Life Sciences Commons^™

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 …

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, …

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

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 …

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 …

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 …

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 …

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.

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, …

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 …

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 …

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 …

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, …

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 …

Shade Trees Preserve Avian Insectivore Biodiversity On Coffee Farms In A Warming Climate, Sarah L. Schooler

Cal Poly Humboldt theses and projects

Coffee is an important export in many developing countries, with a global annual trade value of $100 billion. Climate change is projected to drastically reduce the area where coffee is able to be grown. Shade trees may mitigate the effects of climate change through temperature regulation for coffee growth, temperature regulation for pest control, and increase in pest-eating bird diversity. The impact of shade on bird diversity and microclimate on coffee farms has been studied extensively in the Neotropics, but there is a dearth of research in the Paleotropics. I examined the local effects of shade on bird presence and …

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 …

Elucidating Patterns Of Bat Species Occupancy Across A Disturbed Landscape In California's Central Valley, Trinity N. Smith

Cal Poly Humboldt theses and projects

California’s Central Valley, one of the most productive agricultural regions in the world, is home to 14 species of resident and migratory bats. The Central Valley has been identified as a crisis ecoregion, and a high number of species are at risk due to anthropogenic land use. In addition, the Central Valley has faced severe drought, effects of which are intensified on the natural landscape by agricultural irrigation practices. In response to the historical drought of 2012-2015, California Department of Fish and Wildlife (CDFW) implemented the Terrestrial Species Stressor Monitoring (TSSM) project, which in part aimed to collect information on …

Extending The Fossil Record Of The Polytrichaceae (Bryophyta): Insights From The Early Cretaceous Of Vancouver Island, Canada, Alexander C. Bippus

Cal Poly Humboldt theses and projects

Diverse in modern ecosystems, mosses are dramatically underrepresented in the fossil record. Furthermore, most pre-Cenozoic mosses are known only from compression fossils, which lack detailed anatomical information. Lower Cretaceous deposits at Apple Bay (Vancouver Island, British Columbia, Canada) contain a diverse anatomically preserved flora that includes numerous bryophytes, many of which have yet to be characterized. Among them is a polytrichaceous moss that is described here as Meantoinea alophosioides gen. et sp. nov. Meantoinea alophosioides represents the first occurrence of gemma cups in a fossil moss and is the oldest unequivocal record of Polytrichaceae, providing a hard minimum age for …

Persistence Of Stream Restoration With Large Wood, Redwood National And State Parks, California, Diedra L. Rodriguez

Cal Poly Humboldt theses and projects

The conservation and recovery of anadromous salmonids (Oncorhynchus sp.) depend on stream restoration and protection of freshwater habitats. In-stream large wood dictates channel morphology, increases retention of terrestrial inputs such as organic matter, nutrients and sediment, and enhances the quality of fish habitat. Historic land use/land cover changes have resulted in aquatic systems devoid of large wood. Restoration by placement of large wood jams is intended to restore physical and biological processes. An important question for scientists and restoration managers, in addition to the initial effectiveness of restoration, is the persistence and fate of large wood installations. In this …

The Bee Fauna Of The Horse Mountain And Grouse Mountain Region, Humboldt County, California, Carrie Lopez

Cal Poly Humboldt theses and projects

Recent concerns about the ecological well-being of bee communities in California and elsewhere have increased the need for monitoring programs and studies that evaluate the impact of habitat loss and alteration on bee diversity and abundance. Such studies depend critically on the expertise of people trained in taxonomy, but their numbers have declined in recent years. My primary goal was to gain a comprehensive first-hand experience with bee identification by documenting the fauna of a previously unstudied area in the mountains of northwestern California and by writing an identification key, intended for dedicated non-specialists, to the area’s 35 species of …

A Comparison Of Benthic Macroinvertebrate Assemblages Between Perennial And Intermittent Headwater Streams Of The Mattole River In Northern California, Usa, Mason S. London

Cal Poly Humboldt theses and projects

Intermittent streams are common throughout the world and comprise 60% or more of total river lengths in the conterminous United States. Despite their prevalence, intermittent streams are understudied, particularly first-order headwater streams, which are vital for maintaining the function, health and biotic diversity of river networks. In June 2016, I sampled five intermittent and five perennial headwater streams in the Mattole River watershed in northwestern coastal California, USA, to compare benthic macroinvertebrate (BMI) assemblages between intermittent and perennial streams. BMI samples were collected using a 500µm mesh D-net at eight randomly located riffles along a 150-m reach, and then composited, …