Tag: The Earth Sky & Everything In Between

Examining the Effect of Collection Method on the Microbial Communities Detected by Shotgun Metagenomics in Elephant Dung

Presenter(s): Joshaniel Tan—Environmental Science

Faculty Mentor(s): Claire Goodfellow

Session 6: The Earth, Sky & Everything In Between

The development of new ways to non-invasively monitor and manage endangered, cryptic or otherwise inaccessible wildlife populations is of critical importance to conservation initiatives . New fecal
DNA (fDNA) approaches offer considerable potential to inform these efforts, as the DNA which is present in an animal’s feces contains a wealth of information about that individual’s diet, health, metabolism, and resistance to disease . Specifically, shotgun metagenomic sequencing of DNA from feces represents an exciting new development in molecular analytics, enabling high resolution characterization of microbial communities in samples . In spite of this, no studies have been done to standardize the collection methods of samples from wild animals for shotgun metagenomics or to evaluate whether different collection methods can lead to differences in the microbial communities which are detected in a sample . In this study, I conducted shotgun metagenomic analyses on fecal samples collected from a captive elephant at the Oregon Zoo and developed an efficient bioinformatic pipeline to analyze the microbial communities detected . Each fecal sample was collected from the same elephant using five different, commonly-used collection methods . DNA was then extracted from each of these samples, sequenced on an Illumina MiSeq, and analyzed using the pipeline which I developed . Based on preliminary results, bacteria and archaea were identified to the genus level, and detected community composition varied by collection method . This work emphasizes both the potential and feasibility of shotgun metagenomics for informing conservation efforts and the need to standardize collection methods in shotgun metagenomic studies of wild populations .

Lobodon carcinophaga: Evolutionary constraints on the spatial variability of crabeater seal postcanine teeth for successful filter-feeding foraging strategies

Presenter(s): Megan Pollak—Earth Sciences—Paleontology

Faculty Mentor(s): Kellum Tate-Jones

Session 6: The Earth, Sky & Everything In Between

Pinnipeds, the group that includes true seals, eared seals, and walruses, generally display highly variable tooth spacing . Previous studies have credited this variability to the typical pinniped feeding mechanism, a combination of suction feeding and pierce feeding known as the “grab-and-gulp” method, which does not require precise dental occlusion . However, the crabeater seal (i .e ., Lobodon carcinophaga) is unique among pinnipeds as a filter-feeder . The distinct sieve-like postcanine tooth processes such as high-cuspation and intricate trellis-like morphology allow the crabeater seal to effectively strain small krill from the water . I hypothesize that individuals in this group with unevenly spaced teeth are unlikely to survive ecological pressures and are thus removed from the population by natural selection, leading to lesser variation in crabeater seal tooth spacing than in grab-and-gulp feeders . I test this hypothesis by assessing whether the distinctive feeding method of the crabeater seal constrains tooth spacing by comparing the variability in tooth gaps of crabeater seals to that of bearded seals (i .e ., Erignathus barbatus) . I measured the tooth gaps between the postcanine teeth of 21 specimens of L . carcinophaga and 11 specimens of E . barbatus . I then performed an F test of equal variance on these two datasets . I found that crabeater seal tooth gaps are significantly less variable in spacing than those of bearded seals . This result supports my hypothesis that natural selective processes have generated evolutionary constraints for lower variability in tooth spacing in the filter- feeder, L . carcinophaga, than in grab-and-gulp feeders such as E . barbatus .

The Evolution of Camelids in the Pacific Northwest in Response to the Grassland Expansion

Presenter(s): Eleanor Froehlich—Earth Sciences

Faculty Mentor(s): Samantha Hopkins, Dana Reuter

Session 6: The Earth, Sky & Everything In Between

Camelids, the artiodactyl group including camels, llamas, and alpacas, evolved in North America during the Eocene . The first camelids were smaller than a goat; however, some extinct genera were giraffe sized . Most studies of North American camelids focus on fossils found in the Great Plains and as a result little is known about how camelid diversity responded to climate and vegetation changes in the Pacific Northwest. Horses are a well-studied example of ungulate responses to climactic changes and grassland expansion . They show a general increase in body size that is concurrent with their switch from browsing to mixed feeding and eventually to the grazing we see in modern examples . I suspect that as the environment in the Pacific Northwest dried out, camelids also increased in size due to the grassland expansion . I also believe that camelids incorporated more grasses into their diet . I tested this by documenting camelid diversity in the Pacific Northwest, specifically the states of Idaho, Oregon, and Washington, using the published fossil occurrences on the Paleobiology Database . Body size data was estimated using tooth measurements collected on the Fossilworks database . Camelid species were categorized according to two ecological parameters, body size and diet . I used these to track camelid evolution through time . I found that although body mass does increase there were still small browsing lineages late into the Miocene . This study provides a broader biogeographical picture of how grassland expansion influenced camelid evolution and ecology .

Population Dynamics in Endemic Serpentine Grassland Plant Communities Amid Anthropogenic Environmental Change

Presenter(s): Michaela Fishback—Environmental Science

Faculty Mentor(s): Eliza Hernández, Lauren Hallett

Session 6: The Earth, Sky & Everything In Between

Rising rates of nitrogen deposition are threatening the stability of the serpentine grassland ecosystem around the California Bay Area by changing the soil to be a more accessible habitat for invasive nonnative species . The recent increase in nitrogen is largely attributed to air pollution from automotive traffic throughout the region . This area hosts 10% of California’s endemic species in only 1% of the state’s land, making it a critical area for ecological conservation efforts . The plant species native to this area have persisted by inhabiting the characteristically low-resource soil of the serpentine grasslands, giving them competitive advantage over invasive species that require higher resource levels . To study the variation in reproductive success of these plants under different environmental constraints typical of polluted serpentine grasslands, I worked on a greenhouse experiment using a nitrogen-water resource gradient in serpentine-amended soil . Plantago erecta, a native, resource-conservative herb, was sown in competition with Bromus hordeaceus, a nonnative, resource-acquisitive grass . My preliminary findings show that Plantago produces the most seeds when there is no competition from Bromus, low availability of water, and high levels of nitrogen . With low Bromus competition, water availability had less impact on Plantago, while increased nitrogen continued to increase Plantago seed production, suggesting that Plantago may not inhabit a low- nitrogen niche, but potentially a low-water niche . However, with high Bromus competition, Plantago seed production was consistently low regardless of nitrogen and water treatments, suggesting that Bromus competition was too great for the availability of resources to support the population of Plantago .

Arbuscular Mycorrhizal Fungi Colonization Decreases Under High Precipitation and Compost Treatment in Semi-Arid Rangelands

Presenter(s): Justin Day—Biology

Faculty Mentor(s): Ashley Shaw, Lauren Hallett

Session 6: The Earth, Sky & Everything In Between

In California, the application of compost has been proposed as a management strategy to increase forage production and soil carbon sequestration in semi-arid rangelands . However, given this ecosystem’s highly variable climate, having a holistic knowledge of the impacts of composting practices is imperative for sustainable management . Arbuscular mycorrhizal fungi (AMF) are known to confer many benefits to their vascular plants symbiotes—namely through nutrient acquisition— and have been proposed to be important to manage in agricultural systems . The body of knowledge surrounding the influence of compost and rainfall variability on AMF, however, is very limited . The purpose of this study is to explore the AMF-plant relationship with the application of fertilizer or compost across a precipitation gradient . Our results show that AMF colonization under compost treatment alone was not affected, but in combination with high precipitation, AMF colonization was significantly depressed when compared to the ambient precipitation . Additionally, AMF colonization negatively correlates with plant root biomass under the same conditions, suggesting that plant hosts reduce C delivery to AMF under low stress and high resource conditions .

New specimen of Monosaulax typicus (Mammalia, Castoridae) from the Mascall Formation of Twin Buttes in the Crooked River Basin, Oregon

Presenter(s): Shyla Davison—Earth Science

Faculty Mentor(s): Samantha Hopkins

Session 6: The Earth, Sky & Everything In Between

The Mascall formation of Central Oregon is a rock unit that was formed during the middle Miocene (~15 million years ago) . The Mascall formation was first described from North Central Oregon, but also outcrops to the south in the Crooked River Basin, where it is much older . While these southern outcrops of the Mascall Formation have been known for some time, recent research shows that they are about a million years older than the outcrops of the same formation in the John Day Basin . This particular formation is known for producing many Barstovian-age mammals . Recent collections by University of Oregon field crews have yielded new material from the Crooked River region . I have diagnosed two new specimens recovered from the Mascall formation from Twin Buttes near Paulina, OR, as Monosaulax typicus from the family Castoridae . One specimen is a fragment of a lower right jaw that contains the p4-m2, while the other is a left jaw fragment . These are the most complete remains of M . typicus from the Mascall formation; other known specimens are isolated teeth . The teeth have all the diagnostic characteristic of other previously identified specimens of M . typicus that were found in Southeast Oregon rocks of similar age (Shotwell, 1968) . The information of this new specimen will add to the limited knowledge of this species and the environment of the Crooked River Basin .