<p> Researchers have identified inadequate sleep duration as one of the factors contributing to global obesity. The purpose of this study was to test a hypothesis deduced from a new sleep-duration-based evolutionary theory claiming that sleep extension in response to lengthening night duration in early fall evolved into a behavioral marker of an approaching winter; this adaptive trait was theorized to produce adiposity gain in White men in response to sleep extension. The hypothesis was that White Americans would show a greater increase in the age-adjusted fat mass index per unit of sleep duration compared to that of Black Americans. Data were part of the National Health and Nutrition Examination Survey (NHANES) study between 2005 and 2010. The multiple regression analysis did not support the study hypothesis. The results indicated that habitual sleep duration had no effect on the annual rate of adiposity gain in White men, while in Black men, longer sleep was associated with significantly higher annual rates of adiposity gain. Implications for social change include the case for population-specific antiobesity interventions in Black men, including closer monitoring of sleep duration in order to prevent adverse habitual sleep extension and to improve time budgeting for physical exercise.</p>

<p> I found that in inbred females <i>D. melanogaster,</i> physical condition plays a major role in the amount of polyandry. In some systems there is evidence that the ability to self assess allows inbred females to vary their reproductive behavior to increase promiscuity. I predicted that this may be true in <i>Drosophila melanogaster</i> females, but we found that inbred females behaved less promiscuously in three proxies than outbred females. Inbred females mated with fewer total males, fewer different males, and had longer copulation latency than their outbred conspecifics. However, male mate choice is not predicted in <i>Drosophila melanogaster </i> because males invest less than females, but recently the importance of male preference has been gaining support. How these males are making decisions is an important component to understanding the evolutionary impacts of the male's behaviors. I found that male mate choices are heavily influenced by previous experiences, and the lack of experience causes significant changes in courtship latency and overall preferences.</p>

<p> Comparative and evolutionary cognitive scientists disagree on whether human and nonhuman primate cognition is driven by a general intelligence or more specific, modular mechanisms. Comparative research with chimpanzees is extensive and provides the opportunity to better understand the evolution of human cognition. Little research has been dedicated to individual differences in chimpanzee social and physical cognition. The study of individual differences can be informative in better understanding the generality of primate intelligence. Results supporting a correlation between performances in the social and physical domains would suggest that a domain-general inference system may be responsible. If no relationship is revealed between performances then more compartmentalized, modular mechanisms may be responsible. As a preliminary investigation, I administered four studies focusing on social and physical cognition to a large number of captive chimpanzees. Performance on two tool-using tasks served as indicators of physical intelligence. I administered two social investigations regarding individual variation in social responsiveness and sociability. I did not find a correlation between the social and physical investigations; however strong individual differences in performances were observed. Demographic factors sometimes played a role in the results presented here (e.g. dominance rank and age). While this research does not demonstrate a relationship between sociability and physical intelligence, additional social measures should be utilized in order to measure social cognitive ability in chimpanzees. Focusing on individual differences with a battery of social and physical tasks will be informative regarding the structure of primate intelligence and the underlying cognitive mechanisms that are responsible.</p>

<p> Male katydids produce mating calls through stridulation to attract potential mates. Calls were recorded in the field and analyzed to compare between two related species that occur in overlapping ranges in the northwestern United States. Distinct differences were found between the two species' calls in both dominant frequency and chirp rate. Also, one species interspersed trills amongst the chirps of the call, while the other species' call did not include trills. These distinct call differences can be used for species identification and can be easier to differentiate than physical characteristics. </p><p> The upper limits of sexual selection can be estimated using upper limits on Bateman gradients, which represent how fecundity increases with additional mates. Upper limits on Bateman gradients are expected to be constrained by various factors such as nutrition. These upper limits were estimated using controlled mating experiments with katydids on high and low protein diets (as adults) by measuring how maximum fecundity (fecundity with ideal mates) increased with each mating. Decreases in both maximum fecundity and the potential for sexual selection were expected in males and females due to protein limitation. This would result from decreased potential fecundity in low protein females and decreased value of nuptial gifts given by low protein males. The results did not support our predictions as strongly as hoped, but a decrease in the upper limits of sexual selection was nearly significant in low protein males, evidenced by reduced fecundity gains from remating. Also, spermatophores (the katydid nuptial gift) had a more complicated effect on fecundity than expected. Spermatophore size differed between males' first and second matings, however, larger spermatophores did not always confer more value to females, particularly in second matings. </p><p> Stable isotope analysis was used to examine the lack of significant effects from differences in dietary protein on the upper limits of sexual selection in the previous experiment. Stable isotope ratios were analyzed for three body tissues to infer diet at different life stages by comparison with isotopic values from the foods. Results showed that animals on the low protein diet may have eaten more food to make up for their protein deficit, which would have confounded nutritional effects in the previous study. Sex differences in nutrient processing were present as would be expected if males and females experience different nutritional requirements for reproduction. Nutrient processing in exoskeleton varied across food treatments in males but not in females. This suggests that males experienced greater protein limitation than females and adjusted their nutrient processing accordingly. Further work is underway to determine how much of each type of food was consumed by individuals in different experimental treatments and during different life stages. </p>

<p> The plant hormone auxin plays a major role in shaping plant morphology and development, but the gene networks regulating its synthesis and transport are incompletely known. The maize <i>BARREN INFLORESCENCE 1</i> (<i>BIF1</i>) gene has recently been cloned and shown to play an important role in the early stages of polar auxin transport. Auxin is synthesized in shoot tips and transported basipetally through the plant shoot and acts as a morphogen by facilitating the degradation of transcriptional repressors in a concentration dependent manner. The <i>AUX/IAA</i> gene family encodes transcriptional repressors that regulate a subset of plant developmental responses governed by the transcription of early auxin inducible genes in plants. Although the maize <i>BIF1</i> gene is a member of the <i>AUX/IAA</i> gene family, the co-ortholog(s) of <i> BIF1</i> in <i>Arabidopsis thaliana</i> was not known prior to this research.</p><p> Bayesian phylogenetic reconstruction placed maize <i>BIF1</i> in a clade sister to <i>Arabidopsis thaliana AtIAA15</i>. The <i> BIF1</i> lineage has undergone two gene duplications since the divergence of the early grasses. Molecular evolutionary analyses by maximum likelihood suggest that the <i>BIF1</i> alignment is under strong purifying selection with positive selection acting on a glutamine residue located in a functional region associated with <i>AUX/IAA</i> protein dimerization in one clade of <i>BIF1</i> paralogs, the <i>BIF1-Like2</i> (<i>BIF1L2</i>) clade. A character reconstruction analysis using maximum parsimony estimated an adenine to cytosine transversion at the base of the <i>BIF1L2</i> clade changed a glutamine into an alanine residue in this functional region. Expression of <i>BIF1</i> orthologs is conserved in floral meristems in the eudicot <i>AtIAA15</i> clade containing the taxa <i>Erianthe Guttata, Arabidopsis thaliana, Medicago truncatula</i>, however grass <i>BIF1L2</i> expression has diverged within the PACMAD &ndash; BEP clade, specifically in rice, where <i> BIF1L2</i> expression is reported to have moved into root tissue. These results suggest that <i>BIF1</i> paralogs has changed following a second round of gene duplication in the grasses. Taken together, a change in localized expression in these sequences, and positive selection acting on a glutamine-rich region of the protein-protein binding motif could imply that BARREN INFLORESCENCE1-like2 proteins are probably interacting with a new set or subset of AUXIN RESPONSE FACTOR (ARF) binding partners, and that neofunctionalization has occurred in the <i>BARREN INFLORESCENCE1-like2 </i> clade.</p>

<p>Recombination is the process in which genetic material is exchanged between one's homologous chromosome pairs during egg or sperm development (meiosis). Recombination is necessary for proper segregation of chromosomes during meiosis, and also plays a role in purging deleterious mutations, accelerating adaptation, and influencing the distribution of genomic features over evolutionary time. While recombination is clearly an important process, recombination rate is known to vary within and between individuals, populations, and species. Furthermore, what causes this variation remains relatively unknown. Using empirical and sequenced based estimates of recombination rate for the closely related species <italic>Drosophila pseudoobscura</italic> and <italic>Drosophila miranda</italic>, I seek to understand where recombination happens across the genome, to what extent recombination changes between species, and what genomic features are responsible for these changes. These data will deepen our understanding of mechanisms determining the recombination landscape, and shed light on generalized patterns and exceptions of recombination rate variation across the tree of life.</p> / Dissertation

Thesis (M.S.)--Rutgers University, 2008. / "Graduate Program in Ecology and Evolution." Includes bibliographical references (p. 73-77).

Thesis (Ph.D.)--Indiana University, Dept. of Biology 2009. / Title from home page (viewed on Jul 8, 2010). Source: Dissertation Abstracts International, Volume: 70-10, Section: B, page: 5957. Advisers: Loren H. Rieseberg; Scott D. Michaels.

abstract: Skeletal diseases related to reduced bone strength, like osteoporosis, vary in frequency and severity among human populations due in part to underlying genetic differentiation. With >600 disease-associated mutations (DAMs), COL1a1, which encodes the primary subunit of type I collagen, the main structural protein in bone, is most commonly associated with this phenotypic variation. Although numerous studies have explored genotype-phenotype relationships with COL1a1, surprisingly, no study has undertaken an evolutionary approach to determine how changes in constraint over time can be modeled to help predict bone-related disease factors. Here, molecular population and comparative species genetic analyses were conducted to characterize the evolutionary history of COL1a1. First, nucleotide and protein sequences of COL1a1 in 14 taxa representing ~450 million years of vertebrate evolution were used to investigate constraint across gene regions. Protein residues of historically high conservation are significantly correlated with disease severity today, providing a highly accurate model for disease prediction, yet interestingly, intron composition also exhibits high conservation suggesting strong historical purifying selection. Second, a human population genetic analysis of 192 COL1a1 nucleotide sequences representing 10 ethnically and geographically diverse samples was conducted. This random sample of the population shows surprisingly high numbers of amino acid polymorphisms (albeit rare in frequency), suggesting that not all protein variants today are highly deleterious. Further, an unusual haplotype structure was identified across populations, but which is only associated with noncoding variation in the 5' region of COL1a1 where gene expression alteration is most likely. Finally, a population genetic analysis of 40 chimpanzee COL1a1 sequences shows no amino acid polymorphism, yet does reveal an unusual haplotype structure with significantly extended linkage disequilibrium >30 kilobases away, as well as a surprisingly common exon duplication that is generally highly deleterious in humans. Altogether, these analyses indicate a history of temporally and spatially varying purifying selection on not only coding, but noncoding COL1a1 regions that is also reflected in population differentiation. In contrast to clinical studies, this approach reveals potentially functional variation, which in future analyses could explain the observed bone strength variation not only seen within humans, but other closely related primates. / Dissertation/Thesis / Ph.D. Biology 2010

Recent advances in high-throughput, genomic sequencing allow unprecedented insight into the evolution of biodiversity. Chapter 1 of this thesis is a phylogenetic study of 1,145 sequenced loci, isolated using a novel high-throughput sequence capture methodology to address the phylogenetic position of turtles within tetrapods. The results reported here unambiguously place turtles as sister to archosaurs and resolve this long-standing question. Chapter 2 investigates the genetic basis of colorful pigmentation in the Green anole (Anolis carolinensis) by sequencing complete transcriptomes from the green dorsal, white ventral and pink dewlap skin. Anoles comprise an adaptive radiation of more than 400 species and color plays a central role in their ecology and evolution, but little is known about the genetic basis of colorful pigmentation in any vertebrate. This study identified 1,719 differentially expressed genes among the three differently colored tissues. Twenty-three of these genes are involved in melanin, pteridine, and carotenoid pigmentation pathways that contribute to the coloration of anole skin. Identifying candidate genes for colorful pigmentation is a significant advance that opens the field for comparative analysis in other taxa. To determine if the genes identified in Chapter 2 are involved in population divergence and speciation, Chapter 3 investigates the complete genomes of twenty individuals from two closely related subspecies of Anolis marmoratus. While the two subspecies differ markedly in pigmentation, this study found few genetic differences between populations except in five regions of the genome, which together contained 447 genes. Of these genes, only two, melanophilin (mlph) and 'cluster of differentiation 36' (cd36), are associated with pigmentation. The intersection of the genes identified in Chapter 2 and Chapter 3 includes both cd36 and mlph, suggesting that both are involved in divergence of coloration. Cd36 is of particular interest because it regulates the uptake of carotenoid pigments and is an important candidate gene contributing to carotenoid pigmentation. Together, this research demonstrates the power of genomic approaches to address fundamental questions in systematics, micro-evolution, and speciation. The findings bolster the emerging field of phylogenomics and broadly impact future research into the genetic basis of coloration in vertebrates.