Genetics and Genomics Commons^™

Microrna Profiling In The Weddell Seal Suggests Novel Regulatory Mechanisms Contributing To Diving Adaptation, Luca Penso-Dolfin, Wilfried Haerty, Allyson Hindle, Federica Di Palma

Life Sciences Faculty Research

Background:The Weddell Seal (Leptonychotes weddelli) represents a remarkable example of adaptation to diving among marine mammals. This species is capable of diving... (See full abstract in article).

Unexpected Predicted Length Variation For The Coding Sequence Of The Sleep Related Gene, Bhlhe41 In Gorilla Amidst Strong Purifying Selection Across Mammals, Krishna Unadkat, Justen B. Whittall

Biology

There is a molecular basis for many sleep patterns and disorders involving circadian clock genes. In humans, “short-sleeper” behavior has been linked to specific amino acid substitutions in BHLHE41 (DEC2), yet little is known about variation at these sites and across this gene in mammals. We compare BHLHE41 coding sequences for 27 mammals. Approximately half of the coding sequence was invariable at the nucleotide level and close to three-quarters of the amino acid alignment was identical. No other mammals had the same “short-sleeper” amino acid substitutions previously described from humans. Phylogenetic analyses based on the nucleotides of the coding sequence …

Evolutionary Ecology Of Host-Parasite Relationships: Role Of Host Ecology, Phylogeny, And Demographics In Shaping Parasite Evolution, Erika Taylor Gendron

Biology ETDs

Host-parasite systems exist across complex and ecologically heterogeneous landscapes, and may occur across taxonomically and ecologically disparate host species. Under these conditions, mechanisms underlying microevolutionary processes (i.e. gene flow, genetic drift) are not always clear, and may be mediated by numerous co-occurring factors specific to individual hosts. Host traits such as host immunology, demographics, phylogeny and ecology may act in concert to shape host-parasite relationships, and ultimately evolutionary processes. The research described herein used phylogeographic, phylogenomic, and population genetic methods to further understanding of how host traits impact the evolutionary ecology of trematode systems, using avian schistosomes (Digenea: Schistosomatidae) as …

Relative Model Fit Does Not Predict Topological Accuracy In Single-Gene Protein Phylogenetics, Stephanie J. Spielman

College of Science & Mathematics Departmental Research

It is regarded as best practice in phylogenetic reconstruction to perform relative model selection to determine an appropriate evolutionary model for the data. This procedure ranks a set of candidate models according to their goodness of fit to the data, commonly using an information theoretic criterion. Users then specify the best-ranking model for inference. Although it is often assumed that better-fitting models translate to increase accuracy, recent studies have shown that the specific model employed may not substantially affect inferences. We examine whether there is a systematic relationship between relative model fit and topological inference accuracy in protein phylogenetics, using …

Delineation Of Undescribed, Morphologically Cryptic Cave Beetles Of The Pseudanophthalmus Pubescens Species-Group (Coleoptera: Carabidae: Trechinae), Jedidiah John Nixon

Masters Theses & Specialist Projects

The genus Pseudanophthalmus Jeannel is a widespread and extremely diverse taxon of troglobiont beetle endemic to the karst of eastern North America, with its distribution centered in Tennessee and Kentucky. Despite lying near the heart of this region, the pubescens species-group was thought to contain many undescribed species. In this study, the validities of several of the late Dr. Thomas Barr’s unpublished putative new species in the pubescens-group were tested both morphologically and molecularly. Body measurements (length and width for head, thorax, and abdomen), as well as male genital morphology were compared to see if they reflected theorized species limits.. …

An Intergrative Ecological And Taxonomic Assessment Of The Stoneflies (Insecta, Plecoptera) Of The Black Mountains, North Carolina, Usa, Madeline Lake Metzger

Masters Theses & Specialist Projects

The Black Mountains are a part of the Blue Ridge region of the Appalachian Mountains and include Mount Mitchell, the highest peak east of the Mississippi River at 2,037 m (= 6,684 ft). A comprehensive inventory of the stonefly fauna was conducted between 2014-2019 within Mt. Mitchell State Park and adjacent Pisgah National Forest. Collections occurred seasonally from 44 unique locations, covering a broad range of stream sizes and elevations in the region. Sequencing of the mitochondrial cytochrome c oxidase subunit I (mtCOI) gene was completed to assist with making positive determinations to species for females of taxonomically challenging genera …

Diversity Of The Major Histocompatibility Complex In African Penguins (Spheniscus Demersus) In Situ, Athena Schalk

Undergraduate Honors Thesis Projects

The Major Histocompatibility Complex (MHC) is responsible for the immune response in all jawed vertebrates and protects individuals against a variety of pathogens and diseases. Maintaining genetic diversity within the MHC exons is critical to protecting endangered species. African penguins (Spheniscus demersus) are in danger of losing their MHC diversity in isolated populations due to reductions in population size associated with environmental changes and human activity. This study analyzes the diversity within the exons in the DNA encoding the MHC by amplifying the exons through polymerase chain reaction and identifying alleles through denaturing gradient gel electrophoresis. Wild populations of …

Distortion Of The Local Magnetic Field Appears To Neither Disrupt Nocturnal Navigation Nor Cue Shelter Recognition In The Amblypygid Paraphrynus Laevifrons, Daniel D. Wiegmann, Patrick Casto, Eileen Hebets, Verner P. Bingman

Eileen Hebets Publications

Many arthropods are known to be sensitive to the geomagnetic field and exploit the field to solve spatial problems. The polarity of the geomagnetic field is used, for instance, as an orientation cue by leafcutter ants as they travel on engineered trails in a rainforest and by Drosophila larvae as they move short distances in search of food. A ubiquitous orientation cue like the geomagnetic field may be especially useful in complex, cluttered environments like rainforests, where the reliability of celestial cues used to navigate in more open environments may be poor. The neotropical amblypygid Paraphrynus laevifrons is a nocturnal …

Molecular Differentiation Of Astragalus Species And Varieties From The Western United States: The Chloroplast Dna Bridge Between Evolution And Molecular Systematics, Marwa Neyaz, Daniel Cook, Rebecca Creamer

Poisonous Plant Research (PPR)

Locoweeds are the most widespread poisonous plant problem in the world and have been reported in the Western United States since the 1800s, causing tremendous losses in livestock. Consumption of locoweeds by grazing animals stimulates the neurological disease, locoism, characterized by weight loss, ataxia, and lack of muscular coordination. The name locoweed is used for Astragalus and Oxytropis species known to contain swainsonine, the toxic principle produced by the plant endophytic fungus Undifilum. Astragalus includes 2,500-3,000 species and many varieties that have almost identical morphological characteristics that overlap among species, leading to improper identification. Therefore, the aim of this study …

Natural Variation And Evolutionary Responses To Climate Change Stressors In Marine Invertebrates, Joanna Sarah Griffiths

LSU Doctoral Dissertations

Our rapidly changing climate is putting many species at risk of extinction and there is an urgent need to understand how species will respond to these changes. In this dissertation, I evaluate how three species of marine invertebrates (corals, oysters, and copepods) respond to stressful conditions in their current environments and how plasticity and evolutionary adaptation could alter their response to future climate change stressors. I first employed a space for time study to elucidate population differences in the response of cold-water corals, Balanophyllia elegans, to future ocean acidification. I found evidence that upwelling history (natural low pH exposure) influences …

Genetic Parameters Of Growth And Adaptive Traits In Aspen (Populus Tremuloides): Implications For Tree Breeding In A Warming World, Chen Ding, Andreas Hamann, Rong-Cai Yang, Jean S. Brouard

Aspen Bibliography

Aspen (Populus tremuloides Michx) is a widespread commercial forest tree of high economic importance in western Canada and has been subject to tree improvement efforts over the past two decades. Such improvement programs rely on accurate estimates of the genetic gain in growth traits and correlated response in adaptive traits that are important for forest health. Here, we estimated genetic parameters in 10 progeny trials containing >30,000 trees with pedigree structures based on a partial factorial mating design that includes 60 half-sibs, 100 full-sib families and 1,400 clonally replicated genotypes. Estimated narrow-sense and broad-sense heritabilities were low for height …

Geographic Life History Differences Predict Genomic Divergence Better Than Mitochondrial Barcodes Or Phenotype, Daniel P. Duran, Robert A. Laroche, Harlan M. Gough, Rodger A. Gwiazdowski, Charles B. Knisley, David P. Herrmann, Stephen J. Roman, Scott P. Egan

School of Earth & Environment Departmental Research

Species diversity can be inferred using multiple data types, however, results based on genetic data can be at odds with patterns of phenotypic variation. Tiger beetles of the Cicindelidia politula (LeConte, 1875) species complex have been taxonomically problematic due to extreme phenotypic variation within and between populations. To better understand the biology and taxonomy of this group, we used mtDNA genealogies and multilocus nuclear analyses of 34,921 SNPs to elucidate its evolutionary history and evaluate the validity of phenotypically circumscribed species and subspecies. Genetic analyses recovered two divergent species that are also ecologically distinct, based on adult life history. These …

Mitochondrial Dna Diversity And Evolutionary History Of Native Human Populations Of Northwest Patagonia (Argentina), María Bárbara Postillone, Virginia Agustina Cobos, Celmira Urrutia, Cristina Beatriz Dejean, Paula N. Gonzalez, Sergio Ivan Perez, Valeria Bernal

Human Biology Open Access Pre-Prints

The genetic composition of Amerindian descendants from Patagonia has long been a focus of interest, although the information available is still scarce for many geographic areas. Here, we report the first analysis of the variation in the mtDNA control region for an area of northwestern Patagonia, the North of Neuquén, with the aim of studying the processes and historical events that modeled the evolutionary history of these human groups. We analyzed 113 individuals from two localities of northern Neuquén, along with 6 from southern Neuquén and 223 mtDNA sequences previously published from neighboring areas from Argentina and Chile. We estimated …

On The Distribution Of Genetic Variation In Ecological Communities, Isaac Overcast

Dissertations, Theses, and Capstone Projects

Biodiversity in ecological communities is structured hierarchically across spatial and temporal scales. Many open questions remain as to how this structure accumulates. For example, what are the relative contributions of dispersal versus in situ speciation? Or, how important are stochastic drift versus deterministic processes? Up to this point, these questions have been investigated by isolated disciplines (e.g. macroecology, comparative phylogeography, macroevolution) using tools and data that tend to focus on only one axis of community scale data (e.g. phylogenies, relative abundances, and/or trait information). Yet we know that there are feedbacks among processes that respond on short, medium, and long …

Contrasting Root System Structure And Belowground Interactions Between Black Spruce (Picea Mariana (Mill.) B.S.P) And Trembling Aspen (Populus Tremuloides Michx) In Boreal Mixedwoods Of Eastern Canada, Claudele Ghotsa Mekontchou, Daniel Houle, Yves Bergeron, Igor Drobyshev

Aspen Bibliography

This study explored the underground interactions between black spruce and trembling aspen in pure and mixed stands to understand how their soil resource use help these species coexist in the boreal mixedwoods of Western Quebec. We analyzed species-specific fine root foraging strategies (root biomass and root tissue density) along three soil layers (organic, top 0–15 cm, and bottom 15–30 cm mineral soil), using 180 soil cores. We collected cores in three sites, each containing three 20 × 50 m2 plots of pure spruce, pure aspen, and mixed spruce and aspen stands. Spruce had a shallow rooting, whereas aspen had a …

Gene Expression Pattern Analysis Of Anterior Hox Genes During Zebrafish (Danio Rerio) Embryonic Development Reveals Divergent Expression Patterns From Other Teleosts, Adam Davis

Georgia Journal of Science

The regional identity of organs and organ systems along the anterior-posterior axis during embryonic development is patterned, in part, by Hox genes, which encode transcription factor proteins that activate or repress the expression of downstream target genes. Divergent nested Hox gene expression patterns may have had a role in facilitating morphological divergence of structures, such as the pharyngeal jaw apparatus, among evolutionarily divergent teleost fishes. Recent studies from several evolutionarily divergent teleosts, such as the Japanese Medaka (Oryzias latipes) and the Nile Tilapia (Oreochromis niloticus), have shown the presence of divergent expression patterns of several Hox …

Landscape Genetics Of Salamander Populations At Mammoth Cave National Park, Jackson Resser

Mahurin Honors College Capstone Experience/Thesis Projects

Habitat connectivity affects the distribution of genetic diversity among populations by influencing the movements of individuals and the resulting pattern of gene flow across landscapes. It has become evident that amphibians are experiencing a period of worldwide population declines brought about by environmental change. An understanding of the effects of habitat structure on landscape connectivity is important for developing effective amphibian conservation strategies. The purpose of this study is to investigate the effect of landscape characteristics on gene flow and population structure of the marbled salamander (Ambystoma opacum) in Mammoth Cave National Park, Kentucky, USA. Salamander larvae were …

Genetic Analysis Of The Endangered Gray Bat Species (Myotis Grisescens), Emma Fitzgerald

Lewis Honors College Capstone Collection

This study attempts to analyze the genetics using specific haplotype sequences of the endangered gray bat to determine genetic events that have happened in the past as well as determining how the species population has changed over time. We were able to conduct a Tajima’s D test to investigate whether a potential bottleneck has occurred. A linear regression of the genetic vs. geographical distance was produced to investigate the patterns of haplotype distribution. The species past distribution was compared to the current distribution using known collected specimens. A map of future predictions was constructed using present and future climate layers …

Demonstrating Mate Choice Copying In Spiders Requires Further Research, R. Tucker Gilman, Kasey Fowler-Finn, Eileen A. Hebets

Eileen Hebets Publications

Mate choice copying—when individuals learn to prefer mates or mate types that have been chosen by others—can influence trait evo-lution and speciation (Varela et al. 2018; Dion et al. 2019). Most examples of mate choice copying are from fish, birds, and mammals including humans (Varela et al. 2018). However, 2 invertebrate examples—fruit flies and wolf spiders—have been used to argue that the phenomenon may be phylogenetically widespread, and perhaps the rule rather than the exception in nature (Varela et al. 2018). Here, we revisit the evidence for mate choice copying in wolf spiders (Fowler-Finn et al. 2015) in light of …

Examining Biodiversity Metrics And The Utility Of Dna Barcoding In The Northern Great Plains, Sarah Herzog

Electronic Theses and Dissertations

Due to heavy threats to remaining global floral and faunal diversity, it is imperative we can identify species and quantify ecosystem health to find best practices for land management and conservation. The tallgrass prairies of the Northern Great Plains are one example of a heavily imperiled ecosystem. The tallgrass prairies have been reduced to less one percent of their historical extent and are facing continued loss. Genetic approaches and evolutionary theory offer insights for identifying species and assessing how biodiversity metrics may correlate with ecosystem processes. My two projects aim to address two facets imperative to conservation in the tallgrass …

The Origin And Evolution Of Flower Characters In Angiosperms With A Case Study On The Genetic Basis Of Zygomorphic Corolla Development In Bee And Hummingbird Pollinated Species Of Schizanthus (Solanaceae), Ghadeer Bukhari

Theses and Dissertations

This Ph.D. dissertation investigates two main projects separated into two chapters, one for each. The first chapter explores the evolution of flowering plants (angiosperms), a macro-scale study. The second project is on a micro-scale that focus on exploring the genes that regulate the similarities and the differences of flower morphology reflecting their different pollination syndromes in two species of Schizanthus (Solanaceae), i.e., S. pinnatus, a bee-pollinated flower, and S. grahamii, a hummingbird- pollinated flower.

In the first chapter, I used floral diagrams to study the origin and the evolution of floral traits in angiosperms, a new set of morphological data …

Patterns Of Epiphytic Lichen Abundance On Aspen Stands In Proximity To Roads Of Varying Vehicular Traffic, D. Aragon, C. Castillo, J. Moffroid, G. Thomas

Aspen Bibliography

Although present in nearly any wild space with available moisture and on a wide variety of substrates, lichen, and its importance as a bioindicator for an ecosystem, is often overlooked. As air pollution becomes a greater concern for flora, fauna, and even humans, the story told by lichen growth becomes more useful as we try to make sense of the downstream effects of anthropogenic contributions to poor air quality. One such human-driven pollutant is the level of emissions that result from vehicular travel. The Jackson Hole area has experienced a large increase in vehicular traffic in the past five to …

Pando Clone Recovery: Repeat Photos 2014-2019, Mary O'Brien, Marc Coles-Ritchie

Aspen Bibliography

The world's largest known clone of aspen (Populus tremuloides), called the "Pando Clone" is located in the Fishlake National Forest in central Utah. For many decades, significant pressure from ungulate (deer and cattle) browsing has prevented growth of young aspen stems in to trees that would replace the mature trees as they die of natural causes. There has been concern that this impressive 104-acre Pando Clone could be lost altogether due to the excessive browsing of young aspen stems. In 2013, 16 acres of this clone were fenced to exclude all ungulates (deer and cattle) so that recovery …

Geographic Distribution Of Bacillus Thuringiensis Cry1f Toxin Resistance In Western Bean Cutworm (Lepidoptera: Noctuidae) Populations In The United States, Brad S. Coates, Craig A. Abel, Katharine A. Swoboda-Bhattarai, Debra E. Palmquist, Débora Goulart Montezano, Sarah N. Zukoff, Yangzhou Wang, Jeffery D. Bradshaw, Christina D. Difonzo, Elson Shields, Kelley J. Tilmon, Thomas Hunt, Julie A. Peterson

West Central Research and Extension Center, North Platte

The western bean cutworm (WBC), Striacosta albicosta (Lepidoptera: Noctuidae), can be a severe pest of transgenic corn in the western Plains and Great Lakes regions of North America, including on hybrids expressing the Bacillus thuringiensis (Bt) Cry1F toxin. The level and geographic distribution of Cry1F resistance are not completely known. Neonate S. albicosta from 10 locations between Nebraska and New York state were subjected to dose–response trypsin-activated native Cry1F toxin overlay bioassays. In 2017, the mean estimated lethal concentration causing 50% larval mortality (LC50) ranged from 15.1 to 18.4 μg Cry1F cm−2, and were not significantly different among locations. In …

Temperate Eurasian Origins Of Hawaiian Chenopodium (Amaranthaceae) Plus Description Of A New Species Endemic To Moloka‘I, Jason T. Cantley, Angela J. Mcdonnell, J Branson, S R. Long, W Garnett, Christopher T. Martine

Faculty Journal Articles

Chenopodium taxa of Hawai‘i are tetraploids distinguished from other members of the circumglobally distributed genus by minute morphological characters. Because of these reasons, the geographic origin of Hawaiian Chenopodium has remained unclear. Across the Hawaiian Archipelago, Chenopodium taxa are morphologically variable and grow in highly disparate xeric habitats, especially in terms of precipitation, temperature, wind, salt spray, and solar irradiation. Habitats include dry subalpine shrublands, sandy beach strand of atolls in the Northwest Hawaiian Islands, dry forests, and precipitously tall sea cliffs of northwestern Moloka‘i. From the Moloka‘i sea cliffs, which are battered by high energy winds, salt spray, and …

Predicting Patterns Of Gene Family Evolution In Taxa With Similar Ecological Niches, Kim Vertacnik

Theses and Dissertations--Biology

To fully understand the genetic basis of adaptation, we need to know its predictability—the extent to which specific selective pressures and contexts can yield corresponding genetic changes. In particular, the repeated colonization of similar, specialized environments by different taxa is ideal for assessing the frequency of reoccurring changes in the same genes or functions. But compared to a growing body of literature on the convergent evolution of individual genes, far less is known about the repeatability of gene family evolution, where families (defined here as groups of genes that share sequence and functional similarity from common ancestry) can expand (gain …

Current Dog Breeding Practices Impacts On Health And Preservation Of Purebred Dogs, Bridget E. Baker

Honors Theses and Capstones

No abstract provided.

Monitoring Mammal Community Shifts Across Silvicultural Treatments Utilizing Camera Traps And The Development Of Invertebrate- Derived Dna In Hardwood Forests Of North America, Shallen Gurtler

Dissertations, Master's Theses and Master's Reports

Mammal distribution and diversity is quickly changing as humans modify the landscape. In particular, silviculture, which is the practice of controlling the growth, structure, and quality of forests to meet the needs of society and the landowner, influences the habitat usage of mammals. Utilizing camera traps, I monitored shifts in mammal communities across different silviculture treatments in the northern hardwood forests of the Great Lakes region in North America. I assessed the community composition across six canopy treatments and three understory treatments with a total of 2,018 active camera trap nights with 3,321 detections over the course of 147 days. …

Spatial And Temporal Genetic Structure Of Winter-Run Steelhead (Oncorhynchus Mykiss) Returning To The Mad River, California, Steven R. Fong

Cal Poly Humboldt theses and projects

Distinct populations of steelhead in the wild are in decline. The propagation of steelhead in hatcheries has been used to boost population numbers for recreational fisheries and for use in conservation. However, hatchery breeding practices of steelhead can result in changes in genetic structure. I investigated the genetic structure of winter-run steelhead (Oncorhynchus mykiss) returning to the Mad River, California, where a hatchery has been used enhance production for recreational fisheries since 1971. Genetic variability in Mad River steelhead was evaluated using 96 single nucleotide polymorphisms (SNPs) among 4203 individuals, including the Mad River and nearby locations, and …

Sampling The Local Fare: Fishes At The Sam Israel House Pit (45gr76), Soap Lake, Washington, Adam Fruge

All Master's Theses

The Sam Israel site is a precontact archaeological complex with numerous fish bones at the north end of Soap Lake, Washington. Excavated in 1976, the fish remains recovered from there were never fully analyzed prior to this research. Since this inland Columbia Plateau site had thousands of fish bones, it contained untapped potential for our understanding of ancient local fish procurement. As such, I conducted a detailed analysis of 2,862 fish bone specimens from the Sam Israel House Pit locus to: study a larger sample of fish bones in greater detail than was done before; compare the distribution of fishes …