Population Biology Commons^™

A Genetic Analysis Of The Rare Endemic Astragalus Ripleyi Barneby, Juan Antonio Jaramillo-Chico

Master's Theses

Astragalus ripleyi Barneby is a rare endemic species found in the San Luis Valley of the southern portions of the Rocky Mountains in Colorado and New Mexico. Though not federally listed as endangered, the species is on the Bureau of Land Management’s Sensitive Species List, warranting protection and continued management. This study aims to provide information about the genetic health of the species to inform conservation efforts and provide updated management recommendations. A genetic health analysis was conducted investigating the levels of diversity present in the species, how genetic diversity is structured across the known range of the species and …

From Genes To Streams: Mitochondrial Approaches To Population Monitoring Of The Santa Ana Sucker Catostomus Santaanae, Mariana Antonio

Electronic Theses, Projects, and Dissertations

This study was developed to use aquatic environmental DNA (eDNA) as a tool to detect the presence of the Santa Ana sucker (Catostomus santaanae), a federally threatened fish species, across the Santa Ana River in Southern California. Environmental DNA is any genetic material that an organism sheds into the environment. We can get an idea of what aquatic species are present when sampling water at a given site. We sequenced the complete mitochondrial genome (mitogenome) of the Santa Ana sucker and designed custom DNA primers to improve eDNA detection accuracy. These primers were selected based on high genetic …

Adapting Population Genetics, Practice, And Policy For Plant Conservation In A Changing World, Cooper M. Kimball-Rhines

Graduate Doctoral Dissertations

Biodiversity conservation is an inherently interdisciplinary goal that requires effective collaboration among academics, ecosystem managers, policymakers, and other stakeholders. Codesigning research with these groups ensures experiments are useful and improves adoption of policy and practice recommendations while advancing our understanding of basic science. This dissertation explores the power of codesigned research in shaping plant conservation strategies using stakeholder engagement, causal inference, demographic modeling, and multi-omic sequencing techniques. In chapter 1 I discuss the history of New England ecosystems and the need for research-driven changes to plant conservation policy and practice in the face of global change. In chapter 2, I …

Popgenhelpr: An R Package To Streamline And Facilitate Informed Population Genomic Analyses And Visualization Of Genetic Ancestry, Diversity And Differentiation, Keaka Farleigh, Mason O. Murphy, Christopher Marie Blair, Tereza Jezkova

Publications and Research

Analysing large population genomic datasets requires an interdisciplinary skillset. Beyond a knowledge base in genetics and population biology, population genomic analyses involve computer science and statistics, representing a barrier for researchers without experience in those fields. PopGenHelpR seeks to lower this barrier by enabling researchers to perform population genomic analyses and generate near-publication quality figures in a streamlined and informed fashion. PopGenHelpR allows users to estimate genetic diversity within populations as well as differentiation among populations and individuals from single nucleotide polymorphism data. PopGenHelpR includes commonly used measures such as observed heterozygosity and FST. PopGenHelpR also provides five …

Investigating Cryptic Diversity In The Hawaiian Endemic Plant, Psychotria Mariniana (Rubiaceae), Uyen Thi Hoang Nguyen

Master's Theses

Islands, with their isolation and steep environmental gradients, serve as natural laboratories for studying speciation. Molecular phylogenetic and population genetic methods utilizing Next-Generation Sequencing (NGS) have revolutionized our ability to document patterns of genetic divergence and diversity. Cryptic diversity, genetically distinct populations that were previously unrecognized as unique, and cryptic speciation, where divergent genetic populations may be deserving of status as unique species, have been observed in many taxa. The Hawaiian Islands provide an ideal setting for studying divergence and speciation due to their extreme isolation, known ages, and volcanic origin. Previous work has investigated the evolutionary relationships of the …

Quantifying Genetic Diversity In Nematode Feeding Rate, Jacob King

Honors Theses

Understanding how populations persist under changing environmental conditions is a central question in ecology and evolutionary biology. Variation in traits related to resource acquisition may play a key role in determining population survival when resources are limited or fluctuate over time. In this study, I investigated how variation in feeding-related traits influences population persistence using a combination of computational modeling and laboratory experiments. I developed a stochastic, individual-based consumer–resource model to simulate population dynamics across varying levels of trait variance and resource regimes. Across 60,000 simulated populations, increased trait variation consistently reduced extinction risk and extended persistence time, although the …

Fisheries Management Paper No.312: Discussion Paper On Management And Licensing Options For The Charter Industry - Statewide Strategic Review Of Western Australia’S Charter Fishing Sector, Department Of Primary Industries And Regional Development, Western Australia

Fisheries Management Papers

This consultation paper has been prepared to support the statewide strategic review of Western Australia’s (WA) charter fishing sector, which was initiated as a government commitment.

The paper details issues and proposals relating to the management and licensing framework, development opportunities and representation model for the charter fishing industry. The proposals have been developed in consultation with the Charter Review Working Group. The Department of Primary Industries and Regional Development (DPIRD) now seeks comment from relevant stakeholders on the issues and proposals outlined within this paper.

Comments provided will assist in providing advice and recommendations to the Minister for Fisheries …

Equid Major Histocompatibility Complex (Mhc) Evolution & Genome Organization, Lauren C. Johnson

Theses and Dissertations--Veterinary Science

The evolution of modern horses has a well-documented fossil record and has long been of interest to the genetics community. Although non-caballine equids (e.g. zebras, donkeys, and asses) can hybridize with horses, the resulting offspring are typically infertile. Despite these reproductive barriers, genomic analyses reveal regions of high sequence similarity among equid species. This dissertation investigates the role of historical introgression in the evolution of modern Equus species. The first chapter re-evaluates earlier findings derived from a limited horse population and a single reference genome. The variants of the identified regions were pushed through Ensembl’s Variant Effect Predictor to assess …

Phylogeography, Fungal Host Specificity, And Fitness In The Corallorhiza Maculata Species Complex, Hana Thixton-Nolan

Graduate Theses, Dissertations, and Problem Reports (ETD)

Mycoheterotrophic plants exploit fungi for most or all nutritional needs, providing a compelling system to address the evolutionary consequences of genome reduction, population-level variation, and germination requirements. I am using the widespread Corallorhiza maculata species complex to address questions of genomic variation, fungal host specificity, morphological variation, and germination requirements across the broad geographic range from Mexico to northern North America. This complex contains C. bulbosa, C. macrantha, and C. mertensiana, the latter with three varieties (maculata, occidentalis, and mexicana). These taxa vary in flowering time, floral morphology, and fungal associations. However, the degree …

Genomic Signatures Of Decline And Recovery In An Endangered Bat, Myotis Grisescens, Marxe Altman-Orbach

Graduate Theses/Dissertations

Tremendous population declines may result in the loss of genetic diversity, which can, in turn, lead to reduced adaptive potential, overexpression of deleterious phenotypes, and further population declines. In this way, genetic drift from a severe demographic decline may ultimately lead to an extinction vortex. However, populations that avoid the loss of genetic diversity may remain viable, despite demographic crashes. Therefore, understanding genetic diversity is vital for assessing the conservation status of species that have undergone declines, and can even reflect the effectiveness of management actions. I investigated signatures of genetic bottlenecks in the gray bat (Myotis grisescens), …

Population Structure Analysis Of Four Basal Higher-Attines Using Bioinformatic Approaches, Gabriel Mcdanield

Biology Theses

Metapopulations within the family Formicidae are unique among other animals due to the large colonies they build, and the mating strategies required to fertilize a specialized reproductive caste that will often produce young for the life of the colony. One group of ants, the fungus-gardeners (tribe Attini). The population structure of North American non-leafcutting, fungus-gardening ants has been understudied, especially in the southwest of the United States. Additionally, not much is known about their dispersal biology, so the dynamics of dispersal of these species and how they affect population structure is likewise not well known. To shed light on the …

Exploring The Role Of Ecological Traits In Shaping Spatial Patterns Of Genetic Diversity, Rilquer Mascarenhas Da Silva

Dissertations, Theses, and Capstone Projects

The field of comparative phylogeography aims at uncovering common underlying causes for shared patterns of diversity and diversification at the population level. However, it is now widely accepted that intraspecific genetic diversity patterns can differ considerably across co-occurring taxa due to ecological processes acting at the population level (and influencing individual movement and abundance). To model the processes underlying lineage diversification and demographic shifts in response to environmental changes, phylogeographers and population geneticists are now faced with the challenge of incorporating measurements of species ecological traits into their molecular studies. This dissertation aimed at investigating how different types of ecological …

Update To: Advancing Butterfly Systematics Through Genomic Analysis, Jing Zhang, Qian Cong, Jinhui Shen, Leina Song, Nick Grishin

The Taxonomic Report of the International Lepidoptera Survey

In this update, we propose (type species or type localities in parentheses): Lochris Grishin, nom. nov. (Lasaia oileus Godman, 1903; Lepidoptera: Riodinidae) as a new substitute name for Locris Grishin, 2025 preoccupied by Locris Stål, 1866 (Cercopis rubra Fabricius, 1794; Hemiptera: Cercopidae), 5 new species, and 5 new subspecies: Emesis (Mandania) mandarina Grishin, sp. n. (Brazil: Santa Catarina) and Emesis (Mandania) mandela Grishin, sp. n. (Venezuela, Carabobo) in Riodinidae Grote, 1895 (1827); others in Hesperiidae Latreille, 1809: Telegonus (Rhabdoides) flavifimbro Grishin, sp. n. (Colombia), Urbanus (Urbanoides) dolus Grishin, sp. n. (Colombia: …

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 …

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 …

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 …

Microsatellites Reveal The Population Genetic Structure Of Yellow Perch In Minnesota, Megan Boche

Journal of Earth and Life Science

When analyzing a population’s genetic makeup, looking at variation of individuals and populations is a crucial factor. The management of yellow perch will be aided by this information particularly in regard to stocking or relocation. Microsatellite loci were used to analyze the genetic population structure of yellow perch Perca flavescens within and among 29 sampling areas throughout Minnesota’s basins. Seven microsatellite DNA loci were evaluated, with heterozygosities ranging from 0.41 to 0.78. The Lower Mississippi basin samples showed higher numbers of alleles per locus and greater expected heterozygosities compared to other basins, with Lake Pepin (PEP) exhibiting the highest average …

Marine Heatwave Response Plan For Western Australia’S Wild Capture Fisheries And Aquaculture, Department Of Primary Industries And Regional Development, Western Australia

Fisheries Management Papers

The purpose of the Western Australian wild capture fisheries and aquaculture marine heatwave response plan (the Plan) is to document the Department’s approach for identifying and responding to the hazard of a marine heatwave on wild catch fisheries (commercial, recreational, charter and customary) and aquaculture resources within the geographic boundaries of WA. It provides risk reduction strategies and establishes best-practice processes for each stage of the hazard management and response continuum, ensuring that DPIRD is able to adequately prepare for, respond to, and recover from marine heatwave events. This Plan operates in conjunction with WA’s existing aquatic resource management framework, …

History, Annotated Gazetteer, And Bibliography Of Ornithology In Kalimantan, Indonesian Borneo, Frederick H. Sheldon, Mohammad Irham, Daisy G. S. Kho, Erik Meijaard, Subir B. Shakya, Dewi M. Prawiradilaga, Sebastianus (Bas) Van Balen

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

Kalimantan comprises nearly three quarters of the island of Borneo and is the place where scientific study of Bornean birds began. We describe the history of bird research in Kalimantan from its beginning, highlighting the ornithologists who explored the region and how their interests and methods changed over time, from a concentration on specimen collection, to examinations of community ecology, to conservation in the face of habitat change and species depletion, to the latest investigations using satellite, genetic, and digital technology. We also highlight some future directions for research, especially the need for more work on basic ecology and biogeography. …

‘Who’S Your Daddy?’: Ddradseq Parentage In Broodstock-Offspring Pairs Of Diadema Antillarum In A Population Restoration Initiative, Bianca R. Rosendahl

Undergraduate Scholarship and Creative Works

In the early 1980s Diadema antillarum, or the long-spined urchin, was hit by a catastrophic mass mortality event across the western Atlantic and Gulf of Mexico, inclusive of the Florida Keys. The cause of this die-off event was likely triggered by a pathogen or environmental stressor that decimated native populations by up to 98%. The species has not yet fully recovered and is struggling with recruitment success which is why it may benefit from an ex-situ recovery program. In this study, I used single nucleotide polymorphisms (SNPs) to identify genetic variation and analyze parentage in a captive population of …

Tricolored Bat (Perimyotis Subflavus) Population Genetic Structure In The Southeastern United States, Laura Henderson

Master's Theses

Tricolored bats (Perimyotis subflavus) have experienced substantial population losses from white-nose syndrome (WNS), a disease caused by the pathogenic fungus Pseudogymnoascus destructans (Pd) which infects hibernating bats. Determining population genetic structure helps assess genetic diversity and the impacts of wildlife threats to populations. Pre-WNS data shows weak-to-negligible structure and panmictic P. subflavus populations at core portions of their range. However, current genetic data from their southeastern U.S. range is lacking. I sought to determine whether recent genetic data help resolve genetic structure among southeastern populations and assess genetic differences at two stages of impact: post-WNS and …

Hidden Markov Model For Identifying Local Variants In Human Genomes Using Simulated Data, Scott Mccallum

Electronic Theses and Dissertations

Identifying adaptive mutations in genetic data is challenging due to the low frequency of occurrence of such events, and because signatures of selection are intertwined with the footprints of various other evolutionary forces that shape our genomes. Even when a larger region appears to be under selection, genomic sites that are linked to adaptive mutations have similar statistical signals, and thus can obfuscate the identification of the actual adaptive mutation. The new method described here uses a Hidden Markov Model that allows for classification of neutral, linked, and sweep (adaptive mutation) genomic sites. This model is general and can be …

Pilbara Demersal Scalefish Resource Recovery Plan 2023- 2043 (Phase 1), Department Of Primary Industries And Regional Development, Western Australia

Fisheries Management Papers

The Pilbara Demersal Scalefish Resource (PDSR) includes over 60 demersal scalefish species. The resource is accessed by the Pilbara Trap Managed Fishery, Pilbara Fish Trawl (Interim) Managed Fishery, and the Pilbara Line Fishery (PTMF, PFTIMF & PLF respectively) as well as the recreational and charter fisheries.

The PDSR is managed in accordance with the North Coast Demersal Scalefish Resource Harvest Strategy (Harvest Strategy). The sustainability objectives of the PDSR are set out in the Harvest Strategy and monitored via the use of an indicator species approach, whereby the status of key species is considered representative of the status of the …

From Turf To Turf: Fungal Invasion Of Ascocoryne Turficola In A Northern Michigan Bog, Evan L. Coscarelli-Trott

All NMU Master's Theses

This is the first paper to report Ascocoryne turficola Boud. 1905 (Helotiales: Ascomycota) within the United States. It is an obligate bog fungus native to Europe and Siberia, where it is extremely rare across most of its range. A. turficola appeared at Lily Pond Bog in Marquette, Michigan (87.47º W, 46.59º N) in 2019, almost contemporaneous with anecdotal reports in Minnesota and Ontario. Since 2019, the Lily Pond population has exploded and become the dominant fungus in this bog but has yet to spread to similar bogs nearby. This species is adapted to long distance dispersal and carries the potential …

The Influence Of Environmental Change On Genetic Diversity Across Spatial And Taxonomic Scales, Connor M. French

Dissertations, Theses, and Capstone Projects

The spatial distribution of genetic diversity is of interest to biodiversity scientists and conservationists and is a fundamental metric of biodiversity. Genetic diversity patterns across spatial and taxonomic scales contain information about population and assemblage dynamics that can convey their resilience to environmental change. Ectotherms are especially linked to their environments and may be especially sensitive to fluctuations in the environment over time. Herein, I investigate global and regional patterns of genetic diversity in two groups of ectotherms, insects and lizards, to understand the relationship between environmental change and genetic diversity, from populations to assemblages. Overall, my research aims to …

Hybridization Between The Rare Gray-Headed Chickadee And The Abundant Boreal Chickadee In The Midst Of Shifting Climate, Matthew R. Armstrong

School of Natural Resources: Dissertations, Theses, and Student Research

As species respond to changing climate, distributions and abundances may shift and alter species interactions. Hybridization, a relatively widespread phenomenon becoming more common with climate change, can have beneficial and detrimental effects on population growth rates and genetic integrity. Beneficial effects due to the introduction of advantageous alleles and increased genetic diversity may result from hybridization. Species may also accrue fitness costs associated with changing climates if mismatches occur between environmental variables and phenotypes. The gray-headed chickadee, Poecile cinctus lathami, is an extremely rare songbird that has experienced marked declines in recent decades within its restricted distribution in Alaska …

New Insights On Hybridization In Potamogeton Floridanus (The Florida Pondweed), Kaitlyn R. Sampson

Graduate Theses and Dissertations (2019 - present)

Freshwater ecosystems are some of the most important and highest threatened habitats in the world, and aquatic plants play an important, but often-overlooked, role in maintaining them. Potamogeton is a diverse and ecologically important aquatic plant genus well known for taxonomic difficulty and rampant hybridization. lbis study aimed to 1) test the hypothesis that Potamogeton jloridanus (Florida pondweed) is a hybrid between P. oakesianus and P. pulcher, and 2) to investigate correlations in ecological conditions for the focal species. This study revealed the discovery of a new population of P. jloridanus in Big Coldwater Creek in Santa Rosa Co., FL, …

Omani Camels From A Cultural And Genomics Perspective, Al Muatasim Al Zadjali

Electronic Theses and Dissertations

The Dromedarian camel, Camelus dromedarius, is native to the Arabian Peninsula, including the Sultanate of Oman. These camels are used for food, milk, as well as show and racing competitions. Despite their economic and cultural importance research on camels in Oman is limited. The goal of this study was to examine their genomic variation, relationship with camels in other parts of the Arabian Peninsula, and to determine if selective breeding has led to the establishment of distinct breeds in Oman. Information was compiled from multiple sources to produce a comprehensive review on the breeding, management, economic and cultural use, …

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 …