Life Sciences Commons^™

Phylogeography Of The California Sheephead, Semicossyphus Pulcher: The Role Of Deep Reefs As Stepping Stones And Pathways To Antitropicality, Marloes Poortvliet, Gary C. Longo, Kimberly Selkoe, Paul H. Berber, Crow White, Jennifer E. Caselle, Alejandro Perez-Matus, Steven D. Gaines, Giacomo Bernardi

Biological Sciences

In the past decade, the study of dispersal of marine organisms has shifted from focusing predominantly on the larval stage to a recent interest in adult movement. Antitropical distributions provide a unique system to assess vagility and dispersal. In this study, we have focused on an antitropical wrasse genus, Semicossyphus, which includes the California sheephead, S. pulcher, and Darwin's sheephead, S. darwini. Using a phylogenetic approach based on mitochondrial and nuclear markers, and a population genetic approach based on mitochondrial control region sequences and 10 microsatellite loci, we compared the phylogenetic relationships of these two species, as well …

Luxs In Bacteria Isolated From 25- To 40-Million-Year-Old Amber, Tasha M. Santiago-Rodriguez, Ana R. Patrício, Jessica I. Rivera, Mariel Coradin, Alfredo Gonzalez, Gabriela Tirado, Raúl J. Cano, Gary A. Toranzos

Biological Sciences

Interspecies bacterial communication is mediated by autoinducer-2, whose synthesis depends on luxS. Due to the apparent universality of luxS (present in more than 40 bacterial species), it may have an ancient origin; however, no direct evidence is currently available. We amplified luxS in bacteria isolated from 25- to 40-million-year-old amber. The phylogenies and molecular clocks of luxS and the 16S rRNA gene from ancient and extant bacteria were determined as well. Luminescence assays using Vibrio harveyi BB170 aimed to determine the activity of luxS. While the phylogeny of luxS was very similar to that of extant Bacillus spp., …

Rov-Based Tracking Of A Shallow Water Nocturnal Squid, Samuel Yim, Christopher M. Clark, Timothy Peters, Vladimir Prodanov, Pat Fidopiastis

Biological Sciences

This paper describes the use of a Remotely Operated Vehicle (ROV) equipped with a monocular vision system to find and track the squid Euprymna scolopes, so that motion behaviors of the squid could be characterized through the use of off-line image processing and state estimation. The ROV was deployed for several nights at several nearshore locations off Oahu, resulting in 10 hours of squid footage. Using blob-tracking image processing techniques and a Particle Filter state estimator, the squid can be detected and tracked. The position, velocity, and acceleration of the squid relative to the stationary ROV can be determined. Experiment …

Evaluation Of Species Distribution Models By Resampling Of Sites Surveyed A Century Ago By Joseph Grinnell, Adam B. Smith, Maria J. Santos, Michelle S. Koo, Karen M.C. Rowe, Kevin C. Rowe, James L. Patton, John D. Perrine, Steven R. Beissinger, Craig Moritz

Biological Sciences

Species distribution models (SDMs) are commonly applied to predict species’ responses to anticipated global change, but lack of data from future time periods precludes assessment of their reliability. Instead, performance against test data in the same era is assumed to correlate with accuracy in the future. Moreover, high-confidence absence data is required for testing model accuracy but is often unavailable since a species may be present when undetected. Here we evaluate the performance of eight SDMs trained with historic (1900–1939) or modern (1970–2009) climate data and occurrence records for 18 mammalian species. Models were projected to the same or the …

Traversing Swanton Road, 13th Ed., James A. West

Academic, Government & Associated Organizational Research Resources

Situated at the northwest end of Santa Cruz County and occupying circa 30 square miles of sharply contrasted terrain, the Scott Creek Watershed concentrates within its geomorphological boundaries, at least 10-12% of California's flora, both native and introduced. Paradoxically, the use/abuse that the watershed has sustained over the past 140+ years, has not necessarily diminished the biodiversity and perhaps parallels the naturally disruptive but biologically energizing processes (fire, flooding, landslides and erosion), which have also been historically documented for the area for +60 years. This is an early edition of an extensive document by James A. West. Please visit the …

Life Support: Long Term Storage Of Solid Waste In An Enclosed Membrane System, Emmy O. Trieu, Michael Flynn, Rocco Mancinelli

STAR Program Research Presentations

In deep space missions, maintaining life support is of the utmost priority. In such a closed system, human waste must be stored and treated. Simulated feces (ersatz) will be inoculated with microbes representing normal fecal flora, mixed with urine brine and shredded refuse of products typically used in space missions. Composting methods often use alternating layers of waste with scraps of carboniferous materials (finely shredded refuse). By preparing membrane bags with a homogenized ersatz and carboniferous refuse mixture and membrane bags with alternating layers of ersatz and carboniferous refuse, it may be possible to monitor anaerobic thermophillic digestion of the …

Identifying Molecular Markers Associated With Salt And Boron Tolerance In Poplar Trees, Darshanpreet Gill, Nathan Follen, Davis W. Cheng, Kyan Salehi, Gary Banuelos, James P. Prince

STAR Program Research Presentations

Standard irrigation practices promote salt and boron accumulation in soils on the Westside of Central California. The build-up of these inorganic salts leads to the degradation of arable land and reduction of crop production. Different clones of poplar trees have been shown to grow in salt- and boron-contaminated soils, and in doing so, gradually remove significant amounts of these inorganic salts from the soil. In an effort to identify molecular markers linked with salt and boron tolerance in poplars, 31 PCR primer pairs have been designed based on candidate genes identified from the literature, and an additional 31 PCR primer …

Jellyfish Identification And Quantification In The San Francisco Estuary, Amalia Borson, Lindsay L. Sullivan, Wim Kimmerer

STAR Program Research Presentations

As potential predators and competitors of plankton-eating fish, jellyfish have the potential to negatively impact fish populations. Jellyfish were collected weekly with plankton tows from the RombergTiburonCenterpier in Tiburon, CA. Since some jellyfish were too small to identify, one tow was collected and preserved to record abundances, and a second tow was collected to rear jellyfish until distinguishing characteristics were visible enough for identification. Jellyfish in the preserved tows were then identified, measured, and counted, and their abundance (number m^-3) was calculated. Jellyfish from the second tows were reared in plastic buckets that were lightly bubbled using aquarium …

Preservation Of Biosignature Molecules In Potential Sample Return Container Of The Mars 2020 Mission, Kimberly E. Lykens, Fei Chen Ph.D

STAR Program Research Presentations

Preservation of Biosignature Molecules in Potential Sample Return Container of the Mars 2020 Mission

Kimberly Lykens¹ and Fei Chen²

¹Wittenberg University, Springfield, Ohio 45501 ²Jet Propulsion Laboratory, Pasadena, California, 91109

One requirement for sustainable life on terrestrial planets includes the presence of organic polymers, compounds that are essential for major biological functions such as replication and catalysis. An identified goal of the Mars mission in the year 2020 is to implement a sample-return to identify and validate signs of life on Mars through the discovery of biosignature molecules in Martian core samples. Martian core samples recovered …

Behavioral Variation Between Two Clades Of Leptasterias Spp., Ashley N. Contreras

STAR Program Research Presentations

Leptasterias spp. are six-rayed sea stars found along the rocky intertidal of the northeast Pacific Alaska to Santa Catalina Island, southern California. In central California, three clades of Leptasterias are found in separate or mixed populations, in diverse habitats that range from shallow pools of seagrass and algae to bare rock exposed to crashing waves. Initial field observations of two clades from different locations suggested that behavioral variation may relate to habitat differences among clades. To measure differences in activity, the righting response was timed at both field sites. As a result of behavioral variation observed in the field, more …

Temporal Variation In Larval Release In Botrylloides Violaceous, Damion J. Delton, Sarah Cohen

STAR Program Research Presentations

Despite Botrylloides violaceous being a globally invasive species in temperate marine habitats, little is known about it’s natural dispersal behavior. Previous work (Delton et al, 2011) suggests behavioral inferences based on a related and much more commonly studied species may not be appropriate, potentially due to a large size difference between the non-feeding larvae of these two species. Here, we consider factors that may affect dispersal potential. To study how light affects larval release, we measured timing of larval release in the field and compared larval size and time of release. Colonies were collected from floating docks in Richmond, CA …

Leatherback Hatchling Fitness, Violet Campbell, Shane Morales, Kelly Stewart

STAR Program Research Presentations

Leatherback hatchling fitness on land is essential for their success in entering the ocean without being predated. Two ways fitness on land may be measured are by how fast hatchlings crawl as well as how fast their righting responses are when they are flipped onto their carapaces. Hatchlings from certain nests have slower righting response times along with slower crawl times, both of which would increase the odds of predation and hinder the success of hatchlings reaching the ocean.

Hatchling crawling speed was determined by timing 12 randomly selected hatchlings from each nest to crawl a distance of two meters. …

Assessing Coral Reef Fish Population And Community Changes In Response To Marine Reserves In The Dry Tortugas, Florida, Usa, Jerald S. Ault, Steven G. Smith, James A. Bohnsack, Jiangang Luo, Natalia Zurcher, David B. Mcclellan, Tracy A. Ziegler, David E. Hallac, Matt Patterson, Michael W. Feeley, Benjamin I. Ruttenberg, John Hunt, Dan Kimball, Billy Causey

Biological Sciences

The efficacy of no-take marine reserves (NTMRs) to enhance and sustain regional coral reef fisheries was assessed in Dry Tortugas, Florida, through 9 annual fishery-independent research surveys spanning 2 years before and 10 years after NTMR implementation. A probabilistic sampling design produced precise estimates of population metrics of more than 250 exploited and non-target reef fishes. During the survey period more than 8100 research dives utilizing SCUBA Nitrox were optimally allocated using stratified random sampling. The survey domain covered 326 km², comprised of eight reef habitats in four management areas that offered different levels of resource protection: the …

Microbial Communities In Pre-Columbian Coprolites, Tasha M. Santiago-Rodriguez, Yvonne M. Narganes-Storde, Luis Chanlatte, Edwin Crespo-Torres, Gary A. Toranzos, Rafael Jiménez-Flores, Alice Hamrick, Raul J. Cano

Biological Sciences

The study of coprolites from earlier cultures represents a great opportunity to study an “unaltered” composition of the intestinal microbiota. To test this, pre-Columbian coprolites from two cultures, the Huecoid and Saladoid, were evaluated for the presence of DNA, proteins and lipids by cytochemical staining, human and/or dog-specific Bacteroides spp. by PCR, as well as bacteria, fungi and archaea using Terminal Restriction Fragment analyses. DNA, proteins and lipids, and human-specific Bacteroides DNA were detected in all coprolites. Multidimensional scaling analyses resulted in spatial arrangements of microbial profiles by culture, further supported by cluster analysis and ANOSIM. Differences between the microbial …

Achieving The Triple Bottom Line In The Face Of Inherent Trade-Offs Among Social Equity, Economic Return, And Conservation, Benjamin S. Halpern, Carissa J. Klein, Christopher J. Brown, Maria Beger, Hedley S. Grantham, Sangeeta Mangubhai, Mary Ruckelshaus, Vivitskaia J. Tulloch, Matt Watts, Crow White, Hough P. Possingham

Biological Sciences

Triple–bottom-line outcomes from resource management and conservation, where conservation goals and equity in social outcomes are maximized while overall costs are minimized, remain a highly sought-after ideal. However, despite widespread recognition of the importance that equitable distribution of benefits or costs across society can play in conservation success, little formal theory exists for how to explicitly incorporate equity into conservation planning and prioritization. Here, we develop that theory and implement it for three very different case studies in California (United States), Raja Ampat (Indonesia), and the wider Coral Triangle region (Southeast Asia). We show that equity tends to trade off …

Marine Protected Areas And Resilience To Sedimentation In The Solomon Islands, B. S. Halpern, K. A. Selkoe, Crow White, S. Albert, S. Aswani, M. Lauer

Biological Sciences

The ability of marine protected areas (MPAs) to provide protection from indirect stressors, via increased resilience afforded by decreased impact from direct stressors, remains an important and unresolved question about the role MPAs can play in broader conservation and resource management goals. Over a five-year period, we evaluated coral and fish community responses inside and outside three MPAs within the Roviana Lagoon system in Solomon Islands, where sedimentation pressure from upland logging is substantial. We found little evidence that MPAs decrease impact or improve conditions and instead found some potential declines in fish abundance. We also documented modest to high …

Evaluating Tradeoffs Among Ecosystem Services To Inform Marine Spatial Planning, Sarah E. Lester, Christopher Costello, Benjamin S. Halpern, Steven D. Gaines, Crow White, John A. Barth

Biological Sciences

A central challenge for natural resource management is developing rigorous yet practical approaches for balancing the costs and benefits of diverse human uses of ecosystems. Economic theory has a long history of evaluating tradeoffs in returns from different assets to identify optimal investment strategies. There has been recent progress applying this framework to the delivery of ecosystem services in land use planning. However, despite growing national and international interest in marine spatial planning, there is a lack of parallel frameworks in the marine realm. This paper reviews an ecosystem service tradeoff analysis framework and provides a more comprehensive synthesis for …

Traversing Swanton Road, 12th Ed., James A. West

Academic, Government & Associated Organizational Research Resources

Situated at the northwest end of Santa Cruz County and occupying circa 30 square miles of sharply contrasted terrain, the Scott Creek Watershed concentrates within its geomorphological boundaries, at least 10-12% of California's flora, both native and introduced. Paradoxically, the use/abuse that the watershed has sustained over the past 140+ years, has not necessarily diminished the biodiversity and perhaps parallels the naturally disruptive but biologically energizing processes (fire, flooding, landslides and erosion), which have also been historically documented for the area for +60 years. This is an early edition of an extensive document by James A. West. Please visit the …

A Socratic Method For Surveying Students’ Readiness To Study Evolution, William D. Stansfield

Biological Sciences

Before beginning a series of presentations on evolution, it would be prudent to survey the general level of students’ understanding of prerequisite basic concepts of reproduction, heredity, ontology, and phenotypic diversity so that teachers can avoid devoting time to well-known subjects of general knowledge and can spend more time on subjects that are unknown, forgotten, or misunderstood by most students. This article outlines a Socratic method for surveying and teaching to address these concerns.

Teaching Evolution & The Nature Of Science Via The History Of Debates About The Levels At Which Natural Selection Operates, William D. Stansfield

Biological Sciences

Students should not graduate from high school without understanding that scientific debates are essential components of scientific methodology. This article presents a brief history of ongoing debates regarding the hypothesis that group selection is an evolutionary mechanism, and it serves as an example of the role that debates play in correcting faulty ideas and stimulating new research in the pursuit of extending scientific knowledge.

Traversing Swanton Road, 11th Ed., James A. West

Academic, Government & Associated Organizational Research Resources

Situated at the northwest end of Santa Cruz County and occupying circa 30 square miles of sharply contrasted terrain, the Scott Creek Watershed concentrates within its geomorphological boundaries, at least 10-12% of California's flora, both native and introduced. Paradoxically, the use/abuse that the watershed has sustained over the past 140+ years, has not necessarily diminished the biodiversity and perhaps parallels the naturally disruptive but biologically energizing processes (fire, flooding, landslides and erosion), which have also been historically documented for the area for +60 years. This is an early edition of an extensive document by James A. West. Please visit the …

Detection Of Viable Microorganisms Using Propidium Monoazide, Erik J. Mcfarland, Adrian Ponce Dr.

STAR Program Research Presentations

Propidium monoazide (PMA) is a molecular tool used to assess viability of microorganisms. Currently, PMA is thought to discern viability through membrane permeability; PMA enters only membrane compromised cells, irreversibly crosslinks to theirDNAand precipitates theDNAout of solution, preventing it from being amplified during polymerase chain reaction (PCR). Using PMA on a sample of live and dead microorganisms results in only theDNAof living organisms being amplified and identified. Therefore, a comparison ofPCRresults with and without PMA allows one to determine the live fraction and total population, respectively.

Current literature provides conflicting evidence as to the effectiveness of the technique. Our research …

Using Stable Isotope Analysis Of Zooplankton To Document Trophic And Biogeochemical Changes In The San Francisco Estuary, Steven C. Westbrook, Julien Moderan

STAR Program Research Presentations

Zooplankton represent a vital link between phytoplankton and fish, like the endangered Delta Smelt. Human interferences (nitrates from waste water, flow alteration, invasive species introduction…) have altered the structure of the San Francisco Estuary (SFE) ecosystem. We use stable isotope analysis to improve our knowledge of the planktonic food web in the SFE and gain insights into its evolution over the past decades. We use the ratios of certain isotopes (Nitrogen, Carbon, Sulfur, etc.) in different species of zooplankton to tell us what it is feeding on as well as the trophic level it feeds in. My research focused on …