Genetics and Genomics Commons^™

West Coast Rock Lobster 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 by the Department of Primary Industries and Regional Development (DPIRD, the Department) 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) and the Aquatic Resources Management Act …

Survey Of The Bolctes From Fish River Nature Preserve, Noah T. Nelson

Honors Theses

Boletes are a special kind of mushroom inside of the Kingdom Fungi that are distinguished from other mushrooms by their uniquely pored hymenium, as opposed to gills. Many boletes are ectomycorrhizal, meaning they are mutualists with vascular plants, and thus beneficial to the overall health of the terrestrial ecosystem. Some are well-known for their edibility and are of economic importance. In the United States 59 genus-level clades comprising 290 operational taxonomic units have been reported. The southeastern US and Gulf Coast regions however are less researched and recorded for their mushroom ecology. In Alabama, only 56 bolete species have been …

Examining Population Structure Of Cismontane And Desert Populations Of Zebra-Tailed Lizards (Callisaurus Draconoides) Using Mitochondrial And Nuclear Intron Dna., Lauren Nicole Morrison

Electronic Theses, Projects, and Dissertations

Callisaurus draconoides, also known as the Zebra-Tailed lizard, belongs to the family Phrynosomatidae family (Pianka, et al. 1972). C. draconoides is a widespread desert lizard found western North America. In California, this species can be found in the Mojave and Colorado Deserts. There are currently several populations that reside in the San Bernardino basin on the cismontane side of the Transverse and Peninsular ranges. These mountain ranges have the potential to have isolated the cismontane populations from their typical desert ranges. In addition, geological passes have the potential to serve as migration corridor between the Deserts and cismontane regions. The …

Documenting The Southern Range Terminus Of The Wood Frog (Lithobates Sylvaticus) In North America, Christian Braswell

Theses

The Wood Frog (Lithobates sylvaticus) holds a remarkable position in North American amphibian biology, with its range extending from the Arctic Circle down to the near sub-tropical southeastern United States. This thesis presents a novel quantitative polymerase chain reaction analysis (qPCR) primer specific to L. sylvaticus and a survey effort regarding the southernmost distribution and detection of this species in Alabama through the application of environmental DNA (eDNA) sampling techniques. By investigating historical data and employing advanced genetic methodologies, this research provides insights into the contemporary status and distribution of the Wood Frog. This research is important to …

Analysis Of The Population Structure And Migrationhabits Of The Northern Leopard Frog (Lithobates Pipiens) At Midewin National Tallgrass Prairie, Gretchen A. Brinkman

ELAIA

Massive amphibian declines of recent years have pushed researchers to pursue population genetics surveys and assess the status of these essential components of many ecosystems. The Northern Leopard Frog (Lithobates pipiens) has continuously experienced population declines across the continental United States due to a combination of habitat losses and environmental changes. Midewin National Tallgrass Prairie houses a considerable portion of L. pipiens in Illinois, and the two creek watersheds studied within this location provide ideal conditions to support these animals. Because this prairie restoration project is a relatively recent development, further assessments regarding the population structure and degree of migration …

Surveys Of Aphonopelma Hentzi In Missouri: Conservation Efforts Through Population, Genetics, And Habitat Studies, Anderson B. Spencer Mr., Becky Hansis-O'Niell

Undergraduate Research Symposium

Aphonopelma hentzi and other tarantula species are greatly understudied organisms. In the Missouri regions there is little knowledge on their mating patterns, gene diversity, or population sizes. The focal glades in this experiment display regional fragmentation, which could prevent tarantulas from traveling and mating between regions of their glades. Due to the lack of knowledge surrounding them, methods for determining gene diversity are harmful to the organism. Our recent work has shown that it is possible to extract genetic information from the molts of burrowing tarantulas. This will allow us to safely determine the lineages and interbreeding patterns of the …

Diving At High Altitude: O2 Transport And Utilization In The Ruddy Duck And Torrent Duck In The Andes, Kevin G. Mccracken, Graham R. Scott, Luis Alza, Andrea Astie, Ciska Bakkeren, Emil Bautista, Mariana Bulgarella, Rebecca Cheek G. Cheek, Beverly A. Chua, Neal J. Dawson, Alexis Diaz, Catherine M. Ivy, Peter B. Frappell, Cecilia Kopuchian, Sabine L. Laguë, John N. Maina, Violeta Muñoz-Fuentes, Elizabeth R. Schell, Matthew M. Smith, Ryan J. Sprenger, Pablo L. Tubaro, Elizabeth R. Schell, Matthew M. Smith, Ryan J. Sprenger, Pablo L. Tubaro, Thomas Valqui, Roy E. Weber, Daniela Wilner, Robert E. Wilson, Julia M. York, William K. Milsom

Occasional Papers of the Museum of Natural Science, Louisiana State University

Hypoxia and cold temperatures create unique physiological challenges for high-altitude organisms that can vary depending on lifestyle. While nearly all studies of air-breathing animals at high altitude are from terrestrial species, species that breath-hold dive underwater at high altitude encounter a very different set of selective pressures influencing their phenotype. The goal of this publication is to highlight the changes in O2 transport and utilization in high-altitude diving birds relative to divers at sea level, and the extent to which these changes are qualitatively distinct from phenotypic changes in non-diving species at high altitude. For example, while high capacities for …

South Coast Offshore Crustacean Resource Of Western Australia Harvest Strategy, Department Of Primary Industries And Regional Development, Western Australia

Fisheries management papers

Harvest strategies for aquatic resources in Western Australia (WA) that are managed by the Department of Primary Industries and Regional Development (DPIRD, the Department) are formal documents that ensures decision-making processes are consistent with the principles of Ecologically Sustainable Development (ESD; Fletcher 2002) and Ecosystem Based Fisheries Management (EBFM; Fletcher et al. 2012). The objectives of ESD are reflected in the objects of the Fish Resources Management Act 1994 (FRMA) and the Aquatic Resources Management Act 2016 (ARMA), which is anticipated replace the FRMA once enacted. At this point, the Fish Resources Management Regulations 1995 (FRMR) is also anticipated to …

Population Genomics, Ecology And Conservation Of Asterias Sea Stars In The North Atlantic, Melenia I. Giakoumis

Dissertations, Theses, and Capstone Projects

Uncovering how species respond to environmental change is a central question in biology (Ehrlén & Morris 2015; Habibullah et al. 2022). It is the key to elucidating the past, understanding the present and predicting the future of species’ population dynamics. This dissertation investigates the influence of environmental change on intertidal species’ distributions and genomics at several timescales, with implications for conservation.

Environmental changes have occurred throughout history, on a geological scale, and have shaped the global patterns of species’ distributions and population sizes. Biologists have long studied how geological history has shaped species distributions (Sanmartín 2012) in both terrestrial (Liu …

Diversity And Dispersal Among Eastern Continental Divide Headwater Stream Fishes In Gwinnett County, Georgia., James E. Russell, Molly M. Botting, Ryan M. Davenport, Emilee J. Story, Mark Patterson

Georgia Journal of Science

The eastern continental divide that bisects Georgia runs through Gwinnett County, separating headwater streams of the western Chattahoochee River watershed from headwater streams of the eastern Ocmulgee and Oconee River watersheds. This landscape feature was used to test hypotheses regarding headwater habitat, fish diversity and gene flow. Headwater habitats are dominant components of river network ecosystems delivering vital ecosystem services and biodiversity. Three headwater streams, one in the Chattahoochee watershed and two in the Oconee watershed, on Gwinnett County Park property, were sampled for differences in physical and chemical properties and fish inter- and intraspecific diversity. Our results suggest the …

Mechanistic Examination Of Protist-Mediated Plant Growth Through The Comparative Development Of Medicago Truncatula, Shane Connolly

University Scholar Projects

Protists are known to increase plant growth through two main mechanisms: the microbial loop and the alteration of the root microbiome. The microbial loop is a nutrient recycling method in which protists provide inorganic nitrogen ions to the plant. Alteration of root microbiome leads to the removal of plant pathogens and shifting communities towards plant growth-promoting bacteria (PGPB). This study aimed to elicit which mechanism could produce the largest boost in shoot weight for Medicago truncatula. A series of microcosm experiments were explored in which M. truncatula was grown with variable microbiome structures to allow for mechanism differentiation. The …

Du Undergraduate Showcase: Research, Scholarship, And Creative Works, Caitlyn Aldersea, Justin Bravo, Sam Allen, Anna Block, Connor Block, Emma Buechler, Maria De Los Angeles Bustillos, Arianna Carlson, William Christensen, Olivia Kachulis, Noah Craver, Kate Dillon, Muskan Fatima, Angel Fernandes, Emma Finch, Colleen Cassidy, Amy Fishman, Andrea Francis, Stacia Fritz, Simran Gill, Emma Gries, Rylie Hansen, Shannon Powers, Jacqueline Martinez, Zachary Harker, Ashley Hasty, Mykaela Tanino-Springsteen, Kathleen Hopps, Adelaide Kerenick, Colin Kleckner, Ci Koehring, Elijah Kruger, Braden Krumholz, Maddie Leake, Lyneé Alves, Seraphina Loukas, Yatzari Lozano Vazquez, Haley Maki, Emily Martinez, Sierra Mckinney, Mykaela Tanino-Springsteen, Audrey Mitchell, Kipling Newman, Audrey Ng, Megan Lucyshyn, Andrew Nguyen, Stevie Ostman, Casandra Pearson, Alexandra Penney, Julia Gielczynski, Tyler Ball, Anna Rini, Christina Rorres, Simon Ruland, Helayna Schafer, Emma Sellers, Sarah Schuller, Claire Shaver, Kevin Summers, Isabella Shaw, Madison Sinar, Claudia Pena, Apshara Siwakoti, Carter Sorensen, Madi Sousa, Anna Sparling, Alexandra Revier, Brandon Thierry, Dylan Tyree, Maggie Williams, Lauren Wols

DU Undergraduate Research Journal Archive

DU Undergraduate Showcase: Research, Scholarship, and Creative Works

Past And Present Patterns Of Neutral And Adaptive Genetic Diversity In Wild Mandrills (Mandrillus Sphinx), Anna Weber

University of New Orleans Theses and Dissertations

Although primates have fascinated researchers and the public alike for generations, one species that has remained enigmatic is the mandrill (Mandrillus sphinx), a large Cercopithecine monkey endemic to Central Africa. Mandrills are currently in decline due to bushmeat hunting, urbanization, and habitat loss. Neutral and adaptive genetic diversity are important tools for understanding evolutionary history and future viability, since diversity influences a species’ ability to adapt to a changing environment. However, thus far, minimal genetic information has been available for wild mandrills. Because of the dense vegetation in their tropical forest habitat, studying wild mandrills has proven to …

Analysis Of The Population Structure And Migration Habits Of The Northern Leopard Frog (Lithobates Pipiens) At Midewin National Tallgrass Prairie, Gretchen A. Brinkman

Honors Program Projects

Massive amphibian declines of recent years have pushed researchers to pursue population genetics surveys and assess the status of these essential components of many ecosystems. The Northern Leopard Frog (Lithobates pipiens) has continuously experienced population declines across the continental United States due to a combination of habitat losses and environmental changes. Midewin National Tallgrass Prairie houses a considerable portion of L. pipiens in Illinois, and the two creek watersheds studied within this location provide ideal conditions to support these animals. Because this prairie restoration project is a relatively recent development, further assessments regarding the population structure and degree …

History, Annotated Gazetteer, And Bibliography Of Sarawak Ornithology, Frederick H. Sheldon, Dency F. Gawain, Daisy G. S. Kho, Rosalina Regai, Subir B. Shakya, Chin Aik Yeap

Occasional Papers of the Museum of Natural Science, Louisiana State University

Sarawak is Malaysia’s largest state, covering most of northern Borneo. It has a remarkable history of scientific bird study, starting in the 1840s and growing ever since. To set the stage for the gazetteer, which is the core of this paper, we start with a review of this history and discuss various forces that have influenced the direction of bird research in the state. Following this introduction comes the gazetteer, which is an annotated list of c. 865 sites in Sarawak where birds have been collected, studied, or regularly observed. The gazetteer provides the latitude, longitude, and elevation of each …

Placing The Evolutionary History Of Desmognathus Salamanders In Context: A Phylogeographic Approach, Kara Jones

Theses and Dissertations--Biology

Patterns of genetic variation do not arise in a vacuum but are instead shaped by the interplay between evolutionary forces and ecological constraints. Here, I use a phylogeographic approach to examine the role that ecology played in lineage divergence in the Desmognathus quadramaculatus species complex (Family: Plethodontidae), which consists of three nominal species: D. quadramaculatus, D. marmoratus, and D. folkertsi. Previous phylogenetic studies have shown that individuals from these species do not form clades based on phenotype. My approach to reconciling phylogenetic discordance was two-fold, using (1) genome-wide markers to provide insight into the …

Sympatric Carnivores And Vegetation Structure Influence The Distribution And Abundance Of Humboldt Martens In Northern California, Erika L. Anderson

Cal Poly Humboldt theses and projects

The Humboldt marten (Martes caurina humboldtensis) is a species facing conservation concern in Oregon and California. Historical populations were subjected to unregulated fur trapping and timber harvest throughout the late 19^th and early 20^th centuries leading to a 90% decline in their distribution. As such, the Humboldt marten is listed as a state endangered species in California, and the analogous ‘coastal marten’ is listed as federally threatened under the Endangered Species Act and classified as a Species of Greatest Conservation Need in Oregon and California. Contemporary populations are small, and isolated, and threatened by habitat loss …

Effects Of Riverine Barriers On Avian Evolution In The Amazon Basin, Andre Eugene Moncrieff

LSU Doctoral Dissertations

The high biodiversity found in the Amazon Basin has long captivated the attention of naturalists and evolutionary biologists seeking to explain its origins. Early observations by Alfred Wallace highlighted the role of rivers in delimiting the geographic ranges of many species; furthermore, where rivers narrow towards their headwaters, he noted that some species cross rivers freely. A major goal of this dissertation is to investigate how these and other observations about riverine barriers might inform our understanding of how speciation unfolds in Amazonia. My approach involved generating genomic data with dense geographic sampling for manakins in the genus Lepidothrix, …

Potential Fitness Trade-Offs Of Elevated Esterase Activity Associated With Insecticide Resistance In The Mosquito Culex Quinquefasciatus, Timothy Schulte

Electronic Theses, Projects, and Dissertations

One of the current major issues in the control of vector-borne disease is resistance to insecticides. Resistance to one or more insecticides has appeared in over 580 different arthropod species. Widespread resistance has led to the field of Insecticide Resistance Management (IRM). The goal of IRM is to develop insecticide-use strategies that prevent or slow down the evolution of resistance. Computer models have shown that more effective IRM strategies rely on the assumption that resistance carries a fitness cost in the absence of insecticide use.

In the mosquito Culex quinquefasciatus resistance to certain organophosphate insecticides is caused by an increased …

Variability And Genetic Structure Of The Montezuma Quail Cyrtonyx Montezumae In The Northern Limit Of Its Distribution, Eduardo Sánchez Murrieta, Alberto Macías-Duarte, Reyna A. Castillo-Gámez, Angel B. Montoya, Alejandro Varela-Romero, Nohelia G. Pacheco Hoyos

National Quail Symposium Proceedings

A species’ geographic distribution of genetic variability is influenced by different factors including size of geographic distribution, dispersal capability, mating system, and migration. For instance, a low migration rate among populations may cause a decrease in genetic variation. Such is the case of the Montezuma quail (Cyrtonyx montezumae), a popular game bird with a limited flight capacity that prevents long-distance dispersal. In the northern limit of the species’ distribution in Arizona, New Mexico, and Texas in the United States, the species inhabits oak forests that are separated from one another by deserts. Consequently, Montezuma quail populations are distributed …

Evaluating Non-Invasive Environmental Methods For Detecting Tropical African Pangolin Species To Inform Conservation Actions, Ichu Godwill Ichu

Theses and Dissertations

Tropical African pangolin species are threatened throughout their range due to habitat loss and illegal take. Limited knowledge on distribution has rendered conservation efforts challenging. Methods commonly used for other wildlife species need to be tested for each pangolin species as each has variable ecologies requiring specific detection and monitoring techniques. This thesis evaluates the efficacy of two non-invasive environmental methods for detecting tropical African pangolin species, and consists of two complementary studies; a proof of concept study using soil sourced eDNA from a white-bellied pangolin enclosure in the Columbus Zoo, Ohio, to detect the species, and a field study …

Chromosome Number Evolution, Phylogeography, And The Effects Of Climate Change On Species Distributions In Polyploid Plant Systems, Courtney H. Babin

University of New Orleans Theses and Dissertations

Polyploidy, a term used to describe organisms with cells having more than two paired sets of chromosomes, is a significant driver of diversification among land plants. Over a century of research has advanced our understanding of polyploidization in some taxa, but polyploid organisms remain understudied. In this dissertation, I investigate chromosome number evolution, phylogeographic structure, genetic differentiation, and the effects of climate change on ploidy level distribution using polyploid plant systems. In the first chapter, I inferred a molecular phylogeny of Allium, an economically important genus that includes cultivated crops and ornamentals, to investigate evolutionary transitions in chromosome number …

Population Genetics Of Cownose Rays, Rhinoptera Spp. In The Western Atlantic, Helen Weber

Master's Theses

Using molecular tools (e.g., the NADH subunit II mitochondrial gene), this study was the first to document the Brazilian cownose ray, Rhinoptera brasiliensis, within the northwestern Atlantic (NWA), and was the first study to examine population structure in R. brasiliensis within the NWA or northern Gulf of Mexico (GMX), revealing novel insights into the population biology of the animal and extending its range by nearly 1,500 km. This study also examined the sympatrically occurring American cownose ray, R. bonasus, and found population structure between the NWA and the GMX and the NWA and the southwestern Atlantic (SWA). High …

Genomic Insights Into Mechanisms Of Microbial Evolution And Evolution-Inspired Strategies To Combat Pathogen Diversity, Saymon Akther

Dissertations, Theses, and Capstone Projects

We live in an era of emerging infectious diseases that are increasingly common, rapidly spreading, and gravely devastating. Lyme disease, caused by bacteria belonging to the genus Borreliella, is rapidly rising in the Northern Hemisphere because of geographic range expansion of both the tick vectors and the pathogens. Evolutionary comparative analysis of Borreliella genomes is a key to understanding the phylogeographic history and mechanisms of their global diversification. Moreover, genomic variations in Borreliella associated with human pathogenicity, e.g., at loci encoding cell-surface antigens interacting with the vertebrate hosts, have not been fully identified. Similarly, the ongoing COVID-19 pandemic, caused …

Gene Drives And The Consequences Of Over-Suppression, Cole Butler

Biology and Medicine Through Mathematics Conference

No abstract provided.

Analysis Of Water Quality And Fish Communities Of Crooked Creek, Tributary To The Allegheny River In Southwestern Pennsylvania, Katherine Stupar

Electronic Theses and Dissertations

Crooked Creek is a tributary of the Allegheny River with a drainage area of 292 square miles. It has been historically affected by mine drainage pollution. Extensive cleanup and monitoring efforts by the Commonwealth of Pennsylvania and the U.S. Army Corps of Engineers (USACE) have taken place over the last four decades. Unconventional oil extraction, or fracking, presents an emerging threat to the water quality of this stream and the health of its fish communities. Here we perform an analysis of the Crooked Creek watershed utilizing backpack electrofishing, eDNA metabarcoding, and various methods of water quality analysis. Seven sites on …

Microbial Diversity And Community Structure In Sediments Associated With The Seagrass (Thallassia Testudinum) In Apalachicola Bay, Florida, Rahma Ahmed, Thomas Mcelroy, Troy Mutchler

Symposium of Student Scholars

Seagrass is an angiosperm which provides many ecosystem services in coastal areas, such as providing food, shelter and nurseries for many species, and decreasing the impact of waves on shorelines. A global assessment reported that 29% of known seagrass meadows are in a state of decline due to the effects of human activity. Seagrass is commonly found in shallow marine waters where they form meadows containing a microbiome that plays an important role in providing nutrients for seagrass growth, though little is known about the microorganisms within the seagrass meadow sediments. Our project collected sediments from seagrass meadows and adjacent …

The Influence Of Climate Change On The Ecology Of The Arctic Ground Squirrel In Denali National Park, Ak., Nigel A. Golden

Doctoral Dissertations

This dissertation research focuses on the ecology of the Arctic ground squirrel (Urocitellus parryii) in Denali National Park and Preserve, AK. The Arctic ground squirrels is a species of interest for monitoring efforts under the National Park Services’ Vital Signs Monitoring Program under the Vital Signs Monitoring program. The focus of this program is to monitor what is considered to be the most significant indicators of ecological conditions of the specific park resources that are of the greatest concern. The CAKN designated the Arctic ground squirrel (Urocitellus parryii) as one indicator species of park ecosystems. Despite being easy to observe …

Conservation Status Assessment Of The Egg-Mimic Darter (Percidae: Etheostoma Pseudovulatum) Using A Multi-Faceted Approach, Zachary L. Wolf, John W. Johansen, Rebecca E. Blanton

Southeastern Fishes Council Proceedings

The imperiled Egg-mimic Darter (Etheostoma pseudovulatum) is a headwater-adapted fish restricted to an area less than 1000 km² in Tennessee. It is found in only six tributaries of the Duck River and the large, mainstem of this system may act as a barrier to dispersal, restricting population connectivity. The only status assessment of this species was over two decades ago; genetic diversity and the degree of population connectivity have never been evaluated. We conducted a conservation status assessment using a multi-faceted approach to better inform conservation management plans, including examining its current distribution, assessing habitat quality, estimating …

An Analysis Of The Spatial Genetic Structure Of A Hybrid Zone Between Two Species Of Killifish, Fundulus Heteroclitus And F. Grandis, Andrew Lee Hardy

UNF Graduate Theses and Dissertations

Hybridization offers unique insight into the evolutionary process of speciation and the forces that maintain barriers to reproduction. In northeast Florida, a hybrid zone between two species of killifish, Fundulus heteroclitus and F. grandis, has been identified near Flagler Beach, FL, although the exact boundaries of the hybrid zone remain unknown (Gonzalez et al. 2009). This study aims to determine the fine-scale spatial genetic patterns of the hybrid zone and test the hypothesis that species ranges are influenced by changes in dominant vegetation. Results from an ADMIXTURE analysis and F_ST data indicated the boundary of the area of …