Open Access. Powered by Scholars. Published by Universities.®
- Institution
-
- City University of New York (CUNY) (3)
- Cal Poly Humboldt (2)
- Bucknell University (1)
- Old Dominion University (1)
- The University of Maine (1)
-
- The University of Southern Mississippi (1)
- University of Connecticut (1)
- University of Denver (1)
- University of Montana (1)
- University of Nebraska - Lincoln (1)
- University of New Mexico (1)
- University of North Florida (1)
- University of Richmond (1)
- University of South Florida (1)
- University of Tennessee, Knoxville (1)
- Keyword
-
- Biodiversity (2)
- Conservation (2)
- Fisheries (2)
- Microbial ecology (2)
- Population genomics (2)
-
- Abstracts (1)
- Amplicon sequencing (1)
- Anaerobic (1)
- Animals (1)
- Annotation (1)
- Atlantic killifish (1)
- Australia (1)
- Axial elongation (1)
- Biodiversity hot spots (1)
- Biofertilizer (1)
- Biogeography (1)
- Bioinformatics (1)
- Biomonitoring (1)
- Botany (1)
- Breeding systems (1)
- Bush tomato (1)
- Caudal Type Homeobox (1)
- Cave fauna (1)
- Caves (1)
- Cdx (1)
- Classification (1)
- Climate change (1)
- Community ecology (1)
- Cosexuality (1)
- Cytochrome-c oxidase (1)
- Publication
-
- Dissertations, Theses, and Capstone Projects (3)
- Cal Poly Humboldt theses and projects (2)
- Biological Sciences Faculty Publications (1)
- Branch Mathematics and Statistics Faculty and Staff Publications (1)
- DU Undergraduate Research Journal Archive (1)
-
- Doctoral Dissertations (1)
- Electronic Theses and Dissertations (1)
- Faculty Journal Articles (1)
- Graduate Student Theses, Dissertations, & Professional Papers (1)
- Honors Theses (1)
- International Journal of Speleology (1)
- Master's Theses (1)
- The Taxonomic Report of the International Lepidoptera Survey (1)
- UNF Graduate Theses and Dissertations (1)
- University Scholar Projects (1)
- Publication Type
Articles 1 - 18 of 18
Full-Text Articles in Genetics and Genomics
Novel Microbial Guilds Implicated In N2o Reduction, Guang He
Novel Microbial Guilds Implicated In N2o Reduction, Guang He
Doctoral Dissertations
N2O is a long-recognized greenhouse gas (GHG) with potential in global warming and ozone depletion. Terrestrial ecosystems are a major source of N2O due to imbalanced N2O production and consumption. Soil pH is a chief modulating factor controlling net N2O emissions, and N2O consumption has been considered negligible under acidic conditions (pH <6). In this dissertation, we obtained solids-free cultures reducing N2O at pH 4.5. Furthermore, a co-culture (designated culture EV) comprising two interacting bacterial population was acquired via consecutive transfer in mineral salt medium. Integrated phenotypic, metagenomic and metabolomic analysis dictated that the Serratia population excreted certain …6).>
Book Review: Habitantes De La Obscuridad (Fauna Ibero-Balear De Las Cuevas) – Inhabitants Of The Darkness (Ibero-Baleric Fauna Of Caves), Oana Teodora Moldovan
Book Review: Habitantes De La Obscuridad (Fauna Ibero-Balear De Las Cuevas) – Inhabitants Of The Darkness (Ibero-Baleric Fauna Of Caves), Oana Teodora Moldovan
International Journal of Speleology
NA
Population Genomics, Ecology And Conservation Of Asterias Sea Stars In The North Atlantic, Melenia I. Giakoumis
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 …
Predicting Marine Teleost Responses To Ocean Warming And Pollution, Akila Harishchandra
Predicting Marine Teleost Responses To Ocean Warming And Pollution, Akila Harishchandra
Electronic Theses and Dissertations
Ocean warming and pollution are two detrimental anthropogenic factors causing rapid marine ecosystem degradation recorded in the past decades. These factors alter the marine environment intolerable for many marine species, forcing them to either adapt or shift their contemporary habitat ranges to reduce the extinction risk embedded with environmental degradation. Estimating marine species’ habitat range shifts, and their potential for developing adaptive mechanisms are critical for ecosystem conservation and management, human health risk assessment, and climate change vulnerability assessments. Given that, for the first chapter of this thesis, we focused on developing a species distribution model (SDM) integrating marine species …
Annotation Of Non-Model Species’ Genomes, Taiya Jarva
Annotation Of Non-Model Species’ Genomes, Taiya Jarva
Master's Theses
The innovations in high throughput sequencing technologies in recent decades has allowed unprecedented examination and characterization of the genetic make-up of both model and non-model species, which has led to a surge in the use of genomics in fields which were previously considered unfeasible. These advances have greatly expanded the realm of possibilities in the fields of ecology and conservation. It is now possible to the identification of large cohorts of genetic markers, including single nucleotide polymorphisms (SNPs) and larger structural variants, as well as signatures of selection and local adaptation. Markers can be used to identify species, define population …
Illuminating The Drivers Of Genomic Diversification In Lamprologine Cichlids Of The Lower Congo River, Naoko P. Kurata
Illuminating The Drivers Of Genomic Diversification In Lamprologine Cichlids Of The Lower Congo River, Naoko P. Kurata
Dissertations, Theses, and Capstone Projects
Freshwater fishes are extraordinarily diverse, considering their available habitats represent a tiny proportion of the earth’s surface. Rivers connect heterogeneous habitats in a linear form and provide excellent simplified models to understand how aquatic biodiversity evolves. In particular, the lower Congo River (LCR) in west Central Africa consists of a dynamic hydroscape exhibiting extraordinary aquatic biodiversity, endemicity, and morphological and ecological specialization. This system is thus an excellent natural laboratory for understanding complex speciation and population diversification processes. In my research, I explore various drivers of diversification, and adaptive evolution in rheophilic lamprologine cichlids endemic to the LCR, including Lamprologus …
A Foundational Population Genetics Investigation Of The Sexual Systems Of Solanum (Solanaceae) In The Australian Monsoon Tropics Suggests Dioecious Taxa May Benefit From Increased Genetic Admixture Via Obligate Outcrossing, Jason T. Cantley, Ingrid E. Jordon-Thaden, Morgan Roche, Daniel S. Hayes, Stephamie Kate, Christopher T. Martine
A Foundational Population Genetics Investigation Of The Sexual Systems Of Solanum (Solanaceae) In The Australian Monsoon Tropics Suggests Dioecious Taxa May Benefit From Increased Genetic Admixture Via Obligate Outcrossing, Jason T. Cantley, Ingrid E. Jordon-Thaden, Morgan Roche, Daniel S. Hayes, Stephamie Kate, Christopher T. Martine
Faculty Journal Articles
Solanum section Leptostemonum is an ideal lineage to test the theoretical framework regarding proposed evolutionary benefits of outcrossing sexual systems in comparison to cosexuality. Theoretically, non-cosexual taxa should support more genetic diversity within populations, experience less inbreeding, and have less genetic structure due to a restricted ability to self-fertilize. However, many confounding factors present challenges for a confident inference that inherent differences in sexual systems influence observed genetic patterns among populations. This study provides a foundational baseline of the population genetics of several species of different sexual systems with the aim of generating hypotheses of any factor—including sexual system—that influences …
Mechanistic Examination Of Protist-Mediated Plant Growth Through The Comparative Development Of Medicago Truncatula, Shane Connolly
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 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
Role Of Cdx4 And Sp5l In Zebrafish Development, Wesley Tsai
Role Of Cdx4 And Sp5l In Zebrafish Development, Wesley Tsai
Honors Theses
The Caudal Type Homeobox transcription factors cdx are a family of genes found in vertebrates that regulates body regionalization and anterior-posterior patterning. They are also responsible for regulating axial elongation, but the mechanisms behind this behavior are not known. Previous studies in mouse embryonic stem cells have shown that the cdx genes are necessary for upregulating the gene sp5 which may be linked to axial elongation. Sp5 is a zinc-finger transcription factor belonging to the specificity protein (sp) family. Our group has used in-situ hybridization experiments on zebrafish embryos to show that sp5-like (sp5l) is transcribed within tailbud tissues that …
Additional Taxonomic Refinements Suggested By Genomic Analysis Of Butterflies, Jing Zhang, Qian Cong, Jinhui Shen, Leina Song, Paul A. Opler, Nick V. Grishin
Additional Taxonomic Refinements Suggested By Genomic Analysis Of Butterflies, Jing Zhang, Qian Cong, Jinhui Shen, Leina Song, Paul A. Opler, Nick V. Grishin
The Taxonomic Report of the International Lepidoptera Survey
Comparative analyses of genomic data reveal further insights into the phylogeny and taxonomic classification of butterflies presented here. As a result, 2 new subgenera and 2 new species of Hesperiidae are described: Borna Grishin, subgen. n. (type species Godmania borincona Watson, 1937) and Lilla Grishin, subgen. n. (type species Choranthus lilliae Bell, 1931) of Choranthus Scudder, 1872, Cecropterus (Murgaria) markwalkeri Grishin, sp. n. (type locality in Mexico: Sonora), and Hedone yunga Grishin, sp. n. (type locality in Bolivia: Yungas, La Paz). The lectotype is designated for Aethilla toxeus Plötz, 1882. The type locality of Dion uza (Hewitson, 1877) is likely …
American Eel (Anguilla Rostrata) And Other Fishes As Surveyed By Environmental Dna In The Bronx River And Hudson River Watershed, Sam C. Chin
Dissertations, Theses, and Capstone Projects
Mounting an effective response to the threats faced by freshwater fish may require expansions to aquatic biomonitoring in excess of what is feasible using the capture-based survey techniques currently relied upon by natural resource managers. Methods for analyzing environmental DNA (eDNA) are emerging as a minimally invasive and cost-effective approach for surveying fish and other organisms. By detecting taxon-specific DNA sequences recovered from environmental samples (e.g. water, sediment), eDNA methods are able to infer species presence from samples that can be collected rapidly with simple equipment. In many cases, eDNA detection rates of fish species have been shown to meet …
Microbial Communities In The Guana Tolomato Matanzas National Estuarine Research Reserve: An Assessment Of The Responses Of Spartina Alterniflora Epiphytes To Nitrogen Enrichment, And A Characterization Of Benthic Cyanobacterial Diversity, Anne C. Hurley
UNF Graduate Theses and Dissertations
Elevated nitrogen and phosphorus inputs from anthropogenic sources, which can lead to significant increases in algal biomass and changes in algal community composition, poses a serious threat to estuarine ecosystems worldwide. While numerous studies have addressed the impacts of nutrient enrichment on epiphytic algae in seagrass habitats, few have investigated potential nutrient-driven changes to epiphytes on emergent salt marsh plants, such as Spartina alterniflora. Epiphytic microalgae on S. alterniflora play an important role in food availability in salt marsh ecosystems, and epiphytic nitrogen-fixing cyanobacteria also provide an important source of nitrogen for salt marsh consumers. The first study included …
Biodiversity Of Philippine Marine Fishes: A Dna Barcode Reference Library Based On Voucher Specimens, Katherine E. Bemis, Matthew G. Girard, Mudjekeewis D. Santos, Kent E. Carpenter, Jonathan R. Deeds, Diane E. Pitassy, Nicko Amor L. Flores, Elizabeth S. Hunter, Amy C. Driskell, Kenneth S. Macdonald Iii, Lee A. Weigt, Jeffrey T. Williams
Biodiversity Of Philippine Marine Fishes: A Dna Barcode Reference Library Based On Voucher Specimens, Katherine E. Bemis, Matthew G. Girard, Mudjekeewis D. Santos, Kent E. Carpenter, Jonathan R. Deeds, Diane E. Pitassy, Nicko Amor L. Flores, Elizabeth S. Hunter, Amy C. Driskell, Kenneth S. Macdonald Iii, Lee A. Weigt, Jeffrey T. Williams
Biological Sciences Faculty Publications
Accurate identification of fishes is essential for understanding their biology and to ensure food safety for consumers. DNA barcoding is an important tool because it can verify identifications of both whole and processed fishes that have had key morphological characters removed (e.g., filets, fish meal); however, DNA reference libraries are incomplete, and public repositories for sequence data contain incorrectly identified sequences. During a nine-year sampling program in the Philippines, a global biodiversity hotspot for marine fishes, we developed a verified reference library of cytochrome c oxidase subunit I (COI) sequences for 2,525 specimens representing 984 species. Specimens were primarily purchased …
[Research Note] The Random Somatic Mutation Is Not Quite Random, Florentin Smarandache
[Research Note] The Random Somatic Mutation Is Not Quite Random, Florentin Smarandache
Branch Mathematics and Statistics Faculty and Staff Publications
This research note challenges the idea that Random Somatic Mutations are entirely random, highlighting their non-equiprobable nature and their influence on evolution, involution, or indeterminacy. It recalls the Neutrosophic Theory of Evolution, extending Darwin’s theory, and emphasizes the importance of distinguishing between different senses of “random mutation” in evolutionary theory.
Use Of Foreign Edna Tracers To Resolve Site- And Time-Specific Edna Distributions In Natural Streams, Braden A. Herman
Use Of Foreign Edna Tracers To Resolve Site- And Time-Specific Edna Distributions In Natural Streams, Braden A. Herman
Cal Poly Humboldt theses and projects
Substantial uncertainty in how to interpret eDNA observations motivates a need for a technique to effectively and efficiently measure of system- and time-specific eDNA distributions. Using a technique to robustly calibrate eDNA dynamics in a given system would improve established eDNA methods such as presence and absence and has the potential to refine estimates of organism abundance using eDNA concentration that are less well understood. Particles of eDNA are present in a wide variety of size and type resulting in varying transport dynamics, persistence, decay, among others. This variation likely makes eDNA transport more complex than that of conservative tracers …
Host-Microbe Interactions In Non-Native Estuarine Anemones: Biogeography And Temperature, Parker K. Lund
Host-Microbe Interactions In Non-Native Estuarine Anemones: Biogeography And Temperature, Parker K. Lund
Cal Poly Humboldt theses and projects
Non-native species are increasing in prevalence around the world, resulting in negative economic and ecological impacts. However, the broad distributions of non-native species also offer a system for investigating the response of host-associated microbial communities to environmental factors across a range of ecological scales. At the broadest scale, I investigated the geography of microbial communities in the non-native estuarine anemone Diadumene lineata on the west coast of the United States of America. Across latitudes, microbial community composition was very similar and displayed a high percentage of Klebsiella spp. at all sites. However, the communities in California tended to exhibit higher …
Genetic And Environmental Contributions To Wolbachia-Induced Cytoplasmic Incompatibility, Kelley Van Vaerenberghe
Genetic And Environmental Contributions To Wolbachia-Induced Cytoplasmic Incompatibility, Kelley Van Vaerenberghe
Graduate Student Theses, Dissertations, & Professional Papers
Maternally-transmitted Wolbachia infect the cells of most insect species, but their frequencies in host populations vary. While much of their success can be attributed to their ability to manipulate host reproduction, these manipulations are context-dependent, varying due to several biotic and abiotic factors. Wolbachia’s most common manipulation, cytoplasmic incompatibility (CI), is a conditional sterility phenotype where male-female host compatibility depends on their infection status. Specifically, CI occurs when infected males produce modified sperm that cause increased embryonic lethality unless the female carries a similar infection. Rescuing their eggs from CI increases the relative fitness of infected females, promoting Wolbachia spread …