Genetics and Genomics Commons^™

Influence Of Increasing Fires On Mixed Conifer Stand Dynamics In The U.S. Southwest, Simon D. Baker, Kristen M. Waring, David Auty, Nicholas Wilhelmi

Aspen Bibliography

(1) Stand-replacing fires may threaten the continued stability of mixed conifer forests in the U.S. Southwest. Increasing fire frequency and severity have made post-fire forest recovery trajectories uncertain for many coniferous species, potentially leading to long-term shifts in forest structure and composition. (2) The purpose of this study was to examine post-fire stand dynamics over a 10-year period, using a network of permanent plots established prior to wildfire events across Arizona and New Mexico. We assessed changes in over story composition, regeneration, and fuel loading across different fire severities. (3) High severity fire caused near-total over story mortality, with little …

Experiments To Enhance Post-Fire Aspen Seedling Survival And Growth, Larissa L. Yocom, Mark R. Kreider, Owen T. Burney, Tammy Parsons, Ryan T. Choi, Emily K. Liese, Karen E. Mock

Aspen Bibliography

Aspen forests provide wildlife, watershed, and aesthetic value, and the potential for reduced fire occurrence, behavior, and severity. There is interest in planting aspen to achieve various management objectives. However, few studies have investigated the optimal conditions for aspen seedlings in the western US. We conducted two experiments to address this knowledge gap. First, we tested the effects of shading structures (i.e., logs) and biochar on the survival and growth of 960 outplanted aspen seedlings in three exclosures in a recent fire footprint. Second, we tested whether experimentally placing logs near 120 naturally-occurring post-fire aspen seedlings affected survival or growth. …

Individual, Social, And Environmental Factors Associated With Patterns Of Parasitic Infection In Capuchin Monkeys (Cebus Imitator), Megan C. Henriquez

Dissertations, Theses, and Capstone Projects

Parasites, and the infectious diseases they carry, are thought to have significantly impacted our evolutionary trajectory for millennia. Exploring how parasites are acquired and transmitted by their hosts in wild, natural populations is integral to understanding how similar processes may have shaped host-parasite co-evolutionary relationships over time. However, parasitological studies in humans and in non-human primates have produced inconsistent results, highlighting the dynamic, nuanced, and unique relationships individual parasites have with their hosts. These relationships are largely regulated by variation in factors at host, social, and environmental levels. Characteristics unique to the host (e.g., age and sex), factors pertaining to …

Comparative Methylation Analyses Across Juglans Species To Investigate Epigenetic Contributions To Fungal Resistance, Keertana Chagari

Honors Scholar Theses

Juglans cinerea (butternut) is a critically threatened North American tree species experiencing severe declines due to the fungal pathogen Ophiognomonia clavigignentijuglandacearum. In contrast, its Asian relative, Juglans ailantifolia (Japanese walnut), shows natural resistance. To investigate the genomic and epigenetic factors underlying this difference, we constructed and analyzed high-quality, chromosome-level genome assemblies for both species from long-read sequencing data (J. ailantifolia: 527Mb; J. cinerea: 586Mb), focusing on transposable element (TE) content, DNA methylation patterns, and regulation of pathogen resistance genes (PRGs).

Repeat analysis revealed that J. cinerea has a slightly higher overall transposable element (TE) content, with …

Sexual And Vegetative Recruitment Of Trembling Aspen Following A High-Severity Boreal Wildfire, Denyse A. Dawe, Ellen Whitman, Michael Michaelian, Alan J. Tepley, Marc-André Parisien

Aspen Bibliography

Background High-severity fire is rare in trembling aspen-dominated forests of the boreal region. The post-fire recruitment strategy of aspen, by either vegetative suckering or sexually (i.e., by seed), has considerable implications for subsequent forest structure, genetic diversity, and ecological resilience to shifting climatic and disturbance regimes. In this study, we take advantage of the unique opportunity provided by the Chuckegg Creek Wildfire Fire (310,000 ha) in northern Alberta, Canada, which burned at high severity through aspen stands before and after spring green-up, to document how phenology, fire severity, and stand characteristics affect recruitment one year following the fire.

Results We …

Factors Impacting The Variability Of Post-Fire Forest Regeneration In Central European Pine Plantations, Florent Jouy, Maren Schüle, Yojana Adhikari, Anja Binder, Danica Clerc, Werner Gerwin, Thilo Heinken, Thomas Raab, Frank Repmann, Susanne Rönnefarth, Marina Schirrmacher, Marie-Therese Schmehl, Jens Schröder, Pierre L. Ibisch

Aspen Bibliography

Fire is increasingly posing a risk to forests and plantations, even in the temperate latitudes of central Europe. Little is known about fire ecology in this region, and therefore, appropriate approaches for the management and reforestation of burned sites are mostly lacking. In a Scots pine plantation region in Brandenburg (northeast Germany), the early tree regeneration of two nearby areas that burned 1 year apart was investigated. We observed that 3 years after the fire events, the forest in one study area showed a relatively high regeneration with a mean density of 7765 saplings/ha, clearly dominated by European aspen (93%); …

Network Analysis Of Antimicrobial Resistance In Staphylococcus Aureus: Characterization Of Hub Genes And Their Functional Implications, Md Imran Hasan, Davida Smyth, Jeong Yang, Ashley Teufel

Masters Theses (Archived)

Antimicrobial resistance is a major cause of morbidity and mortality in patients with S. aureus infections. In this study, we analyzed genes, molecular mechanisms, and pathways driving drug resistance in S. aureus using network analysis. Using whole-genome sequencing (WGS) data and systems biology approaches, we identified 229 AMR-associated genes and constructed a protein-protein interaction network among these genes. Through network topology and functional enrichment analyses, we not only confirmed their association with resistance, but also highlighted the central roles of these genes in resistance pathways, such as efflux, target replacement, and target protection, which are directly linked to multiple drug …

A Phylogenomic Investigation Of The Historical Biogeography Of Livebearers (Cyprinodontiformes: Poeciliidae), Sheila Rodríguez Machado

LSU Doctoral Dissertations

The Neotropics contain several biodiversity hotspots and harbor the highest diversity of freshwater fishes globally. Yet, recognizing the patterns and processes driving this richness remains a challenge. Similarly, all groups and subregions have not received the same attention, especially in the genomics era. Addressing these knowledge gaps will help us to better understand the region’s evolutionary and biogeographic complexity. The goal of this dissertation is to examine phylogenetic and biogeographic patterns of Neotropical freshwater fishes, with emphasis on the Greater Antilles, across multiple taxonomic and geographic scales. To achieve this goal, I generated a genomic dataset of hundreds of ultraconserved …

Causes Of Heterozygosity Excess: The Case Of Mexican Populations Of Populus Tremuloides, Javier Hernández-Velasco, José Ciro Hernández-Díaz, Sergio Leonel Simental-Rodríguez, Juan P. Jaramillo-Correa, David S. Gernandt, José Jesús Vargas-Hernández, Ilga Porth, Roos Goessen, M. Socorro Gonzáles-Elizondo, Matthias Fladung, Cuauhtémoc Sáenz-Romero, José Guadalupe Martínez-Ávalos, Artemio Carrillo-Parra, Eduardo Mendoza-Maya, Arnulfo Blanco-García, Christian Wehenkel

Aspen Bibliography

The presence of heterozygous individuals in a population is crucial for maintaining genetic diversity, which can positively affect fitness and adaptability to environmental changes. While inbreeding generally reduces the proportion of heterozygous individuals in a population, polyploidy tends to increase the proportion. North American Populus tremuloides is one of the most widely distributed and ecologically important tree species in the Northern Hemisphere. However, genetic variation in Mexican populations of P. tremuloides, including the genetic signatures of their adaptation to a variety of environments, remains largely uncharacterized. The aim of this study was to analyze how inbreeding coefficient (F …

Sex, Skulls, And Selection: An Exploration Of Blakely Island's Deer Population And Their Ecology Through Genetic Sex Differentiation Of Juvenile Crania, Blair P. Graves

Honors Projects

As an isolated landmass with no natural predators, Blakely Island serves as an effective study site for the study of evolutionary factors relating to insular populations of large mammals. A disparity in the adult sex ratio of local deer has been observed, but the demographics of juveniles must still be ascertained through genetic methods. This study aims to further research concerning the development of a replicable and non-toxic procedure through which undergraduate students can identify the sex of numerous juvenile deer crania. Specifically, differing decalcification lengths, DNA extraction kit methods, and amelogenin primer sets were evaluated for relative success in …

Genomic Structure Among Populations Of A Regionally Rare Perennial Plant Indicates The Need For Reevaluation Of Management Units, Cheyenne Moore, Angela J. Mcdonnell, Scott Schuette, Christopher T. Martine

Faculty Journal Articles

Conservation of rare species often relies on the delineation of management units and genomic tools can now be applied for this purpose. However, this is not as common on a local scale, where populations are often small and fragmented, despite the utility of informing conservation and management practice at the regional level. We use a genotyping by sequencing (GBS) approach to assess the perennial riparian plant species Baptisia australis (Fabaceae) in Pennsylvania, where the taxon is at the edge of its natural distribution and considered threatened. In this system, we investigate whether sampled subpopulations exhibit genetic structure. We find that …

Elucidating The Role Of Transposable Element Derived Gene, Dplg3, In Drosophila Melanogaster, Kaisy A. Martinez

2025 Spring Honors Capstone Projects - Archive

A big fraction of most eukaryotic genomes is comprised of transposable elements (TEs). TEs are mobile genetic sequences often causing deleterious effects as they increase in copy number. On rare occasions, TEs can undergo molecular domestication, where the TE proteins are co-opted by the host to serve cellular functions. In Drosophila melanogaster, domestication from PIF/Harbinger TEs has resulted in five Drosophila PIF-Like Genes (DPLG1-4 and 8). This study focuses on investigating the function of DPLG3. In DPLG3 knock out lines, DPLG3-KO, a fraction of the progeny shows an abnormal gonad phenotype. We sought to confirm …

Uncovering The Evolutionary Origins Of Neo-Sex Chromosomes In The Insect Family Membracidae, Mary Kumah

2025 Spring Honors Capstone Projects - Archive

This research explores the evolution of the neo-XX/XY sex chromosome system of Amblyophallus exaltatus, a treehopper insect in the family Membracidae. Neo-XX/XY sex chromosome systems can evolve from an XX/X0 sex chromosome system via fusion events between the X chromosome and an autosome. Although cytological work has indicated the presence of a neo-XX/XY system within A.exaltatus, the chromosomal identity of the fused autosome and the molecular drivers behind this chromosomal fusion remain poorly understood. By performing a coverage analysis with whole genome sequence data, the parts of the A.exaltatus genome that fused with the X chromosome will be better …

Life History Inhibits Deleterious Effects Of Dams On Genetic Health And Structure Of A Headwater Stream Fish, Riley Phelps

Electronic Theses and Dissertations

Habitat loss, fragmentation, and land use changes in river networks are common globally. The resulting fragmentation of landscapes and riverscapes threatens biodiversity and can affect dispersal and subsequently, gene flow and genetic health of species. Headwater streams are an integral part of river networks and contribute to biodiversity by providing habitat for temporary and permanent residents, yet they are easily altered and fragmented. The sandhills chub (Semotilus lumbee) is an endemic headwater leuciscid that lives in highly fragmented streams of the sandhills ecoregion in North and South Carolina, USA. New knowledge on the population genetics of the sandhills chub is …

A Genetic And Spatial Analysis Of The Last Megafaunal Species (Tapirus Terrestris) In The Paraguayan Dry Chaco Forest, Emily Bowers

LSU New Orleans Theses and Dissertations

No abstract provided.

Sibship Analysis Of Fall And Spring Spawn Gulf Sturgeon Eggs In The Choctawhatchee River, Florida, Lyric Mccullouch

Honors Theses

The Gulf sturgeon (Acipenser oxyrinchus desotoi) is an anadromous species that inhabits rivers along the northern Gulf of Mexico. Facing challenges from overfishing and habitat alteration, the Gulf sturgeon is listed as threatened under the Endangered Species Act. This study investigated the genetic distinctiveness of fall and spring spawning groups of Gulf sturgeon in the Choctawhatchee River, a critical habitat for the species. In this study, I used microsatellite loci to analyze Gulf sturgeon eggs previously collected in the fall and spring of 2019 and 2020. The goals of this study were to verify the genetic identity of …

Chromosome Evolution Model Reveals Hidden Variation In Karyotype-Driven Speciation In Ferns, Thomas Buchloh

All Theses

Because karyotype change commonly generates reproductive isolation between diverging species, rapid karyotype evolution, like that seen in plants, may increase the total rate of diversification. However, few studies have investigated this predicted relationship. Tests of this prediction have identified a positive correlation between the rate of karyotype change (specifically whole genome duplications) and diversification, but tests have been restricted to relatively small and young clades. Fortunately, novel macroevolutionary models have recently become available to investigate patterns of karyotype evolution in large phylogenies, providing new opportunity to investigate variation in karyotype driven diversification. Ferns are one of the most karyotype rich …

Intraspecific Genetic Variation In Green Salamanders (Aneides Aeneus) At Bays Mountain Park, Brianna Drake

Electronic Theses and Dissertations

Accurate taxonomy is crucial for conserving vulnerable cryptic species like the green salamander (Aneides aeneus) in the Southern Appalachian Mountains. Prior studies identified three distinct lineages within the A. aeneus complex: Northern Appalachians, Southern Appalachians, and Blue-Ridge Escarpment. One previously collected sample indicated green salamanders in northeast Tennessee fit within the Northern lineage. The present study uses molecular data of A. aeneus at Bays Mountain Park (BMP) in Kingsport, Tennessee, to determine where the BMP population fits within these lineages. It was hypothesized that individuals from BMP belong in the northern lineage. Tail tips were collected from thirty-four …

Below-Ground Carbon Gradients Surrounding Saskatchewan's Native Agricultural Copses, Andrea V. Cline, Colin P. Laroque

Aspen Bibliography

As carbon markets develop, understanding the carbon storage capabilities of agricultural land is imperative to maximizing carbon storage. Ecosystems store two-thirds of their carbon below ground. Shrubland and shelterbelt carbon storage have been well documented in agricultural settings, yet little is known about the carbon stored under the native woody vegetation scattered across the Prairies. This study aims to be the first to quantify the below-ground carbon under and around these native trembling aspen (Populus tremuloides) copses in the Canadian Prairies. For this study, the leaf, fibric, humic layer (LFH) and soil samples up to 60cm were collected …

Robust Sex Determination In The Caenorhabditis Nigoni Germ Line, Jonathan P Harbin, Yongquan Shen, Shin-Yi Lin, Kevin Kemper, Eric S Haag, Erich M Schwarz, Ronald E Ellis

Rowan-Virtua School of Osteopathic Medicine Departmental Research

Sexual characteristics and reproductive systems are dynamic traits in many taxa, but the developmental modifications that allow change and innovation are largely unknown. A leading model for this process is the evolution of self-fertile hermaphrodites from male/female ancestors. However, these studies require direct analysis of sex-determination in male/female species, as well as in the hermaphroditic species that are related to them. In Caenorhabditis nematodes this has only become possible recently, with the discovery of new species. Here, we use gene editing to characterize major sex-determination genes in C. nigoni, a sister to the widely studied hermaphroditic species C. briggsae. These …

Life After Death: Investigating The Resistance And Recovery Of Fungal Communities To Foundation Tree Mortality, Jessie F. Marlenee

Biology ETDs

Tree mortality can have cascading effects on the composition and resilience of interacting fungal communities. Yet, little is known about the impact tree mortality, distinct from abiotic drivers (i.e., drought), has on these communities. This dissertation focuses on the resilience of fungal communities to experimental tree mortality in a piñon-juniper woodland. In chapter one, I found that piñon mortality reduced piñon fine root biomass and piñon mycorrhizal fungal diversity, whereas juniper mycorrhizal fungi were unaffected by juniper mortality. In chapter two, I revealed that piñon mortality altered the composition and spatial structure of mycorrhizal and saprotrophic fungi in the soil, …

Effectiveness Of Silvicultural Options In Renewal Of Trembling Aspen–Jack Pine Mixedwood Stands, 21 Years After Treatment, Rongzhou Man

Aspen Bibliography

Regenerating conifers after harvest through planting and postharvest broadcast application of herbicide is effective in ensuring the survival and growth of seedlings, but faces challenges in meeting broad social and ecological objectives of forest management. This study reports the effectiveness of alternative options in regenerating jack pine (Pinus banksiana Lamb.), 21 years after harvest of trembling aspen (Populus tremuloides Michx.)-dominated boreal mixedwood stands. The treatment options included (i) preharvest spray—aerial broadcast spray prior to harvest, (ii) postharvest partial spray—ground herbicide application in strips, (iii) partial harvest in strips, (iv) postharvest aerial broadcast, and (v) uncut reference. Twenty-one years …

Fisheries Management Paper No.286: Western Australian Octopus Resource Harvest Strategy, Department Of Primary Industries And Regional Development, Western Australia

Fisheries Management Papers

Harvest strategies for Western Australia’s (WA) aquatic resources are formal documents developed to support decision-making processes that ensure the outcomes are consistent with the principles of Ecologically Sustainable Development (ESD; Fletcher 2002a) and Ecosystem Based Fisheries Management (EBFM; Fletcher et al. 2012). Harvest strategies are a key component of all contemporary fishery management systems and a requirement for certification under the Marine Stewardship Council (MSC). The objectives of ESD are reflected in the objectives of the Fish Resources Management Act 1994 (FRMA).

This Octopus Resource Harvest Strategy (Harvest Strategy) has been developed and revised in line with the Harvest Strategy …

Ecological Restoration And Ecosystem Memory Of Wildlife Forage And Understory Diversity In A Young Pine Monoculture Plantation In Central-Interior British Columbia, Julia Claire Bizon

Aspen Bibliography

Ecological restoration has recently taken center stage in the rehabilitation of degraded forest ecosystems to improve multifunctionality, biodiversity, and wildlife habitat conservation. The research summarized herein assessed the efficacy of variable stand density thinning (200, 400, and 600 stems/ha) and artificial canopy gaps (0.2, 0.5, 1.0, 2.0 ha in size) as potential restoration treatments to enhance wildlife forage and native biodiversity in a young lodgepole pine (Pinus contorta var. latifolia Engelm. ex S. Wats.) forest in central-interior British Columbia. Field data collection was conducted from May-August, 2023 to assess the early response (1-3 years post-treatment) of the forest …

Aspen Health On National Forests In The Northern Rocky Mountain Region (2008/2009 To 2024), James T. Blodgett, Kurt K. Allen, Megan Wilson, Bradley Lalande

Aspen Bibliography

Quaking aspen (Populus tremuloides) is a widely distributed species in the western United States, but in the northern Rocky Mountain Region it is a rare forest component. In national forests (NF) of the northern Rocky Mountain Region this species comprises only 1% of the Bighorn, 3% of the Black Hills, and 1% of the Shoshone cover types (DeBlander 2002, Menlove 2008, Witt 2008). Since aspen forests provide increased species richness, support wildlife, are an important component of watersheds, and have aesthetic value, there are concerns regarding the health of this relatively rare forest cover type.

Contrasting Effects Of Climate Warming On Hosts And Parasitoids: Insights From Rocky Mountain Aspen Leaf Miners And Their Parasitoids, Alisha A. Shah, Emily Hamant, Juan G. Rubalcaba, Beau Larkin, Andrew A. Forbes, H. Arthur Woods

Aspen Bibliography

Because temperature has pervasive effects on biological rates, climate warming may alter the outcomes of interactions between insect hosts and their parasitoids, which, for many host species, constitute the single largest source of mortality. Despite growing interest in parasitoid-host responses due to climate change, there are few empirical tests of thermal tolerance differences between non-model lepidopteran hosts and their parasitoids and almost none from mountain ecosystems where warming is occurring more rapidly. We examined the thermal ecology of a host–parasitoid interaction in the Rocky Mountains using the wild populations of the aspen leaf miner (Phyllocnistis populiella) and a …

Draft Genome Data Including Functional Annotation Of An Emerging Fungal Pathogen (Neodothiora Populina) Causing A Canker Disease Of Trembling Aspen In Interior Alaska, Ursel M. E. Schütte, Mace Wages, Aaron Buechlein, Jorda P. Kovash, Danielle C. Wrenn, Tereza Smrhova, Andrea Zubrova, Doug B. Rusch, Loretta M. Winton, Gerard C. Adams, Roger W. Ruess, Mary Beth Leigh, Devin M. Drown

Aspen Bibliography

Neodothiora populina is a black yeast-like fungus in the family Dothioraceae. It causes an aggressive canker disease of trembling aspen that results in widespread mortality of aspen across the boreal forest of Interior Alaska. Here we report a high-quality draft genome including functional annotation of this emerging fungal pathogen based on Oxford Nanopore Technologies long-read sequences. Our initial genome assembly totaled 23,960,169 bp and contained 18 contigs, and we identified 7,343 genes. This resource announcement provides new genomic data that are useful long term for improving our understanding of forest health in Alaska.

Bryce Canyon Aspen: Recent Trends, Future Actions, Paul C. Rogers

Aspen Bibliography

In cooperation with Bryce Canyon National Park, we undertook a survey of quaking aspen (Populus tremuloides Michx.) conditions throughout the Park with the intention of better understanding conditions and prescribing corrective measures where needed. There are clear disparities within the Park between sustainable aspen conditions and failing stands. Based on condition of mature trees, but most importantly regeneration and recruitment of juvenile stems, most aspen forests within Bryce Canyon are in poor condition. Aspen recruitment—generally sapling-sized trees that have survived browsing ungulates—is the most important metric of future stand resilience and here we found 83% of all aspen sample …

Changing Fire Regimes In The Great Basin Usa, Eva K. Strand, Kori Blankenship, Corey Gucker, Mark Brunson, Eugénie Montblanc

Aspen Bibliography

Wildfire is a natural disturbance in landscapes of the Western United States, but the effects and extents of fire are changing. Differences between historical and contemporary fire regimes can help identify reasons for observed changes in landscape composition. People living and working in the Great Basin, USA, are observing altered fire conditions, but spatial information about the degree and direction of change and departure from historical fire regimes is lacking. This study estimates how fire regimes have changed in the major Great Basin vegetation types over the past 60 years with comparisons to historical (pre-1900) fire regimes. We explore potential …

Variation In Thermal Tolerance Plasticity And The Costs Of Heat Exposure In The Estuarine Sea Hare, Phyllaplysia Taylori, Richelle L. Tanner, Rauri C. K. Bowie, Cynthia Y. Wang-Claypool, Jonathan H. Stillman

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Climate change is increasing average temperatures and the frequency and intensity of thermal extremes in coastal marine environments. Organisms in coastal marine habitats are accustomed to environmental fluctuations and possess physiological plasticity that may be advantageous in response to increased occurrence of extremes. To examine whether such plasticity is locally adapted to environmental conditions, we investigated the relationship between genetic diversity and thermal tolerance plasticity in 11 populations of the direct-developing intertidal sea hare, Phyllaplysia taylori, on the western coast of the United States. Using whole-organism metrics of muscle function and metabolic rate and a ddRADseq genomic approach, we …