Life Sciences Commons^™

I Also Survived A Debate With A Creationist (With Reflections On The Perils Of Democratic Information), Kelly C. Smith

Kelly C Smith

A personal narrative is presented which explores the author's experience of debating with a creationist.

Development Of An Interactive Course Module: "Teaching And Learning Molecular Basis Of Evolution To Human Body", Soma Mukhopadhyay, Rachel Bishop, Brittany Blocker

Soma Mukhopadhyay Ph.D.

Today’s youth expect to use technology in every aspect of their lives, including their education. Instead of being challenged by their considerable skills, educators should embrace the technology and use it to make the classroom experience more enjoyable for students, thereby improving learning outcomes. Evolution is no different – students must know the basics of evolution in order to be well-read members of society, and technology can help the students learn. The study of evolution today is incredibly interesting, particularly with new evidence coming to light almost daily. Human evolution, in particular, is the subject of copious amounts of research. …

Were Neandertal Humeri Adapted For Spear Thrusting Or Throwing? A Finite Element Study, Michael Anthony Berthaume

Masters Theses

An ongoing debate concerning Neandertal ecology is whether or not they utilized long range weaponry. The anteroposteriorly expanded cross-section of Neandertal humeri have led some to argue they thrusted their weapons, while the rounder cross-section of Late Upper Paleolithic modern human humeri suggests they threw their weapons. We test the hypothesis that Neandertal humeri were built to resist strains engendered by thrusting rather than throwing using finite element models of one Neandertal, one Early Upper Paleolithic (EUP) human and three recent human humeri, representing a range of cross-sectional shapes and sizes. Electromyography and kinematic data and articulated skeletons were used …

Characterization Of The Transcriptome, Nucleotide Sequence Polymorphism, And Natural Selection In The Desert Adapted Mouse Peromyscus Eremicus, Matthew D. Macmanes, Michael B. Eisen

Molecular, Cellular & Biomedical Sciences

As a direct result of intense heat and aridity, deserts are thought to be among the most harsh of environments, particularly for their mammalian inhabitants. Given that osmoregulation can be challenging for these animals, with failure resulting in death, strong selection should be observed on genes related to the maintenance of water and solute balance. One such animal, Peromyscus eremicus, is native to the desert regions of the southwest United States and may live its entire life without oral fluid intake. As a first step toward understanding the genetics that underlie this phenotype, we present a characterization of the …

Ecological Niches, Species Distributions, And Biogeographic Processes In Rodents On Neotropical Sky Islands, Mariano Soley

Dissertations, Theses, and Capstone Projects

This dissertation focused on the methodological and theoretical improvement of correlative ecological niche models (ENMs) to better understand the processes governing species distributions and associated evolutionary divergence in rodents inhabiting mesic conditions in the Neotropics. Focusing on a widespread rodent from northern South America (Heteromys anomalus), in the first chapter I proposed and tested a methodological approach to surmount the challenge of incorporating environmental information from the margins of species geographic ranges into ENMs. In so doing, I argue how populations that exist on the borders of species' local ranges (spatial margins) can lead to exaggerated estimates of their niches …

Herbert W. Conn: Formative Decades Of Microbiology And Evolutionary Biology, Frederick M. Cohan, Alexa Boesel

Frederick M. Cohan

Herbert W. Conn (1859–1917) made outstanding contributions to both microbiology and evolutionary biology, reflecting his intellectual command of several biological disciplines. Conn endeavored to make the unseen world of microbes familiar, real, and consequential to members of the general public. He presciently considered the role of bacteria in our own bodies, describing them as being both harmful and beneficial to our health. He also contributed to our understanding of the concept of species, how they originate, and what those ideas might mean in terms of bacterial speciation. In Conn’s spirit, microbial ecologists studying speciation eschew the “species” taxa of bacterial …

Acceptance Of Evolution By America’S Educators Of Prospective Teachers, Guillermo Paz-Y-Miño-C, Avelina Espinosa

New England Science Public: Series Evolution

Paz-y-Miño-C G & Espinosa A. 2014. Acceptance of Evolution by America’s Educators of Prospective Teachers. New England Science Public: Series Evolution 2(1): 1-92 (ISSN: 2326-0971). In NESP Series Evolution Vol 2 No 1, Paz-y-Miño-C and Espinosa use the conceptual framework of the Incompatibility Hypothesis (i.e. science/evolution and belief in supernatural causation are incompatible) to document the patterns of acceptance of evolution of 495 Educators of Prospective Teachers affiliated with 281 colleges and universities widely distributed in 4 regions, 9 divisions, and 50 states in the United States. These higher-education professionals (65% PhD-, 22% doctorate-holders) were polled in five areas: (i) …

A Homogenizing Process Of Selection Has Maintained An 'Ultra-Slow' Acetylation Nat2 Variant In Humans, Blandine Patillon, Pierre Luisi, Estella S. Poloni, Sotiria Boukouvala, Pierre Darlu, E. Genin, Audrey Sabbagh

Human Biology Open Access Pre-Prints

N-acetyltransferase 2 (NAT2) is an important enzyme involved in the metabolism of a wide spectrum of naturally occurring xenobiotics, including therapeutic drugs and common environmental carcinogens. Extensive polymorphism in NAT2 gives rise to a wide interindividual variation in acetylation capacity which influences individual susceptibility to various drug-induced adverse reactions and cancers. Striking patterns of geographic differentiation have been described for the main slow acetylation variants of the NAT2 gene, suggesting the action of natural selection at this locus. In the present study, we took advantage of the whole-genome sequence data available from the 1000 Genomes project to investigate the …

The Reproduction And Ecology Of Hypericum Edisonianum: An Endangered Florida Endemic, Warren G. Abrahamson Ii, Sam P. Vander Kloet

Warren G. Abrahamson, II

The reproduction and ecology of the narrow endemic and Florida endangered shrub Hypericum edisonianum (Edison’s St. John's Wort) was investigated through field and greenhouse studies. Hypericum edisonianum exhibits a number of traits common to rare and geographically limited plant species including heavy reliance on clonal propagation to maintain local stands; passive seed dispersal resulting in a near-parent seed shadow; limited numbers of genetically unique individuals in its isolated seasonal-pond habitat; and likely self-incompatibility. In the field study, most flowers were produced by a small subset of the monitored ramets. Indeed, three ramets belonging to a single genetic individual accounted for …

Phylogenetics And Mating System Evolution In The Southern South American Valeriana (Valerianaceae), Lauren A. Gonzalez

University of New Orleans Theses and Dissertations

Species of Valerianaceae in South America represent one of the best examples of rapid diversification on a continental scale. The phylogeny of Valerianaceae has received a lot of attention within the last 10 years, but relationships among the South American species are fairly unresolved. Results from previous studies have not been well resolved with traditional genetic markers, most likely due to its recent and rapid radiation. Species in this clade exhibit a variety mating systems and inflorescence types. For the first part of this research I used several traditional plastid markers, and 3 new low copy nuclear markers to better …

Linking Dna Polymorphisms And Populations' Evolutionary History, Ivan Juric

Doctoral Dissertations

This dissertation seeks to provide an understanding of how different evolutionary forces can affect the DNA polymorphism patterns. I use a combination of individual-based simulations and analytical to examine polymorphism patterns during divergence with gene flow, hybridization and territory expansion. In the first chapter, I show how during divergence with gene flow the appearance and maintenance of “Genomic Islands of Divergence” can be explained using standard population genetics terminology, thus removing some of the confusion recently introduced in that literature. In the second chapter I derive the expressions for the distribution of coalescent times and pairwise differences in a hybridization …

Quantitative Characterization Of Proteins And Post-Translational Modifications In Complex Proteomes Using High-Resolution Mass Spectrometry-Based Proteomics, Zhou Li

Doctoral Dissertations

Mass spectrometry-based proteomics is focused on identifying the entire suite of proteins and their post-translational modifications (PTMs) in a cell, organism, or community. In particular, quantitative proteomics measures abundance changes of thousands of proteins among multiple samples and provides network-level insight into how biological systems respond to environmental perturbations. Various quantitative proteomics methods have been developed, including label-free, metabolic labeling, and isobaric chemical labeling. This dissertation starts with systematic comparison of these three methods, and shows that isobaric chemical labeling provides accurate, precise, and reproducible quantification for thousands of proteins. Based on these results, we applied this approach to characterizing …

Biogeographical Patterns, Ecological Drivers, And Evolutionary Mechanisms Of Plant Invasions, Rafael Dudeque Zenni

Doctoral Dissertations

Understanding and predicting organisms’ responses to novel environments is a key issue for global change biology. In this dissertation, I study biogeographical patterns of plant invasions in Brazil, explore some of their ecological drivers, and disentangle the gene-level mechanisms that cause introduced organisms to become successful or failed invaders. I found that, for the invasive flora of Brazil, species were not introduced to new regions at random and that a species’ reason for introduction and continent of origin were associated. Asian ornamental and African forage plants are overrepresented, and two families (Poaceae and Fabaceae) dominate the invasive flora of Brazil. …

Push Me – Pull You: Experimental Biomechanics Of Immobile Suspension Feeders On Soft Substrates, Roy Plotnick, Benjamin Dattilo, Joshua Corrie, Daniel Piquard, Jennifer Bauer

Benjamin F. Dattilo

Immobile suspension feeders on soft substrates (ISOSS; Thayer 1979) although rare in modern marine habitats, were relatively common in the Paleozoic. Numerous Paleozoic taxa have been interpreted as dwelling on soft unconsolidated sediments and possessing morphologic features that either anchor them to the sea floor (e.g., crinoid holdfasts) or prevent them from sinking in (strophomenid brachiopods). Thayer (1975) reviewed the morphologic adaptations for forms living on soft-muddy bottoms and provided a quantitative expression of the static stresses involved. The same quantitative expression can also be used to describe the forces involved in anchoring. With the exception of Leighton and Savarese …

Dinosaur Tracksites Of The Paluxy River Valley (Glen Rose Formation, Lower Cretaceous), Dinosaur Valley State Park, Somervell County, Texas., James O. Farlow, Mike O'Brien, Glenn J. Kuban, Benjamin F. Dattilo, K. T. Bates, Peter L. Falkingham, L. Pinuela, Amanda Rose, A. Freels, C. Kumagai, Courtney Libben, Justin Smith, J. Whitcraft

Benjamin F. Dattilo

In 1940 R.T. Bird of the American Museum of Natural History collected segments of a sauropod and a theropod trackway from a site in the bed (Glen Rose Formation; Lower Cretaceous) of the Paluxy River, in what is now Dinosaur Valley State Park (Glen Rose, Texas, USA). However, Bird left undocumented thousands of other dinosaur footprints from this and other Paluxy tracksites. In 2008 and 2009 our international team carried out fieldwork to create detailed photomosaics of extant Paluxy tracksites, using GIS technology to combine these with historic maps and photographs. We also made photographs, tracings, LiDAR images, and measurements …

The Curse Of Rafinesquina: Negative Taphonomic Feedback Exerted By Strophomenid Shells On Storm-Buried Lingulids In The Cincinnatian (Katian, Ordovician) Series Of Ohio, Rebecca Freeman, Benjamin Dattilo, Aaron Morse, Michael Blair, Steve Felton, John Pojeta

Benjamin F. Dattilo

Thousands of lingulid brachiopods were found clustered beneath hundreds of individual valves of the strophomenid brachiopod Rafinesquina in the Upper Ordovician of Ohio. This association suggested a relationship between the two brachiopods, but the nature of this relationship was unclear. We utilized serial thin sectioning to examine these brachiopods and to determine the origin of the bed in which they were found. Sedimentary structures, mixed taphonomies, and stratigraphic and paleogeographic setting suggest that the lingulids occupied a hiatal concentration that had previously been reworked, but not significantly transported, by tropical storms. The final burial event was a storm that exhumed …

The Orientation Of Strophomenid Brachiopods On Soft Substrates, Roy Plotnick, Benjamin Dattilo, Daniel Piquard, Jennifer Bauer, Joshua Corrie

Benjamin F. Dattilo

Strophomenid brachiopods have long been interpreted as ‘‘snowshoe’’ strategists, with their flattened concavoconvex valves providing resistance to foundering in very soft sediments. There has been a sharp difference of opinion in whether the shells were oriented with their convex or their concave surface in contact with the sediment. This study, along with independent evidence from sedimentology, ichnology, and morphology, indicates that the strophomenids lived with their shells concave down (convex up). Experiments indicate the force required to push shells into soft cohesive muds is much greater for the convex up than for the convex down orientation. Forces also increase with …

The Brachiopod Trap: What Their Oldest (Upper Ordovician, Ohio) Failed Escape Burrows Tell Us About The Evolution Of Burrowing In Lingulids, Rebecca Freeman, Benjamin Dattilo, Aaron Morse, Michael Blair, Bryan Utesch, Steve Felton, John Pojeta

Benjamin F. Dattilo

Infaunal organisms living in shallow marine settings are vulnerable to exhumation during storms or entombment by storm-deposited sediments. Cambrian­–Early Ordovician lingulids included epifaunal as well as possible infaunal forms. However, many epifaunal forms became extinct during the Middle Ordovician, and Late Ordovician lingulids were similar in their infaunal habits and marginal habitats. Modern infaunal lingulids are able to reorient themselves after burial in sediments, but it is unclear when this ability evolved. Initial burrowing of juvenile lingulids, as well as re-burrowing of exhumed modern lingulids involves digging downwards and then back up in a u-shape, but successful escape burrowing involves …

The Fossilized Birth–Death Process For Coherent Calibration Of Divergence-Time Estimates, Tracy A. Heath, John P. Huelsenbeck, Tanja Stadler

Tracy Heath

Comparative Population Assessments Of Nautilus Sp. In The Philippines, Australia, Fiji, And American Samoa Using Baited Remote Underwater Video Systems, Gregory Jeff Barord, Frederick Dooley, Andrew Dunstan, Anthony Ilano, Karen N. Keister, Heike Neumeister, Thomas Preuss, Shane Schoepfer, Peter D. Ward

Publications and Research

The extant species of Nautilus and Allonautilus (Cephalopoda) inhabit fore-reef slope environments across a large geographic area of the tropical western Pacific and eastern Indian Oceans. While many aspects of their biology and behavior are now well-documented, uncertainties concerning their current populations and ecological role in the deeper, fore-reef slope environments remain. Given the historical to current day presence of nautilus fisheries at various locales across the Pacific and Indian Oceans, a comparative assessment of the current state of nautilus populations is critical to determine whether conservation measures are warranted. We used baited remote underwater video systems (BRUVS) to make …

Early Back-To-Africa Migration Into The Horn Of Africa, Jason A. Hodgson, Connie J. Mulligan, Ali Al-Meeri, Ryan L. Raaum

Publications and Research

Genetic studies have identified substantial non-African admixture in the Horn of Africa (HOA). In the most recent genomic studies, this non-African ancestry has been attributed to admixture with Middle Eastern populations during the last few thousand years. However, mitochondrial and Y chromosome data are suggestive of earlier episodes of admixture. To investigate this further, we generated new genome-wide SNP data for a Yemeni population sample and merged these new data with published genome-wide genetic data from the HOA and a broad selection of surrounding populations. We used multidimensional scaling and ADMIXTURE methods in an exploratory data analysis to develop hypotheses …

The Effect Of Population History On Hominoid Intraspecific Cranial Shape Diversity: Combining Population Genetic And 3d Geometric Morphometric Data, Julia Marie Zichello

Dissertations, Theses, and Capstone Projects

Cranial shape diversity within hominoids has been previously studied with the aim of understanding how levels of diversity in extant species compare with extinct hominin specimens. This dissertation addresses the question of why cranial shape diversity differs among extant hominoids. Levels of intraspecific cranial shape diversity are highly varied among hominoids. For example, Sumatran orangutan cranial shape diversity is more than twice that of all living humans. Here, the population history of each species, or sub-species, is considered as a force potentially structuring phenotypic variation. It is already well established that population history has shaped patterns of modern human cranial …

Early Song Discrimination By Nestling Sparrows In The Wild, Daizaburo Shizuka

School of Biological Sciences: Faculty Publications

Songs play an important role in premating isolation in birds. However, when songs are learned, expe- rience with both conspecific and heterospecific songs in early life could lead to the development of both mixed songs and mixed preferences. One way that such learning errors can be prevented is if birds can discriminate between songs of different species prior to learning and preferentially memorize conspe- cific songs. Prior captive studies have shown that white-crowned sparrows, Zonotrichia leucophrys, are able to discriminate songs early in the process of song memorization, after about 10 days since hatching. I studied early song discrimination in …

The Evolution Of Respiratory O2/No Reductases: An Out-Of-The-Phylogenetic-Box Perspective, Anne-Lise Ducluzeau, Barbara Schoepp-Cothenet, Robert Van Lis, Frauke Baymann, Michael J. Russell, Wilfgang Nitschke

Department of Biochemistry: Faculty Publications

Complex life on our planet crucially depends on strong redox disequilibria afforded by the almost ubiquitous presence of highly oxidizing molecular oxygen. However, the history of O₂-levels in the atmosphere is complex and prior to the Great Oxidation Event some 2.3 billion years ago, the amount of O₂ in the biosphere is considered to have been extremely low as compared with present-day values. Therefore the evolutionary histories of life and of O₂-levels are likely intricately intertwined. The obvious biological proxy for inferring the impact of changing O₂-levels on life is the evolutionary history …

Photosynthetic Thermal Tolerance And Recovery To Short Duration Temperature Stress In Desert And Montane Plants: A Comparative Study, David William Gallagher

Master's Theses

• Climate change models predict an increase in frequency and amplitude of extreme weather events, including heat waves. To better predict how the composition and distribution of plant assemblages might respond to these changes in temperature, it is important to understand how species currently respond to these extremes. Photosynthetic thermal tolerance (T₂₅)and photosynthetic recovery (RT₂₅) were quantified in 27 species. We also studied the relationships between T₂₅, RT₂₅ and leaf mass per area (LMA). Leaf temperature was also monitored in the field.
• Leaves used in this study were collected from two distinct …

Joint Phenotypes, Evolutionary Conflict And The Fundamental Theorem Of Natural Selection, David C. Queller

Biology Faculty Publications & Presentations

Multiple organisms can sometimes affect a common phenotype. For example, the portion of a leaf eaten by an insect is a joint phenotype of the plant and insect and the amount of food obtained by an offspring can be a joint trait with its mother. Here, I describe the evolution of joint phenotypes in quantitative genetic terms. A joint phenotype for multiple species evolves as the sum of additive genetic variances in each species, weighted by the selection on each species. Selective conflict between the interactants occurs when selection takes opposite signs on the joint phenotype. The mean fitness of …

A Male Spider’S Ornamentation Polymorphism Maintained By Opposing Selection With Two Niches, Bo Deng, Alex Estes, Brett Grieb, Douglas Richard, Brittney Hinds, Eileen Hebets

Eileen Hebets Publications

The Levene mechanism to maintain genotypic polymorphism by opposing selection on genotypes in multiple niches was proposed 60 years ago, and yet no systems were found to satisfy the mechanisms rather restrictive conditions. Reported here is such an example that a wolf spider population lives in a habitat of mixed rocks and leafy litter for which the females are phenotypically indistinguishable and the males have two distinct phenotypes subject to opposing selection with respect to the substrates. Census data is best-fitted to a population genetics model of the Levene type. A majority of the best fit support polymorphism, with many …

Adaptive Radiation Along A Benthic/Pelagic Ecological Axis In North America’S Most Diverse, Endemic Clade Of Freshwater Fishes, Phillip Ray Hollingsworth Jr.

Doctoral Dissertations

Eastern North America is unparalleled throughout the temperate world in terms of freshwater fish biodiversity. A monophyletic group of approximately 250 cyprinid fishes, known as the open posterior myodome (OPM) clade, dominates the fish species richness in the freshwater ecosystems of this region. In this dissertation, I explore the influence of eco-evolutionary divergence along a benthic/pelagic habitat axis on the generation of this hyper-diverse group of fishes. My three chapters work synergistically to address the question: Did a historical shift from benthic to pelagic habitats by OPM cyprinids represent the invasion of an open adaptive zone and result in the …

Inter-And Intra-Population Variability Across The Transcriptome Of Lake Baikal’S Endemic Copepod With Ramifications For Adapting To Climate Change, Larry L. Bowman Jr

Electronic Theses and Dissertations

The future of Lake Baikal’s biodiversity is uncertain in response to climate change. Unlike its diverse benthos, Lake Baikal’s zooplankton is species poor, with up to 96% of its biomass being composed of a single Calanoid copepod species, Epischura baikalensis. This study characterizes the genetic differentiation and differential gene expression of E. baikalensis. Using partial-transcriptome sequences obtained by 454 Rosche and Illumina sequencing technologies, the genetic differentiation at inferred single nucleotide polymorphism (SNP) sites and differential gene expression in populations sampled from various parts of the lake were analyzed. The functional genomics of genes showed significant differential …

Evolutionary Pressures On Primate Intertemporal Choice, Jeffrey R. Stevens

Department of Psychology: Faculty Publications

From finding food to choosing mates, animals must make intertemporal choices that involve fitness benefits available at different times. Species vary dramatically in their willingness to wait for delayed rewards. Why does this variation across species exist? An adaptive approach to intertemporal choice suggests that time preferences should reflect the temporal problems faced in a species' environment. Here, I use phylogenetic regression to test whether allometric factors (relating to body size), relative brain size, and social group size predict how long 13 primate species will wait in laboratory intertemporal choice tasks. Controlling for phylogeny, a composite allometric factor that includes …