Life Sciences Commons^™

A Novel Body Coloration Phenotype In Anolis Sagrei: Implications For Physiology, Fitness, And Predation, Yasmeen Erritouni, Beth Reinke, Ryan Calsbeek

Beth Reinke

Repeats Of Unusual Size In Plant Mitochondrial Genomes: Identification, Incidence And Evolution, Emily L. Wynn, Alan C. Christensen

School of Biological Sciences: Faculty Publications

Plant mitochondrial genomes have excessive size relative to coding capacity, a low mutation rate in genes and a high rearrangement rate. They also have abundant non-tandem repeats often including pairs of large repeats which cause isomerization of the genome by recombination, and numerous repeats of up to several hundred base pairs that recombine only when the genome is stressed by DNA damaging agents or mutations in DNA repair pathway genes. Early work on mitochondrial genomes led to the suggestion that repeats in the size range from several hundred to a few thousand base pair are underrepresented. The repeats themselves are …

Long-Term Experimental Hybridisation Results In The Evolution Of A New Sex Chromosome In Swordtail Fish, Paolo Franchini, Julia C. Jones, Peiwen Xiong, Susanne Kneitz, Zachariah Gompert, Wesley C. Warren, Ronald B. Walter, Axel Meyer, Manfred Schartl

Biology Faculty Publications

The remarkable diversity of sex determination mechanisms known in fish may be fuelled by exceptionally high rates of sex chromosome turnovers or transitions. However, the evolutionary causes and genomic mechanisms underlying this variation and instability are yet to be understood. Here we report on an over 30-year evolutionary experiment in which we tested the genomic consequences of hybridisation and selection between two Xiphophorus fish species with different sex chromosome systems. We find that introgression and imposing selection for pigmentation phenotypes results in the retention of an unexpectedly large maternally derived genomic region. During the hybridisation process, the sex-determining region of …

Effects Of Evolution On Laboratory Sublines Of Myxococcus Xanthus Dk1622, Mackenzie Ryan, Francesca Scribano, Kimberly Murphy

Celebration of Learning

Microbes have served as effective models for studying evolution because of their ability to be easily replicated, stored, and manipulated. Myxococcus xanthus is a soil bacterium that has served as a model organism in many laboratories. The unique social and motile behaviors exhibited by this bacterium make it ideal for phenotypic assays. A wild-type strain of M. xanthus, DK1622, has been distributed to laboratories across the United States and therefore we now have DK1622 sublines. The genomes of a number of these sublines have been sequenced and their social and motile phenotypes have been analyzed. When nine of these sublines …

Hypoplectrus Liberte, A New And Endangered Microendemic Hamlet From Haiti (Teleostei: Serranidae), Benjamin C. Victor, Kenneth W. Marks

Marine & Environmental Sciences Faculty Articles

The hamlets of the genus Hypoplectrus comprise a species flock of about 20 species found on coral reefs of the tropical western Atlantic Ocean, distinguished by complex color patterns and sharing mitochondrial DNA haplotypes within the Caribbean Sea (Gulf of Mexico and Florida-centered species are about 3% divergent in the COI marker). The species show a variety of biogeographic patterns, from widespread common species to relatively rare species limited to small parts of the Greater Caribbean region. We describe here a distinctive striped morph of barred hamlet, apparently limited to Fort-Liberté Bay in northeastern Haiti, as the new species Hypoplectrus …

Achilles And The Tortoise: Some Caveats To Mathematical Modeling In Biology, Scott F. Gilbert

Biology Faculty Works

Mathematical modeling has recently become a much-lauded enterprise, and many funding agencies seek to prioritize this endeavor. However, there are certain dangers associated with mathematical modeling, and knowledge of these pitfalls should also be part of a biologist's training in this set of techniques. (1) Mathematical models are limited by known science; (2) Mathematical models can tell what can happen, but not what did happen; (3) A model does not have to conform to reality, even if it is logically consistent; (4) Models abstract from reality, and sometimes what they eliminate is critically important; (5) Mathematics can present a Platonic …

The Positive Effect Of Role Models In Evolution Instruction, Emily A. Holt, T. Heath Ogden, Susan L. Durham

Ecology Center Publications

Background: Previous research has identified numerous factors to explain why students have difficulty learning about evolution. Some of these factors include a student’s background (including their religion and major of study), the type of evolution instruction, and the inclusion of the nature of science (NOS) instruction. Sparse but more recent work has investigated the impact of a religious-scientist role model to help dampen perceptions of conflict between evolutionary science and worldview. We had two research goals: (1) to identify which of these factors influence students’ learning of evolution in post-secondary education; and (2) to describe the relationships among incoming …

Eco-Evolutionary Implications Of Environmental Change Across Heterogeneous Landscapes, Jared J. Homola

Electronic Theses and Dissertations

Species use a variety of mechanisms to adapt to environmental change. These range from spatially tracking optimal environments, to phenotypically plastic responses and evolutionary adaptation. Due to increases in anthropogenic influence on environments, characteristics of change such as their duration and magnitude are undergoing fundamental shifts away from the natural disturbance regimes that shaped species’ evolution. This dissertation uses empirical data and simulation models to examine the ecological and evolutionary consequences of environmental change across real, heterogeneous landscapes for multiple species, with an emphasis on anthropogenic changes. I used landscape genetics to evaluate the effects of urbanization on two native …

The Effect Of An Historical Geology Course On Students’ Attitudes Towards Science And Their Knowledge Of Deep Time As A Threshold To Their Knowledge Of Evolution, Allan Nolan

Dissertations

In America there exists a conflict between a small group of its citizens and the concept of evolution. Researchers have studied this conflict and the ways in which teachers might approach educational methodologies that not only address evolution in a sensitive manner, but also remain legally acceptable.

This research was designed to address teaching evolution in the context of deep time – the concept that time is vast and that geology and biology operate in a timescale of hundreds of millions to billions of years. In previous peer-reviewed works, it has been stated that deep time acts as a threshold …

The Crs Ekinds Research Initiative: Where We Have Been And Where We Are Headed From Here, Jean K. Lightner, Kevin Anderson

Proceedings of the International Conference on Creationism

The eKINDS research initiative began in 2016 in an effort to accelerate research on numerous outstanding questions related the diversification and speciation of plants and animals. The research encompasses three broad topics: a) identification of created kinds, b) identification of mechanisms that drive diversification and speciation within created kinds, and c) detailed analysis of individual created kinds in an attempt to propose a robust natural history that delineates key events as organisms reproduced and filled the earth following the time of the Flood.

As part of the eKINDS project, a new statistical tool is being developed to take advantage of …

Investigations On The Role Of The Immune System In Mammary Development And Maternal Immunity In The Marsupial, Monodelphis Domestica, Bethaney Fehrenkamp

Biology ETDs

All newborn mammals are highly dependent upon milk for nourishment and immune protection. This is especially true for marsupials, a lineage of mammals with a short gestation, limited placental development, and an increased reliance on an extended lactation period. Most newborn marsupials do not receive passive maternal immunity in utero and therefore are entirely dependent upon factors within the milk for immune protection until capable of mounting their own response. In this project we seek to characterize the complex lactation program utilized by marsupials, and seek greater understanding of the maternal role in the establishment of the developing immune system …

Ongoing Transposon-Mediated Genome Reduction In The Luminous Bacterial Symbionts Of Deep-Sea Ceratioid Anglerfishes, Tory Hendry, Lindsay L. Freed, Dana Fadera, Dante Fenolio, Tracey Sutton, Jose Lopez

Marine & Environmental Sciences Faculty Articles

Diverse marine fish and squid form symbiotic associations with extracellular bioluminescent bacteria. These symbionts are typically free-living bacteria with large genomes, but one known lineage of symbionts has undergone genomic reduction and evolution of host dependence. It is not known why distinct evolutionary trajectories have occurred among different luminous symbionts, and not all known lineages previously had genome sequences available. In order to better understand patterns of evolution across diverse bioluminescent symbionts, we de novo sequenced the genomes of bacteria from a poorly studied interaction, the extracellular symbionts from the “lures” of deep-sea ceratioid anglerfishes. Deep-sea anglerfish symbiont genomes are …

Evolutionary And Population Dynamics Of Crustaceans In The Gulf Of Mexico, Laura Timm

FIU Electronic Theses and Dissertations

Evolution occurs and can be conceptualized along a spectrum, bounded on one extreme by the relationships between deep lineages – such as phyla, classes, and orders – and on the other by the molecular dynamics of operational taxonomic units within a species, defined as population genetics. The purpose of this dissertation was to better understand the evolutionary and population dynamics of crustaceans within the Gulf of Mexico. In the second chapter of my dissertation, I provide a guide to best phylogenetic practice while reviewing infraordinal relationships within Decapoda, including the promise held by next-generation sequencing (NGS) approaches such as Anchored …

Modeling Stochastic Viral Evolution: A Multiscale Wright Fisher Model, Marco Hamins-Puertolas

Biology and Medicine Through Mathematics Conference

No abstract provided.

Geometry Of The Sample Frequency Spectrum And The Perils Of Demographic Inference, Zvi H. Rosen

Biology and Medicine Through Mathematics Conference

No abstract provided.

Digging Biomechanics In Geomyoid Rodents, Alexis Moore Crisp

UNLV Theses, Dissertations, Professional Papers, and Capstones

Subterranean digging behaviors provide opportunities for protection, access to prey, and predator avoidance for a diverse array of vertebrates, yet studies of the biomechanics of burrowing have been limited by the technical challenges of measuring kinetics and kinematics of animals moving within a substrate. Prior studies of burrowing have recorded a single axis of x-ray video and/or force. However, empirical observations show that burrowing is not restricted to a single axis or plane. I describe a new system called a ‘tunnel-tube’ for measuring 3D reaction force during burrowing. This tunnel-tube has two separate tubes, one ‘entry tube’ that has no …

Evolution Of Voltage-Gated Ion Channels, Kevin Gregory Bennett, Kevin Bennett

Master of Science in Integrative Biology Theses

Voltage-gated Ion Channels (VICs) form a superfamily of energy-independent membrane transporters that facilitate the transfer of charged sodium, calcium, and potassium ions across the cell membrane (Hodgkin & Huxley 1952). The channels contain a selective ion-conducting pore along with several other structural and gating features that come together to form a functional hetero- or homotetramer. A comprehensive phylogenetic study of all available proteins aimed at finding unknown distribution and illuminating evolutionary paths would be immensely useful in understanding relationships of structure, function, and organismal distribution. This phylogenetic analysis of VICs will be immensely useful in characterizing functional and structural distribution, …

Sequencing And Analysis Of Centromere Protein B In Wallaby And The Rapid Evolution Of The Centromere, Alexander Tedeschi

Honors Scholar Theses

Using a combination of Sanger sequencing and RNA-seq data, this project aims to determine the nucleotide and amino acid sequence of Centromere Protein B (CENP-B), an important protein involved in the assembly of the kinetochore protein complex at the centromere, in several species of marsupials, specifically wallabies. Despite their recent evolutionary history, these species have been shown to have surprisingly divergent centromeric DNA sequences. Through comparative analysis of these sequences, this project, along with analysis of several other CENPs, aims to determine if this divergence extends to the proteins closely associated with these sequences and possibly even further into the …

Hormonebase, A Population-Level Database Of Steroid Hormone Levels Across Vertebrates, Maren N. Vitousek, Michele A. Johnson, Jeremy W. Donald, C. D. Francis, M. J. Fuxjager, W. Goymann, M. Hau, Jerry F. Husak, Bonnie K. Kircher, R. Knapp, L. B. Martin, E. T. Miller, L. A. Schoenle, J. J. Uehling, T. D. Williams

Biology Faculty Research

Hormones are central regulators of organismal function and flexibility that mediate a diversity of phenotypic traits from early development through senescence. Yet despite these important roles, basic questions about how and why hormone systems vary within and across species remain unanswered. Here we describe HormoneBase, a database of circulating steroid hormone levels and their variation across vertebrates. This database aims to provide all available data on the mean, variation, and range of plasma glucocorticoids (both baseline and stress-induced) and androgens in free-living and un-manipulated adult vertebrates. HormoneBase (www.HormoneBase.org) currently includes >6,580 entries from 476 species, reported in 648 publications from …

Phylogeny And Evolutionary Genomics Of Non-Photosynthetic Diatoms, Anastasiia Onyshchenko

Graduate Theses and Dissertations

Diatoms are prolific photosynthesizers responsible for some 20% of global primary production. In real terms, the oxygen in one of every five breaths traces back to photosynthesis by marine diatoms. Among the tens of thousands of diatom species, a small handful of colorless diatom species in the genus Nitzschia have lost photosynthesis altogether and rely exclusively on extracellular organic carbon for growth. I used DNA sequence data to reconstruct the phylogeny of this group, and found that nonphotosynthetic diatoms are monophyletic, indicating that photosynthesis was lost just one time over the course of some 200 million years of diatom evolution. …

Hip Extensor Mechanics And The Evolution Of Walking And Climbing Capabilities In Humans, Apes, And Fossil Hominins, Elaine E. Kozma, Nicole M. Webb, William Harcourt-Smith, David A. Raichlen, Kristiaan D’Août, Mary H. Brown, Emma M. Finestone, Stephen R. Ross, Peter Aerts, Herman Pontzer

Publications and Research

The evolutionary emergence of humans’ remarkably economical walking gait remains a focus of research and debate, but experi- mentally validated approaches linking locomotor capability to postcranial anatomy are limited. In this study, we integrated 3D morphometrics of hominoid pelvic shape with experimental mea- surements of hip kinematics and kinetics during walking and climbing, hamstring activity, and passive range of hip extension in humans, apes, and other primates to assess arboreal–terrestrial trade-offs in ischium morphology among living taxa. We show that hamstring-powered hip extension during habitual walking and climbing in living apes and humans is strongly predicted, and likely constrained, by …

Selection Perception: Views On The Theory Of Evolution Among Residents Of Moshi, Tanzania, Robin Waterman

Independent Study Project (ISP) Collection

The theory of evolution is a major tenet of biological science and has many practical applications, particularly in agriculture, medicine, and conservation. Nevertheless, there is significant opposition to the theory and its incorporation into school curricula, largely on religious grounds. This disconnect between public opinion and scientific opinion has been studied at length in the US and to some extent in other industrialized nations, but little is known about the issue in other communities around the world. This paper will use the town of Moshi, Tanzania as a case study in community views and knowledge about the theory of evolution. …

The Evolutionary Significance Of Body Size In Burying Beetles, Ashlee Nichole Momcilovich

Theses and Dissertations

Body size is one of the most commonly studied traits of an organism, which is largely due to its direct correlation with fitness, life history strategy, and physiology of the organism. Patterns of body size distribution are also often studied. The distribution of body size within species is looked at for suggestions of differential mating strategies or niche variation among ontogenetic development. Patterns are also examined among species to determine the effects of competition, environmental factors, and phylogenetic inertia. Finally, the distribution of body size across the geographic range of a species or group of closely related is looked at …

Impacts Of Genome And Nuclear Architecture On Molecular Evolution In Eukaryotes, Xyrus Maurer-Alcalá

Doctoral Dissertations

The traditional view of genomes suggests that they are static entities changing slowly in sequence and structure through time (e.g. evolving over geological time-scales). This outdated view has been challenged as our understanding of the dynamic nature of genomes has increased. Changes in DNA content (i.e. polyploidy) are common to specific life-cycle stages in a variety of eukaryotes, as are changes in genome content itself. These dramatic genomic changes include chromosomal deletions (i.e. paternal chromosome deletion in insects; Goday and Esteban 2001; Ross, et al. 2010), developmentally regulated genome rearrangements (e.g. the V(D)J system in adaptive immunity in mammals; Schatz …

Evolution Of Alu Elements In The Saimiri And Papio Lineages Of Primates, Jasmine Nicole Brown Baker

LSU Doctoral Dissertations

Alu elements are approximately 300 base pair (bp) primate specific non- autonomous retrotransposons. Alu elements, a short interspersed element (SINE), account for high copy numbers in all primate genomes. Numerous Alu element subfamilies have undergone varying degrees of activity and amplification within primates. Identification of these subfamilies has proved to be very informative in elucidating phylogenies and as phylogenomic markers. Squirrel monkeys, genus Saimiri, are one of the most well-known neotropical primates and the second most commonly used laboratory monkey. Squirrel monkey species diverged approximately 1.5 million years ago and are native to South America. Despite being well-known, there …

A Biogeographic Perspective On The Evolution Of Fire Syndromes In Pine Trees (Pinus: Pinaceae), Kevin J. Badik, Joshua P. Jahner, Joseph S. Wilson

Biology Faculty Publications

Our goals were to explore the relationship between biogeography and the evolution of fire-adaptive syndromes in the genus Pinus. We used a previously published time-calibrated phylogeny and conducted ancestral trait reconstruction to estimate the likely timing of diversification in Pinus, and to determine when fire-adaptive syndromes evolved in the lineage. To explore trait conservation among fire syndromes and to investigate historical biogeography, we constructed ancestral state reconstructions using the program RASP and estimated the degree of conservatism for fire-adapted traits in the program BaTS. Our reconstructions suggest that the Bering land bridge, which connected North America and Asia, probably played …

Does Body Size Affect Fitness The Same Way In Males And Females? A Test Of Multiple Fitness Components, Ashlee N. Smith, Mark C. Belk

Faculty Publications

Body size generally has an important relationship with fitness, whereby larger body size leads to an increase in fitness through competition, reproductive output and survivorship. However, the traits through which body size increases fitness often differ between the sexes. We tested for the effects of body size on fitness in both sexes using three separate experiments on competitive ability, reproductive output and starvation resistance in the burying beetle Nicrophorus marginatus. Results varied between sexes as follows: (1) larger body size increased competitive ability differentially between sexes; (2) female body size, but not male body size, significantly affected reproductive output …

Allometry Of Individual Reproduction And Defense In Eusocial Colonies: A Comparative Approach To Trade-Offs In Social Sponge- Dwelling Synalpheus Shrimps, Sarah L. Bornbusch, Jonathan S. Lefcheck, J. Emmett Duffy

VIMS Articles

Eusociality, one of the most complex forms of social organization, is thought to have evolved in several animal clades in response to competition for resources and reproductive opportunities. Several species of snapping shrimp in the genus Synalpheus, the only marine organisms known to exhibit eusociality, form colonies characterized by high reproductive skew, and aggressive territoriality coupled with cooperative defense. In eusocial Synalpheus colonies, individual reproduction is limited to female 'queens', whose fecundity dictates colony growth. Given that individual reproduction and defense are both energetically costly, individual and colony fitness likely depend on the optimal allocation of resources by these reproducing …

Using Introduced Species Of Anolis Lizards To Test Adaptive Radiation Theory, James T. Stroud

FIU Electronic Theses and Dissertations

Adaptive radiation – the proliferation of species from a single ancestor and diversification into many ecologically different forms – has long been heralded as an important process in the generation of phenotypic diversity. However, the early stages of adaptive radiation are notoriously elusive to observe and study. In this dissertation, I capitalize on communities of introduced non-native Anolis lizards as analogues of early stage adaptive radiations. In Chapter II, I begin by reviewing the concept of “ecological opportunity” – a classic hypothesis put forward as a potential key to understanding when and how adaptive radiation occurs. In Chapter III, I …

Redescription And Phylogenetic Analysis Of The Materials Assigned To The Taxon "Captorhinikos" Chozaensis, Jason Paul Jung

Electronic Theses, Projects, and Dissertations

“Captorhinikos” chozaensis is a multiple-tooth-rowed captorhinid reptile from the Lower Permian Clear Fork Group, undivided formation. Upon re-examination of the materials associated with the species from both the Chicago Field Museum of Natural History, and the Smithsonian United States National Museum, I reaffirm their affinity and collective identity as a valid taxon. “Captorhinikos” chozaensis does not, however, belong with either of the two members of its genus, C. valensis or “C.” parvus, instead occupying its own branch on the phylogenetic tree of the Captorhinidae. This conclusion is based in strong results from a combined phylogenetic parsimony analysis combined with …