<p> Key to understanding the transition that vertebrates made from water to land is determining the developmental and genomic bases for the changes. New bioinformatic tools provide an opportunity to automate the discovery, broaden the number of, and provide an evidence-based ranking for potential candidate genes. I sought to explore this potential for the fin/limb transition, using the substantial genetic and phenotypic data available in model organism databases. Model organism data was used to hypothesize candidate genes for the fin/limb transition. In addition, 131 fin/limb candidate genes from the literature were extracted and used as a basis for comparison with candidates from the model organism databases. Additionally, seven genes specific to limb and 24 genes specific to fin were identified as future fin/limb transition candidates.</p>

<p> Lipid-producing microalgae are a feedstock for commercial products such as nutritional supplements, aquatic animal feed, and biofuels. Unlike most algal phyla, the diatoms (Bacillariophyta) characteristically produce storage lipids throughout their entire lifecycle. In this study, lipids were extracted via chloroform-methanol and quantified as percent dry weight, &mgr;g/mL, and pg/100 &mgr;m³ and then analyzed for a phylogenetic signal by comparing the variability between lineages to the variability within lineages for each metric. These ten taxa were then paired with data gathered from the literature and examined for a phylogenetic signal using previously described methods. In the first analysis, there was greater variability between than within lineages during stationary growth when using percent dry weight as a metric. In the second analysis, a statistically significant phylogenetic signal was detected for nutrient-deplete growth experiments when examining the genus-level phylogeny (P = 0.013).</p>

<p> Historical biogeography has a diversity of methods for inferring ancestral geographic ranges on phylogenies, but many of the methods have conflicting assumptions, and there is no common statistical framework by which to judge which models are preferable. Probabilistic modeling of geographic range evolution, pioneered by Ree and Smith (2008, <i>Systematic Biology</i>) in their program LAGRANGE, could provide such a framework, but this potential has not been implemented until now. </p><p> I have created an R package, "BioGeoBEARS," described in chapter 1 of the dissertation, that implements in a likelihood framework several commonly used models, such as the LAGRANGE Dispersal-Extinction-Cladogenesis (DEC) model and the Dispersal-Vicariance Analysis (DIVA, Ronquist 1997, <i> Systematic Biology</i>) model. Standard DEC is a model with two free parameters specifying the rate of "dispersal" (range expansion) and "extinction" (range contraction). However, while dispersal and extinction rates are free parameters, the cladogenesis model is fixed, such that the geographic range of the ancestral lineage is inherited by the two daughter lineages through a variety of scenarios fixed to have equal probability. This fixed nature of the cladogenesis model means that it has been indiscriminately applied in all DEC analyses, and has not been subjected to any inference or formal model testing. </p><p> BioGeoBEARS also adds a number of features not previously available in most historical biogeography software, such as distance-based dispersal, a model of imperfect detection, and the ability to include fossils either as ancestors or tips on a time-calibrated tree. </p><p> Several important conclusions may be drawn from this research. First, formal model selection procedures can be applied in phylogenetic inferences of historical biogeography, and the relative importance of different processes can be measured. These techniques have great potential for strengthening quantitative inference in historical biogeography. No longer are biogeographers forced to simply assume, consciously or not, that some processes (such as vicariance or dispersal) are important and others are not; instead, this can be inferred from the data. Second, founder-event speciation appears to be a crucial explanatory process in most clades, the only exception being some intracontinental taxa showing a large degree of sympatry across widespread ranges. This is not the same thing as claiming that founder-event speciation is the <i>only</i> important process; founder event speciation as the only important process is inferred in only one case (<i>Microlophus</i> lava lizards from the Galapagos). The importance of founder-event speciation will not be surprising to most island biogeographers. However, the results are important nonetheless, as there are still some vocal advocates of vicariance-dominated approaches to biogeography, such as Heads (2012, <i>Molecular Panbiogeography of the Tropics</i>), who allows vicariance and range-expansion to play a role in his historical inferences, but explicitly excludes founder-event speciation <i> a priori.</i> The commonly-used LAGRANGE DEC and DIVA programs actually make assumptions very similar to those of Heads, even though many users of these programs likely consider themselves dispersalists or pluralists. Finally, the inclusion of fossils and imperfect detection within the same likelihood and model-choice framework clears the path for integrating paleobiogeography and neontological biogeography, strengthening inference in both. </p><p> Model choice is now standard practice in phylogenetic analysis of DNA sequences: a program such as ModelTest is used to compare models such as Jukes-Cantor, HKY, GTR+I+G, and to select the best model before inferring phylogenies or ancestral states. It is clear that the same should now happen in phylogenetic biogeography. BioGeoBEARS enables this procedure. Perhaps more importantly, however, is the potential for users to create and test new models. Probabilistic modeling of geographic range evolution on phylogenies is still in its infancy, and undoubtedly there are better models out there, waiting to be discovered. It is also undoubtedly true that different clades and different regions will favor different processes, and that further improvements will be had by linking the evolution of organismal traits (e.g., loss of flight) with the evolution of geographic range, within a common inference framework. In a world of rapid climate change and habitat loss, biogeographical methods must maximize both flexibility and statistical rigor if they are to play a role. This research takes several steps in that direction. </p><p> BioGeoBEARS is open-source and is freely available at the Comprehensive R Archive Network (http://cran.r-project.org/web/packages/BioGeoBEARS/index.html). A step-by-step tutorial, using the <i>Psychotria</i> dataset, is available at PhyloWiki (http://phylo.wikidot.com/biogeobears). </p><p> (Abstract shortened by UMI.)</p>

<p> Human development and health involves the complex and coordinated regulation of gene expression across diverse tissues. Gene regulation is therefore an essential process in human biology. In the field of human genetics, this has only become more apparent as genomic technologies have made genome-wide surveys of genetic variation underlying human traits possible. In my thesis work, I studied the impact of variation in gene regulation on human traits from three distinct perspectives of human genetics. I first examined the contribution of gene regulation to human disease susceptibility by combining gene expression data with a genome-wide association study to identify novel asthma susceptibility candidate genes. I then studied the effects of depleting specific transcription factors from the cell on downstream gene expression by incorporating gene expression data (following cellular depletion of those factors) with genomic transcription factor binding data. Finally, I considered the role of gene regulation in human evolution by integrating RNA-seq data collected in human, chimpanzee, and rhesus macaque lymphoblastoid cell lines with promoter reporter assays conducted in the same lines. Throughout this work, I have synthesized multiple genomic data sets and multiple distinct sub-disciplines of human genetics in order to arrive at a unified view of the role of gene regulation in determining human traits.</p>

Thesis (Ph.D.)--Indiana University, Dept. of Biology, 2009. / Title from PDF t.p. (viewed on Jul 20, 2010). Source: Dissertation Abstracts International, Volume: 70-12, Section: B, page: 7343. Adviser: Justin P. Kumar.

<p> Interpreting the taxonomic and behavioral implications of variation in the inferred limb proportions of fossil hominin taxa is contingent upon assessing how much variation exists in extant primate taxa and, by extension, how much of that variation is associated differences in their locomotor behaviors. However, the majority of evidence linking limb proportions to behavior in extant primates is based on taxonomically-restricted samples, or on species means as opposed to individual values, or does not account for field observations that capture the complexity of locomotor behavior in a primate taxon (see Napier &amp; Napier, 1967; Fleagle, 1988; see also Preuschoft, 2002). With regards to extinct taxa, the problem is compounded by a necessary reliance on relatively few associated skeletons, most of which are incomplete, or fragmented or both. </p><p> This thesis addresses the aforementioned issues using a) multivariate methods to quantify the relationships between limb proportions and behavioral repertoires in extant anthropoids; b) machine-learning methods to select relevant extant models with which to interpret the limb proportions of extinct taxa; and c) resampling methods to evaluate hypotheses regarding major adaptive shifts in inferred locomotor behavior.</p><p>

abstract: Evolution is the foundation of biology, yet it remains controversial even among college biology students. Acceptance of evolution is important for students if we want them to incorporate evolution into their scientific thinking. However, students’ religious beliefs are a consistent barrier to their acceptance of evolution due to a perceived conflict between religion and evolution. Using pre-post instructional surveys of students in introductory college biology, Study 1 establishes instructional strategies that can be effective for reducing students' perceived conflict between religion and evolution. Through interviews and qualitative analyses, Study 2 documents how instructors teaching evolution at public universities may be resistant towards implementing strategies that can reduce students' perceived conflict, perhaps because of their own lack of religious beliefs and lack of training and awareness about students' conflict with evolution. Interviews with religious students in Study 3 reveals that religious college biology students can perceive their instructors as unfriendly towards religion which can negatively impact these students' perceived conflict between religion and evolution. Study 4 explores how instructors at Christian universities, who share the same Christian backgrounds as their students, do not struggle with implementing strategies that reduce students' perceived conflict between religion and evolution. Cumulatively, these studies reveal a need for a new instructional framework for evolution education that takes into account the religious cultural difference between instructors who are teaching evolution and students who are learning evolution. As such, a new instructional framework is then described, Religious Cultural Competence in Evolution Education (ReCCEE), that can help instructors teach evolution in a way that can reduce students' perceived conflict between religion and evolution, increase student acceptance of evolution, and create more inclusive college biology classrooms for religious students. / Dissertation/Thesis / Doctoral Dissertation Biology 2018

<p> Natural selection, the driving force behind evolution, acts on individual phenotypes. Phenotypes are the result of an individual&rsquo;s genotype, but the development from genotype to phenotype is not always accurate and precise. Developmental instability (DI: random perturbations in the microenvironment during development) can result in a phenotype that misses its genetic target. In the current study I assert that developmental instability may itself be an evolvable trait. Here I present evidence for DI&rsquo;s heritability, selectability, and phenotypic variation in the form of empirical data and evidence from the literature from the years 2006 through 2016. Phenotypic variation contributed by DI was estimated using fluctuating asymmetry and was found to contribute up to 60% of the phenotypic variation in certain trait types. I suggest that selection against developmental instability in some traits may result in higher evolvabilities (i.e., rates of evolution) for those traits or for entire taxonomic groups.</p><p>

Gnathostome novelties include jaws, paired appendages, and true teeth. Dlx genes encode transcription factors indispensable for embryonic development of these novelties. Gnathostomes possess at least 6 Dlx genes organized in 3 bi-gene clusters, a physical arrangement which is proposed to affect their expression though shared enhancer elements. I studied the Dlx genes of Cyclostomes, the evolutionary sister group of Gnathostomes. I identified 4 novel members of the Dlx gene family in hagfish (Eptatretus stoutii), and confirmed the presence of 6 Dlx genes in lamprey ( Petromyzon marinus). I found that Cyclostomes have only 1 gene cluster and several orphan genes. This lack of conserved arrangement is coincident with an absence of conserved Dlx enhancers. Irregardless, some regulatory conservation is still apparent as lamprey non-coding DNA is able to drive dlx specific expression patterns of reporter genes in zebrafish. Therefore Cyclostome and Gnathostome Dlx are both organized and regulated differently. The causes and consequences of these changes in Chordate evolution are discussed.

<p> The earliest-diverged multicellular animals are decentralized organisms capable of growing to indeterminate sizes and highly variable morphologies. These organisms must coordinate activity among their constitutive cells at the scale of the organism in order to to leverage the benefits of multicellularity, and must do so using decentralized mechanisms that are robust to uncertainty in size and shape. This thesis investigates how coordination within the Placozoa&mdash;arguably the simplest animals&mdash;scales with organism size, quantifies the extent to which different developmental processes affect size regulation, and creates a framework for measuring morphological variability in what had been considered amorphous animals. In Chapter 1 I develop a method by which one can measure coordination and information propagation within an animal's body plan, and investigate how this propagation is affected by changes in size. I argue that such animals are poised at criticality, with evidence presented to suggest that this facilitates optimal information transmission, but that the physical constraints of multicellularity create a size-coordination trade-off in such decentralized organisms. The presence of size-induced trade-offs brings forth the question of how size is regulated, which in Placozoa occurs through growth and asexual fission. In Chapter 2 I investigate whether size is regulated in response to changing environmental nutrient conditions and find that animals adjust their sizes to match their environments. I further find that this change comes about primarily due to changing dynamics of growth rather than fission, and identify that growth is highly dependent on nutrient conditions, but find evidence that asexual fission could be an emergent phenomenon of poor coordination beyond certain sizes. Finally, in Chapter 3 I investigate the morphological variability in Placozoa and find evidence for allometric growth in such animals. In addition, Chapter 3 sets the groundwork for future comparative morphological studies between individuals and for behavioral stereotyping by developing a size and rotation invariant shape representation, which I use to identify the presence of idiosyncratic morphologies. I close the thesis with some remarks regarding future directions in exploring the effects of scaling on coordination, morphology, and behavior in this small yet evolutionarily significant Metazoa phylum.</p><p>