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<title>Biological Sciences</title>
<copyright>Copyright (c) 2013 California Polytechnic State University All rights reserved.</copyright>
<link>http://digitalcommons.calpoly.edu/bio_fac</link>
<description>Recent documents in Biological Sciences</description>
<language>en-us</language>
<lastBuildDate>Sat, 16 Mar 2013 01:44:49 PDT</lastBuildDate>
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<title>A New Niche for &lt;i&gt;Vibrio logei&lt;/i&gt;, the Predominant Light Organ Symbiont of Squids in the Genus &lt;i&gt;Sepiola&lt;/i&gt;</title>
<link>http://digitalcommons.calpoly.edu/bio_fac/413</link>
<guid isPermaLink="true">http://digitalcommons.calpoly.edu/bio_fac/413</guid>
<pubDate>Thu, 14 Mar 2013 14:24:40 PDT</pubDate>
<description>
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	<p>Two genera of sepiolid squids—<em>Euprymna</em>, found primarily in shallow, coastal waters of Hawaii and the Western Pacific, and <em>Sepiola</em>, the deeper-, colder-water-dwelling Mediterranean and Atlantic squids—are known to recruit luminous bacteria into light organ symbioses. The light organ symbiont of <em>Euprymna</em> spp. is <em>Vibrio fischeri</em>, but until now, the light organ symbionts of <em>Sepiola</em> spp. have remained inadequately identified. We used a combination of molecular and physiological characteristics to reveal that the light organs of <em>Sepiola affinis</em> and <em>Sepiola robusta</em> contain a mixed population of <em>Vibrio logei</em> and <em>V. fischeri</em>, with <em>V. logei</em> comprising between 63 and 100% of the bacteria in the light organs that we analyzed. <em>V. logei</em> had not previously been known to exist in such symbioses. In addition, this is the first report of two different species of luminous bacteria co-occurring within a single light organ. The luminescence of these symbiotic <em>V. logei</em> strains, as well as that of other isolates of <em>V. logei</em> tested, is reduced when they are grown at temperatures above 20°C, partly due to a limitation in the synthesis of aliphatic aldehyde, a substrate of the luminescence reaction. In contrast, the luminescence of the <em>V. fischeri</em> symbionts is optimal above 24°C and is not enhanced by aldehyde addition. Also, V. fischeri strains were markedly more successful than V. logei at colonizing the light organs of juvenile <em>Euprymna scolopes</em>, especially at 26°C. These findings have important implications for our understanding of the ecological dynamics and evolution of cooperative, and perhaps pathogenic, associations of <em>Vibrio</em> spp. with their animal hosts.</p>

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<author>Pat M. Fidopiastis et al.</author>


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<title>Addressing biased occurrence data in predicting potential Sierra Nevada red fox habitat for survey prioritization</title>
<link>http://digitalcommons.calpoly.edu/bio_fac/412</link>
<guid isPermaLink="true">http://digitalcommons.calpoly.edu/bio_fac/412</guid>
<pubDate>Thu, 14 Mar 2013 14:24:38 PDT</pubDate>
<description>
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	<p>The Sierra Nevada red fox <em>Vulpes vulpes necator</em> is listed as a threatened species under the California Endangered Species Act. It originally occurred throughout California’s Cascade and Sierra Nevada mountain regions. Its current distribution is unknown but should be determined in order to guide management actions. We used occurrence data from the only known population, in the Lassen Peak region of northern California, combined with climatic and remotely sensed variables, to predict the species’ potential distribution throughout its historic range. These model predictions can guide future surveys to locate additional fox populations. Moreover, they allow us to compare the relative performances of presence-absence (logistic regression) and presence-only (maximum entropy, or Maxent) modeling approaches using occurrence data with potential false absences and geographical biases. We also evaluated the recently revised Maxent algorithm that reduces the effect of geographically biased occurrence data by subsetting background pixels to match biases in the occurrence data. Within the Lassen Peak region, all models had good fit to the test data, with high values for the true skill statistic (76–83%), percent correctly classified (86–92%), and area under the curve (0.94–0.96), with Maxent models yielding slightly higher values. Outside the Lassen Peak region, the logistic regression model yielded the highest predictive performance, providing the closest match to the fox’s historic range and also predicting a site where red foxes were subsequently detected in autumn 2010. Subsetting background pixels in Maxent reduced but did not eliminate the effect that geographically biased occurrence data had on prediction results relative to the Maxent model using full background pixels.</p>

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<author>Casey Cleve et al.</author>


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<title>Characterization of a &lt;i&gt;Vibrio fischeri&lt;/i&gt; Aminopeptidase and Evidence for Its Influence on an Early Stage of Squid Colonization</title>
<link>http://digitalcommons.calpoly.edu/bio_fac/411</link>
<guid isPermaLink="true">http://digitalcommons.calpoly.edu/bio_fac/411</guid>
<pubDate>Thu, 28 Feb 2013 15:48:32 PST</pubDate>
<description>
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	<p>Vibrio fischeri cells are the sole colonists of a specialized light organ in the mantle cavity of the sepiolid squid Euprymna scolopes. The process begins when the bacteria aggregate in mucus secretions outside the light organ. The cells eventually leave the aggregate, enter the light organ, and encounter a rich supply of peptides. The need to dissociate from mucus and presumably utilize peptides led us to hypothesize that protease activity is integral to the colonization process. Protease activity associated with whole cells of Vibrio fischeri strain ES114 was identified as the product of a putative cell membrane-associated aminopeptidase (PepN). To characterize this activity, the aminopeptidase was cloned, overexpressed, and purified. Initial steady-state kinetic studies revealed that the aminopeptidase has broad activity, with a preference for basic and hydrophobic side chains and <em>k</em><sub>cat</sub> and <em>K<sub>m</sub></em> values that are lower and smaller, respectively, than those of Escherichia coli PepN. A V. fischeri mutant unable to produce PepN is significantly delayed in its ability to colonize squid within the first 12 h, but eventually it establishes a wild-type colonization level. Likewise, in competition with the wild type for colonization, the mutant is outcompeted at 12 h postinoculation but then competes evenly by 24 h. Also, the PepN-deficient strain fails to achieve wild-type levels of cells in aggregates, suggesting an explanation for the initial colonization delay. This study provides a foundation for more studies on PepN expression, localization, and role in the early stages of squid colonization.</p>

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<author>Pat M. Fidopiastis et al.</author>


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<title>LitR, a new transcriptional activator in &lt;i&gt;Vibrio fischeri&lt;/i&gt;, regulates luminescence and symbiotic light organ colonization</title>
<link>http://digitalcommons.calpoly.edu/bio_fac/410</link>
<guid isPermaLink="true">http://digitalcommons.calpoly.edu/bio_fac/410</guid>
<pubDate>Thu, 28 Feb 2013 15:48:30 PST</pubDate>
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	<p><em>Vibrio fischeri</em> is the bacterial symbiont within the light-emitting organ of the sepiolid squid <em>Euprymna scolopes</em> . Upon colonizing juvenile squids, bacterial symbionts grow on host-supplied nutrients, while providing a bioluminescence that the host uses during its nocturnal activities. Mutant bacterial strains that are unable to emit light have been shown to be defective in normal colonization. A 606 bp open reading frame was cloned from <em>V. fischeri</em> that encoded a protein, which we named LitR, that had about 60% identity to four related regulator proteins: <em>Vibrio cholerae</em> HapR, <em>Vibrio harveyi</em> LuxR, <em>Vibrio parahaemolyticus</em> OpaR and <em>Vibrio vulnificus</em> SmcR. When grown in culture, cells of <em>V. fischeri</em> strain PMF8, in which <em>litR</em> was insertionally inactivated, were delayed in the onset of luminescence induction and emitted only about 20% as much light per cell as its parent. Protein-binding studies suggested that LitR enhances quorum sensing by regulating the transcription of the <em>luxR</em> gene. Interestingly, when competed against its parent in mixed inocula, PMF8 became the predominant symbiont present in 83% of light organs. Thus, the <em>litR</em> mutation appears to represent a novel class of mutations in which the loss of a regulatory gene function enhances the bacterium's competence in initiating a benign infection.</p>

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<author>Pat Fidopiastis et al.</author>


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<title>Characterizing the resident, fermentative microbial consortium in the hindgut of the temperate-zone herbivorous fish, &lt;i&gt;Hermosilla azurea&lt;/i&gt; (Teleostei: Kyphosidae)</title>
<link>http://digitalcommons.calpoly.edu/bio_fac/409</link>
<guid isPermaLink="true">http://digitalcommons.calpoly.edu/bio_fac/409</guid>
<pubDate>Thu, 28 Feb 2013 15:48:29 PST</pubDate>
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	<p>The zebraperch, <em>Hermosilla azurea</em> Jenkins and Evermann, a warm-temperate marine fish species with a strictly macroalgal diet, has a relatively long digestive tract with an enlarged hindgut and an associated blind caecum (HC). In zebraperch sampled off Santa Catalina Island, California (33°19′42′′N; 118°18′37′′W) in years 1995 through 2001, direct cell counts, gut epithelium assessment of bacterial attachment, and short-chain fatty acid (SCFA) analyses verified that the zebraperch HC possesses a dense and morphologically diverse, fermentative microbiota. Bacterial cell counts and morphological diversity were significantly higher in HC contents compared to anterior gut regions, suggesting that microbial populations were growing along the digestive tract. Similarly, electron micrographs of the HC epithelium revealed attached microbes, further supporting the possibility that these organisms constitute resident microbiota. Five different SCFAs were detected in all three regions of the digestive tract, but levels were up to three times greater in HC contents. Acetate was consistently the prevailing SCFA in all gut regions. Sequence analysis of bacterial 16S rDNA was used to identify predominant bacterial groups in HC contents. Of the seven main bacterial types identified, <em>Enterovibrio</em> spp. were the dominant bacteria in HC contents followed by species of <em>Bacteroides</em>,<em>Faecalibacterium</em>, and <em>Desulfovibrio</em>. Taken together, our findings show that the zebraperch HC harbors a consortium of microbes that appears to assist in the breakdown of algal polysaccharides in the herbivorous diet of the fish.</p>

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<author>Pat M. Fidopiastis et al.</author>


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<title>A Novel &lt;i&gt;lux&lt;/i&gt; Operon in the Cryptically Bioluminescent Fish Pathogen &lt;i&gt;Vibrio salmonicida&lt;/i&gt; Is Associated with Virulence</title>
<link>http://digitalcommons.calpoly.edu/bio_fac/408</link>
<guid isPermaLink="true">http://digitalcommons.calpoly.edu/bio_fac/408</guid>
<pubDate>Thu, 28 Feb 2013 15:48:27 PST</pubDate>
<description>
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	<p>The cold-water-fish pathogen <em>Vibrio salmonicida</em> 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 <em>lux</em> operon and (ii) test whether the bioluminescence gene cluster is associated with virulence. Cloning and sequencing of the <em>V. salmonicida lux</em> operon revealed that homologs of all of the genes required for luminescence are present: <em>luxAB</em> (luciferase) and <em>luxCDE</em> (aliphatic-aldehyde synthesis). The arrangement and sequence of these structural <em>lux</em> genes are conserved compared to those in related species of luminous bacteria. However, <em>V. salmonicida</em> strains have a novel arrangement and number of homologs of the <em>luxR</em> and <em>luxI</em> quorum-sensing regulatory genes. Reverse transcriptase PCR analysis suggests that this novel arrangement of quorum-sensing genes generates antisense transcripts that may be responsible for the reduced production of bioluminescence. In addition, infection with a strain in which the <em>luxA</em> gene was mutated resulted in a marked delay in mortality among Atlantic salmon relative to infection with the wild-type parent in single-strain challenge experiments. In mixed-strain competition between the <em>luxA</em> mutant and the wild type, the mutant was attenuated up to 50-fold. It remains unclear whether the attenuation results from a direct loss of luciferase or a polar disturbance elsewhere in the <em>lux</em> operon. Nevertheless, these findings document for the first time an association between a mutation in a structural <em>lux</em> gene and virulence, as well as provide a new molecular system to study <em>Vibrio</em> pathogenesis in a natural host.</p>

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<author>Eric J. Nelson et al.</author>


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<title>Cryptic luminescence in the cold-water fish pathogen &lt;i&gt;Vibrio salmonicida&lt;/i&gt;</title>
<link>http://digitalcommons.calpoly.edu/bio_fac/407</link>
<guid isPermaLink="true">http://digitalcommons.calpoly.edu/bio_fac/407</guid>
<pubDate>Thu, 28 Feb 2013 15:48:25 PST</pubDate>
<description>
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	<p>The recent discovery that the fish pathogen <em>Vibrio salmonicida</em> is closely related to the luminous bacteria <em>Vibrio fischeri</em> and <em>Vibrio logei</em> suggested that <em>V. salmonicida</em> might also be capable of bioluminescence. Interestingly, cells of <em>V. salmonicida</em> were found to produce light in culture, but only when exposed to either an aliphatic aldehyde and/or the major <em>V. fischeri</em> autoinducer <em>N</em>-(3-oxo-hexanoyl)-l-homoserine lactone, a transcriptional activator of the luminescence (<em>lux</em>) genes. An extract of spent medium of <em>V. salmonicida</em> that should contain any <em>V. salmonicida</em> acyl-homoserine lactone autoinducer, when added to <em>V. fischeri</em> cells, led to an induction of their luminescence. These results show that <em>V. salmonicida</em> is a newly recognized luminous bacterial species that apparently both produces an autoinducer activity and responds to exogenous <em>V. fischeri</em> autoinducer</p>

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<author>P. M. Fidopiastis et al.</author>


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<title>Meeting the Challenges: The Western Section&apos;s Role in Developing Tomorrow&apos;s Resource Management Professionals</title>
<link>http://digitalcommons.calpoly.edu/bio_fac/406</link>
<guid isPermaLink="true">http://digitalcommons.calpoly.edu/bio_fac/406</guid>
<pubDate>Thu, 28 Feb 2013 15:48:24 PST</pubDate>
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	<p>The following is a slightly edited version of a plenary address delivered at the Western Section annual meeting in January 2009. The plenary theme was “The view from the future: wildlife management challenges and opportunities of the next 100 years.” Key references are listed at the end of the address. Readers will also be interested in the Winter 2009 (Vol. 3, No. 4) issue of The Wildlife Professional, which contains a special section on the preparation and training of future wildlife professionals.</p>

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<author>John D. Perrine</author>


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<title>Use of Cover and Response to Cover Type Edges by Female Sierra Nevada Red Foxes in Winter</title>
<link>http://digitalcommons.calpoly.edu/bio_fac/405</link>
<guid isPermaLink="true">http://digitalcommons.calpoly.edu/bio_fac/405</guid>
<pubDate>Thu, 28 Feb 2013 15:48:23 PST</pubDate>
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	<p>Red foxes (Vulpes vulpes) use a variety of habitats across their range, including semiarid deserts, tundra, boreal forests, farmland, and urban areas (Larivière and Pasitschniak-Arts 1996). Within these habitats there is much variation in the use of different cover types among populations of red foxes (Jones and Theberge 1982, Halpin and Bissonette 1988, Theberge and Wedeles 1989, St-Georges et al. 1995). In Maine, red foxes used coniferous stands and open areas more than expected (Halpin and Bissonette 1988). In British Columbia, red foxes used shrub communities more than expected and open areas less than expected (Jones and Theberge 1982). In the Yukon Territory, red foxes used shrub habitats more than forests or open areas (Theberge and Wedeles 1989). Edge habitat, between forest and shrub stands, was important for red foxes in Quebec (St-Georges et al. 1995). Variation in use of cover by this species necessitates populationspecific studies of red fox habitat relations for use in conservation and management.</p>

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<author>John F. Benson et al.</author>


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<title>A New Wildlife Sighting Reporting and Database System for Lassen Volcanic National Park</title>
<link>http://digitalcommons.calpoly.edu/bio_fac/404</link>
<guid isPermaLink="true">http://digitalcommons.calpoly.edu/bio_fac/404</guid>
<pubDate>Thu, 28 Feb 2013 15:48:22 PST</pubDate>
<description>
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	<p>Visitors and employees in national parks may observe species of interest to wildlife biologists and resource managers. These sightings are useful to researchers and managers only if the data can be efficiently acquired, stored and retrieved for analysis.· We identified several problems in the wildlife sightings reporting system at Lassen Volcanic National Park, including a confusing array of reporting forms; incomplete contact information for the reporter; insufficient reporting of the animal's description, behavior and location; and a cumbersome data entry and retrieval system. We developed a new system to correct these problems. A single reporting form corrects the aforementioned data gaps and includes a park map so the reporter can mark the approximate location of the sighting. Resource Management staff use a clear overlay with a numbered 1 mP grid to assign a location code for each sighting. This code and the report information are entered into a Microsoft Access database. Queries can be conducted for individual species and the location codes can be used to create sighting-distribution maps. The new system, in place since July 1999, has proven easier to implement and to query and therefore more useful than the previous system. A total of 553 sighting reports was received in 1999 and 2000, representing 720 animals of 39 species. These reports reflect several important biases inherent to wildlife sighting reporting data.</p>

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<author>John D. Perrine et al.</author>


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<title>Lassen Volcanic National Park Small Vertebrate Inventory Project: Preliminary Results 2000-2004</title>
<link>http://digitalcommons.calpoly.edu/bio_fac/403</link>
<guid isPermaLink="true">http://digitalcommons.calpoly.edu/bio_fac/403</guid>
<pubDate>Fri, 22 Feb 2013 11:31:09 PST</pubDate>
<description>
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	<p>Biologists at Lassen Volcanic National Park in northern California conducted an inventory of non-flying small mammals, amphibians and reptiles from 2000 through 2004. The four primary habitat types in the park (brush, forest, riparian and subalpine) were each sampled at one high elevation and one mid-elevation site in the park. Each of the eight sites was sampled for four six-day periods between June and September each year using a combination of pitfall, Sherman and Tomahawk traps, coverboards and unbaited automatic camera stations. This effort yielded 12,150 captures and 776 photo detections. A total of 649 voucher specimens, representing 19 mammal, one amphibian and two reptile species, was collected and accessioned to the Museum of Vertebrate Zoology at the University of California, Berkeley.</p>

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<author>John D. Perrine</author>


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<title>Sierra Nevada Red Fox (&lt;i&gt;Vulpes vulpes necator&lt;/i&gt;): A Conservation Assessment</title>
<link>http://digitalcommons.calpoly.edu/bio_fac/402</link>
<guid isPermaLink="true">http://digitalcommons.calpoly.edu/bio_fac/402</guid>
<pubDate>Fri, 22 Feb 2013 11:31:06 PST</pubDate>
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	<p>One goal of the Sierra Nevada Forest Plan Amendment (SNFPA) 2001 and 2004 Records of Decision was to protect and recover native Sierra Nevada red fox (Vulpes vulpes necator) populations in the Sierra Nevada (USDA Forest Service 2001 p. 14). To accomplish this goal, the ROD commits the U.S. Department of Agriculture (USDA) Forest Service to completing a conservation assessment for the Sierra Nevada red fox in cooperation with other federal, state, and local agencies, as well as Tribal governments. This conservation assessment synthesizes the best available scientific information and thought concerning habitat relationships, population status and trends, historical and current distributions, and key threats potentially affecting the distribution, abundance and persistence of the Sierra Nevada red fox. Biologists and resource managers from the Forest Service, US Department of the Interior (USDI) National Park Service, USDI Fish and Wildlife Service, US Geological Survey, University of California, and California Department of Fish and Game, along with private research scientists, worked cooperatively to develop this assessment. This conservation assessment provides a scientifically sound, comprehensive assessment of the status of the Sierra Nevada red fox population and its habitat. It identifies and evaluates key threats affecting viability and describes management considerations that could form the basis of a strategy to conserve and recover populations throughout the range of this species.</p>

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<author>John D. Perrine et al.</author>


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<title>North American montane red foxes: expansion, fragmentation, and the origin of the Sacramento Valley red fox</title>
<link>http://digitalcommons.calpoly.edu/bio_fac/401</link>
<guid isPermaLink="true">http://digitalcommons.calpoly.edu/bio_fac/401</guid>
<pubDate>Fri, 22 Feb 2013 11:31:04 PST</pubDate>
<description>
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	<p>Most native red foxes (<em>Vulpes vulpes</em>) in the western contiguous United States appear to be climatically restricted to colder regions in the major mountain ranges and, in some areas, have suffered precipitous declines in abundance that may be linked to warming trends. However, another population of unknown origin has occurred in arid habitats in the Sacramento Valley of California well outside this narrow bioclimatic niche since at least 1880. If native, this population would be ecologically distinct among indigenous North American red foxes. We used mitochondrial and microsatellite markers from historical and modern samples (modes: 1910–1930 and 2000–2008, respectively) obtained throughout the western United States to determine the origins of the Sacramento Valley red fox, and assess the historical and modern connectivity and genetic effective population sizes of Sacramento Valley and montane red foxes. We found clear and consistent evidence supporting the indigenous origin of the Sacramento Valley population, including the phylogenetic positioning of the dominant, endemic mtDNA clade and microsatellite clustering of the Sacramento Valley population with the nearest montane population. Based on both mitochondrial and microsatellite AMOVAs, connectivity among Western populations of red foxes declined substantially between historical and modern time periods. Estimates based on temporal losses in gene diversity for both marker types suggest that both the Sierra Nevada (including the Southern Cascades population) and the Sacramento Valley populations have small genetic effective population sizes. Significant heterozygote excesses also indicate the occurrence of recent bottlenecks in these populations. Both substitutions distinguishing the 2 endemic Sacramento Valley haplotypes from the dominant montane haplotype were in the coding region and nonsynonymous, consistent with adaptive differences. These findings along with previously reported body size distinctions between Sacramento Valley and montane red foxes argue for distinct subspecific status for the Sacramento Valley red fox, for which we propose the designation <em>V. v. patwin</em> n. subsp. The small genetic effective population size estimates for the Sierra Nevada red fox and Sacramento Valley red fox are cause for concern, as is the possibility of genetic introgression into the latter population from an adjacent, recently established nonnative population.</p>

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<author>Benjamin N. Sacks et al.</author>


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<title>Phylogeography of the North American red fox: vicariance in Pleistocene forest refugia</title>
<link>http://digitalcommons.calpoly.edu/bio_fac/400</link>
<guid isPermaLink="true">http://digitalcommons.calpoly.edu/bio_fac/400</guid>
<pubDate>Fri, 22 Feb 2013 11:30:59 PST</pubDate>
<description>
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	<p>Fossil, archaeological, and morphometric data suggest that indigenous red foxes in North America were derived from vicariance in two disjunct refugia during the last glaciation: one in Beringia and one in the contiguous USA. To test this hypothesis, we conducted a phylogeographical analysis of the North American red fox within its presettlement range. We sequenced portions of the mitochondrial cytochrome <em>b</em> (354 bp) gene and D-loop (342 bp) from 220 historical red fox specimens. Phylogenetic analysis of the cytochrome <em>b</em> gene produced two clades that diverged <em>c</em>. 400 000 years before present (bp): a Holarctic and a Nearctic clade. D-loop analyses of the Nearctic clade indicated three distinct subclades (≥ 99% Bayesian posterior probability); two that were more recently derived (rho estimate <em>c</em>. 20 000 bp) and were restricted to the southwestern mountains and the eastern portion of North America, and one that was older (rho estimate <em>c</em>. 45 000 bp) and more widespread in North America. Populations that migrated north from the southern refugium following deglaciation were derived from the colonization of North America during or prior to the Illinoian glaciation (300 000–130 000 bp), whereas populations that migrated south from the northern refugium represent a more recent colonization event during the Wisconsin glaciation (100 000–10 000 bp). Our findings indicate that Nearctic clade red foxes are phylogenetically distinct from their Holarctic counterparts, and reflect long-term isolation in two disjunct forest refugia during the Pleistocene. The montane lineage, which includes endangered populations, may be ecologically and evolutionarily distinct.</p>

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<author>Keith B. Aubry et al.</author>


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<title>Genetic evidence for the persistence of the critically endangered Sierra Nevada red fox in California</title>
<link>http://digitalcommons.calpoly.edu/bio_fac/399</link>
<guid isPermaLink="true">http://digitalcommons.calpoly.edu/bio_fac/399</guid>
<pubDate>Fri, 22 Feb 2013 11:30:54 PST</pubDate>
<description>
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	<p>California is home to both the native state-threatened Sierra Nevada red fox (<em>Vulpes vulpes necator</em>), 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-<em>b</em> haplotypes of the only currently-known high-elevation population (<em>n</em> = 9 individuals) to samples from 3 modern lowland populations (<em>n</em> = 35) and historic (1911–1941) high-elevation (<em>n</em> = 22) and lowland (<em>n</em> = 7) populations. We found no significant population differentiation among the modern and historic high-elevation populations (average pairwise <em>F</em> <sub>ST</sub> = 0.06), but these populations differed substantially from all modern and historic lowland populations (average pairwise <em>F</em> <sub>ST</sub> = 0.52). Among lowland populations, the historic and modern Sacramento Valley populations were not significantly differentiated from one another (<em>F</em> <sub>ST</sub> = −0.06), but differed significantly from recently founded populations in the San Francisco Bay region and in southern California (average pairwise <em>F</em> <sub>ST</sub> = 0.42). Analysis of molecular variance indicated that 3 population groupings (mountain, Sacramento Valley, and other lowland regions) explained 45% of molecular variance (<em>F</em> <sub>CT</sub> = 0.45) whereas only 4.5% of the variance was partitioned among populations within these groupings (<em>F</em> <sub>SC</sub> = 0.08). These findings provide strong evidence that the native Sierra Nevada red fox has persisted in northern California. However, all nine samples from this population had the same haplotype, suggesting that several historic haplotypes may have become lost. Unidentified barriers have apparently prevented gene flow from the Sacramento Valley population to other eastern or southern populations in California. Future studies involving nuclear markers are needed to assess the origin of the Sierra Nevada red fox and to quantify levels of nuclear gene flow.</p>

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<author>John D. Perrine et al.</author>


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<title>The Scientific Foundations of Habitat Conservation Plans: a Quantitative Assessment</title>
<link>http://digitalcommons.calpoly.edu/bio_fac/398</link>
<guid isPermaLink="true">http://digitalcommons.calpoly.edu/bio_fac/398</guid>
<pubDate>Fri, 22 Feb 2013 11:30:50 PST</pubDate>
<description>
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	<p>The number of habitat conservation plans ( HCP) has risen dramatically since the first plan was written over 18 years ago. Until recently, no studies have quantitatively investigated the scientific foundations underlying these documents. As part of a larger study of HCPs, we examined 43 plans primarily to assess the availability and use of scientific data and secondarily to determine the extent of involvement by, and influence of, independent scientists within the process. Specifically, our analysis focused on five key steps taken when an HCP is developed: assessing status of a species, determining take, predicting the project effects, mitigating for those effects, and monitoring of take and mitigation. In general, we found that the preparers of HCPs utilized existing scientific information fairly well, with 60% of plans not missing any available information described by our study as “starkly necessary.” The most common types of underutilized available data included those describing the influence of stochastic processes and habitat quality or quantity on species persistence. For many species, however, data on biology or status simply did not exist, as demonstrated by the fact that we could locate quantitative population estimates for only 10% of the species. Furthermore, for 42% of the species examined we had insufficient data and analysis to determine clearly how predicted take might affect the population. In many cases, mitigation measures proposed to offset take frequently addressed the most important local threats to the species with moderately reliable strategies. Species with monitoring programs rated as sufficient had plans that proposed to collect a greater amount of “quantitative” data than did those programs rated insufficient. Finally, when species “experts” were consulted, plan quality was generally higher. Overall, available scientific information in a majority of categories was fairly well utilized, but for many species additional studies and more in-depth analyses were required to provide adequate support for issuance of an incidental take permit.</p>

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<author>Elaine K. Harding et al.</author>


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<title>A Socratic Method for Surveying Students’ Readiness to Study Evolution</title>
<link>http://digitalcommons.calpoly.edu/bio_fac/397</link>
<guid isPermaLink="true">http://digitalcommons.calpoly.edu/bio_fac/397</guid>
<pubDate>Fri, 22 Feb 2013 11:30:48 PST</pubDate>
<description>
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	<p>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.</p>

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</description>

<author>William D. Stansfield</author>


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<title>Gene transcripts encoding hypoxia-inducible factor (HIF) exhibit tissue- and muscle fiber type-dependent responses to hypoxia and hypercapnic hypoxia in the Atlantic blue crab, &lt;i&gt;Callinectes sapidus&lt;/i&gt;</title>
<link>http://digitalcommons.calpoly.edu/bio_fac/396</link>
<guid isPermaLink="true">http://digitalcommons.calpoly.edu/bio_fac/396</guid>
<pubDate>Wed, 30 Jan 2013 10:43:37 PST</pubDate>
<description>
	<![CDATA[
	<p>Hypoxia inducible factor (HIF) is a transcription factor that under low environmental oxygen regulates the expression of suites of genes involved in metabolism, angiogenesis, erythropoiesis, immune function, and growth. Here, we isolated and sequenced partial cDNAs encoding <em>hif</em>-α and <em>arnt</em>/<em>hif</em>-β from the Atlantic blue crab, <em>Callinectes sapidus</em>, an estuarine species that frequently encounters concurrent hypoxia (low O<sub>2</sub>) and hypercapnia (elevated CO<sub>2</sub>). We then examined the effects of acute exposure (1 h) to hypoxia (H) and hypercapnic hypoxia (HH) on relative transcript abundance for <em>hif</em>-α and <em>arnt</em>/<em>hif</em>-β in different tissues (glycolytic muscle, oxidative muscle, hepatopancreas, gill, and gonads) using quantitative real-time RT-PCR. Our results indicate that <em>hif</em>-α and <em>arnt</em>/<em>hif</em>-β mRNAs were constitutively present under well-aerated normoxia (N) conditions in all tissues examined. Further, H and HH exposure resulted in both tissue-specific and muscle fiber type-specific effects on relative <em>hif</em>-α transcript abundance. In the gill and glycolytic muscle, relative <em>hif</em>-α mRNA levels were significantly lower under H and HH, compared to N, while no change (or a slight increase) was detected in oxidative muscle, hepatopancreas and gonadal tissues. H and HH did not affect relative transcript abundance for <em>arnt</em>/<em>hif</em>-β in any tissue or muscle fiber type. Thus, in crustaceans the HIF response to H and HH appears to involve changes in <em>hif</em> transcript abundance, with variation in <em>hif</em>-α and <em>arnt</em>/<em>hif</em>-β transcriptional dynamics occurring in both a tissue- and muscle fiber type-dependent manner.</p>

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</description>

<author>Kristin M. Hardy et al.</author>


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<title>Environmental stress proteomics of two blue mussel (genus &lt;i&gt;Mytilus&lt;/i&gt;) congeners</title>
<link>http://digitalcommons.calpoly.edu/bio_fac/395</link>
<guid isPermaLink="true">http://digitalcommons.calpoly.edu/bio_fac/395</guid>
<pubDate>Wed, 30 Jan 2013 10:43:35 PST</pubDate>
<description>
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	<p>Abstract of paper presented at the 28th Congress of the New European Society of Comparative Physiology and Biochemistry Proceedings: Bilbao, Spain.</p>

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</description>

<author>Lars Tomanek</author>


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<title>How do host sex and reproductive state affect host preference and feeding duration of ticks?</title>
<link>http://digitalcommons.calpoly.edu/bio_fac/394</link>
<guid isPermaLink="true">http://digitalcommons.calpoly.edu/bio_fac/394</guid>
<pubDate>Tue, 04 Dec 2012 15:07:39 PST</pubDate>
<description>
	<![CDATA[
	<p>Parasitism is one of the most notable forms of symbiosis in the biological world, with nearly all organisms hosting parasites. In many vertebrates, males have higher ectoparasite burdens than females, especially when testosterone concentrations are elevated. Furthermore, reproductive females may have higher ectoparasite burdens than non-reproductive females. It is possible that testosterone-stimulated behaviors in males and offspring investment by females incur energetic costs that inhibit immune function. If questing ticks can sense host sex or reproductive condition prior to attachment, they could potentially choose hosts with the poorest immune function, thereby leading to improved feeding success and decreased feeding duration. In this study, we examined the host–parasite relationship between western fence lizards (<em>Sceloporus occidentalis</em>) and the western black-legged tick (<em>Ixodes pacificus</em>) to test the following hypotheses: (1) ticks prefer male lizards to female lizards. (2) Ticks prefer male lizards with higher testosterone. (3) Ticks prefer reproductive female lizards to non-reproductive female lizards. (4) Ticks feed to repletion more rapidly (decreased feeding duration) on reproductive females and males with higher testosterone. In all three experiments, ticks failed to show a preference for one group over another as demonstrated by similar attachment rates between groups. This suggests that observed differences in ectoparasite loads in free-ranging lizards is due to some other factor than host choice. However, tick feeding duration on female lizards was shorter when hosts were reproductive, suggesting that host reproductive condition alters tick feeding, possibly due to a decreased immune response. Interestingly, ticks fed more slowly on male lizards with elevated testosterone, suggesting that testosterone may actually improve immune function against ectoparasites.</p>

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</description>

<author>Nicholas B. Pollock et al.</author>


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