bluuebunny/crossref_metadata_2025_split huggingface dataset:
Species‐specific oligonucleotide probes for macroalgae: molecular discrimination of two marine fouling species of Enteromorpha (Ulvophyceae)
Authors: Blomster J. , Hoey E. M. , Maggs C. A. , Stanhope M. J. 
Published: March 2003

AbstractThe green seaweeds Enteromorpha intestinalis and E. compressa are important fouling organisms commonly found in polluted and nutrient‐enriched marine and brackish water habitats, where they are used in environmental monitoring. Discrimination of the two species is extremely difficult because of overlapping morphological characters. In this study a quick molecular method for species identification was developed based on the nuclear rDNA ITS2 sequence data of 54 E. intestinalis samples and 20 E. compressa samples from a wide geographical range. Oligonucleotide probes were designed for species‐specific hybridization to dot‐blots of the PCR‐amplified ITS1, 5.8S gene and ITS2 fragment of both E. intestinalis and E. compressa. Specificity of the oligonucleotide probes was confirmed by tests with taxonomically diverse species that could morphologically be confused with E. intestinalis or E. compressa. This is the first use of species‐specific probes for macroalgae. The restriction endonuclease NruI digested specifically the amplified PCR product from E. compressa into two fragments detectable on agarose gels, but no suitable restriction sites were identifiable in the PCR product of E. intestinalis.
Molecular tracking of mountain lions in the Yosemite Valley region in California: genetic analysis using microsatellites and faecal DNA
Authors: Ernest H. B. , Penedo M. C. T. , May B. P. , Syvanen M. , Boyce W. M. 
Published: March 2003

AbstractTwelve microsatellite loci were characterized in California mountain lions (Puma concolor) and sufficient polymorphism was found to uniquely genotype 62 animals sampled at necropsy. Microsatellite genotypes obtained using mountain lion faecal DNA matched those from muscle for all of 15 individuals examined. DNA from potential prey species and animals whose faeces could be misidentified as mountain lion faeces were reliably distinguished from mountain lions using this microsatellite panel. In a field application of this technique, 32 faecal samples were collected from hiking trails in the Yosemite Valley region where seven mountain lions previously had been captured, sampled, and released. Twelve samples yielded characteristic mountain lion genotypes, three displayed bobcat‐type genotypes, and 17 did not amplify. The genotype of one of the 12 mountain lion faecal samples was identical to one of the mountain lions that previously had been captured. Three of the 12 faecal samples yielded identical genotypes, and eight new genotypes were detected in the remaining samples. This analysis provided a minimum estimate of 16 mountain lions (seven identified by capture and nine identified by faecal DNA) living in or travelling through Yosemite Valley from March 1997 to August 1998. Match probabilities (probabilities that identical DNA genotypes would be drawn at random a second time from the population) indicated that the samples with identical genotypes probably came from the same mountain lion. Our results demonstrate that faecal DNA analysis is an effective method for detecting and identifying individual mountain lions.
Microdiversity of uncultured marine prokaryotes: the SAR11 cluster and the marine Archaea of Group I
Authors: García‐Martínez J. , Rodríguez‐Valera F. 
Published: March 2003

AbstractThe SAR11 cluster and the Group I of marine Archaea represent probably the best two examples of uncultured marine prokaryotes of widespread occurrence. To study their microdiversity and distribution, a total of 81 and 48 clones, respectively, were sequenced from Mediterranean and Antarctic waters at different locations and depths. The DNA regions chosen for the analysis were the last third, approximately, of the 16S rRNA gene and the 16S–23S intergenic spacer (also known as internal transcribed spacer [ITS]). There was a high concordance in both, even with the extremely variable ITS, where potential probes have been proposed for the identification and isolation of these micro‐organisms. In terms of community structure, our results show that although depth‐related factors seem to be predominant in the final associations of the clones, geography also plays a significant role. A major group of surface‐associated sequences was found in both SAR11 and marine Archaea. In both cases this group was relatively homogeneous containing little diversity in terms of sequence, while sequences retrieved from deep samples and some surface clones contained much more heterogeneity. As a whole, both groups of prokaryotes seem to fall within the limits of well‐defined taxonomic units.
Increase of genetic variation over time in a recently founded population of great reed warblers (Acrocephalus arundinaceus) revealed by microsatellites and DNA fingerprinting
Authors: Hansson B. , Bensch S. , Hasselquist D. , Lillandt B.‐G. , Wennerberg L. , Von Schantz T. 
Published: March 2003

AbstractGenetic similarity within pairs of individuals was examined using both 10 polymorphic microsatellite loci and multi‐locus DNA fingerprinting profiles in a semi‐isolated population of great reed warblers at Lake Kvismaren, south Central Sweden, in 1987–1993. The population was founded by a few individuals in 1978, followed by a gradual increase in numbers until 1988, since when the population has remained relatively stable with about 60 breeding birds. We have previously found that high genetic similarity between pair‐mates in the population during the early part of the study period reduced egg hatching success, and hence reproductive success. The measures of pairwise genetic similarity, microsatellite allele sharing and DNA fingerprinting band sharing, were highly correlated with pedigree‐based relatedness. Both microsatellite and DNA fingerprinting similarities between pair‐mates declined significantly over the study period, and the pattern was most pronounced in the DNA fingerprinting data. Analyses restricted to the microsatellite data showed that the average annual microsatellite similarity between pairwise combinations of individuals, as well as individual homozygosity in males, declined significantly over the study period, and that several immigrants carrying novel alleles entered the population during the study. Hence, the temporal decline in genetic similarity of mates in the population is probably a consequence of increased immigration, facilitated by the recent expansion of the species in the region. These results suggest that the population has now recovered genetically, or is in the process of recovering, from a recent founder event.
The use of amplified fragment length polymorphism in determining species trees at fine taxonomic levels: analysis of a medically important snake, Trimeresurus albolabris
Authors: Giannasi Nicholas , Thorpe Roger S. , Malhotra Anita 
Published: March 2003

AbstractThere are a huge number of phylogenetic studies based on mitochondrial DNA (mtDNA); however, these may represent gene trees that may not be congruent with the species tree. A solution to this problem is to include additional, independent, loci from the nuclear genome. At fine taxonomic levels, i.e. between populations and closely related species, previously suggested nuclear markers such as intron sequence data may not be appropriate. In this study we investigate the use of amplified fragment length polymorphisms (AFLP) to aid determination of the species tree for 24 specimens of a medically important snake, Trimeresurus albolabris. This is of particular importance for many venomous snakes as venom often varies intraspecifically. Five different primer combinations produced 434 bands and were analysed by constructing a phylogenetic tree using neighbour joining and principal component analysis. Results were similar across all methods and found distinct groupings. The results were compared with mtDNA data and a reconciled tree was constructed in order to determine the species tree for T. albolabris. We found that T. albolabris (sensu lato) is not monophyletic. Specimens from the Indonesian islands (except West Java) form a distinct clade and we propose elevation to species level. A specimen from Nepal is also distinct and suggests that this population also deserves specific status. We suggest that AFLPs may prove a valuable aid in determining species trees as opposed to gene trees at fine taxonomic levels and this should facilitate the incorporation of molecular data into such activities as antivenom production and conservation management.
Abundance and diversity of Schizophyllum commune spore clouds in the Caribbean detected by selective sampling
Authors: James Timothy Y. , Vilgalys Rytas 
Published: March 2003

AbstractSelective spore trapping and molecular genotyping methods were employed to examine potential long‐distance gene flow among Caribbean populations of the common mushroom Schizophyllum commune. Spore‐trap samples from five locations were analysed using restriction fragment polymorphisms of five enzymatically amplified gene regions. Successful trappings suggested S. commune spores to be abundant in the air, with an estimated sedimentation rate of ≈ 18 spores/m2/h. High levels of genetic diversity characterized the spore‐trap samples, with as many as 12 alleles observed at a single locus (chitin synthase) over all samples. In addition, spore‐trap samples showed significant among sample heterogeneity including geographical population substructure. The ribosomal DNA (rDNA) intergenic spacer displayed the greatest allele frequency differences among samples, clearly separating the samples into those possessing only a South American‐type allele and those segregating for both North and South American‐type alleles. The molecular variation provided no clear evidence for dispersal over large, aquatic barriers within the Caribbean region, and instead suggested that spore‐trapping experiments are primarily reflective of the local, established population.
Deep molecular divergence in the absence of morphological and ecological change in the Californian coastal dune endemic trapdoor spiderAptostichus simus
Authors: Bond J. E. , Hedin M. C. , Ramirez M. G. , Opell B. D. 
Published: March 2003

AbstractAptostichus simusis a trapdoor spider endemic to the coastal dunes of central and southern California and, on morphological grounds, is recognized as a single species. Mitochondrial DNA 16S rRNA sequences demonstrate that most populations are fixed for the same haplotype and that the population haplotypes from San Diego County, Los Angeles County, Santa Rosa Island, and Monterey County are extremely divergent (6–12%), with estimated separation times ranging from 2 to 6 million years. A statistical cluster analysis of morphological features demonstrates that this genetic divergence is not reflected in anatomical features that might signify ecological differentiation among these lineages. The species status of these divergent populations ofA. simusdepends upon the species concept utilized. If a time‐limited genealogical perspective is employed,A. simuswould be separated at the base into two genetically distinct species. This study suggests that species concepts based on morphological distinctiveness, in spider groups with limited dispersal capabilities, probably underestimate true evolutionary diversity.
Diamondback moth compensatory consumption of protease inhibitor‐transformed plants
Authors: Winterer Juliette , Bergelson Joy 
Published: March 2003

AbstractPrior study of the effect of protease inhibitors (PIs) on diamondback moths suggests that moths are resistant to them, so PIs represent an ineffective defence against moths. However, our data suggest that diamondback moths do suffer lower growth rates when they consume plants transformed with potato protease inhibitor (PI2), but that effect is hidden by compensatory consumption. Plants, instead of gaining an advantage by lowering the insect growth rate, suffer a disadvantage as moths consume more tissue to mitigate the effect. Furthermore, PI2, when used in conjunction with another transgenic pesticidal protein, Bt (from Bacillus thuringiensis) counteracts the effectiveness of Bt at protecting plant tissue. Thus, transgenic PIs are not only less effective than previously thought in protecting Brassica plants from diamondback moths, they may actually lead to increased plant damage by the moths.
Genetic characterization of hybridization and introgression between anadromous rainbow trout (Oncorhynchus mykiss irideus) and coastal cutthroat trout (O. clarki clarki)
Authors: Young William P. , Ostberg Carl O. , Keim Paul , Thorgaard Gary H. 
Published: March 2003

AbstractInterspecific hybridization represents a dynamic evolutionary phenomenon and major conservation problem in salmonid fishes. In this study we used amplified fragment length polymorphisms (AFLP) and mitochondrial DNA (mtDNA) markers to describe the extent and characterize the pattern of hybridization and introgression between coastal rainbow trout (Oncorhynchus mykiss irideus) and coastal cutthroat trout (O. clarki clarki). Hybrid individuals were initially identified using principle coordinate analysis of 133 polymorphic AFLP markers. Subsequent analysis using 23 diagnostic AFLP markers revealed the presence of F1, rainbow trout backcross, cutthroat trout backcross and later‐generation hybrids. mtDNA analysis demonstrated equal numbers of F1 hybrids with rainbow and cutthroat trout mtDNA indicating reciprocal mating of the parental types. In contrast, rainbow and cutthroat trout backcross hybrids always exhibited the mtDNA from the recurrent parent, indicating a male hybrid mating with a pure female. This study illustrates the usefulness of the AFLP technique for generating large numbers of species diagnostic markers. The pattern of hybridization raises many questions concerning the existence and action of reproductive isolating mechanisms between these two species. Our findings are consistent with the hypothesis that introgression between anadromous populations of coastal rainbow and coastal cutthroat trout is limited by an environment‐dependent reduction in hybrid fitness.
Microsatellite variation and fine‐scale population structure in the wood frog (Rana sylvatica)
Authors: Newman Robert A. , Squire Tina 
Published: March 2003

AbstractWe investigated genetic population structure in wood frogs (Rana sylvatica) from a series of Prairie Pothole wetlands in the northern Great Plains. Amphibians are often thought to exist in demographic metapopulations, which require some movement between populations, yet genetic studies have revealed strong subdivision among populations, even at relatively fine scales (several km). Wood frogs are highly philopatric and studies of dispersal suggest that they may exhibit subdivision on a scale of ≈ 1–2 km. We used microsatellites to examine population structure among 11 breeding assemblages separated by as little as 50 m up to ≈ 5.5 km, plus one population separated from the others by 20 km. We found evidence for differentiation at the largest distances we examined and among a few neighbouring ponds, but most populations were strikingly similar in allele frequencies, suggesting high gene flow among all but the most distant populations. We hypothesize that the few significant differences among neighbouring populations at the finest scale may be a transient effect of extinction–recolonization founder events, driven by periodic drying of wetlands in this hydrologically dynamic landscape.
Microsatellite variation in naturalDrosophila melanogasterpopulations from New South Wales (Australia) and Tasmania
Authors: Agis M. , Schlötterer C. 
Published: March 2003

AbstractMicrosatellite variation was studied at 48 microsatellite loci in 10Drosophila melanogasterpopulations to investigate the population structure on the Australian east coast. Low, but statistically significant population differentiation was observed among most populations. The populations on the Australian mainland did not show evidence for isolation by distance. We conclude that the population structure ofD. melanogasteron the Australian mainland is probably the result of a shared history (recent colonization). The observed differences between localD. melanogasterpopulations probably reflect variation in effective population sizes rather than patterns of gene flow. Two populations from Tasmania were more differentiated from the Australian mainland than a population from Israel, raising the question whether they are derived from the Australian mainland or colonized from a different source population.
Hierarchical genetic structure of the introduced wasp Vespula germanica in Australia
Authors: Goodisman Michael A. D. , Matthews Robert W. , Crozier Ross H. 
Published: March 2003

AbstractThe wasp Vespula germanica is a highly successful invasive pest. This study examined the population genetic structure of V. germanica in its introduced range in Australia. We sampled 1320 workers and 376 males from 141 nests obtained from three widely separated geographical areas on the Australian mainland and one on the island of Tasmania. The genotypes of all wasps were assayed at three polymorphic DNA microsatellite markers. Our analyses uncovered significant allelic differentiation among all four V. germanica populations. Pairwise estimates of genetic divergence between populations agreed with the results of a model‐based clustering algorithm which indicated that the Tasmanian population was particularly distinct from the other populations. Within‐population analyses revealed that genetic similarity declined with spatial distance, indicating that wasps from nests separated by more than ~25 km belonged to separate mating pools. We suggest that the observed genetic patterns resulted from frequent bottlenecks experienced by the V. germanica populations during their colonization of Australia.
Geographical and genetic distances among zooplankton populations in a set of interconnected ponds: a plea for using GIS modelling of the effective geographical distance
Authors: Michels E. , Cottenie K. , Neys L. , De Gelas K. , Coppin P. , De Meester L. 
Published: March 2003

AbstractIn systems of interconnected ponds or lakes, the dispersal of zooplankton may be mediated by the active population component, with rivulets and overflows functioning as dispersal pathways. Using a landscape‐based approach, we modelled the effective geographical distance among a set of interconnected ponds (De Maten, Genk, Belgium) in a Geographic Information System (GIS) environment. The first model (the Landscape Model; LM) corrects for the presence of direct connections among ponds and was based on the existing landscape structure (i.e. network of connecting elements among ponds, travelling distance and direction of the current). A second model (the Flow Rate Model; FRM) also incorporated field data on flow rates in the connecting elements as the driving force for the passive dispersal of the active zooplankton population component. Finally, the third model (the Dispersal Rate Model; DRM) incorporated field data on zooplankton dispersal rates. An analysis of the pattern of genetic differentiation among Daphnia ambigua populations inhabiting 10 ponds in the pond complex reveals that the effective geographical distance as modelled by the flow rate and the dispersal rate model provide a better approximation of the true rates of genetic exchange among populations than mere Euclidean geographical distances or the landscape model that takes into account solely the presence of physical connections.
Sharp genetic breaks among populations of Haptosquilla pulchella (Stomatopoda) indicate limits to larval transport: patterns, causes, and consequences
Authors: Barber P. H. , Palumbi S. R. , Erdmann M. V. , Moosa M. K. 
Published: March 2003

AbstractTo help stem the precipitous decline of coral reef ecosystems world‐wide, conservation efforts are focused on establishing interconnected reserve networks to protect threatened populations. Because many coral reef organisms have a planktonic or pelagic larval dispersal phase, it is critical to understand the patterns of ecological connectivity between reserve populations that result from larval dispersal. We used genetics to infer dispersal patterns among 24 Indo‐West Pacific populations of the mantis shrimp, Haptosquilla pulchella. Contrary to predictions of high dispersal facilitated by the strong currents of the Indonesian throughflow, mitochondrial DNA sequences from 393 individuals displayed striking patterns of regional genetic differentiation concordant with ocean basins isolated during periods of lowered sea level. Patterns of genetic structuring indicate that although dispersal within geographical regions with semicontiguous coastlines spanning thousands of kilometres may be common, ecologically meaningful connections can be rare among populations separated by as little as 300 km of open ocean. Strong genetic mosaics in a species with high dispersal potential highlight the utility of genetics for identifying regional patterns of genetic connectivity between marine populations and show that the assumption that ocean currents will provide ecological connectivity among marine populations must be empirically tested in the design of marine reserve networks.
Using nested clade analysis to assess the history of colonization and the persistence of populations of an Iberian Lizard
Authors: Paulo Octávio S. , Jordan William C. , Bruford Michael W. , Nichols Richard A. 
Published: March 2003

AbstractThe distribution of the lizard Lacerta schreiberi is likely to have been severely affected by the climatic cycles that have influenced the Iberian Peninsula. Information about the species ecology and Iberian physiogeography was used to generate specific hypotheses about episodes of colonization and subsequent population persistence. These hypotheses generated predictions about the distribution of genetic variation, which were tested using nested clade analysis (NCA) supplemented by analysis of molecular variance (amova). Two predictions were confirmed by NCA; that is those that specified multiple and allopatric refugia. However, the remaining three predictions were not corroborated by the analyses. Firstly, a simple analysis of the distribution of genetic variability failed to detect an expected difference in the pattern of colonization between the inland mountain system and the coastal region. Moreover, while NCA did detect the expected genetic pattern in southern coastal populations, it was explained in terms of long‐distance migration, which seems implausible because of the extent of unsuitable habitat. A more likely cause of the pattern is population fragmentation and a reduction in population size caused during the Holocene. Finally, NCA also failed to detect a northwestern population expansion, which is supported by other evidence. We conclude that NCA has a limited ability to detect range expansion led by individuals with more ancestral (interior) haplotypes.
Mesobuthus gibbosus (Scorpiones: Buthidae) on the island of Rhodes — hybridization between Ulysses’ stowaways and native scorpions?
Authors: Gantenbein B. , Largiadèr C. R. 
Published: March 2003

AbstractAllozyme data suggest that the Rhodes population of Mesobuthus gibbosus is a hybrid population of recent origin. Namely, it is a mixture between an autochthonous population and an artificially introduced population probably from the Greek mainland. All samples were mainly composed of F1 hybrid genotypes and genotypes either fixed for autochthonous or introduced alleles. Back‐cross hybrid genotypes were very rare. Mitochondrial DNA analysis, in contrast, revealed only one group of closely related haplotypes that are unique for the Rhodes populations, thus suggesting asymmetric introgression of the two marker classes.