Biology Commons^™

Molecular Cloning And Sequence Analysis Of Multiple Cdna Variants For Thyroid-Stimulating Hormone Β Subunit (Tshβ) In The Fathead Minnow (Pimephales Promelas), Sean C. Lema, Jon T. Dickey, Penny Swanson

Biological Sciences

We cloned and sequenced full-length cDNAs encoding the β subunit of thyroid-stimulating hormone (TSHβ) from the pituitary of fathead minnow (Piephales promelas)using 5'-and 3'-rapid amplification of cDNA ends (RACE). Three cDNA variants for TSHβ with lengths of 1184-, 1093-, and 818-bp were identified. The cDNA variant of 1184-bp included 453-bp of open-reading frame and 610-bp of 3' UTR followed by a poly(A)site. This cDNA encodes 150 amino acids including a 19 residue signal peptide and a mature TSHβ protein of 131 residues with sequence identities of 97–53% to other fishes and 42–39% to mammals. The 1093-bp cDNA variant …

Correlated Evolution Of Genome Size And Cell Volume In Diatoms (Bacillariophyceae), Jessica A. Connolly, Matthew J. Oliver, Jeremy M. Beaulieu, Charles A. Knight, Lars Tomanek, Mark A. Moline

Biological Sciences

A correlation between genome size and cell volume has been observed across diverse assemblages of eukaryotes. We examined this relationship in diatoms (Bacillariophyceae), a phylum in which cell volume is of critical ecological and biogeochemical importance. In addition to testing whether there is a predictive relationship across extant species, we tested whether evolutionary divergences in genome size were correlated with evolutionary divergences in cell size (using independent contrasts). We estimated total DNA content for 16 diatom species using a flow cytometer and estimated cell volumes using critical dimensions with scaling equations. Our independent contrast analyses indicated a significant correlated evolution …

Sub-Kilometer Length Scales In Coastal Waters, Shelley M. Blackwell, Mark A. Moline, Andrew Schaffner, Thomas Garrison, Grace Chang

Biological Sciences

Patchiness or spatial variability is ubiquitous in marine systems. With increasing anthropogenic impacts to coastal resources and coastal systems being disproportionately large contributors to ocean productivity, identifying the spatial scales of this patchiness, particularly in coastal waters, is of critical importance to understand coastal ecosystem dynamics. The current work focuses on fine scale structure in three coastal regions. More specifically, we utilize variogram analyses to identify sub-kilometer scales of variability in biological and physical parameters measured by an autonomous underwater vehicle (AUV) in the Mid-Atlantic Bight, Monterey Bay, and in San Luis Obispo Bay between 2001 and 2004. Critical scales …

A Journey Through The Scott Creek Watershed, James A. West

Academic, Government & Associated Organizational Research Resources

This PDF contains content captured from: West, James. A Journey Through the Scott Creek Watershed, https://swanton.ucscarboretum.org/index.html. Accessed 9 July 2020. The website was created for the University of California Santa Cruz Arboretum and Botanic Garden. It serves as the beginnings and provides a basic outline of the content within "Traversing Swanton Road," an essay by James A. West. A most recent version of the essay can be found at https://digitalcommons.calpoly.edu/spr_assocres/1/

Metacommunity Patterns In Larval Odonates, Shannon J. Mccauley, Christopher J. Davis, Rick A. Relyea, Kerry L. Yurewicz, David K. Skelly, Earl E. Werner

Biological Sciences

The growth of metacommunity ecology as a subdiscipline has increased interest in how processes at different spatial scales structure communities. However, there is still a significant knowledge gap with respect to relating the action of niche-and dispersal-assembly mechanisms to observed species distributions across gradients. Surveys of the larval dragonfly community (Odonata: Anisoptera) in 57 lakes and ponds in southeast Michigan were used to evaluate hypotheses about the processes regulating community structure in this system. We considered the roles of both niche- and dispersal-assembly processes in determining patterns of species richness and composition across a habitat gradient involving changes in the …

Predator Induction Of Spine Length In Larval Leucorrhinia Intacta (Odonata), Shannon Mccauley, Christopher J. Davis, Earl E. Werner

Biological Sciences

Questions: Do larvae of a dragonfly with a broad habitat distribution have longer abdominal spines when they co-exist with fish, and are these differences the result of phenotypic plasticity?
Hypothesis: Phenotypic plasticity will result in larvae having longer spines when they are exposed to cues from predatory fish.
Organism: Larvae of Leucorrhinia intacta (Odonata: Libellulidae).
Research site: Natural ponds and cattle tanks on the E.S. George Reserve in southeast Michigan.
Methods: We compared the morphology of larvae collected from two natural ponds before and after a drought resulted in the extirpation of fish from one pond. We also compared …

Creationism, Catastrophism, And Velikovsky, William D. Stansfield

Biological Sciences

No abstract provided.

A Fossil Skull Of The Extant Blue Marlin (Makaira Nigricans Lacapède, 1802) From The Late Miocene Of Orange County, California, Harry L. Fierstine

Biological Sciences

A nearly complete fossil skull, including the rostrum, of blue marlin, Makaira nigricans Lacapède, 1802 (Perciformes: Xiphioidei: Istiophoridae), was collected from the Oso Member (latest Miocene) of the Capistrano Formation, Mission Viejo, Orange County, California. The specimen is compared with extant and fossil istiophorids, and 19 of its 20 morphological variables are within the range of values observed for extant M. nigricans, whereas only 13 or less variables are within the observed range of other extant istiophorids. Because extant M. nigricans usually inhabits a water column with a height of about 200 m or more and is the most …

High Latitude Changes In Ice Dynamics And Their Impact On Polar Marine Ecosystems, Mark A. Moline, Nina J. Karnovsky, Zachary Brown, George J. Divoky, Thomas K. Frazer, Charles A. Jacoby, Joseph J. Torres, William R. Fraser

Biological Sciences

Polar regions have experienced significant warming in recent decades. Warming has been most pronounced across the Arctic Ocean Basin and along the Antarctic Peninsula, with significant decreases in the extent and seasonal duration of sea ice. Rapid retreat of glaciers and disintegration of ice sheets have also been documented. The rate of warming is increasing and is predicted to continue well into the current century, with continued impacts on ice dynamics. Climate-mediated changes in ice dynamics are a concern as ice serves as primary habitat for marine organisms central to the food webs of these regions. Changes in the timing …

Spatial And Temporal Approaches In Analyzine Recreational Groundfish Data From Southern Central California And Their Application Toward Marine Protected Areas, Steven J. Rienecke, John S. Stephens Jr., Royden Nakamura, Erin Nakada, Dean E. Wendt

Biological Sciences

Many nearshore rockfish species have small homerange sizes and therefore may be affected by heavier localized fishing in nearport areas. For this study we examined longterm trends in rockfish and lingcod landings from the commercial passenger fishing vessel (CPFV) fishery along the south central coast (SCC) of California using data from two sources: California Department of Fish and Game (CDFG) surveys from 1988–98 and California Polytechnic State University (Cal Poly) surveys in 2003–04. The objective was to make comparisons between areas close to port (that receive greater fishing effort) and those far from port (areas receiving less fishing effort). We …

An Automated Temperature-Based Option For Estimating Surface Activity And Refuge Use Patterns In Free-Ranging Animals, J R. Davis, E N. Taylor, D F. Denardo

Biological Sciences

Accurately assessing free-ranging animals’ patterns of surface activity and refuge use is critical, yet fundamentally challenging for biologists and wildlife managers. We evaluate the accuracy of an automated technique—temperature-based activity estimation (TBAE)—in estimating surface activity and refuge use patterns of two sympatric reptiles, the western diamond-backed rattlesnake (Crotalus atrox) and the Gila monster (Heloderma suspectum) in the Sonoran Desert. TBAE derived from a comparison of body temperature to shaded air temperature was effective in estimating the overall percent surface activity for both rattlesnakes (observed surface activity 51.8%, TBAE estimated surface activity 48.2%) and Gila monsters (observed …

The Phenotypic Plasticity Of Death Valley's Pupfish: Desert Fish Are Revealing How The Environment Alters Development To Modify Body Shape And Behavior, Sean C. Lema

Biological Sciences

Death Valley seems an unlikely spot to go fishing. Nonetheless, seven species of pupfish survive in North America's lowest, hottest spot as remnants from the cooler, damper Pleistocene Epoch. For the most part, these species exist in isolation and have been left to adapt to minute details of their local environment—sort of the fish version of Darwin's finches. Surprisingly, however, even within a species, when environmental variables such as water temperature or food supply vary, morphological changes are evident within a few generations. This phenotypic plasticity calls into question not only environmental management practices for species preservation but also just …

Franklin's Electric Kite Experiment, William D. Stansfield

Biological Sciences

No abstract provided.

Lichens Of Pine Hill, A Peridotite Outcrop In Eastern North America, Tanner B. Harris, Fred C. Olday, Nishanta Rajakaruna

Biological Sciences

Despite a large body of work on the serpentine-substrate effect on vascular plants, little work has been undertaken to describe lichen communities growing on serpentine soils derived from peridotite and other ultramafic rocks. Most such work has been conducted in Europe and western North America. Only one study to date has examined the lichen flora of an ultramafic outcrop in eastern North America. The current paper examines the lichen flora of a peridotite outcrop from Deer Isle, Hancock County, Maine, U.S.A. The lichen flora is presented along with relevant ecological and geochemical data. Sixty-three species were found, comprising 35 genera. …

Bioluminescence In A Complex Coastal Environment: 2. Prediction Of Bioluminescent Source Depth From Spectral Water-Leaving Radiance, Matthew J. Oliver, Mark A. Moline, Curtis D. Mobley, Lydia Sundman, Oscar M.E. Schofield

Biological Sciences

Many bioluminescence observations are made from the ocean's surface. However, the depth of the bioluminescent source is difficult to estimate on the basis of surface observations alone, given the variable light attenuation of unknown concentrations of water column constituents such as phytoplankton, colored dissolved organic matter, and detritus. Part 1 of this paper showed that bioluminescent water-leaving radiance signals are detectable, even in extremely turbid and dynamic coastal waters. Here, in part 2 of this paper, we analyze the water-leaving radiance patterns of bioluminescence modeled by HydroLight 4.2 to determine if the depth of the bioluminescent source can be estimated …

Temperature Effects On Metabolic Rate Of Juvenile Pacific Bluefin Tuna Thunnus Orientalis, Jason M. Blank, Jeffery M. Morrissette, Charles J. Farwell, Mathew Price, Robert J. Schallert, Barbara A. Block

Biological Sciences

Pacific bluefin tuna inhabit a wide range of thermal environments across the Pacific ocean. To examine how metabolism varies across this thermal range, we studied the effect of ambient water temperature on metabolic rate of juvenile Pacific bluefin tuna, Thunnus thynnus, swimming in a swim tunnel. Rate of oxygen consumption (M_O2) was measured at ambient temperatures of 8–25°C and swimming speeds of 0.75–1.75 body lengths (BL) s^–1. Pacific bluefin swimming at 1 BL s^–1 per second exhibited a U-shaped curve of metabolic rate vs ambient temperature, with a thermal minimum zone between …

Fuzzy Data Sets, William D. Stansfield

Biological Sciences

No abstract provided.

Genetic Evidence For The Persistence Of The Critically Endangered Sierra Nevada Red Fox In California, John D. Perrine, John P. Pollinger, Benjamin N. Sacks, Reginald H. Barrett, Robert K. Wayne

Biological Sciences

California is home to both the native state-threatened Sierra Nevada red fox (Vulpes vulpes necator), which historically inhabited high elevations of the Sierra Nevada and Cascade mountains, and to multiple low-elevation red fox populations thought to be of exotic origin. During the past few decades the lowland populations have dramatically expanded their distribution, and possibly moved into the historic range of the native high-elevation fox. To determine whether the native red fox persists in its historic range in California, we compared mitochondrial cytochrome-b haplotypes of the only currently-known high-elevation population (n = 9 individuals) to samples …

Protective Capactiy Of Mangroves During Tropical Storms: A Case Study From 'Wilma' And 'Gamma' In Belize, Elise F. Granek, Benjamin I. Ruttenberg

Biological Sciences

Globally threatened mangrove forest habitat is often considered an important buffer protecting coastlines from wave and storm impacts and coastal erosion. However, there is little empirical data quantifying the protective effects of mangroves during storms, primarily because of the difficulty of predicting where and when a storm will intersect the shoreline, to facilitate data collection before and after storm events. In 2005, opportunistic results from an ongoing study quantifying differences between intact and cleared mangrove areas on Turneffe Atoll, Belize, provided such pre- and post-storm data from tropical storms ‘Wilma’ (later a Category 5 Hurricane) and ‘Gamma’. We compared differences …

The Relationship Between Disperal Ability And Geographic Range Size, Sarah E. Lester, Benjamin I. Ruttenberg, Steven D. Gaines, Brian P. Kinlan

Biological Sciences

There are a variety of proposed evolutionary and ecological explanations for why some species have more extensive geographical ranges than others. One of the most common explanations is variation in species’ dispersal ability. However, the purported relationship between dispersal distance and range size has been subjected to few theoretical investigations, and empirical tests reach conflicting conclusions. We attempt to reconcile the equivocal results of previous studies by reviewing and synthesizing quantitative dispersal data, examining the relationship between average dispersal ability and range size for different spatial scales, regions and taxonomic groups. We use extensive data from marine taxa whose average …

Recombination And Positive Selection Contribute To Evolution Of Listeria Monocytogenes Inla, R. H. Orsi, D. R. Ripoll, M. Yeung, K. K. Nightingale, M. Wiedmann

Biological Sciences

The surface molecule InlA interacts with E-cadherin to promote invasion of Listeria monocytogenes into selected host cells. DNA sequencing of inlA for 40 L. monocytogenes isolates revealed 107 synonymous and 45 nonsynonymous substitutions. A frameshift mutation in a homopolymeric tract encoding part of the InlA signal peptide was identified in three lineage II isolates, which also showed reduced ability to invade human intestinal epithelial cells. Phylogenies showed clear separation of inlA sequences into lineages I and II. Thirteen inlA recombination events, predominantly involving lineage II strains as recipients (12 events), were detected and a number of amino acid residues were …

The Phd Degree And Biblical Fundamentalism, William D. Stansfield

Biological Sciences

No abstract provided.

Biofouling Likely Serves As A Major Mode Of Dispersal For The Polychaete Tubeworm Hydroides Elegans As Inferred From Microsatellite Loci, J. B. Pettengill, D. E. Wendt, M. D. Schug, M. G. Hadfield

Biological Sciences

The polychaete tubeworm Hydroides elegans (Haswell) is a biofouling species with relatively limited larval dispersal. Four highly polymorphic microsatellite loci were used to make inferences about the migration and global population structure of 137 individuals from seven sub-populations located in the Atlantic, Pacific, and Indian Oceans and in the Mediterranean Sea. The results of the genetic analyses suggest minimal population sub-structure (F_st = 0.09). Estimates of pairwise F_st and migration rates using the coalescent-based method of MIGRATE suggest that there is little genetic differentiation between certain populations. Variation in relatedness among pairs of populations is consistent with a …

Neural Defects And Cardiac Arrhythmia In Fish Larvae Following Embryonic Exposure To 2,2',4,4'-Tetrabromodiphenyl Ether (Pbde 47), Sean C. Lema, Irvin R. Schultz, Nathaniel L. Scholz, John P. Incardona, Penny Swanson

Biological Sciences

Polybrominated diphenyl ethers (PBDEs) are added to plastics, polyurethane foam, and textiles as a flame retardant. While PBDEs play a key role in reducing loss of human life and property from fires, these flame retardants have become pervasive organic contaminants in the environment and in the tissues of fish, birds, marine mammals, and humans. Levels of PBDEs in wildlife and humans continue to rise, raising concerns about potential ecological and health risks associated with exposure to these chemicals. Nevertheless, there is little currently known about the toxicological effects of PBDE exposure. Here, we examined the developmental toxicity of the PBDE …

Human Sex Ratios And Sex Distribution In Sibships Of Size 2, William D. Stansfield, Matthew A. Carlton

Biological Sciences

We previously analyzed data from the U.S. National Health Interview Survey (NHIS, 1998 to 2002) on families with two biological children (10 years of age and younger) and found that the distribution of families with two boys, two girls, and one boy + one girl did not statistically conform to a binomial distribution regardless of the boy/girl sex ratio used. Using the best estimate of the sex ratio from the data, we found that there were significantly more families with opposite-sex siblings than families with same-sex siblings. No biological mechanism could explain these results at the time. In the present …

Environmental And Genetic Influences On Mating Strategies Along A Replicated Food Availability Gradient In Guppies (Poecilia Reticulata), Gita R. Kolluru, Gregory F. Grether, Heidy Contreras

Biological Sciences

Food availability is expected to influence the relative cost of different mating tactics, but little attention has been paid to this potential source of adaptive geographic variation in behavior. Associations between the frequency of different mating tactics and resource availability could arise because tactic use responds directly to food intake (phenotypic plasticity), because populations exposed to different average levels of food availability have diverged genetically in tactic use, or both. Different populations of guppies (Poecilia reticulata) in Trinidad experience different average levels of food availability. We combined field observations with laboratory “common garden” and diet experiments to examine how this …

Specimens Of The Billfish Xiphiorhynchus Van Beneden, 1871, From The Yazoo Clay Formation (Late Eocene), Louisiana, Harry L. Fierstine, Gary L. Stringer

Biological Sciences

No abstract provided.

Influence Of Swimming Speed On Metabolic Rates Of Juvenile Pacific Bluefin Tuna And Yellowfin Tuna, Jason M. Blank, Charles J. Farwell, Jeffery M. Morrissette, Robert J. Schallert, Barbara A. Block

Biological Sciences

Bluefin tuna are endothermic and have higher temperatures, heart rates, and cardiac outputs than tropical tuna. We hypothesized that the increased cardiovascular capacity to deliver oxygen in bluefin may be associated with the evolution of higher metabolic rates. This study measured the oxygen consumption of juvenile Pacific bluefin Thunnus orientalis and yellowfin tuna Thunnus albacares swimming in a swim-tunnel respirometer at 20°C. Oxygen consumption ( Mo₂) of bluefin (7.1–9.4 kg) ranged from 235 ± 38 mg kg^-1 h^-1 at 0.85 body length (BL) s^-1 to 498 ± 55 mg kg^-1 h^-1 at 1.80 …

A Novel Lux Operon In The Cryptically Bioluminescent Fish Pathogen Vibrio Salmonicida Is Associated With Virulence, Eric J. Nelson, Hege S. Tunsjø, Pat M. Fidopiastis, Henning Sørum, Edward G. Ruby

Biological Sciences

The cold-water-fish pathogen Vibrio salmonicida expresses a functional bacterial luciferase but produces insufficient levels of its aliphatic-aldehyde substrate to be detectably luminous in culture. Our goals were to (i) better explain this cryptic bioluminescence phenotype through molecular characterization of the lux operon and (ii) test whether the bioluminescence gene cluster is associated with virulence. Cloning and sequencing of the V. salmonicida lux operon revealed that homologs of all of the genes required for luminescence are present: luxAB (luciferase) and luxCDE (aliphatic-aldehyde synthesis). The arrangement and sequence of these structural lux genes are conserved compared to those in related species of …

Genome Size Evolution In Relation To Leaf Strategy And Metabolic Rates Revisited, Jeremy M. Beaulieu, Ilia J. Leitch, Charles A. Knight

Biological Sciences

• Background and AimsIt has been proposed that having too much DNA may carry physiological consequences for plants. The strong correlation between DNA content, cell size and cell division rate could lead to predictable morphological variation in plants, including a negative relationship with leaf mass per unit area (LMA). In addition, the possible increased demand for resources in species with high DNA content may have downstream effects on maximal metabolic efficiency, including decreased metabolic rates.

• MethodsTests were made for genome size-dependent variation in LMA and metabolic rates (mass-based photosynthetic rate and dark respiration rate) using our own …