genetic and plastic contributions to oceanic stickleback phenotypes body shape and life histories across two types in close geographic proximity which correlates with salinity regime suggest a flexible dual stem in the oceanic group(s). This could then influence evolution within the freshwater radiation. Thus, depending upon the freshwater populations (or watersheds) studied, the choice of representative oceanic type would need to be carefully considered. These data suggest that any near shore or inland sea areas within the stickleback oceanic distribution which experience a wide range of salinities is likely to show associated clinal variation in stickleback population reaction norms for (at least) body shape, life history strategies, and likely many other traits which are sensitive to salinity, such as genes involved in osmoregulation. Recent studies of Baltic and Sea of Japan oceanic stickleback further support this conclusion.</p>

<p> Grandparental investment in grandchildren is a topic of interest within the field of evolutionary psychology. Studies have shown a consistent pattern of differences when it comes to each grandparent&rsquo;s investment levels (Danielsbacka, Tanskanen, Jokela, &amp; Rotkirch, 2011; DeKay, 1995; Laham, Gonsakorale, &amp; Von Hippel, 2005; Michaski &amp; Shackelford, 2005; Pollet, Nettle, &amp; Nelisson, 2006). The pattern is as follows: the maternal grandmother invests the most, followed by the maternal grandfather, the paternal grandmother, and finally the paternal grandfather. The current hypotheses and theories behind this pattern are based on previous evolutionary theories of relatedness (Hamilton, 1964) and relational certainty (Trivers, 1972). The large and consistent difference between maternal grandmothers and paternal grandfathers can be explained relatively directly based on relational uncertainty, as the maternal grandmother is the most certain that the grandchild is her genetic relative and the paternal grandfather is least certain. This explanation is widely accepted. However, the smaller but consistent differences in investment patterns by maternal grandfathers versus paternal grandmothers, in favor of the former, is not as easily explained. The two currently competing theories are as follows: (1) although maternal grandfathers and paternal grandmothers are equally uncertain of their relatedness, they invest differently depending on which generation their uncertainty lies in &ndash; the grandparent generation for the grandfather and the parent generation for the grandmother; and (2) paternal grandparents have other grandchildren for which they are maternal grandparents, and they will choose to invest more in these more certain relatives. The current research was designed to test a new hypothesis, that patterns of grandparent investment are affected by whether or not grandparents are nested (coupled and sharing resources). A survey measuring grandparent investment across four dimensions was administered and found no significant differences between certain nested and unnested grandparents in terms of investment. Results instead revealed a different overall pattern of investment entirely, indicating multiple design flaws and providing some direction for future research.</p>

<p> The larval nutritional mode of marine invertebrates is an important life history trait that has strong effects on their ecology and evolution. Increases in egg size and transitions from feeding to nonfeeding larvae have happened repeatedly. In Spiralia, a change in cytoplasm allocated to macromeres at the 8-cell stage (that could delay the development of a functional gut) may accompany these transitions. The first part of this thesis describes the development of the gastropod <i>Crepidula williamsi</i> and compares it to the closely related <i>C. fornicata,</i> with a focus on changes in allocation to macromeres and the development of a functional gut. The second part is a phylogenetic comparison of egg size and allocation to macromeres in 44 species of spiralians, which revealed a significant correlation between the two. A phylogenetic comparison like this one has not previously been done on the development of such diverse marine invertebrate taxa.</p>

Although population genetics has a long history and firm theoretical basis, until recently little data was available for empirical hypothesis testing. The unprecedented growth of sequencing methodologies has transformed the discipline from data-poor and theory rich field into one virtually unlimited by the available of suitable data. In this thesis, we develop bioinformatic methods to address a variety of longstanding questions in the field of evolutionary genetics. Specifically, we use data derived from model organisms to study the evolution of inversion polymorphisms, segregation distorters and fitness epistasis. In the first chapter, we develop methods for detecting chromosomal inversions using next-generation sequencing data. Subsequently, we show that chromosomal inversions in Drosophila melanogaster are evolutionarily young, and at least one has likely achieved polymorphic frequencies via sex-ratio segregation distortion. In the third chapter, we develop a method of surveying the genome for segregation distortion in an unbiased manner, and show that segregation distortion does not contribute to hybrid male sterility in one pair of house mouse populations. Finally, we show that contrary to expectations, gene-gene interactions are widespread within species, which challenges a central paradigm of speciation research.

A study of the marine dinoflagellate Glenodinium foliaceum is presented which attempts to provide information on the process of host-endosymbiont integration in a unicellular system that may be of relevance to current hypotheses on chloroplast evolution. An experimental ultrastructural review of G. foliaceum supports the proposal that the chloroplasts and supernumerary nucleus belong to a morphologically reduced, endosymbiotic chromophyte. DAPI staining shows that the endosymbiont nucleus is fragmented in some cells and appears to be randomly divided by the host's cleavage furrow at cytokinesis. A quantification of the intensity of mithramycin fluorescence from single cells by flow cytometry suggests that both nuclei synthesize their ENA in synchrony. Protocols are outlined for isolating the chloroplasts and dinoflagellate nucleus from G. foliaceum and a method is given for fractionating whole cell lysates to prepare chloroplast, host nuclear, and endosymbiont nuclear DNAs. It is estimated that the symbiont and dinoflagellate nuclei contain about 34 pg and 40 pg of ENA respectively. There is no evidence of amplified genesized ENA molecules in the symbiont nucleus. The results of preliminary re-association experiments show only the presence of highly repeated ENA and sequences of intermediate repetitiveness in total cell ENA, which together comprise about half the genome. The chloroplast DNA is shown to a molecular weight of approximately 103 kb by restriction endonuclease analysis but an attempt to localize the rbc S gene in either the chloroplast or nuclear DNAs using a cloned pea ENA probe proved unsuccessful. Two other anomalously pigmented dinoflagellates, Gyrodinium aureolum and Gymnodinium galatheanum, are demonstrated to lack endosymbionts by electron and fluorescence microscopy, but the atypical ultrastructural or cytological characters of their chloroplasts are considered to indicate an endosymbiotic origin. The possibility that Glenodinium foliaceum could evolve into a similar uninucleate species is discussed in relation to the conservation of genetic information for nuclear-encoded, chloro-plast proteins.

<p> This study examines how the different behavioral, environmental and physiological factors might be influencing the essential physiological trait of erythrocyte mean cell diameters (MCD). At present no other study has explored the effects of these factors. Erythrocyte MCD for 153 species were collected from recent literary sources and compared to erythrocyte MCDs collected by Gulliver (1875), genome sizes and spleen sizes were also collected from a variety of literary sources. This data was analyzed using R with phylogenetic generalized least square analyses against several different behavioral, environmental and physiological factors. From these analyses, I found that as mammal mass and length increase the erythrocyte MCD also increases and as mammals move into higher elevations and warmer climates erythrocyte MCD decreases. All other behavioral, environmental, and physiological factors did not have an influence on erythrocyte MCD. These data did not support hypotheses previously offered by the other studies done on erythrocytes. Further research needs to be conducted on this topic because other factors that influence erythrocyte MCD may still exist that were not examined in this study.</p><p>

<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>

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

This work sequenced the placental microbiome of preterm and full-term pregnancies, and related preterm/full-term variations in placental microbiome composition and function to maternal inflammation in order to evaluate the proximate roles of the placental microbiome in responding to maternal immune stress and determining gestation length. These findings were situated in an evolutionary life history framework based on reproductive-immune trade-offs in order to develop an ultimate explanation for why natural selection has left us vulnerable to preterm birth, and why some populations are more affected than others. The preterm placental microbiome was found to be characterized by an inflammatory microbiome, dominated by bacteria that multiply in the context of energetic stress. The presence of such high numbers of these bacteria at the preterm placenta suggests that energetic and immune stresses are occurring in preterm birth, and that there may be a bidirectional relationship between stressful conditions and the microbiome. That is, inflammation or other stressors that contribute to energy imbalance may encourage shifts in the microbiome, which in turn creates more inflammation and energy imbalance. When that happens, pregnancy may become unsustainable before reaching term. Conversely, term pregnancies were characterized by greater numbers of beneficial, anti-inflammatory bacteria, hinting at possible roles for a healthy placental microbiome in nourishing and protecting the fetus. These findings underscore the need for a more holistic view of the role of microbes in pregnancy, as well as the need for health interventions that identify and address root sources of energetic and immune stress. / Anthropology