bluuebunny/crossref_metadata_2025 huggingface dataset:
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

The 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

The 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

Phylogenetic 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

Although 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

Regions 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

For 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

Glacial 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

Two 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

We 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

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

In 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

As 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

DNA 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

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

Spatial 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.
Detection and analysis of genetic variation in Hordeum spontaneum populations from Israel using RAPD markers
Authors: DAWSON I. K. , CHALMERS K. J. , WAUGH R. , POWELL W.
Published: April 2008

Randomly amplified polymorphic DNA (RAPD) markers were used to analyse genetic diversity within and between Hordeum spontaneum populations sampled from Israel. Nei's index of genetic differentiation was used to partition diversity into within and between population components. Fifty‐seven per cent of the variation detected was partitioned within 10 H. spontaneum populations. Using principal component and multiple regression analysis, part of the variation detected between populations was seen to be associated with certain ecogeographical factors. Fifty‐eight per cent of the distribution of the phenotypic frequencies of three RAPD phenotypes detected using a single primer in 20 H. spontaneum populations could be accounted for by four ecogeographical variables, suggesting adaptive variation at certain RAPD loci.
Phylogeny and historical aspects of the ecology of eastern Australian scrubwrens Sericornis spp. — evidence from mitochondrial DNA
Authors: JOSEPH L. , MORITZ C.
Published: April 2008

A phylogeny of mainland eastern Australian scrubwrens (Sericornis citreogularis, S. frontalis, S. keri, S. tnagnirostris and S. beccarii) was constructed using presence or absence of phylogenetically informative restriction sites in 15 mitochondrial DNA (mtDNA) haplotypes. MtDNA sequence divergences between species were generally large (mostly between 10 and 18%) emphasizing the antiquity of this radiation. Phylogenetic analysis of the mtDNA resulted in a strongly supported phylogeny concordant with relationships suggested by a previous study of allozyme variation, but conflicting with concepts based on morphological similarity. The mtDNAs grouped the species into two lineages, one containing beccarii and tnagnirostris and the other comprising citreogularis, frontalis and keri. The mtDNAs of beccarii and tnagnirostris were paraphyletic with a northern variant of tnagnirostris being more similar to beccarii than other magnirostris. The mtDNA from keri was most closely related to that of frontalis and then citreogularis. The strongly corroborated molecular phylogeny confirms and extends the previous (Christidis et al. 1988; Auk 105 > 616) reinterpretation of morphological and ecological shifts in the group. This suggests considerable plasticity and parallelism in the plumage characters previously used to associate species. The low divergence and close relationship between the montane rain‐forest specialist keri and the widely distributed generalist frontalis demonstrate the capacity for evolutionarily rapid and dramatic shifts in habitat use. This contrasts with the assumption of fixed habitat preference that underlies refuge‐based models of diversification of rain‐forest fauna.
Plasmid DNA in a groundwater aquifer microcosm ‐adsorption, DNAase resistance and natural genetic transformation of Bacillus subtilis
Authors: ROMANOWSKI G. , LORENZ M. G. , WACKERNAGEL W.
Published: April 2008

Prokaryotes can exchange chromosomal and plasmid genes via extracellular DNA in a process termed genetic transformation. This process has been observed in the test tube for several bacterial species living in the environment but it is not clear whether transformation occurs in natural bacterial habitats. A major constituent of terrestrial environments are solid particles such as quartz, silt and clay, which have considerable surface areas and which make up the solid‐liquid interfaces of the habitat. In previous experiments the adsorption of DNA to chemically purified quartz and clay minerals was shown and the partial protection of adsorbed DNA against DNAase I. In a microcosm consisting of natural groundwater aquifer material (GWA) sampled directly from the environment and groundwater (GW) both linear duplex and supercoiled plasmid DNA molecules bound rapidly and quantitatively to the minerals. The divalent cations required to form the association were those present in the GWA/GW microcosm. The association was stable to extended elution over one week at 23°C. Upon adsorption, the DNA became highly resistant against enzymatic degradation. About 1000 times higher DNAase I concentrations were needed to degrade bound DNA to the same extent as DNA dissolved in GW. Furthermore, chromosomal and plasmid DNA bound on GWA transformed competent cells of Bacillus subtilis. However, in contrast to DNA in solution, on GWA the chromosomal DNA was more active in transformation than the plasmid DNA. The studies also revealed that in the transformation of B. subtilis Mg2+ can be replaced by Na+, K+ or NH4 The observations suggest that in soil and sediment environments, mineral material with inorganic precipitates and organic matter can harbour extracellular DNA leaving it available for genetic transformation.
Mitochondrial DNA phylogeography in northern grasshopper mice (Onychomys leucogaster) — the influence of Quaternary climatic oscillations on population dispersion and divergence
Authors: RIDDLE B. R. , HONEYCUTT R. L. , LEE P. L.
Published: April 2008

The details of mitochondrial DNA (mtDNA) phylogenetic structure of the northern grasshopper mouse Onychomys leucogaster were examined using populations from a postulated area of endemism that includes three arid regions (Colorado Plateaus, Interior Plains, and Wyoming Basins) in western North America. Fifteen tetra‐ and heptanucleotide restriction enzymes were used to assay restriction‐site variation in a 2150‐bp PCR‐amplified fragment of mtDNA representing the ND2 and part of the COI gene regions. A total of 18 mtDNA haplotypes were detected. Although overall genetic divergence among these haplotypes was low (average = 1.1%), phylogeographic structuring was apparent. Notably, a clear phylogenetic split separated one group of haplotypes restricted to the Wyoming Basins from all others. This phylogenetic split was further corroborated by examination of nucleotide sequence variation from a 270‐bp stretch of the mtDNA cytochrome b gene. Overall geographic and phylogenetic patterns suggest a complex history of geographic structuring and subsequent mixing of populations of grasshopper mice throughout the late Pleistocene. These patterns of variation are evaluated relative to alternative hypotheses about biotic responses to Quaternary climatic oscillations in western North American arid regions.
Assessing the risks of transgene escape through time and crop‐wild hybrid persistence
Authors: LINDER C. R. , SCHMITT J.
Published: April 2008

Transgenes introduced into crops can escape in time, as well as space, via the seed bank. For annual plants, especially ruderals, seed bank behaviour may be the most important factor determining population persistence. Crop seeds may exhibit some dormancy and germination cueing in the soil but are expected to be less able to persist than their wild relatives, which often have considerable dormancy and longevity, as well as effective germination cueing responses. Crop‐wild hybrids may have seed bank characteristics more suited to persistence, and maternal effects may favour persistence of hybrids having wild plants for their female parent. Escape of transgenes via crop‐wild hybrids presents unique concerns not present for crops. Hybrids can undergo natural selection and may back‐cross with wild plants. We suggest methods that can be used in conjunction with evaluation of the relative fitness of crop‐wild hybrids that will determine the likelihood of back‐crossing. Accurate assessment of escape in time and transgene persistence via crop‐wild hybrids requires proper plant materials. We emphasize the use of null segregants as controls for transgenic crops and for generating crop‐wild hybrid controls for transgenic hybrids. Since good empirical and theoretical understanding of how individual genes influence the fate of plants in different environments is lacking, evaluation of escape in time and the persistence of transgenes via crop‐wild hybrids should be on a case‐by‐case basis.
The impact of hybrids between genetically modified crop plants and their related species: general considerations
Authors: DALE P.J.
Published: April 2008

Factors influencing the fate and impact of hybrids between crop plants and their related species operate from the early zygote, through to plant establishment in different habitats, to their ability to form self‐sustaining populations. Many of the classes of genes being introduced by modern methods of genetic modification are similar to those manipulated by conventional plant breeding. In assessing the impact of transgenes in hybrids between crops and related species, therefore, it is important to be informed about the consequences of hybridization between conventionally bred varieties and their relatives. Some transgenes will have novel effects (e.g. production of pharmaceutical substances or certain fatty acids) on plants, and are likely to need specific assessment studies to determine their impact on hybrids. This will be particularly important if there is the possibility of these transgenes becoming established in wild populations. Some recommendations for further research are outlined.
Release of transgenic plants: biodiversity and population‐level considerations
Authors: ANGLE J. SCOTT
Published: April 2008

Many transgenic plant gene products introduced into soil are likely to degrade so quickly that they will have little impact upon the ecosystem. Some products, however, will be more recalcitrant and thus may exhibit potentially adverse effects upon the soil ecosystem. Potential changes in specific groups of organisms, functional groups of organisms and biodiversity are discussed. Methods to detect changes and the impact of changes are considered.
Assessing the impact of transgenic plant products on soil organisms
Authors: MORRA M.J.
Published: April 2008

Little is known about the impact of transgenic plant products on soil organisms. However, previous research with synthetic organics, allelochemicals, and extracellular enzymes can be used to guide future research in this area. Projects designed to quantify the impact of transgenic plants on soil organisms must clearly establish that the gene products are responsible for any observed changes. This can only be achieved by determining the fate of transgenic plant gene products during the period of the soil bioassay. The overall impact of transgenic plants will be dictated by not only the primary gene product, but secondary products resulting from abiotic and biotic soil reactions. Primary and secondary products may exhibit both acute and chronic impacts. Such impacts are best quantified using a soil microcosm in which fungal populations and micro‐ and mesofauna are monitored.
Transgenic plants and biogeochemical cycles
Authors: TREVORS J.T. , KUIKMAN P. , WATSON B.
Published: April 2008

The purpose of this manuscript is to consider interactions between transgenic (TG) plants and biogeochemical cycles, with an emphasis on how microorganisms involved in soil nutrient cycles may be influenced by transgenic plant gene products. We have also attempted to identify research areas considered a priority to fill existing information requirements on use of TG plants in the environment.
Community response to transgenic plant release: using mathematical theory to predict effects of transgenic plants
Authors: ANDOW D. A.
Published: April 2008

Predicting the potential effects of introductions of plants on the structure of plant communities has been elusive. I suggest that mathematical models of resource competition might be useful for identifying categories of plants that either are unlikely to alter community structure or that have the potential for altering community structure. Assuming that the transgenic plant will escape and establish viable populations in nontarget habitats, this theory suggests that species that have a high minimum resource requirement are unlikely to alter community structure. The theory is elaborated to evaluate the potential effects on community structure of transgenic plants with resistance to primary consumers. Results indicate that the greatest reduction in the minimum resource requirement caused by resistance will occur when consumers are consuming enough plant biomass that the plant can no longer grow. If resistance to such a consumer were incorporated into a plant, it could lower the minimum resource requirement sufficiently that a transgenic plant would be able to alter community structure substantially. Examples of introductions of exotic plants, plant pathogens, and insect herbivores are given to support the conceptual basis of the theory. Not all transgenic plants with resistance, however, have the potential to alter community structure. Resistance to primary consumers that strongly reduce the biomass producing ability of a plant will probably be able to alter community structure, whereas resistance that reduces most other types of yield loss is less likely to alter community structure. The theory should be elaborated to incorporate more‐realistic assumptions, such as those regarding reproduction, dormancy, and dispersal of the transgenic plants, and provide more detailed characterization of the potential hazard of transgenic plants to plant communities.
Community response to transgenic plant release: predictions from British experience of invasive plants and feral crop plants
Authors: WILLIAMSON M.
Published: April 2008

The ten‐ten rule can be used to predict the community consequences of releasing GMOs. This, combined with data on the feral state of British crop plants, predicts that almost all GMOs will become at least casual, that more than 10% will establish, and about 10% of those will become pests. Which constructs will fall into which category cannot be predicted from their characters. In particular, Baker characters have no predictive value for weediness. The fourteen most troublesome invasive plant pests show a remarkably diverse set of characters. GMOs, being mainly derived from crop plants, and in some cases with genes that are likely to enhance survival, can be expected to have an appreciable effect on nonagricultural ecosystems, once a range of different constructs have been released. Familiarity is unlikely to be an effective defence against new ecological effects.
Test systems to determine the ecological risks posed by toxin release fromBacillus thuringiensisgenes in crop plants
Authors: JEPSON P. C. , CROFT B. A. , PRATT G. E.
Published: April 2008

Procedures for the selection of species for ecotoxicological risk assessment ofBacillus thuringiensis(Bt) gene products in the epigeal and hypogeal environments are proposed. Although species can be selected on the basis of ecological realism and functional importance, the number of organisms requiring testing and the nature of the test procedures remain uncertain with such a selectively toxic material. The heterogeneity of the soil environment, the stratification of plant material at different stages of breakdown and decomposition and the aggregation and patterns of movement of the soil fauna and flora impose problems for the design of ecologically relevant test methods. Similarly, the impact upon beneficial invertebrates, if toxic effects are detected, will be mediated by the scale and pattern of transgenic plant release in the fragmented agricultural landscape. To properly assess the ecological risks posed by a widely released toxin with a narrow spectrum of effects, a combination of laboratory tests, field experiments and longer‐term monitoring will be required.
Parent and larval RAPD fingerprints reveal outcrossing in freshwater bryozoans
Authors: JONES C. S. , OKAMURA B. , NOBLE L. R.
Published: April 2008

The occurrence of outcrossing in benthic hermaphroditic colonial invertebrates has received much historical debate and little demonstration. Direct genetic study of this question using routine techniques has been limited by both the amount of material required and the detection of adequate DNA polymorphisms. However, the recent development of molecular techniques that require no a‐priori sequence data provides new approaches to the characterization of both tiny and genetically similar individuals. Random amplification of polymorphic DNA (the RAPD assay) was used to amplify fragments of DNA (via the polymerase chain reaction) to obtain fingerprints of parental colonies and larval offspring of the hermaphroditic freshwater bryozoan Cristatella mucedo. Here we report the first positive and direct genetic evidence for outcrossing in bryozoans. However, we find that outcrossing generates only low levels of genetic variation in populations that are highly clonal.
Genetic stability in a population of a plant pathogenic fungus over time
Authors: CHEN R.‐S. , BOEGER J. M. , MCDONALD B. A.
Published: April 2008

Collections of the plant pathogenic fungus Mycosphaerella graminicola were made from the same field of wheat over a 3‐year period. The field was planted with small plots containing four varieties of wheat grown in pure stand and in all possible two‐, three‐ and four‐way mixtures. In each year, the wheat field was recolonized by a local source of inoculum of unknown origin. Allele frequencies at 10 RFLP loci were compared at two different times within a growing season and over the 3‐year period. No significant differences in allele frequencies were found for any of the RFLP loci over any of the time periods. DNA fingerprints were used to identify clones produced by asexual reproduction. Genotypic diversity based on the frequency of each clone was compared for each collection. No significant changes in genotypic diversity were found within a year or between years. Identical genotypes were found in the field at different times within a season, but no clones were conserved between years. No clone existed in a high frequency in any year, suggesting that selection for particular asexual lineages was weak. The founding population each year probably originated from wind‐borne ascospores of the teleomorph, which may exist as an indigenous population on alternative hosts, such as Poa annua (annual bluegrass).
Variation in mitochondrial DNA and population structure of the Taipei treefrog Rhacophorus taipeianus in Taiwan
Authors: YANG YI‐JU , LIN YAO‐SUNG , WU JEN‐LEIH , HUI CHO‐FAT
Published: April 2008

Mitochondrial DNA (mtDNA) from 40 samples of the Taipei treefrog Rhacophorus taipeianus collected from seven populations in Taiwan were sequenced to document the DNA sequence variation in anuran mtDNA and to elucidate the phylogeographic population structure in the Taipei treefrog. Sequences of 722–764 bases in length, including a 108‐bp segment of the cytochrome b gene and a 614–656‐bp D‐loop segment, were obtained by direct sequencing using polymerase chain reaction (PCR). The variation in length was due to a 40‐bp region that tandemly repeated four to five times in the D‐loop region. The first repeat is the most conserved one among the five repeats because there are no variable sites in this repeat. Besides the 40‐bp length variation, 28 positions in the 764‐bp sequences are variable and distributed evenly in the cytochrome b gene fragment and D‐loop region. Variation in the D‐loop of the Taipei treefrog is comparable to those of other vertebrates. Two well‐differentiated lineages (northern and central) differing by mean sequence divergence of 1.7% are identified and concordant with their geographic distributions. The two lineages are inferred to have split from a common ancestral population in the early Pleistocene. However, the interpopulation divergence of the northern lineage (< 0.33%) is apparently lower than that of the central lineage (1.11%), implying that the two lineages evolved independently and had different demographic histories after divergence. This study reveals that anuran D‐loop has potential as a genetic marker in phylogenetic and population genetic analyses of anurans.
No evidence for extrapair fertilizations in the merlin revealed by DNA fingerprinting
Authors: WARKENTIN I. G. , D.‐CURZON A. , CARTER R. E. , WETTON J. H. , JAMES P. C. , OLIPHANT L. W. , PARKIN D. T.
Published: April 2008

Broods of young merlins were compared with the adults in attendance at their nest by DNA fingerprinting. No offspring were found that mismatched genetically suggesting that intraspecific brood parasitism and extrapair fertilization are very rare in this population. The results are discussed in the light of the Paternity Assurance Hypothesis.
Insertion sequence (IS) hybridization supports classification of Rhizobium meliloti by phage typing
Authors: BARRAN L. R. , BROMFIELD E. S. P. , LABERGE S. , WHEATCROFT R.
Published: April 2008

Sixty‐one isolates of Rhizobium meliloti from two field sites which had been previously classified into 15 phage types on the basis of sensitivity to 16 typing phages, were subjected to insertion sequence (IS) hybridization using DNA probes for ISRm3 and ISRm5. Isolates from all but one phage type contained ISRm3 (apparent copy no. 1–11) and all isolates contained ISRm5 (apparent copy no. 3–11). The isolates were placed into 24 IS classes based on differences in their respective ISRm3 and ISRm5 hybridization profiles. At either field site, isolates representing different phage types possessed IS hybridization profiles that differed from each other, while those comprising a specific type had identical or closely related profiles. Isolates from one phage type were unusual since they did not react with any of the typing phages and were shown by IS hybridization to constitute a heterogeneous group. Evidence for spatial effects were provided by isolates from two of six types present at both sites which fell into separate IS classes on the basis of their site of origin. These data have ecological implications and suggest that for a particular site, phage typing may be employed for the rapid assessment of the genetic diversity among field isolates.
DNA variability and parentage testing in captive Waldrapp ibises
Authors: SIGNER E. N. , SCHMIDT C. R. , JEFFREYS A. J.
Published: April 2008

The Waldrapp ibis (Geronticus eretnita) is one of the most endangered birds in the wild. The only real hope for its survival seems to rest with captive propagation, which has fortunately proved straightforward. Preservation of genetic diversity for maintaining viable populations is a major goal in any species conservation programme. Therefore sensitive tools have to be developed for the detection and regular monitoring of population variability. Individual identity has to be verified and each individual's pedigree defined in order to enable effective selective breeding. In this study, extensive DNA fingerprinting technology was applied to a group of 39 captive Waldrapp ibises. Five minisatellite probes were used. Despite the fact that the colony was founded by only six birds and that some of the founders were apparently related, highly polymorphic banding patterns were obtained. The human‐ and pig‐derived probes MS1, MS31, pλg3 and pCMS12 each detected multiple distinct loci suitable for individual identification and resolution of parentage. Probe MS51 was locus‐specific and revealed six different alleles. In addition, MS31 and pλg3 co‐detected a band present in all females but none of the males and thus could be used for sex determination. For all but four individuals both parents could be identified unambiguously. The exceptions were offspring derived from a full sib mating in which DNA results allowed no distinction between the parents and the grandparents. Comparison of the parentage assigned by DNA analysis and by observation of breeding behaviour, respectively, showed agreement in all but five instances. Here, DNA data uncovered interchange of individuals in the stud book. Application of these minisatellite probes therefore offers an extremely sensitive means for individual identification and verification and completion of pedigree records.
Molecular genetics of the most endangered canid: the Ethiopian wolf Canis simensis
Authors: GOTTELLI D. , SILLERO‐ZUBIRI C. , APPLEBAUM G. D. , ROY M. S. , GIRMAN D. J. , GARCIA‐MORENO J. , OSTRANDER E. A. , WAYNE R. K.
Published: April 2008

The world's most endangered canid is the Ethiopian wolf Canis simensis, which is found in six isolated areas of the Ethiopian highlands with a total population of no more than 500 individuals. Ethiopian wolf populations are declining due to habitat loss and extermination by humans. Moreover, in at least one population, Ethiopian wolves are sympatric with domestic dogs, which may hybridize with them, compete for food, and act as disease vectors. Using molecular techniques, we address four questions concerning Ethiopian wolves that have conservation implications. First, we determine the relationships of Ethiopian wolves to other wolf‐like canids by phylogenetic analysis of 2001 base pairs of mitochondrial DNA (mtDNA) sequence. Our results suggest that the Ethiopian wolf is a distinct species more closely related to gray wolves and coyotes than to any African canid. The mtDNA sequence similarity with gray wolves implies that the Ethiopian wolf may hybridize with domestic dogs, a recent derivative of the gray wolf. We examine this possibility through mtDNA restriction fragment analysis and analysis of nine microsatellite loci in populations of Ethiopian wolves. The results imply that hybridization has occurred between female Ethiopian wolves and male domestic dogs in one population. Finally, we assess levels of variability within and between two Ethiopian wolf populations. Although these closely situated populations are not differentiated, the level of variability in both is low, suggesting long‐term effective population sizes of less than a few hundred individuals. We recommend immediate captive breeding of Ethiopian wolves to protect their gene pool from dilution and further loss of genetic variability.