Biodiversity Commons^™

Social Interactions And Spatial Structure Drive Community Assembly Of Bacterial Biofilm, Matthew C. Bond

Dartmouth College Ph.D Dissertations

Despite the critical nature which microbial communities play in the natural world and human civilization, the breadth of understanding remains shallow. Challenged by scale, high variability between environments, and extensive diversity, microbial ecologists strive to understand connections between a community’s structure and function, as well as the ecological and evolutionary mechanisms underlying observed natural patterning of communities. Biofilms are the predominate mode of growth for microbial communities—characterized by cellular attachment to a surface via a self-produced matrix and heterogeneous structure, often resulting in a primary growth front along the biofilm surface due to differential access to bulk nutrients (cite). This …

Advancing The Blue Economy Through Sustainable Mariculture: The Prospect Of Pearl Oyster And Sponge Cultivation In St. Vincent And The Grenadines, Kevin Antonio Providence

Gulf and Caribbean Research

The Blue Economy is estimated to be worth over USD 2.5 trillion annually, or almost 3% of the world’s GDP in 2020. St. Vincent and the Grenadines (SVG) in the Caribbean region has a vast and rich marine space that is underutilized. This study aimed to explore the feasibility of pearl oyster and sponge farming to advance the country’s Blue Economy through sustainable mariculture. A qualitative approach was applied, using a literature review and thematic analysis of data gathered through semi—structured interviews and focus group discussions with relevant stakeholders. Among several species evaluated, the result of the study revealed that …

Building A Coordinated Framework For Research And Monitoring In Large-Scale International Marine Protected Areas: The Ross Sea Region As A Model System, Cassandra Brooks, Sharon Stammerjohn, Grant Ballard, Alice K. Duvivier, Eileen Hofmann, Michelle Larue, Cara Nissen, Alexander J. Orona, B. Jack Pan, Annie E. Schmidt, Nathan Walker, George M. Watters, John Weller

CCPO Publications

To fulfill their conservation potential and provide safeguards for biodiversity, marine protected areas (MPAs) need coordinated research and monitoring for informed management through effective evaluation of ecosystem dynamics. However, coordination is challenging, often due to knowledge gaps caused by inadequate access to data and resources, compounded by insufficient communication between scientists and managers. We propose to use the world's largest MPA in the Ross Sea, Antarctica as a model system to create a comprehensive framework for an interdisciplinary network supporting research and monitoring that could be implemented in other remote large-scale international MPAs. Our proposed framework has three key components: …

Wildlife Conservation And Adaptation To Humans, Valeria Mazza Phd, Claudio Carere

Animal Sentience

For many animal species, the ability to adapt to coexistence with the human species and to the environmental changes that humans cause is a biological imperative. This adaptive capacity varies not only between species, but within species. Studying individual differences in animals’ behavioral, cognitive and physiological adaptability is important for integrating ethology and conservation. Findings about animal cognitive capacities, including learning, need to be applied in conservation—but humans need to be educated about ethology, coexistence and conservation too.

Quick Guide To Aquatic Weeds Of Oregon, Gabriel E. Campbell, Ashley Newcomb, Jacob Rose

Center for Lakes and Reservoirs Publications and Presentations

This document contains a quick, non-technical, pictured-based field guide to aquatic weed species in Oregon and throughout the Pacific Northwest. It contains approximately 50 common, newly emerging, and watch list exotic weeds and common native look-alike plants. The intended audience for this guide includes weed professionals, restoration practitioners, land managers, professional botanists, and amateur naturalists.

Lycosidae Abundance And Diversity Across Lawn And Leaf Litter Substrate, Sage O. Lockett, Dan Albrecht-Mallinger

Undergraduate Research Posters

Significant knowledge gaps exist in how land-cover impacts ground-hunting spider populations. To fill these gaps, this study investigates a common family of ground-hunting spiders, Lycosidae, to determine differences in their abundance and diversity in deciduous leaf litter and managed turfgrass (lawn). The study was conducted within a forested ecosystem at Virginia Commonwealth University's Rice Rivers Center in Charles City County, Virginia. I placed 10 belt transects (1m x 20m) on lawn substrate and 10 identical transects in deciduous forest leaf litter substrate. I performed repeated visual census via eyeshine and manual capture of up to three individuals per transect …

Using Novel And Traditional Survey Techniques To Monitor Small Mammal Species In Northwestern California, Sydney Mccluskey

Cal Poly Humboldt theses and projects

Small mammal species play a critical role in forest ecosystems contributing significantly to overall forest biodiversity and ecological dynamics. Forest-dwelling species are among the most vulnerable to habitat loss and fragmentation. It is essential to develop efficient techniques for monitoring small mammal populations in forested ecosystems to inform conservation efforts and management plans; yet, monitoring small mammals in these habitats can be particularly challenging due to their size, activity patterns, and frequently nocturnal nature. In this study, I aimed to address two primary research objectives: 1) compare the effectiveness of 3 distinct camera-trap survey techniques (i.e., ground, tree, and tube) …

Hite: A Fast And Accurate Dynamic Boundary Adjustment Approach For Full-Length Transposable Element Detection And Annotation, Kang Hu, Peng Ning, Minghua Xu, You Zou, Jianye Chang, Xin Gao, Yaohang Li, Jue Ruan, Bin Hu, Jianxin Wang

Computer Science Faculty Publications

Recent advancements in genome assembly have greatly improved the prospects for comprehensive annotation of Transposable Elements (TEs). However, existing methods for TE annotation using genome assemblies suffer from limited accuracy and robustness, requiring extensive manual editing. In addition, the currently available gold-standard TE databases are not comprehensive, even for extensively studied species, highlighting the critical need for an automated TE detection method to supplement existing repositories. In this study, we introduce HiTE, a fast and accurate dynamic boundary adjustment approach designed to detect full-length TEs. The experimental results demonstrate that HiTE outperforms RepeatModeler2, the state-of-the-art tool, across various species. Furthermore, …

From The Ground Up: A Complex Systems Approach To Climate Change Adaptation In Agriculture, Karen Buchsbaum

Antioch University Dissertations & Theses

Climate change presents an unprecedented challenge to global agriculture and food security. Small farms are especially vulnerable to the local impacts of large-scale drivers of change. Effective adaptation in agriculture requires working across scales, and geographic, political, and disciplinary boundaries to address barriers. I use elements of case study, agent-based modeling and serious games, to design a model of farmer decision-making using the sociocognitive framework of climate change adaptation. I examine how adaptation functions as a process, how complex dynamics influence farmer behavior, and how individual decisions influence collective behavior in response to climate change. This novel approach to adaptation …

Influence Of Landscape Characteristics On Eastern Gray Treefrog (Hyla Versicolor) Occupancy Within Managed Forests Of Pennsylvania And Virginia, Susanna G. Sousa

Antioch University Dissertations & Theses

Understanding the characteristics that influence amphibian occupancy within forest ecosystems is necessary for effective conservation and management. My study focused on how eastern gray treefrog (Hyla versicolor) occupancy is influenced by environmental attributes quantified at various spatial extents. From May through July 2020 and 2021, we deployed autonomous recording units at 986 unique locations within managed forests in Pennsylvania and Virginia. Landcover class and road density were evaluated around each sampling location at ten spatial extents between 60 and 4000 m. Additionally, I measured aspect, elevation, soil drainage class, distance to nearest wetland, and basal area at each …

Pioneering Plant Metabolomic Library Of Indonesian Plants For Research, Conservation, Capacity Building And Economic Development, Isabel Armas, Ernawati Sinaga, Nonon Saribanon, Noverita, Alvira Noer Effendi, Chairil Rohadi, Hanifa Nur Adilah, Vyacheslav Dushenkov, Ilya Raskin

Publications and Research

Indonesia, one of the world’s most biodiverse countries, is undergoing mass deforestation, exacerbating climate change and leading to accelerated loss of species. This project addressed the urgent need to conserve endangered Indonesian biodiversity. Specifically, the potentially life-saving bioactive compounds harbored within its plants. A group of Indonesian researchers from Universitas Nasional (UNAS) in Jakarta received training in RApid Metabolome Extraction and Storage (RAMES) technology, an ethical, low-impact, field-deployable and cost-effective methodology developed by Rutgers University. The team of Indonesian scientists used this technology to create the first metabolomic library of Indonesian plant species and an easily transportable collection containing 501 …

Long Term Trends In Mortality Rates Of A Smallmouth Bass Population, Caleb D. Anderson

Journal of Earth and Life Science

Smallmouth bass Micropterus dolomieu are known as a popular sport fish for anglers. When a known smallmouth bass fishery appears to have a dwindling population, it raises questions about the population health. A common indicator of the health of the population is the mortality rate. By comparing mortality, conclusions can be made on whether smallmouth bass are dying at a different rate in the system over time. Therefore, the objective of this study was to see if there had been a significant change in smallmouth bass mortality over a span of thirty years in Round Lake (DOW:010204), Aitkin County, Minnesota. …

Flowering Rush (Butomus Umbellatus) Id Guide For The Columbia River, Gabriel Campbell, Jacob Rose

Center for Lakes and Reservoirs Publications and Presentations

This is a picture based field guide for how to identify Flowering Rush (Butomus umbellatus) in the Columbia River throughout Oregon and Washington. It includes how to tell this species from commonly co-occurring look-alike species.

Quantifying The Ecological Effects Of Salix Fragilis On Riparian Habitat In Kittitas County, Washington, Landon Shaffer

All Master's Theses

Invasive species threaten plant community structure and function globally. Riparian areas, the zone near streams where water influences vegetation, are especially sensitive to invasive species colonization, suffering large-scale shifts in community composition. Salix fragilis (crack willow) is a nonnative riparian species abundant in the lower elevation tributaries of central Washington. Some speculate whether this willow should be listed as invasive in Washington, despite a lack of regional supporting evidence. I studied riparian communities dominated by either S. fragilis or native species in the Kittitas Valley and measured biodiversity, quantified differences in solar attenuation, and compared leaf decomposition rates to learn …

Diet And Population Genomics Of River Otters (Lontra Canadensis) In West Virginia, Eden Grace Nitza

Graduate Theses, Dissertations, and Problem Reports (ETD)

North American river otters (Lontra canadensis), hereafter, otters, are apex predators in aquatic ecosystems across Appalachia, and thus have important impacts on their ecosystems such as food web regulation, nutrient cycling, and reducing the impacts of invasive species. Otters were extirpated from most of Appalachia, including all of West Virginia, by the mid-1900’s due to habitat destruction and overharvest. The West Virginia Division of Natural Resources (WVDNR) began an otter reintroduction program in 1984 which translocated approximately 250 otters into the state by 1997. This reintroduction program was largely considered successful, and a regulated harvest season was opened …

A Case Of One Step Forward And Two Steps Back? An Examination Of Herbicide-Resistant Weed Management Using A Simple Agroecosystem Dynamics Model, Srinadh Kodali, Chris Flores-Lopez, Isabelle Lobdell, Branson Kim, James C. Russell, Lane Michna, Benjamin L. Turner

Mechanical & Aerospace Engineering Faculty Publications

Global herbicide-resistant weed populations continue rising due to selection pressures exerted by herbicides. Despite this, herbicides continue to be farmers’ preferred weed-control method due to cost and efficiency relative to physical or biological methods. However, weeds developing resistance to herbicides not only challenges crop production but also threatens ecosystem services by disrupting biodiversity, reducing soil health, and impacting water quality. Our objective was to develop a simulation model that captures the feedback between weed population dynamics, agricultural management, profitability, and farmer decision-making processes that interact in unique ways to reinforce herbicide resistance in weeds. After calibration to observed data and …

State Of Coastal And Marine Resources: Sablayan, Occidental Mindoro, Ma Celina J. Añonuevo, Jemelyn Grace P. Baldisimo, Denmark B. Racamara, Mary Joyce P. Velos, Joseph Benedict T. Garcia, Frederico B. Sabban, Joey P. Cabasan, Rhea Mae Luciano, Darryl Anthony Valiño, Lovely Joy Heyres, Hazel O. Arceo

Biological Sciences Faculty Publications

[Introduction] Sablayan, situated on the western side of Mindoro Island facing the WPS (12.8564° N, 120.9101° E), is a first-class municipality in the province of Occidental Mindoro with a total land area of 2,188.8km² that is divided into 22 barangays, nine of which are along the coast. The coastline stretches for 115 km, with municipal waters covering approximately 750,000 km² (LGU-Sablayan 2008).

The Apo Reef Natural Park, one of its most prominent features, is located approximately 33 km off the coast (Figure 2.9-1) The Apo Reef Natural Park is a protected coral reef system under presidential proclamation 868 (1996) encompassing …

Concepts In Animal Parasitology, Chapter 07: Biostatistics For Parasitologists: A Painless Introduction [Parascript Approaches], Jenő Reiczigel, Marco Marozzi, Fábián Ibolya, Lajos Rózsa

Concepts in Animal Parasitology

Covers biostatistics for parasitologists and includes discussion of taking samples, frequency distribution of host individuals across infection classes, sample size, prevalence, mean intesity, median intensity, stochasic equality of intensities, abundance, crowding, levels of aggregation, parasite sex ratio, parasite species richness, interactions between parasite species, and the tool Quantitative Parasitology on the Web (QPweb).

Chapter 7 in Concepts in Animal Parasitology on biostatistics for parasitologists by Jenő Reiczigel, Marco Marozzi, Fábián Ibolya, and Lajos Rózsa. 2024. S. L. Gardner and S. A. Gardner, editors. Zea Books, Lincoln, Nebraska, United States. doi: 10.32873/unl.dc.ciap007

Concepts In Animal Parasitology, Chapter 58: Acanthocephala Rudolphi, 1808 (Phylum), Scott Monks

Concepts in Animal Parasitology

An overview of the phylum Acanthocephala Rudolphi, 1808, also called the thorny-headed or spiny-headed worms, including discussion of their general morphology, life cycles, classification, and phylogenetic relationships.

Chapter 58 in Concepts in Animal Parasitology, by Scott Monks. 2024. S. L. Gardner and S. A. Gardner, editors. Zea Books, Lincoln, Nebraska, United States. doi: 10.32873/unl.dc.ciap058

Movement Behavior And Metapopulation Connectivity Of Stream Salamanders In Response To Disturbance Events, Kathryn M. Greene

Theses and Dissertations--Biology

Metapopulations are shaped by the dispersal between populations in a landscape. Disturbance events can disrupt this connectivity resulting in local population extinction. For my dissertation, I used a combination of empirical and theoretical techniques to examine dispersal in response to disturbance and assessed it’s population-level consequences. My research used capture-mark-recapture sampling techniques to evaluate stream salamander movement in response to (1) a supraseasonal drought and (2) mountaintop-removal-mining (MTR) and valley-filling (VF) and (3) agent-based simulation modeling to evaluate population extinction risk in response to varying dispersal and mortality rates.

First, I evaluated the effects of a supraseasonal drought, a severe …

Co-Divergence Of Lemur Hosts And Gut Microbiomes Across Multiple Evolutionary Scales, Mariah E. Donohue

Theses and Dissertations--Biology

This dissertation bridges micro- and macroevolutionary approaches to understand the co-diversification of animal hosts and their gut microbiomes at different evolutionary timescales. I examined these dynamics using wild lemurs, a diverse Primate clade endemic to the island of Madagascar.

First, I tested the relative effects of host phylogenetic relationships, diet, and habitat in shaping the gut microbiome through deep evolutionary time and across distinct microbial kingdoms. I designed a natural experiment sampling feces from rainforest and dry forest lemur communities with similar phylogenetic assemblages and considerable variation in dietary strategy. Then, I amplified and sequenced two metabarcoding genes, the V4 …

Concepts In Animal Parasitology, Chapter 34: Introduction To Diplostomida Olson Et Al., 2003 (Order) [Platyhelminthes, Trematoda, Digenea, Diplostomida], Lucrecia Acosta Soto, Bernard Fried, Rafael Toledo

Concepts in Animal Parasitology

An introduction to the trematode (fluke) order Diplostomida Olson et al., 2003, one of the two main lineages from which subclass Digenea have diversified. Includes a discussion of Diplostomida systematics, general morphology, and human pathogenesis, including schistosomiasis.

Chapter 34 in Concepts in Animal Parasitology, by Lucrecia Acosta Soto, Bernard Fried, and Rafael Toledo. 2024. S. L. Gardner and S. A. Gardner, editors. Zea Books, Lincoln, Nebraska, United States. doi: 10.32873/unl.dc.ciap034

Concepts In Animal Parasitology, Chapter 52: Oxyurida (Order): Pinworms [Nemata, Secernentea], Haylee J. Weaver

Concepts in Animal Parasitology

An overview of the pinworms, order Oxyurida, discussing their key features, life history, ecology, health effects on hosts, systematics, taxonomy, and including summaries of the main groups.

Chapter 52 in Concepts in Animal Parasitology, by Haylee J. Weaver. 2024. S. L. Gardner and S. A. Gardner, editors. Zea Books, Lincoln, Nebraska, United States. doi: 10.32873/unl.dc.ciap052

Concepts In Animal Parasitology, Part 5: Ectoparasites, Griselda Pulido-Flores, Scott C. Cutmore, Thomas H. Cribb, Alejandro Oceguera-Figueroa, Sebastian Kvist, Marcela Lareschi, Lajos Rózsa, Haylee J. Weaver, Sue Ann Gardner, Darci Moraes Barros-Battesti, Valeria Castilho Onofrio, Filipe Dantas-Torres

Concepts in Animal Parasitology

Part V: Ectoparasites, chapters 60–67, pages 732–841, in Concepts in Animal Parasitology. 2024. Scott L. Gardner and Sue Ann Gardner, editors. Zea Books, Lincoln, Nebraska, United States; part V doi: 10.32873/unl.dc.ciap075

Platyhelminthes

Chapter 60: Monogenea van Beneden, 1858 (Class) by Griselda Pulido-Flores, pages 733–742

Chapter 61: Transversotrematidae Witenberg, 1944 (Family): Ectoparasitic Trematodes by Scott C. Cutmore and Thomas H. Cribb, pages 743–746

Hirudinea

Chapter 62: Hirudinea (Subclass): Parasitic Leeches by Alejandro Oceguera-Figueroa and Sebastian Kvist, pages 747–755

Arthropoda

Chapter 63: Siphonaptera Latreille, 1825 (Order): Fleas by Marcela Lareschi, pages 756–770

Chapter 64: Phthiraptera (Order): Lice by Lajos Rózsa and Haylee …

Concepts In Animal Parasitology, Chapter 33: Aspidogastrea (Subclass) [Platyhelminthes, Trematoda, Aspidogastrea], Klaus Rohde

Concepts in Animal Parasitology

An overview of the trematode (fluke) subclass Aspidogastrea, a very small group of trematodes with around 80 species, none of them of economic importance, but are of great interest because of their unique structure, their simple life cycles (which may well be the most primitive or ancestral one among the trematodes, and the extraordinarily complex sensory/nervous systems found in some species. Includes a desciption of their general morphology, life cycles, taxonomy and phylogeny, infection process, localization in the host, and ecological infection dynamics.

Chapter 33 in Concepts in Animal Parasitology by Klaus Rohde. 2024. S. L. Gardner and S. A. …

Concepts In Animal Parasitology, Chapter 19: Echinococcus (Genus) [Platyhelminthes, Cestoda, Eucestoda], Akira Ito, Scott L. Gardner

Concepts in Animal Parasitology

Discusses the cestode (tapeworm) genus Echinococcus, several species of which infect humans, including their general morphology, taxonomy, systematics, life cycles, host range, and medical and veterinary importance.

Chapter 19 in Concepts in Animal Parasitology on the family Proteocephalidae La Rue, 1911 by Tomáš Scholz and Roman Kuchta. 2024. S. L. Gardner and S. A. Gardner, editors. Zea Books, Lincoln, Nebraska, United States. doi: 10.32873/unl.dc.ciap019

Concepts In Animal Parasitology, Chapter 21: Bothriocephalidea Kuchta Et Al., 2008 (Order) [Platyhelminthes, Cestoda, Eucestoda], Jorge Falcón-Ordaz, Luis García-Prieto

Concepts in Animal Parasitology

An overview of the cestode (tapeworm) order Bothriocephalidea Kuchta et al., 2008, including a discussion of the main morphological characteristics, the description and summary of a representative species, Schyzocotyle acheilognathi (Yamaguti, 1934) Brabec et al., 2015 (also known as the Asian fish tapeworm), including its prevalence, life cycles, host range, and zoogeography.

Chapter 21 in Concepts in Animal Parasitology by Jorge Falcón-Ordaz and Luis García-Prieto. 2024. S. L. Gardner and S. A. Gardner, editors. Zea Books, Lincoln, Nebraska, United States. doi: 10.32873/unl.dc.ciap021

Concepts In Animal Parasitology, Chapter 41: Monorchiata Olson Et Al., 2003 (Suborder): Two Families Separated By Salinity [Platyhelminthes, Trematoda, Digenea, Plagiorchiida], Nicholas Q.-X. Wee

Concepts in Animal Parasitology

An overview of the speciose trematode (fluke) suborder Monorchiata Olson et al., 2003, which parasitizes fishes as adults. Includes general morphology, systematics, taxonomy, life cycles, and biogeography for several groups.

Chapter 41 in Concepts in Animal Parasitology, by Nicholas Q.-X. Wee. 2024. S. L. Gardner and S. A. Gardner, editors. Zea Books, Lincoln, Nebraska, United States. doi: 10.32873/unl.dc.ciap041

Concepts In Animal Parasitology, Chapter 66: Ixodida Leach, 1815 (Order): Ticks -- Keys To The Ticks [Arthropoda], Darci Moraes Barros-Battesti, Valeria Castilho Onofrio, Filipe Dantas-Torres

Concepts in Animal Parasitology

Chapter 66: Ixodida Leach, 1815 (Order): Ticks -- Keys to the Ticks by Darci Moraes Barros-Battesti, Valeria Castilho Onofrio, and Filipe Dantas-Torres.

Supplement to chapter 66 in Concepts in Animal Parasitology. 2024. Scott L. Gardner and Sue Ann Gardner, editors. Zea Books, Lincoln, Nebraska, United States.

Concepts In Animal Parasitology, Chapter 67: Acari Leach, 1817 (Subclass): Mites [Arthropoda], David Evans Walter, Gerald W. Krantz, Evert E. Lindquist

Concepts in Animal Parasitology

A very brief overview from open access sources about mites (subclass Acari Leach, 1817), including discussion of general identifying characteristics, biology, life cycle, scabies (cause by Sarcoptes scabiei var. hominis), and phylogenetic relationships (through 1996).

Chapter 67 in Concepts in Animal Parasitology, by David Evans Walter, Gerald W. Krantz, and Evert E. Lindquist. 2024. S. L. Gardner and S. A. Gardner, editors. Zea Books, Lincoln, Nebraska, United States. doi: 10.32873/unl.dc.ciap067