bluuebunny/crossref_metadata_2025_split huggingface dataset:
Screening techniques for detecting allelic variation in DNA sequences
Authors: LESSA E. P. , APPLEBAUM G. 
Published: April 2008

AbstractThis article reviews four ‘DNA screening techniques’, namely heteroduplex analysis, single‐strand conformational polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) as tools for the study of allelic variation in natural populations. The resolving power, advantages, and limitations of each technique are discussed and compared. We also provide some criteria for choosing among techniques and illustrate some practical issues with examples taken primarily from our own laboratory experience.
VNTR loci reveal differentiation between and structure within populations of the eastern barred bandicoot Perameles gunnii
Authors: ROBINSON N. A. , MURRAY N. D. , SHERWIN W. B. 
Published: April 2008

AbstractThe Eastern Barred Bandicoot Perameles gunnii has declined in abundance within mainland south‐eastern Australia, to a relict wild population of less than 100 individuals in Hamilton, Victoria. It is more common, but is also declining in Tasmania. Genomic DN A variability was compared within and between surviving populations of P. gunnii using variable number of tandem repeat (VNTR) markers in one of two ways. First, average percentage differences (APDs) were determined between profiles for two VNTR probe—endonuclease combinations. Secondly, because one of these combinations revealed two multiallelic VNTR loci, genotypes were assigned and analysed for homogeneity of allele frequencies among subpopulations, for deviation of heterozygosity from Hardy‐Weinberg equilibrium within populations and for genetic structuring among individuals from different subpopulations. The results of both the APD and defined locus approaches showed consistent trends within and between populations. Genetic variability was higher among mainland P. gunnii than in Tasmanian populations (higher APDs, number of alleles, and heterozygosity at one locus), despite the known decline and subdivision of the Hamilton population. Eleven per cent of the variability detected in Hamilton was attributed to genetic differentiation between east and west subdivisions of the population. Departure from random mating indicating local inbreeding within collecting localities was evident for one locus in both north and south Tasmania, particularly at one locality. AH alleles at both loci were unique to either Hamilton or Tasmanian P. gunnii. The initial captive colony contains high heterozygosity for these loci. It is concluded that VNTR markers can be of benefit for use in studies of population differentiation and for conservation management.
A case study of the interpretation of linkage data using DNA fingerprinting probes
Authors: BROOKFIELD J. F. Y. , CARTER R. E. , MAIR G. C. , SKIBINSKI D. O. F. 
Published: April 2008

AbstractThe statistical power of the technique of DNA fingerprinting relies greatly on the ability of the investigator to make an assumption that the presence or absence of different fingerprint bands are independent. Such linkage equilibrium is unlikely if bands are tightly linked to each other. Thus, when a new organism is to be investigated it is helpful to examine the segregation of parental bands into the offspring to confirm that the bands are not linked. By considering families of the tilapia Oreochrotnis niloticus, we produce statistical tests for linkage that can be applied to DNA fingerprint information. The use of these tests is more difficult and complicated if one parent is missing, but some progress can be made. We recommend that at least ten offspring are examined for segregation in families, since smaller numbers of offspring result in coincidental perfect agreements in band distributions in the absence of any linkage.
The perils of single gene trees — mitochondrial versus single‐copy nuclear DNA variation in white‐eyes (Aves: Zosteropidae)
Authors: DEGNAN S. M. 
Published: April 2008

AbstractPhylogenetic relationships among animal populations and species commonly have been inferred from patterns of variation observed within a single gene system, most often the mitochondrial genome. Analysis of restriction site variation in the mitochondrial DNA of two species of white‐eye (Zosterops lateralis and Z. lutea) in Australia produced a single gene tree that does not accurately represent the organismal tree. In contrast, patterns of variation at two anonymous, single‐copy nuclear DNA loci revealed a phylogeography consistent with traditional classification of the species. Discordance between mitochondrial DNA and single‐copy nuclear DNA variation is probably the result of past hybridization between Z. lateralis and Z. lutea, evidence of which has been lost from the nuclear genome by recombination. This study provides a clear empirical demonstration that single gene genealogies cannot be assumed to accurately represent the true phylogenies, and emphasizes the need for composite genetic analyses.
Dominant vs. codominant genetic markers in the estimation of male mating success
Authors: MILLIGAN B. G. , McMURRY C. K. 
Published: April 2008

AbstractAlthough a major component of fitness, male reproductive success is generally extremely difficult to estimate. As a result, genetic methods and maximum likelihood models have been developed to estimate male parentage, but all are limited in practice by the degree of genetic variation observable. Scoring individuals phenotypically at a large number of random loci exhibiting dominance (e.g. RAPD markers) may provide a means of detecting sufficient genetic variation. Dominance, however, represents a loss of information and therefore greater variation in the estimate of paternity. A mixture model describing mating in a population is presented to quantify the trade‐off between marker types when estimates of male fertility are sought. A sample size 1.5‐2.0 times greater is required for dominant markers under some conditions to obtain the same confidence in fertility estimates as for codominant markers, although with large sample sizes the fertility estimates are similar for either marker type. Since the number of dominant DN A markers is not limited in the same manner as is the number of codominant protein markers, one's confidence in the estimates can be increased above that possible from proteins by surveying additional loci. However, for a fixed sample size a trade‐off exists between the number of progeny assayed per female and the number of loci surveyed. In many cases more progeny per female provide better estimates of fertility than more loci.
The cloning and characterization of phage promoters, directing high expression of luciferase in Pseudomonas syringae pv. phaseolicola, allowing single cell and microcolony detection
Authors: WATERHOUSE R. N. , SILCOCK D. J. , WHITE H. L. , BUHARIWALLA H. K. , GLOVER L. A. 
Published: April 2008

AbstractRegions of DNA containing promoter sequences from a Pseudomonas syringae pv. phaseolicola‐specific phage (φ11P) were identified by shotgun cloning into a broad‐host‐range promoter‐probe vector (pQF70). When used in conjunction with the luciferase reporter genes, one of these DNA fragments, 19H, directed gene expression at a level which enabled the subsequent light output (bioluminescence) of single cells of P. syringae pv. phaseolicola to be detected and visualized using a charge‐coupled device (CCD). The P. syringae pv. phaseolicolaφ11P, 19H and P. aeruginosaφPLS27, HcM promoters gave a 50‐fold increase in bioluminescence (maximum relative light output) compared to similar constructs containing other well‐characterized promoters, for example, tetracycline. Similar bioluminescent characteristics of the transformed bacterium, were observed during growth with and without antibiotic‐selection. When lux+ bacteria were inoculated onto French bean leaf (Phaseolus vulgaris L.), the resultant secondary halo blight lesions were bioluminescent and during phylloplane colonization by the lux+ bacterium, bioluminescence on leaf surfaces was detected and imaged by the CCD. Use of these newly identified promoters, combined with the greatly increased sensitivity of bioluminescence detection by the CCD, thus provided a new dimension for the study of natural ecological populations during the bacterial colonization of plants.
The analysis of paternity and maternity in the marine hydrozoan Hydractinia symbiolongicarpus using randomly amplified polymorphic DNA (RAPD) markers
Authors: LEVITAN D. R. , GROSBERG R. K. 
Published: April 2008

AbstractFor organisms in which direct observation of mating and subsequent dispersal of offspring and relatives is impossible, patterns of reproductive success and genealogical relationship can only be established using genetic markers. The ideal genetic assay would (1) employ highly polymorphic genetic markers for distinguishing among individuals; (2) use little tissue for analysing early life‐history stages; and (3) require minimal investment in time and money for population level studies. From this perspective, DNA polymorphisms revealed by PCR amplification using random ten‐base primers [Randomly Amplified Polymorphic DNA (PCR‐RAPD) or Arbitrarily Primed DNA (AP‐PCR)] have great potential. However, the evidence that RAPD/AP markers are both heritable and can be repeatably amplified remains controversial. This study characterizes patterns of inheritance and polymorphism of RAPD markers in the free‐spawning, colonial marine hydrozoan Hydractinia symbiolongicarpus. In all cases, the amplification products were identical among extractions from the same clone. Of 56 primers screened, 13 had sufficient polymorphism and scoreability for an analysis of parentage and higher‐order genetic relationships in three matings. These primers generated 156 unique amplification products (putative loci), of which 133 were polymorphic. All but four of these loci were inherited as dominant mendelian markers. Our study suggests that the presence of a marker represents a single allele at a locus; however, what appear to be single null alleles may actually comprise several segregating alleles. When the identity of neither parent was known a priori, inclusion (unique markers present in offspring and only one of the potential parents) proved to be more efficient than exclusion for assigning offspring to parents. The most powerful approach, however, was cluster analysis of all presence/absence information for the marker bands. Clustering avoided the pitfalls caused by the appearance of occasional nonparental bands, and constructed a hierarchical framework that correctly reflected all genealogical relationships.
Native oak chloroplasts reveal an ancient divide across Europe
Authors: FERRIS C. , OLIVER R. P. , DAVY A. J. , HEWITT G. M. 
Published: April 2008

AbstractGlacial refugia and postglacial migration are major factors responsible for the present patterns of genetic variation we see in natural populations. Traditionally postglacial history has been inferred from fossil data, but new molecular techniques permit historical information to be gleaned from present populations. The chloroplast tRNALeu1 intron contains regions which have been highly conserved over a billion years of chloroplast evolution. Surprisingly, in one of these regions which has remained invariant for all photosynthetic organisms so far studied, we have found intraspecific site polymorphism. This polymorphism occurs in two European oaks, Quercus robur and Q. petraea, indicating hybridisation and introgression between them. Two distinct chloroplast types occur and are distributed geographically as eastern and western forms suggesting that these oaks are each derived from at least two separate glacial refugia.
Molecular genetic evidence for reproductive isolation between sympatric populations of smelt Osmerus in Lake Utopia, south‐western New Brunswick, Canada
Authors: TAYLOR E. B. , BENTZEN P. 
Published: April 2008

AbstractTwo morphologically and ecologically distinct forms of smelt, Osmerus, reside sympatrically in Lake Utopia, south‐western New Brunswick, Canada. The ‘normal‐sized’ form matures at greater than 200 mm standard length, averages about 31–33 gill rakers, and spawns in lake outlets. By contrast, the ‘dwarf‐sized’ form matures at less than 150 mm standard length, averages 34–36 gill rakers, and spawns in small streams 3–5 weeks later than the normal form. We tested whether these sympatric forms represented ecological polymorphism within a single population or two reproductively isolated demes by assaying variation within and between forms by mitochondrial DNA (mtDNA) restriction site and nuclear minisatellite DNA analyses. Analysis of smelt mtDNA with twelve restriction enzymes resolved ten composite genotypes (differing by an average 0.27% sequence divergence) which differed markedly in frequency between the forms. Net percentage sequence divergence between the forms was O.l6%. A Wagner parsimony/ bootstrapping analysis of the restriction site presence/absence matrix, however, suggested that there were no significant distinctions between dwarf and normal smelt based on the phylogeny of composite genotypes. Hybridization studies of genomic DNA digests with a minisatellite probe indicated both that nuclear restriction fragment differentiation and the frequency of specific fragments differed significantly between the forms. Significant genetic differentiation between the sympatric forms demonstrates that they are distinct gene pools and reproductively isolated. Our molecular evidence for reproductive isolation between dwarf and normal smelt in Lake Utopia, coupled with the persistent morphological and ecological differentiation between them, argues strongly that they are behaving as distinct species. The Lake Utopia Osmerus populations provide further illustration of the potential for rapid differentiation to the level of biological species in postglacial environments.
Rapid assessment of single‐copy nuclear DNA variation in diverse species
Authors: SLADE R. W. , MORITZ C. , HEIDEMAN A. , HALE P. T. 
Published: April 2008

AbstractWe investigated the use of PCR primers designed to conserved exons within nuclear DNA to amplify potentially variable regions such as introns or hypervariable exons from a wide range of species. We then explored various approaches to assay population‐level variation in these PCR products. Primers designed to amplify regions within the histone H2AF, myoglobin, MHC DQA, and aldolase (ALD) genes gave clean amplifications in diverse mammals (DQA), and in birds, reptiles and mammals (aldolase, H2AF, myoglobin). The sequenced PCR products generally, but not always, confirmed that the correct locus had been amplified. Several primer sets produced smaller size fragments consistent with preferential amplification of intronless pseudogenes; this was confirmed by sequencing seal and reptile H2AF PCR products. Digestion with randomly selected four‐base recognizing enzymes detected variation in some cases but not in others. In species/gene combinations with either low (e.g. seal H2AF, ALD‐A) or high (e.g. skink ALD‐1) nucleotide diversity it was more efficient to sequence a small number of distantly related individuals (e.g. one per geographic population) and from these data to identify informative or potentially informative restriction enzymes for ‘targeted’ digestion. We conclude that for studies of population‐level variation, the optimal approach is to use a battery of primers for initial PCR of both mtDNA and scnDNA loci, select those that give clean amplifications, and sequence one sample from each population to (i) confirm gene identity, (ii) estimate the amount of variation and, (iii) search for diagnostic restriction sites. This will allow determination of the most efficient approach for a large‐scale study.
Genetic structure of a natural population of Dictyostelium discoideum, a cellular slime mould
Authors: FRANCIS D. , EISENBERG R. 
Published: April 2008

Abstract Dictyostelium discoideum is a eukaryotic microbe feeding on soil bacteria. A first step towards describing the genetic structure of populations of this species was made by examining multiple isolates from a single locale. The isolates were grown clonally and their RFLP patterns compared, using a probe specific for a family of tRNA genes. Thirty‐nine types were distinguished in 54 isolates. To determine if genetic exchange occurs among members of the population, an analysis of linkage disequilibrium was performed on the RFLP data. Little disequilibrium was found, implying gene flow in the population. In conflict with this result is the finding that no recombinant progeny were recovered from many attempted crosses between pairs of isolates. The tentative conclusion is that genetic exchange does not in fact occur, and that the observed shuffling of RFLP bands is caused by insertion and excision of transposons known to be associated with the tRNA genes of Dictyostelium.
Parentage analyses in ant colonies using simple sequence repeat loci
Authors: EVANS J. D. 
Published: April 2008

AbstractIn ants of the genus Myrmica, female progeny may be the offspring of one to several different queens. In addition, both workers and queens are capable of producing haploid male offspring. Even in such complex colonies, parentage can be assigned on the basis of genotypic variation at highly polymorphic simple sequence repeat loci. Methods are described for isolating and screening dinucleotide repeat loci in ants. Three independent loci, Myrt2, Myrt3 and Myrt4, show expected heterozygosities of 0.94, 0.92 and 0.95, respectively. When used in parallel these loci should be sufficient to establish parentage in the vast majority of screened colonies. An initial screening indicates that males are produced by workers in the subalpine ant Myrmica ‘near tahoensis’.
Sexing free‐ranging brown bears Ursus arctos using hairs found in the field
Authors: TABERLET P. , MATTOCK H. , DUBOIS‐PAGANON C. , BOUVET J. 
Published: April 2008

AbstractAs an aid to the management of the Pyrenean population of the brown bear Ursus arctos, a sexing method based on the amplification of a Y chromosome specific sequence has been developed, and tested using hairs found in the field as a source of DNA. This method involves a two‐step polymerase chain reaction (PCR) which allows the detection of a very small amount of DNA, probably a single SRY gene molecule. The sex can reliably be identified using about 50pg of DNA extract as template. It is possible that this approach could, with adjustments, be used to identify the sex of other species of eutherian mammals.
Typing method for N2‐fixing bacteria based on PCR‐F — application to the characterization of Frankia strains
Authors: JAMANN S. , FERNANDEZ M. P. , NORMAND P. 
Published: April 2008

AbstractDNA sequences of an intergenic spacer (IGS) and parts of genes in the nif cluster were amplified by the polymerase chain reaction (PCR) using two primers derived from nifD‐and nifK‐conserved sequences. The PCR products were cleaved by ten 4–base cutting restriction enzymes and the restriction patterns were used as fingerprints to type Frankia strains. The feasability of this PCR‐RFLP method for typing Frankia strains was investigated on Frankia reference strains belonging mainly to the Elaeagnaceae infectivity group but also on new Frankia isolates and on other N2‐fixing microorganisms. By modulating the stringency of the amplifications, we showed the method allowed to target either Frankia strains or the whole N2‐fixing microbial community. DNA digestion patterns were used to estimate the sequence divergence between the Frankia nifD‐K fragment. The estimated relationships deduced from these genotypic data correlated well with established Frankia taxonomic schemes.
Monitoring the diversity of Rhizobium meliloti field and microcosm isolates with a novel rapid genotyping method using insertion elements
Authors: KOSIER B. , PÜHLER A. , SIMON R. 
Published: April 2008

Abstract Rhizobium meliloti strains isolated from alfalfa plants grown in a mining recultivation field, in a model ecosystem (microcosm) and in soil core containers were characterized by two new taxonomic methods, fingerprinting and handprinting, using insertion sequence elements (IS) as hybridization probes. The diversity of strains within the field population could first be detected with IS‐fingerprinting, whereby nearly three times more groups of Rhizobium meliloti strains could be identified in comparison to the groups according to plasmid profiles. This complexity and diversity of the rhizobial population was also detected in microcosm studies. Strains identified among the field population were also detected in the microcosm studies. The persistence of rhizobia in soil was demonstrated in soil core samples held in a cold room for 2 years. A decrease in the genomic diversity of the R. meliloti population upon soil storage was observed. A novel monitoring method, IS‐handprinting, in which the presence of certain endogenous insertion elements within a strain is registered, was successfully employed to characterize genetically the field R. meliloti strains with simplicity and speed. In contrast to IS‐fingerprinting, IS‐handprinting is based on a simple plus‐or‐minus detection, which is sufficient for a taxonomic characterization. Both methods, using a non‐radioactive detection system, are sensitive enough to detect one copy of an insertion element in a strain's genome. IS‐fingerprinting, with its fine resolution, would be suitable for ecological studies of individual strains in any complex ecosystem, whereas IS‐handprinting would be suitable for monitoring strains and characterizing large numbers of strains.
Cytonuclear genetic architecture in mosquitofish populations and the possible roles of introgressive hybridization
Authors: SCRIBNER K. T. , AVISE J. C. 
Published: April 2008

AbstractSpatial genetic structure in populations of mosquitofish (Gambusia) sampled throughout the south‐eastern United States was characterized using mitochondrial (mt) DNA and allozyme markers. Both sets of data revealed a pronounced genetic discontinuity (along a broad path extending from south‐eastern Mississippi to north‐eastern Georgia) that corresponds to a recently recognized distinction between the nominal forms G. affinis to the west and G. holbrooki to the east. However, several populations from the general contact region exhibited unusual allelic associations in high frequency, suggestive of evolutionary processes within a zone of introgressive hybridization. These involve: (i) cytonuclear profiles representing combinations of nuclear and mitochondrial genotypes that tended to be more nearly species‐specific and concordant elsewhere; and (ii) significant nuclear gametic disequilibria, perhaps attributable to positive assortative mating and/or differential fitnesses of homospecific vs. recombinant genotypes. However, outside this suspected hybrid region, ‘heterospecific’ genetic markers also appeared in low frequency, thus complicating interpretations. These discordant alleles on a broader geographic scale may reflect: (a) the retention of polymorphisms from an ancestral gene pool; (b) occasional evolutionary convergence (especially with respect to electrophoretic mobility of allozyme alleles); (c) the ‘footprints’ of a moving hybrid zone; or (d) differential introgressive penetrance across the current hybrid region.