bluuebunny/crossref_metadata_2025_split huggingface dataset:
Geographic and microgeographic genetic differentiation in two aphid species over southern England using the multilocus (GATA)4 probe
Authors: de BARRO P. J. , SHERRATT T. N. , CARVALHO G.R. , NICOL D. , IYENGAR A. , MACLEAN N. 
Published: April 2008

AbstractSamples of the grain aphid Sitobion avenue (F.) and the rose‐grain aphid Metopolophium dirhodum (Walker) were collected in late March from wheat fields and adjacent road‐side grasses at a number of locations in southern England. Unparasitized aphids were DNA fingerprinted using the multilocus (GATA)4 probe. Over all locations, the fingerprints of individual S. avenue caught in wheat had lower overall average distances of band migration (ADBM) and shared a higher proportion of bands, than fingerprints of individuals caught in adjacent road‐side grasses. The ADBM of fingerprints of S. avenue collected on road‐side grasses altered significantly with geographical location, while the ADBM of fingerprints of S. avenue caught on wheat did not. A comparison of the fingerprints of individual M. dirhodum caught in wheat and neighbouring road‐side grasses did not reveal any genetic differentiation. Fingerprints of M. dirhodum that were caught in the same host type did however, show significant variation in ADBM between different locations. With both S. avenue and M. dirhodum, spatial autocorrelation revealed that locations that were close together were no more likely to have individuals with similar ADBM than locations mat were far apart Our results suggest that (i) particular clones of S. avenue prefer to colonize wheat; and/or that (ii) particular clones of S. avenae perform better on wheat man other clones. It is unclear why M. dirhodum did not show any genetic structuring according to host type, but this species appears to engage in sexual reproduction much more frequently than S. avenae in southern England. M. dirhodum is likely to have displayed genetic heterogeneity between locations either because of founder effects, or because of genetic drift.
Species identification of Cecidophyopsis mites (Acari: Eriophyidae) from different Ribes species and countries using molecular genetics
Authors: FENTON B. , MALLOCH G. , JONES A. T. , AMRINE J. W. , GORDON S. C. , A'HARA S. , MCGAVIN W. J. , BIRCH A. N. E. 
Published: April 2008

Abstract Cecidophyopsis mites were studied by PCR amplification of parts of their ribosomal DNA, followed by restriction enzyme analysis. Mite specimens on Ribes nigrum (black currant) from six countries gave the same digestion pattern, which was distinct from the pattern for mites found on R. rubrum from Poland and Finland and for R. grossularia from the USA. This suggests that each Ribes species is host to a different mite species: C. ribis, C. selachodon and C. grossulariae, respectively. Two other mite samples from R. alpinum and R. aureum were identical but were distinct from each of the other species.
A single‐locus minisatellite discriminates chinook salmon (Oncorhynchus tshawytscha) populations
Authors: HEATH D. D. , BERNIERM N. J. , MOUSSEAU T. A. 
Published: April 2008

AbstractA knowledge of genetic structure in natural populations is often necessary for conservation and management purposes, especially in declining Pacific salmon populations. To test for genetic differentiation between nine populations of chinook salmon, Oncorhynchus tshawytscha, from south‐western British Columbia, Canada, DNA was extracted from 603 fish and hybridized with a single‐locus minisatellite probe. Multivariate statistical analyses of the resulting allele size data permitted successful overall population identification of 52% (individual population range: 24–78%; P < 0.005), indicating a high level of genetic differentiation among the nine populations. Two of the nine populations were further analysed using data from a second minisatellite locus. The discrimination success rate improved from 81.1% (one‐locus analyses) to 90.0% (two‐locus analyses), indicating the potential for greatly increased resolution gained by the addition of more loci. These results indicate that variation at minisatellite loci can be used for assessing population‐level genetic structure, even with artificial gene flow.
PCR amplification of intergenic spacers in the ribosomal DNA of Drosophila melanogaster reveals high levels of turnover in length and copy‐number of spacers in geographically separated populations
Authors: BOWEN T. , DOVER G. A. 
Published: April 2008

AbstractA recently described PCR‐based method for the analysis of intergenic spacer (IGS) length variation in the ribosomal (r) DNA of Drosophila melanogaster was used to analyse the distribution of IGS length variants in the rDNA of a number of recently collected D. melanogaster populations. One group of populations, from Europe and North Africa, was shown to have low intrapopulation IGS length variation following maintenance of massed populations in the laboratory for an extended period. However, a greater degree of IGS profile variability was detected at a number of levels in the majority of laboratory‐maintained isofemale lines from two of these populations plus a second group of populations which were collected more recently from the eastern coast of Australia; all of which were immediately divided into isofemale lines following collection. Interestingly, PCR analysis of pooled DNA extracts from 30 individuals of either sex showed almost identical PCR profiles from each of the Australian populations. These preliminary results are discussed with regard to the possible combinations of forces (natural selection, neutral drift and genomic molecular drive) on the patterns of IGS length variation.
Mitochondrial DNA products among RAPD profiles are frequent and strongly differentiated between races of Douglas‐fir
Authors: AAGAARD J. E. , VOLLMER S. S. , SORENSEN F. C. , STRAUSS S. H. 
Published: April 2008

AbstractRacial differentiation and genetic variability were studied between and within the coastal, north interior, and south interior races of Douglas‐fir using RAPD and allozyme markers. Nearly half of all RAPD bands scored (13:45%) were found to be amplified from mitochondrial DNA. They exhibited maternal inheritance among hybrids and back‐crosses between the races, and were much more highly differentiated (GST= 0.62 for haplotype frequencies) than were allozymes (GST= 0.26). No evidence of hybridization or introgression was detected where the coastal and interior races come into proximity in central Oregon.
Patterns of covert infection by invertebrate pathogens: iridescent viruses of blackflies
Authors: WILLIAMS T. 
Published: April 2008

AbstractRecently, it has been recognized that blackfly populations may host two forms of infection by iridescent viruses (IVs); a covert (inapparent, nonlethal) form which was common in springtime populations in the River Ystwyth, Wales, and a patent (obvious, lethal) form which was rare. This study aimed to investigate the changes in frequency of the two types of infection in blackfly populations over the reproductive period of the flies, April‐September 1992. Blackfly larvae sampled from three different sites along the river were bioassayed for the presence of covert IV infection. Of 870 larvae assayed, 17 were found to be infected. All the infected larvae appeared to be Simnulium variegatum, the dominant species during the sampling period. IV infections were common in the spring (17–37% depending on site) but appeared absent in the S. variegatum population for most of the summer months, reappearing again in the autumn (0–20% infected). These fluctuations were concurrent with biotic and abiotic factors: elevated levels of covert infection occurred at low population densities, high water flow rates, low temperatures (and presumably slower growth rates), although it is not clear if any cause‐and‐effect relationship exists. Patent infections occurred immediately after the peak of covert infection in the spring, and again in the autumn. Virus characterization of isolates from covertly infected larvae showed that three distinct groups of isolates were present in the blackfly population. Isolates from the springtime populations were mostly variants of an isolate found in patently infected blackfly larvae in the 1970s (Aberystwyth IV). Isolates from the autumn populations were mostly variants of an isolate from a patently infected larva found in September the previous year. A third group comprised a single novel isolate which was detected in a covertly infected larva. The mechanisms by which IVs persist in blackfly populations remain unknown, although the role of alternative hosts is a possibility which needs to be studied.
RAPD assessment of California phylloxera diversity
Authors: FONG G. , WALKER M. A. , GRANETT J. 
Published: April 2008

AbstractGrape phylloxera, Daktulosphaira vitifoliae Fitch, is a parthenogenetic, aphid‐like pest which attacks the roots and leaves of many Vitis L. species. Feeding on the roots of V. vinifera L. cultivars leads to decreased plant productivity and eventual death. Isolates of phylloxera have been grouped into ‘biotypes’ based on the aggressiveness of their feeding behaviour, relative reproductive rates, and abilities to cause decline on V. vinifera and the grape rootstock AXR1. The goal of our research was to determine whether these bio‐type definitions were reflected in the genetic diversity among laboratory‐cultured colonies of Californian phylloxera. Thirteen phylloxera isolates, encompassing biotypes A, B and non‐A or ‐B types based on their feeding and reproduction, were analysed using the RAPD‐PCR method. Results indicate that there were genetic differences among isolates and that there was as much polymorphism within biotypes as among biotypes. This is surprising in a parthenogenetic organism and leads us to suggest that there have been multiple introductions of phylloxera into California, that phylloxera are not obligately parthenogenetic, or that there are other mechanisms whereby phylloxera may evolve relatively rapidly.
Mitochondrial DNA variation in Moroccan and Spanish honey bee populations
Authors: GARNERY L. , MOSSHINE E. H. , OLDROYD B. P. , CORNUET J. M. 
Published: April 2008

AbstractThe mitochondrial DNAs of 192 Moroccan and 173 Spanish honey bee colonies were characterized by a rapid test involving the restriction by DraI of a PCR‐fragment of the COI‐COII region. In Morocco, we found eight haplotypes, all characteristic of the African (A) lineage, suggesting that most if not all the maternal lineages of the colonies repeatedly imported from Europe over the last 150 years have not contributed mitochondrial genomes to the local population. Using two new genetic distances analogous to the shared allele distance defined for nuclear genes, we showed that Morocco was most probably colonized by two sublineages, one from the north‐east and the other one from the south of the country and that the contact zone between them extends along both sides of the Atlas range. In Spain, we found eight haplotypes characteristic of lineage A (six in common with Morocco) and four of lineage M (the West European lineage). The distribution of haplotypes of both lineages forms a gradient with c. 10% of lineage M in the south of Spain (Seville) and up to 100% in the north (San Sebastian). Three hypotheses are presented to explain the large differences of haplotype frequencies between Moroccan and lineage A Spanish colonies: a non‐Moroccan origin of lineage A in Spain, an ancient Moroccan origin or a recent Moroccan origin with a rapid shift of haplotype frequencies due to a founder effect.
Marked mitochondrial DNA differences between Mediterranean and Atlantic populations of the swordfish, Xiphias gladius
Authors: KOTOULAS G. , MAGOULAS A. , TSIMENIDES N. , ZOUROS E. 
Published: April 2008

AbstractRestriction analysis of mitochondrial DNA (mtDNA) from 204 individuals of swordfish (Xiphias gladius) revealed no differentiation among samples from three sites in the Mediterranean Sea (Greece, Italy, Spain), but a high degree of differentiation between Mediterranean samples and a sample from the Gulf of Guinea. A fifth sample from the Atlantic side of the Straits of Gibraltar (Tarifa) consisted mostly of mitotypes that are common in the Mediterranean, but contained several of mtDNA types of the Guinea sample not found in the Mediterranean. We conclude that, in spite of free migration of swordfish across the Straits of Gibraltar, little genetic exchange occurs between the populations inhabiting the Mediterranean Sea and the tropical Atlantic ocean. This is the first evidence of genetic differentiation among geographic populations of this highly mobile species that supports a world‐wide fishery.
Resolving genetic relationships with microsatellite markers: a parentage testing system for the swallowHirundo rustica
Authors: PRIMMER C. R. , MØLLER A. P. , ELLEGREN H. 
Published: April 2008

AbstractEight polymorphic microsatellite markers from the swallow were isolated and characterized. Extraordinary variability was revealed at theHrU6locus with 45 different alleles scored among 46 unrelated individuals. The probability that the same genotype combination would occur in two random and unrelated individuals at six selected loci was as low as 1.3 × 10‐8and the combined exclusion probability was 0.9996. Stable Mendelian inheritance was observed in about 1000 meioses. No significant linkage was revealed and for almost all combinations of marker‐pairs, linkage closer than 5 cM could be excluded. At two loci, null (nonamplifying) alleles were encountered. Thirteen (30%) extra‐pair offspring were identified in 5 (56%) broods when applying the marker set on a nearly complete swallow colony. We were able to identify a single male from the other families in the colony as the most likely father for nine of the 13 extra‐pair offspring.
Multiple paternity in the red‐eyed treefrog Agalychnis callidryas (Cope)
Authors: D'ORGEIX C. A. , TURNER B. J. 
Published: April 2008

AbstractDNA fingerprinting of tadpoles from two different ‘one female‐two male’ matings of the red‐eyed treefrog, Agalychnis callidryas, revealed multiple paternity of offspring. Offspring were assigned paternity based on bands shared with the putative father, but not shared between putative fathers or with the mother. Paternity was split 44/56% and 36/64% in two matings. These results do not support a hypothesis of sperm priority in access to unfertilized eggs by primary males. Multiple paternity may be commonplace in species of anurans with matings by multiple males.
PCR‐based identification of wheat genomes
Authors: SALLARES R. , ALLABY R. G. , BROWN T. A. 
Published: April 2008

AbstractWe describe a PCR system that distinguishes the A, B and D genomes in wheat DNA extracts. PCRs were directed at the ‘non‐transcribed spacer’ regions of the rDNA loci. The spacers within the D genome locus have a 71‐bp insertion that is absent from the corresponding A and B loci PCR product sizes therefore enable D‐ and D+ genomes to be distinguished. The A and B genomes can be differentiated by PCR with an internal primer which does not anneal to A genome sequences. This work is relevant to the ancient ecology of wheat, as it is often difficult to determine ploidy level from morphological examination of archaeobotanical remains.
Amplification of hypervariable simple sequence repeats (microsatellites) from excremental DNA of wild living bonobos (Pan paniscus)
Authors: GERLOFF U. , SCHLÖTTERER C. , RASSMANN K. , RAMBOLD I. , HOHMANN G. , FRUTH B. , TAUTZ D. 
Published: April 2008

AbstractWe show that nuclear DNA extracted from faeces of free living bonobos (Pan paniscus) can be used to amplify hypervariable simple sequence repeats, which can be used for paternity analysis and kinship studies. Of 130 DNA extractions of samples from 33 different animals, about two‐thirds yielded PCR products at the first attempt. For several samples only a second extraction resulted in positive amplifications. Consistency tests revealed that in some cases only one of the two alleles was amplified. Presumably this is due to a very limited amount of bonobo DNA in the sample and we suggest therefore that a sample found to be homozygous at a given locus should be typed repeatedly for verification.
The phylogenetic distribution of a transposable dioxygenase from the Niagara River watershed
Authors: NAKATSU C. H. , FULTHORPE R. R. , HOLLAND B. A. , PEEL M. C. , WYNDHAM R. C. 
Published: April 2008

AbstractHorizontal gene transfer in the Bacteria has been demonstrated to occur under natural conditions. The ecological impact of gene transfer events depends on the new genetic material being expressed in recipient organisms, and on natural selection processes operating on these recipients. The phylogenetic distribution of cbaAB genes for chlorobenzoate 3,4‐(4,5)‐dioxygenase, which are carried within Tn5271 on the IncPβ plas‐mid pBRC60, was investigated using isolates from freshwater microcosms and from the Niagara River watershed. The latter included isolates from surface water, groundwater and bioremediation reactor samples. The cbaAB genes have become integrated, through interspecific transfer, primarily into species of the β Proteobacteria (44/48 isolates). Only four isolates, identified as Pseudomonas fluorescens (3/48) and Xanthomonas maltophilia (1/48), belonged to the Γ Proteobacteria, despite the observation that pBRC60 was capable of mobilizing these genes into a wide range of β and Γ Proteobacteria in the laboratory. The natural host range correlated with the distribution of the meta‐ring‐fission pathway for metabolism of protocatechuates formed when the cbaAB genes were expressed (45/48 isolates). We proposed the hypothesis that natural selection has favoured recipients that successfully integrate the activity of the transferred dioxygenase with the conserved meta ring‐fission pathway. The hypothesis was tested by transferring a plasmid construct containing the cbaAB genes into type strains representative of the β and γ Proteobacteria. The concept of applying mobile catabolic genes to probe the phylogenetic distribution of compatible degradative pathways is discussed.
Microbial community structure and biogeochemistry of Miocene subsurface sediments: implications for long‐term microbial survival
Authors: FREDRICKSON J. K. , MCKINLEY J. P. , NIERZWICKI‐BAUER S. A. , WHITE D. C. , RINGELBERG D. B. , RAWSON S. A. , LI SHU‐MEI , BROCKMAN F. J. , BJORNSTAD B. N. 
Published: April 2008

AbstractThirty closely spaced cores were obtained from Miocene‐aged fluvial, lacustrine and palaeosol subsurface sediments ranging in depth from 173 to 197 m at a site in south‐central Washington to investigate the size and composition of the microbial community in relation to sediment geochemical and geophysical properties. Total phospholipid fatty acid (PLFA) analysis indicated that the greatest concentrations of microbial bio‐mass were in low‐permeability lacustrine sediments that also contained high concentrations of organic carbon. Community structure, based on lipid analyses and on in situ hybridization of bacterial cells with 16S RNA‐directed DNA probes, also revealed the presence of metabolically active bacteria that respire sulphate and/or Fe(III) in the lacustrine sediments. Concentrations of pore water sulphate were low (4–8 mg/L) and HCI‐extractable Fe was predominantly Fe(II) in the same samples where total biomass and organic carbon were highest. The low hydraulic conductivity (10‐6 to < 10‐9 cm/s) of these sediments has likely contributed to the long term maintenance of both bacteria and organic carbon by limiting the supply of soluble electron acceptors for microbial respiration. These results suggest that the current subsurface microbial population was derived from organisms that were present during lake sedimentation = 6–8 million years ago.
DNA‐based monitoring of total bacterial community structure in environmental samples
Authors: HOLBEN W. E. , HARRIS D. 
Published: April 2008

AbstractDetermining the structure of bacterial communities and their response to stimuli is key to understanding community function and the interactions that occur between microorganisms and the environment. However, bacterial communities often comprise complex assemblages of large numbers of different bacterial populations. An approach is presented which allows bacterial community structure to be determined by fractionation of the complex mixture of total bacterial community DNA using the DNA‐binding dye bisbenzimidazole which imposes G + C‐dependent changes in the buoyant density of DNA. Bacterial community structure presented as percentage of total DNA vs. percentage G + C content of DNA is an indication of the relative abundance of phylogenetic groups of bacteria. Changes in the composition of a soil bacterial community in response to perturbations in the form of carbon amendment and altered water status were monitored.
Molecules are more than markers: new directions in molecular microbial ecology
Authors: LENSKI R. E. 
Published: April 2008

AbstractMacromolecules such as DNA, RNA, and proteins are widely used to quantify diversity in natural communities, to monitor the dispersal of organisms and their genes, and to trace phylogenetic relationships among organisms. With such widespread use of molecules as markers, it is easy to forget that they perform functions that are integral to the survival of organisms. The structural and functional properties of macromolecules have been intensively studied in genetics, biochemistry, and physiology. These fields, however, have not generally focused on the ecological significance of molecular variation, but instead have used defective variants as tools for identifying structure and function. Understanding the significance of molecular variation for organismal success or failure is a central problem in ecology, one whose solution will require the integration of diverse approaches and perspectives from ecology, molecular biology, genetics, physiology, and evolutionary biology. I review several studies of bacterial populations evolving in simple environments that have begun to integrate these approaches and perspectives in order to examine the consequences of molecular variation for ecological performance.
A phylogeographic survey of brook charr (Salvelinus fontinalis) in Algonquin Park, Ontario based upon mitochondrial DNA variation
Authors: DANZMANN R. G. , IHSSEN P. E. 
Published: April 2008

AbstractForty‐nine populations of brook charr (Salvelinus fontinalis) from Algonquin Park lakes and rivers were analysed for mitochondrial DNA variation. Haplotypic distributions of wild fish in the Algonquin Park region of Ontario, Canada, predominantly reflect postglacial dispersal patterns into the region in spite of substantial hatchery plantings. Two major refugial groupings colonized this region. Northern and eastern watersheds (Amable du Fond, Bonnechere, and northern Petawawa), were colonized primarily by haplotype 1 fish (B1 phylogenetic assemblage), while Oxtongue River, southern Petawawa, and York River populations were colonized predominately by fish from the B2 and A mtDNA phylogenetic assemblages. Fish with haplotypes in the A and B2 phylogenetic assemblages are common in the Lake Huron drainage. All watersheds in the Park drain into the Ottawa River, except the Oxtongue drainage (part of the Lake Huron watershed). This suggests that early glacial outflows south of the Algonquin Park region (Kirkfield‐Trent) may have been colonized by fish that initially invaded ‘Ontario island’ (south‐western Ontario), while fish which invaded northern Algonquin Park were derived from a different refugial grouping(s) which may have involved colonization both up the Ottawa River drainage, and/or from a more westerly (Mississippian) refugial grouping. A majority of the populations in Algonquin Park have been planted with hatchery reared brook charr since the 1940s. The Hills Lake or ‘Domestic’ strain was used almost exclusively for these plantings. Comparisons of mtDNA haplotypic distributions in hatchery and wild fish suggests that hatchery females had minimal spawning success and/or their progeny had poor survivorship in the wild.