Biodiversity Commons^™

Do California Rangeland Healthy Soil Practices Offer Co-Benefits For Grassland Birds?, Ximena O. Gil

Cal Poly Humboldt theses and projects

Rangelands are important landscapes in California that support a robust cattle industry and serve as vital grassland habitat for birds. Climate change is projected to impact rangelands, leading to economic and ecological deterioration. In California, the Healthy Soils Program (HSP) incentivizes climate-smart solutions to increase working land resiliency. While the HSP targets soil and range health for livestock, it may also benefit birds. We surveyed rangeland operators to examine whether the implementation and duration of specific range management practices, such as range seeding, prescribed grazing, and silvopasture, are associated with bird community responses, using avian point count data from Point …

Succession And Alpine Plant Habitat Of A Recently Deglaciated Foreland In The Trinity Alps, California, Sebastian Evans

Cal Poly Humboldt theses and projects

The recent extinction of the Salmon Glacier in the Trinity Alps, California, provides a rare opportunity to examine post-glacial succession in a region of high endemism experiencing climatic stress. Using a chronosequence spanning ~150 years since deglaciation, I investigated (1) vegetation successional trajectories in the foreland, (2) whether the foreland functions as a climate refugium for alpine specialists, and (3) whether facilitative interactions between the dominant vascular plant (DVP) and bryophytes occur and persist through succession. I surveyed 100 plots across 11 transects within the foreland and 40 randomized plots in adjacent ecosystems. Successional patterns and refugial potential were analyzed …

From Theory To Ecosystems: Exploring Biodiversity And Ecosystem-Function In Pitcher Plant (Darlingtonia Californica) Microbial Communities, Gavin Sutter

Cal Poly Humboldt theses and projects

The relationship between biodiversity and ecosystem-function (BEF) has been a central focus of ecological research for the last three decades, yet the role of space in shaping BEF relationships remains relatively unknown. Research has shown that community diversity and composition can strongly influence productivity, nutrient cycling, and decomposition, but much of this work treats communities as spatially isolated, leaving open how dispersal and other spatial processes shape BEF at broader scales. To begin addressing this gap, I used microbial communities inhabiting Darlingtonia californica pitcher plant leaves to evaluate how spatial organization and successional change shape biodiversity and ecosystem-functioning. I quantified …

Bacterial Community Function In Pitcher Plant Leaves As An Experimental And Mathematical Model Of Functional Dynamics, Amelia Jackson

Cal Poly Humboldt theses and projects

This work looks at two different sites with differing abiotic factors in measures of altitude, temperature and precipitation. The site with higher altitude, larger temperature range, and lower precipitation, located in Plumas National Forest (Quincy, CA), had a flat BEF trend that suggests functional redundancy The site with lower altitude, more moderate temperatures, and higher precipitation located in Six Rivers National Forest (Gasquet, CA), also had a flat BEF trend. These abiotic factors could correlate to the significantly different bacterial compositions between sites. The second portion of this work is modeling the host antagonist relationship between Eyxra moths and their …

Using Environmental Dna Metabarcoding To Investigate Diversity And Seasonal Variation Of Fishes In Humboldt Bay, California, Johnathon M. Richardson

Cal Poly Humboldt theses and projects

This study applied environmental DNA (eDNA) metabarcoding to characterize fish diversity and temporal patterns in fish assemblage structure within Humboldt Bay, California. This work advances ecological understanding of Humboldt Bay’s ichthyofauna, regional natural history and ecosystem function. Over one year (February 2023–January 2024), triplicate surface-water samples were collected every two weeks from a fixed site in Humboldt Bay (n = 78). DNA was extracted from filters and amplified using MiFish 12S primers in six replicate PCRs per sample. Amplicon concentrations were normalized, pooled and sequenced on an Illumina MiSeq platform (2×150 bp). Sequences were processed using a custom bioinformatics pipeline, …

Examining The Effects Of Songbird Nest Boxes And Habitat On Avian And Arthropod Communities In A Vineyard Ecosystem, Eleanor Macdonald

Cal Poly Humboldt theses and projects

Agricultural expansion threatens biodiversity, but integrating insectivorous birds into vineyard ecosystems may support both conservation and ecosystem services. We tested how nest boxes and habitat composition influence avian and arthropod communities in Napa Valley vineyards using a before-after, control-impact experiment across 20 sites. During the 2023-2024 breeding seasons we conducted avian point counts, sampled key pest and beneficial arthropods, and collected fecal samples from adult and nestling tree swallows (Tachycineta bicolor) and western bluebirds (Sialia mexicana) to detect vineyard pest DNA. Nest boxes significantly increased swallow and bluebird abundance within one year; swallow responses were strongest …

Investigating The Refugial River Mouth Hypothesis: Assessing The Effects Of Low Salinity Conditions On The Microscopic Life Stages Of Nereocystis Luetkeana, Duncan Jackson

Cal Poly Humboldt theses and projects

Populations of Nereocystis luetkeana (bull kelp) have experienced localized extinction events in northern California since 2014 due to multiple stressor events, including the area’s most severe marine heatwave (MHW) to-date. Previous surveys in the region observed that bull kelp recovered and persisted at river mouths following the 2014-2015 MHW, suggesting that river mouths may serve as refugia – the refugial river mouth hypothesis. My study aimed to assess this hypothesis and the long-term stability of these refugia by studying how freshwater influences communities at these sites and bull kelp recruitment. Field surveys of salinity fluctuation and kelp and sea urchin …

Jaguar (Panthera Onca) Population Status And Conservation Needs In Panama Revealed Using Spatial Density And Occupancy Models., Rebeca E. Becdach

Cal Poly Humboldt theses and projects

Jaguars (Panthera onca) are key predators and the largest felid in the Americas. The species is listed as near threatened globally due to habitat loss, fragmentation, and human persecution. Their population decline can negatively affect the structure and functioning of the ecosystems they inhabit. Conservation efforts for jaguars and their habitat require understanding jaguar populations and how they are impacted by human presence across their range. This information is lacking in Panama, a critical portion of the Jaguar range. Panama forms a narrow land bridge connecting Central and South America, integral to wildlife movement, including jaguars, across both …

Associational Seaweed Defense Reduces Sea Urchin Grazing On Bull Kelp: Potential Use In Restoration, Brayden Tate Wiley

Cal Poly Humboldt theses and projects

Kelp forests are declining globally under warming seas, altered predator–prey dynamics, and intensified herbivory, with sea urchins often driving shifts from canopy-dominated forests to persistent urchin barrens. Management commonly relies on labor-intensive urchin removals, with variable success, underscoring the need for complementary, ecosystem-based tools that directly reduce urchin grazing pressure. Focusing on far northern California kelp forests, we combined subtidal surveys, field experiments, and laboratory feeding assays to assess whether the understory alga Desmarestia cf. herbacea can provide associational defense for bull kelp (Nereocystis luetkeana) by physically deterring purple sea urchin (Strongylocentrotus purpuratus) grazing and offering low …

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) …

Assessing The Effects Of Remaining Northern California Kelp Forest Mesopredators On Purple Sea Urchin Abundance, Distribution, And Feeding Activity, Sandra E. Traverso

Cal Poly Humboldt theses and projects

Kelp forests are threatened by regional abiotic and biotic stressors, including overgrazing by sea urchins. On the north coast of California, purple sea urchins (Strongylocentrotus purpuratus) are prolific grazers of kelp and with the regional extinction of their main predator (sunflower stars, Pycnopodia helianthoides), it is unknown whether any remaining mesopredators could exert top-down control of purple urchin populations. Other known predators of purple urchins in northern California include rock crabs, which have been shown to control sea urchin populations in Atlantic urchin barrens and indirectly cause phase shifts back to kelp forests. Yet, little is known …

Interactions Between New Zealand Mud Snails (Potamopyrgus Antipodarum) And Toxic Cyanoabacteria (Anabaena) In Baduwa’T (Mad River), Humboldt County, California, Cecilia F. Kennelly

Cal Poly Humboldt theses and projects

Invasive species in freshwater systems are circulated around the globe, wreaking havoc on natural communities. The New Zealand mud snail (Potamopyrgus antipodarum) is a very successful aquatic invader that has established populations in freshwater streams, lakes, and rivers around the globe. The goal of this project was to evaluate the interactions of invasive New Zealand mud snails (NZMS) and toxic cyanobacteria Anabaena in the Mad River in Humboldt County, California. These two species of concern are found in similar habitats along the river, but their whether NZMS consume Anabaena or affect toxin production is unknown. First, I conducted …

Are Biodiverse Communities More Resistant To Invasion? A Case Study With Marine Fouling Communities, Taylor Robert Bruntil

Cal Poly Humboldt theses and projects

The theory of biotic resistance predicts that more diverse communities should be less susceptible to invasion by novel species, but given the opposing results of multiple observational and experimental studies in marine systems, it is unclear how changes in environmental conditions can affect invasion success in communities that differ in diversity. I used marine fouling communities to test how the diversity of the species present in an initial community (hereafter termed “resident species”) affected the establishment and growth of all species not present in the initial communities (hereafter termed “novel species”) at two locations at the Eureka Public Marina, in …

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 …

Carnivore And Ungulate Occurrence In A Fire-Prone Region, Sara J. Moriarty-Graves

Cal Poly Humboldt theses and projects

Increasing fire size and severity in the western United States causes changes to ecosystems, species’ habitat use, and interspecific interactions. Wide-ranging carnivore and ungulate mammalian species and their interactions may be influenced by an increase in fire activity in northern California. Depending on the fire characteristics, ungulates may benefit from burned habitat due to an increase in forage availability, while carnivore species may be differentially impacted, but ultimately driven by bottom-up processes from a shift in prey availability. I used a three-step approach to estimate the single-species occupancy of four large mammal species: mountain lion (Puma concolor), coyote …

Macrolichen Inventory Of The Horse Mountain Botanical Area, Six Rivers National Forest, California, Usa, Sarah Norvell Conway

Cal Poly Humboldt theses and projects

Macrolichen diversity and community composition was determined for an area of high botanical interest in the Coast Ranges of Northern California – the Horse Mountain Botanical Area (HMBA) in Six Rivers National Forest. The Coast Ranges have been suggested to have high epiphytic macrolichen diversity, yet detailed site-specific macrolichen surveys are lacking for the area. Here we present comprehensive data on macrolichens of the HMBA integrated with environmental metadata at the landscape level. Twenty 0.4 ha sampling plots were positioned across the varying habitats of the HMBA and macrolichens were intensively sampled from all substrata. Out of 888 total collections, …

Diversity And Distribution Of Bryozoans Of The Northern To Central Rocky Outer Coast Of California, Ismael Chowdhury

Cal Poly Humboldt theses and projects

The phylum Bryozoa is one of the most diverse groups of marine invertebrates, with a global distribution that spans marine and fresh waters. This study analyzes the Bryozoa in infralittoral communities on rocky surfaces from northern California (Point Saint George) to central California (Estero Bay), spanning 940 kilometers and encompassing 12 rocky intertidal sites. Although recent studies on bryozoan taxonomy and phylogeny have increased due to scanning electron microscopy (SEM) and high throughput sequencing, there is still a lack of studies on species found in shallow waters at intertidal depths, particularly in the northeastern Pacific. This study aims to expand …

Comparing Mexican Spotted Owl Habitat Suitability In Two Different Habitat Types Using A Multi-Scale Ensemble Learning Framework, Danial Nayeri

Cal Poly Humboldt theses and projects

Habitat fragmentation and loss are major threats to species conservation worldwide. Studying species-habitat relationships is a crucial first step toward understanding species habitat requirements, which is necessary for conservation and management planning. However, some species inhabit a range of habitat types, potentially making the use of range-wide habitat models inappropriate due to non-stationarity. The Mexican spotted owl (Strix occidentalis lucida) (MSO) is a species that inhabits both forests and rocky canyonlands, two habitats with large differences in environmental conditions. It is unclear whether the species uses habitat differently in these two habitat types or if previously builthabitat models …

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 …

Environmental Effects On Constructed Wetland Microbial Diversity And Function In The Context Of Wastewater Management, Sandrine Grandmont-Lemire

Cal Poly Humboldt theses and projects

Microbial communities play a crucial role in ecosystems, yet we know little about how microbial diversity influences ecosystem functioning. An important gap in our understanding is how environmental change affects microbial Biodiversity-Ecosystem Function relationships (BEF). These complex interactions between microbial biodiversity and ecosystem function can influence major biogeochemical processes, such as the nitrogen cycle in wetland ecosystems, which play an important role in managing wastewater. To address the effect of biodiversity on function, my study investigates the BEF relationships between microbial diversity and the function in terms of ammonia removal from wastewater at the Arcata Wastewater Treatment Facility (AWTF) both …

Degradation And Nitrogen Cycling In The Context Of Biodiversity-Ecosystem Function Relationships In The Inquiline Bacterial Community Of Darlingtonia Californica, Megan Teigen

Cal Poly Humboldt theses and projects

Biodiversity-ecosystem function (BEF) research aims to explain how species and their environments interact with each other. Microbial communities engage in vital biogeochemical pathways in a variety of natural ecosystems, and yet there are large knowledge gaps about the specific metabolic pathways in which they are involved. Degradation specifically contributes to nitrogen cycling globally through the breakdown of large organic nitrogen compounds into small inorganic nitrogen that is necessary for the survival of many other organisms. In this study, I focused on the degradative function of the inquiline microbial communities found within the carnivorous pitcher plant, Darlingtonia californica. Darlingtonia grows in …

A Characterization Of The Sandy Beach Surf Zone Fish Community And Their Ecology In Northern California And The Effects Of Marine Protected Areas, Katie B. Terhaar

Cal Poly Humboldt theses and projects

Historically written off as dull and homogenous, the dynamics of the sandy beach surf zone remains under studied world-wide. Northern California has been no exception to this global standard, as the sandy beach surf zone ecosystem in this region has yet to be characterized, and the effect of Marine Protected Areas (MPAs) on the fish and macroinvertebrate community fully ascertained.

Considered data-poor by local wildlife officials, commercially, recreationally and culturally important Amphistichus rhodoterus (redtail surfperch) and common Hyperprosopon ellipticum (silver surfperch) utilize the sandy beach surf zone in Northern California. Little is known about the effect of various environmental factors, …

Phylogenetic And Geographic Relationships Of Cheilostome Bryozoans In The Eastern Pacific, Hannah E. Lee

Cal Poly Humboldt theses and projects

The phylum Bryozoa is an incredibly diverse group of marine invertebrates with a widespread global distribution that is well suited for evolutionary studies but whose phylogenetic relationships are still poorly understood. Although recent studies on bryozoan taxonomies and phylogenies have increased, there is still a lack of assessment of species found at shallow water (<1 m) to intertidal depths. In this study, I aimed to expand the taxonomic sampling and assessment of the phylogenetic diversity of cheilostome bryozoans along the California coastline by utilizing mitochondrial DNA as well as inferring potential correlations between species presence and dispersal range both within and between rocky outer coast and sheltered harbor habitats. Illumina high-throughput sequencing was used to produce mitogenomes for cheilostome bryozoan samples collected off rocks from two rocky intertidal sites and off settlement panels from two harbor sites. Phylogenetic analyses generated evolutionary hypotheses of species relationships alongside geographic mapping of their distribution. This study identified 15 distinct species that represent 10 different families to form the first comprehensive phylogeny for multiple bryozoan families in California across a total range of approximately 973 km of coastline. Three genetically distinct species were found at multiple sites that are separated by a combination of rocky shores and sandy beaches, which indicates that the dispersal range of these species are not limited by geographic barriers along the coast of California. These results provide a future opportunity for further integration of this data with the phylogenies generated in this study to examine more robust evolutionary hypotheses for the phylogenetic and geographic relationships of Californian bryozoan species.

Conifer Encroachment And Removal In A Northern California Oak Woodland: Influences On Ecosystem Physiology And Biodiversity, Gabriel S. Goff

Cal Poly Humboldt theses and projects

Oregon white oak (Quercus garryana) woodlands across their range are becoming increasingly threatened by encroaching Douglas-fir encroachment (Pseudotsuga menziesii) as a result of fire exclusion. Using water potential (Ψ), stomatal conductance (g_s), xylem water stable isotopes (dD), and three metrics of biodiversity, this study investigates the effects of conifer encroachment and removal at the ecosystem-scale. The study was set in an Oregon white oak woodland in northern California and compared three levels of encroachment before and after conifer removal. Findings indicate that heavily encroached stands have the least amount of water stress and gas …

Bird Abundance And Diversity In Shade Coffee And Natural Forest Kenya, Frank J. Ong'ondo

Cal Poly Humboldt theses and projects

Coffee, one of the major traded commodities in the world, has captured attention of both the international business class and conservation community due to its value as a beverage and for the habitat it can provide for wildlife. Previous work in Central Kenya has demonstrated that when cultivated with shade trees, coffee farms can host high levels of bird diversity. However, questions of how the bird community in shade coffee farms compares to those in natural forest remained unanswered. Using three visits to each of 160-point count locations in natural forest (80) and shade coffee sites (80) in Central Kenya, …

Comparison Of Standard And Environmental Dna Methods For Estimating Chinook Salmon Smolt Abundance In The Klamath River, California, Doyle Joseph Coyne

Cal Poly Humboldt theses and projects

Evaluating abundance of juvenile salmonids is critical to conservation and management. Current abundance estimation involves use of rotary screw traps and mark-recapture studies. Use of environmental DNA (eDNA) in water samples offers a noninvasive and less expensive approach that may potentially improve or eventually replace traditional monitoring. Here I evaluate the utility of eDNA to predict weekly abundance estimates of outmigrating Chinook salmon (Oncorhynchus tshawytscha) smolts in the Klamath River, California. A total of 15 water samples were collected per week over the 17-week smolt outmigration in both 2019 and 2020. Chinook salmon eDNA concentration in each water …

Systematics Of Amanita (Amanitaceae, Agaricales, Basidiomycota) From The Guiana Shield And Central Africa, Kennan S. Mighell

Cal Poly Humboldt theses and projects

This study is a systematic assessment of ten species of ectomycorrhizal fungi of the genus Amanita (Amanitaceae, Agaricales, Basidiomycota) from the lowland tropical rainforests of the Guiana Shield and Central Africa. Fungi were collected in each of the above regions, analyzed morphologically, and compared to the literature on Amanita diversity worldwide. All species addressed herein are given full formal taxonomic descriptions including complete macro- and microscopic character profiles, habit, habitat, and distribution. Phylogenetic assessments using ribosomal DNA and protein coding genes are provided for Guiana Shield taxa, and sequence data for two non-protein coding regions, the …

Spatial And Temporal Genetic Structure Of Winter-Run Steelhead (Oncorhynchus Mykiss) Returning To The Mad River, California, Steven R. Fong

Cal Poly Humboldt theses and projects

Distinct populations of steelhead in the wild are in decline. The propagation of steelhead in hatcheries has been used to boost population numbers for recreational fisheries and for use in conservation. However, hatchery breeding practices of steelhead can result in changes in genetic structure. I investigated the genetic structure of winter-run steelhead (Oncorhynchus mykiss) returning to the Mad River, California, where a hatchery has been used enhance production for recreational fisheries since 1971. Genetic variability in Mad River steelhead was evaluated using 96 single nucleotide polymorphisms (SNPs) among 4203 individuals, including the Mad River and nearby locations, and …

The Effects Of Woody Vegetation Encroachment And Removal Within A Coastal Fen, Joseph Saler

Cal Poly Humboldt theses and projects

Early successional wetland habitat is being lost in temperate regions worldwide as a result of changes in disturbance regimes that allow for the establishment and dominance of woody species. In particular, this phenomenon is pronounced in fens, which harbor high numbers of rare herbaceous species that require early successional habitat. I investigated the relationship between woody vegetation encroachment and herbaceous species diversity within a Northern California coastal fen that has been undergoing encroachment by woody vegetation for ca. 80 years by recording species richness and cover data from 338 permanent plots throughout the fen. I also investigated the effect of …

Drought And Coyotes Mediate The Relationship Between Mesopredators And Human Disturbance In California, Molly K. Parren

Cal Poly Humboldt theses and projects

Mesopredators in California are facing two major changes to their ecosystem: drought and the expansion of human disturbance. As a result, mesopredators are likely shifting their habitat use as well as their interspecies interactions to balance resource needs and risk-taking on the landscape. In response to severe drought, the California Department of Fish and Wildlife deployed 585 camera traps throughout the Mojave Desert and Central Valley documenting mammalian mesopredator presence in a drought year (2016) and a post-drought year (2017). The objectives of this study were to examine spatial patterns of mesopredator occurrence and co-occurrence with a dominant predator, the …