bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diving behavior of immature, feeding Pacific bluefin tuna (Thunnus thynnus orientalis) in relation to season and area: the East China Sea and the Kuroshio–Oyashio transition region
Authors: Kitagawa Takashi , Kimura Shingo , Nakata Hideaki , Yamada Harumi 
Published: April 2004

AbstractTwenty‐four archival tags were recovered from Pacific bluefin tuna previously released off Tsushima Island in the East China Sea. By analysis of the time‐series data of the pressure and the ambient and internal temperature from the 24 tags, we examined the relationship between the tuna's pattern of diving and the thermocline depth. In the East China Sea, diving and feeding events occurred throughout almost the entire day in both winter and summer, suggesting that the purpose of diving is for feeding. In summer, the feeding frequency was greater than that in winter, which corresponds to the fact that growth is more rapid in summer than in winter. During summer in the Kuroshio–Oyashio transition region, on the other hand, feeding events were much more frequent than those in the East China Sea, in spite of a lower diving frequency. The mean horizontal distance traveled was also significantly higher and it seems that in this area they may move horizontally to feed on prey accumulated at the surface. We conclude that, in addition to the ambient temperature structure, the vertical and horizontal distribution of prey species plays an important role in the feeding behavior of Pacific bluefin tuna. One bluefin tuna migrated to the Oyashio frontal area, where both the horizontal and the vertical thermal gradients are much steeper. The fish spent most of the time on the warmer side of the front and often traveled horizontally to the colder side during the day, perhaps to feed. This implies that there is a thermal barrier effect, in this case from the Oyashio front, on their behavior. The frequency of feeding events was low, although all the monitored fish dived every dawn and dusk, irrespective of the seasons or location. It is possible that these twice‐daily diving patterns occurred in response to the change in ambient light at sunrise and sunset.
Trends in carbon flux to seabirds in the Peruvian upwelling system: effects of wind and fisheries on population regulation
Authors: Jahncke J. , Checkley D. M. , Hunt G. L. 
Published: April 2004

AbstractWe hypothesized that change in the annual population size of guano‐producing seabirds (cormorant, Phalacrocorax bougainvillii; booby, Sula variegata; pelican, Pelecanus thagus) is a response to changes in primary and secondary production of the Peruvian upwelling system. We tested this hypothesis by modeling nitrate input through upwelling to the upper layers of the ocean off Peru between 6° and 14°S using data on wind stress and sea surface temperature. The model predicted the amount of carbon fixed by primary production each year from 1925 to 2000, which was then apportioned to the Peruvian anchovy (Engraulis ringens) biomass and ultimately to the seabird population and the anchovy fishery, the largest single‐species fishery on Earth. The model predicted a marked increase in primary production as a consequence of increasing wind stress. It overestimated the anchovy biomass after the collapse of the fishery in 1972, but closely predicted the growth of seabird populations from 1925 to the mid‐1960s, and their decline thereafter, explaining about 94% of the variation in seabird numbers from 1925 to 2000. The model indicates the seabirds consumed 14.4% of the available anchovies and, thus, that seabirds consumed 2.3% of the new production, before the development of the anchovy fishery, and only 2.2% of the available anchovies and 0.3% of the new production after the development of the fishery. The model results clarify the roles that environmental and anthropogenic factors may have had in regulating the guano‐producing seabird populations. It indicates that the growth of seabird populations from 1925 to 1955 was likely a response to increased productivity of the Peruvian upwelling system and that the subsequent drastic decline in seabird abundance was likely due to competition for food with the fishery, which caught ∼85% of the anchovies, which otherwise would have been available for the seabirds. This model also shows that an increase in oceanic primary production promotes reproductive success and population growth in higher trophic level organisms.
Simulating larval supply to estuarine nursery areas: how important are physical processes to the supply of larvae to the Aransas Pass Inlet?
Authors: Brown C. A. , Holt S. A. , Jackson G. A. , Brooks D. A. , Holt G. J. 
Published: April 2004

AbstractFactors controlling the movement of fish larvae from coastal spawning environments to estuarine nursery areas are important to fish recruitment. In this paper, the role of physical processes in larval transport to estuarine nursery areas in the Aransas Pass region, Texas, is examined using a circulation model coupled with a fixed‐depth particle transport model. Two phases of transport are examined: transport on the shelf to the tidal inlet and transport through the inlet to estuarine nursery areas. Observed pulsing in the supply of red drum (Sciaenops ocellatus) larvae to the tidal inlet is significantly correlated with modeled particle supply. This pulsing is not correlated with a specific physical process, but results from the interaction of several factors affecting water movement, including low‐frequency variations in water level and wind forcing. Simulations suggest that the primary spawning region for red drum larvae that utilize nursery habitat in the Aransas Pass region is located north of the inlet. Patterns in the trajectories of particles that successfully enter the inlet reveal that they move alongshelf in the nearshore region and then move into the inlet, rather than moving directly across the shelf to the inlet. The approach path of particles outside the inlet determines the spatial transport patterns for inlets with branched channels and multiple bays. This study demonstrates that physical processes play an important role in determining larval supply to a tidal inlet.
Effect of customization of master gutta‐percha cone on apical control of obturation using different techniques: an in vitro study
Authors: Van Zyl S. P. , Gulabivala K. , Ng Y.‐L. 
Published: April 2004

Aims  (i) To compare the prevalence of root filling extrusion placed using three different obturation techniques, each with or without customization of the master gutta‐percha cone; and (ii) to investigate the effects of various factors on the prevalence of root filling extrusion.Methodology  A total of 180 roots were selected and randomly allocated into three groups. Five general dental practitioners were recruited; each obturated one group of the roots using three techniques, namely cold lateral condensation (n = 20), Schilder's warm vertical condensation (n = 20) or continuous wave condensation (n = 20). Each technique was completed with (n = 10) or without (n = 10) customization of the master gutta‐percha cone using chloroform. Two groups of the roots were recycled to allow all five operators to use them. Two observers examined the preinstrumentation, working length, master apical file and postobturation radiographs, and determined the presence of root filling extrusion and voids independently; they were blinded regarding the obturation technique used. The presence of root filling extrusion was also assessed by inspecting the root apex after obturation. The data were analysed using logistic regression models.Results  A total of 300 root fillings were performed and 291 were included for analysis. Most of the root fillings were placed within 0.5 mm of the working length (80%, n = 233); only 20% (n = 58) were placed >0.5 mm beyond the working length. The odds of prevalence of extrusion >0.5 mm were significantly reduced by approximately 50% when cold lateral condensation (OR = 0.50; 95% CI = 0.26, 0.99; P = 0.04) or customization of master gutta‐percha cone (OR = 0.55; 95% CI = 0.30, 0.99; P = 0.04) was used. One operator produced 2.5 times more extruded root fillings than the other operators (OR = 2.50; 95% CI = 1.31, 4.78; P = 0.006). Other factors, such as root canal curvature and length, apical size of the prepared canal, as well as the operator's preferred obturation technique, were shown to have no significant influence on the prevalence of extrusion.Conclusions  The prevalence of extrusion was significantly lower when cold lateral condensation and customization of the master cone were used. The ‘operator’ emerged as a significant factor affecting the prevalence of root filling extrusion.
Population structure of California coyotes corresponds to habitat‐specific breaks and illuminates species history
Authors: Sacks Benjamin N. , Brown Sarah K. , Ernest Holly B. 
Published: April 2004

AbstractLittle is known about the relationship between animal movements and the emergent structure of populations, especially for species occupying large continuous distributions. Some such mammals disperse disproportionately into habitat similar to their natal habitat, a behavioural bias that might be expected to lead to habitat‐conforming genetic structure. We hypothesized that coyotes (Canis latrans) would exhibit such natal‐biased dispersal, and used 13 microsatellite loci to test, correspondingly, whether genetic structure conformed to major habitat breaks. First, we used a model‐based approach to assign coyote genotypes to distinct genetic clusters irrespective of geographical location. Visualization on a geographical information system revealed a strong concordance between the locations of cluster assignments and habitat bioregions, not explainable in terms of physical dispersal barriers or intervening low‐quality habitat. Next, we used a multiple Mantel test, which controlled for effects of geographical distance (itself, marginally significant; P = 0.06), to statistically determine that genetic distance was indeed higher between than within bioregions (P < 0.001). Whereas previously published examples of landscape effects on gene flow have typically been explainable in terms of species‐wide habitat affinities or dispersal barriers, our finding that genetic subdivisions were associated with unobstructed boundaries between contiguous habitats suggests a role for intraspecific variability in habitat affinities as a factor underlying genetic structure. In addition, our data combined with previously published data suggest a pattern of genetic isolation‐by‐distance throughout western North America, consistent with independent evidence that the western half of the coyote range predates European settlement.
Solanum nigrum: A model ecological expression system and its tools
Authors: Schmidt Dominik D. , Kessler André , Kessler Danny , Schmidt Silvia , Lim Michelle , Gase Klaus , Baldwin Ian T. 
Published: April 2004

AbstractPlants respond to environmental stresses through a series of complicated phenotypic responses, which can be understood only with field studies because other organisms must be recruited for their function. If ecologists are to fully participate in the genomics revolution and if molecular biologists are to understand adaptive phenotypic responses, native plant ecological expression systems that offer both molecular tools and interesting natural histories are needed. Here, we present Solanum nigrum L., a Solanaceous relative of potato and tomato for which many genomic tools are being developed, as a model plant ecological expression system. To facilitate manipulative ecological studies with S. nigrum, we describe: (i) an Agrobacterium‐based transformation system and illustrate its utility with an example of the antisense expression of RuBPCase, as verified by Southern gel blot analysis and real‐time quantitative PCR; (ii) a 789‐oligonucleotide microarray and illustrate its utility with hybridizations of herbivore‐elicited plants, and verify responses with RNA gel blot analysis and real‐time quantitative PCR; (iii) analyses of secondary metabolites that function as direct (proteinase inhibitor activity) and indirect (herbivore‐induced volatile organic compounds) defences; and (iv) growth and fitness‐estimates for plants grown under field conditions. Using these tools, we demonstrate that attack from flea beetles elicits: (i) a large transcriptional change consistent with elicitation of both jasmonate and salicylate signalling; and (ii) increases in proteinase inhibitor transcripts and activity, and volatile organic compound release. Both flea beetle attack and jasmonate elicitation increased proteinase inhibitors and jasmonate elicitation decreased fitness in field‐grown plants. Hence, proteinase inhibitors and jasmonate‐signalling are targets for manipulative studies.
On the neutrality of molecular genetic markers: pedigree analysis of genetic variation in fragmented populations
Authors: Van Oosterhout C. , Van Heuven M. K. , Brakefield P. M. 
Published: April 2004

AbstractMany studies employ molecular markers to infer ecological and evolutionary processes, assuming that variation found at genetic loci offers a reliable representation of stochastic events in natural populations. Increasingly, evidence emerges that molecular markers might not always be selectively neutral. However, only a few studies have analysed how deviations from neutrality could affect estimates of genetic variation, using populations with known genealogy. We monitored changes in allozyme variation over eight generations in captive metapopulations of the butterfly Bicyclus anynana. Population demography was recorded by individually marking 35 000 butterflies and constructing pedigrees. We designed a computer program that simulated the inheritance of founder allozyme alleles in butterfly pedigrees. We thus tested whether the observed transmission of allozyme alleles could be explained by random genetic drift alone, or whether there was evidence for positive or negative selection. This analysis showed that in the smallest metapopulations the loss of allozyme variation exceeded the neutral rate. Possibly, linkage disequilibria between deleterious mutations and marker alleles resulted in background selection and a faster erosion of allozyme variation. In larger metapopulations, one locus (MDH) showed a significant heterozygote excess and smaller than expected loss in heterozygosity, observations consistent with (associative) overdominance. This study demonstrates that the neutrality of molecular markers cannot always be assumed, particularly in small populations with a high mutation load.
Genetic diversity ofRanunculus acrisL. (Ranunculaceae) populations in relation to species diversity and habitat type in grassland communities
Authors: Odat Nidal , Jetschke Gottfried , Hellwig Frank H. 
Published: April 2004

AbstractCorrelates between genetic diversity at intra‐ and interpopulation levels and the species diversity in plant communities are rarely investigated. Such correlates may give insights into the effect of local selective forces across different communities on the genetic diversity of local plant populations. This study has employed amplified fragment length polymorphism to assess the genetic diversity within and between 10 populations ofRanunculus acrisin relation to the species diversity (richness and evenness) of grassland communities of two different habitat types, ‘seminatural’ and ‘agriculturally improved’, located in central Germany. Within‐population genetic diversity estimated by Nei's unbiased gene diversity (HE) was high (0.258–0.334), and was not correlated with species richness (Pearson'sr = −0.17;P = 0.64) or species evenness (Pearson'sr = 0.15;P = 0.68) of the plant communities. However, the genetic differentiation betweenR. acrispopulations was significantly correlated with the difference in species evenness (Mantel'sr = 0.62,P = 0.02), but not with difference in species richness of plant communities (r = −0.17,P = 0.22). Moreover, we also found that populations ofR. acrisfrom the ‘seminatural’ habitat were genetically different (amova,P < 0.05) from those in ‘agriculturally improved’ habitats, suggesting that gene flow between these habitat types is limited. The results reported in this study may indicate that habitat characteristics influence the genetic diversity of plant species.
Microsatellite DNA markers: evaluating their potential for estimating the proportion of hatchery‐reared offspring in a stock enhancement programme
Authors: Bravington M. V. , Ward R. D. 
Published: April 2004

AbstractWe describe a statistical method for estimating the effectiveness of a stock enhancement programme using nuclear DNA loci. It is based on knowing the population allele frequencies and the genotypes of the hatchery parents (mother only, or mother and father), and on determining the probability that a wild‐born animal will by chance have a genotype consistent with hatchery origin. We show how to estimate the proportion of released animals in the wild population, and its standard error. The method is applied to a data set of eight microsatellite loci in brown tiger prawns (Penaeus esculentus), prior to the start of a possible enhancement programme. We conclude that, for this particular data set, the effectiveness of such an enhancement programme could be quantified accurately if both maternal and paternal genotypes are known, but not if maternal genotypes only are known. Full paternal genotyping would require offspring genotyping and thus would be expensive, but a partly typed paternal genotype from a mass homogenate of offspring would be almost as effective and much cheaper. The experiment would become feasible based on maternal genotypes alone, if a further three typical microsatellite loci could be found to add to the existing panel of eight. The methods detailed should be of interest to any enhancement project that relies on nuclear DNA markers to provide tags.
Heterogeneous genetic structure in a Fagus crenata population in an old‐growth beech forest revealed by microsatellite markers
Authors: Asuka Y. , Tomaru N. , Nisimura N. , Tsumura Y. , Yamamoto S. 
Published: April 2004

AbstractThe within‐population genetic structure of Fagus crenata in a 4‐ha plot (200 × 200 m) of an old‐growth beech forest was analysed using microsatellite markers. To assess the genetic structure, Moran's I spatial autocorrelation coefficient was calculated. Correlograms of Moran's I showed significant positive values less than 0.100 for short‐distance classes, indicating weak genetic structure. The genetic structure within the population is created by limited seed dispersal, and is probably weakened by overlapping seed shadow, secondary seed dispersal, extensive pollen flow and the thinning process. Genetic structure was detected in a western subplot of 50 × 200 m with immature soils and almost no dwarf bamboos (Sasa spp.), where small and intermediate‐sized individuals were distributed in aggregations with high density because of successful regeneration. By contrast, genetic structure was not found in an eastern subplot of the same size with mature soils and Sasa cover, where successful regeneration was prevented, and the density of the small and intermediate‐sized individuals was low. Moreover, genetic structure of individuals in a small‐size class (diameter at breast height < 12 cm) was more obvious than in a large‐size class (diameter at breast height ≥ 12 cm). The apparent genetic structure detected in the 4‐ha plot was therefore probably the result of the structure in the western portion of the plot and in small and intermediate‐sized individuals that successfully regenerated under the favourable environment. The heterogeneity in genetic structure presumably reflects variation in the density that should be affected by differences in regeneration dynamics associated with heterogeneity in environmental conditions.
Genetic divergence, population structure and historical demography of rare springsnails (Pyrgulopsis) in the lower Colorado River basin
Authors: Hurt Carla R. 
Published: April 2004

AbstractSpringsnails of the genus Pyrgulopsis are the most diverse group of freshwater gastropods in North America and current estimates show that Pyrgulopsis contains ~120 different species, many of which are at risk of extinction. Some factors contributing to their exceptional diversity include poor dispersal ability and extreme habitat specificity based on water availability, chemistry and depth. Most taxa exhibit high degrees of endemism, with many species occurring only in a single spring or seep, making springsnails ideal for studies of speciation and population structure. Here I present data from a survey of genetic variation at the mitochondrial gene cytochrome oxidase I from 37 populations and over 1000 individuals belonging to 16 species of Pyrgulopsis distributed throughout the lower Colorado River basin. High levels of interspecific sequence divergence indicate that Pyrgulopsis may have colonized this region multiple times beginning in the late Miocene (~6 Ma); earlier than previous estimates based on fossil evidence. Estimates of nucleotide diversity differ greatly among species and may reflect differences in demographic processes. These results are used to identify factors contributing to radiation of species in this region. The implications of this evolutionary history and genetic variation are discussed in relation to future management and conservation.
Genetic variation in piñon pine, Pinus edulis, associated with summer precipitation
Authors: Mitton Jeffry B. , Duran Kristy L. 
Published: April 2004

AbstractThree previous reports of microgeographical variation of glycerate dehydrogenase (Gly) frequencies in piñon, Pinus edulis, established the hypothesis that Gly frequencies contribute to adaptation to heterogeneous environments, specifically to variation in soil moisture. In each of these studies, the frequency of the Gly‐3 allele or of Gly‐33 homozygotes was higher on dry sites than on nearby moist sites. Here we attempt to extend these observations by testing the hypothesis that Gly frequencies respond to soil moisture variation on a range‐wide scale. Gly frequencies were surveyed in 11 natural populations, and the frequency of the Gly‐3 allele varied from 0.27 to 0.65 among the sample sites. Elevation varied from 1650 to 3100 m, and summer precipitation, defined as precipitation from April to August, varied from 13.7 to 26.4 cm. The soil types at the collection sites were schist, quaternary volcanic or a mixture of shale and sandstone. Logistic regression revealed that Gly frequencies did not respond to either elevation or soil type, but were related to summer precipitation (P < 0.01). The correlation between summer precipitation and the frequency of the Gly‐3 allele was r = −0.92 (P < 0.001). Thus, the patterns of differentiation on microgeographical scales are consistent with greater differentiation on a range‐wide scale.