bluuebunny/crossref_metadata_2025_split huggingface dataset:
Low mitochondrial DNA variation and recent colonization of Scandinavia by the wood lemming Myopus schisticolor
Authors: FEDOROV V. , JAAROLA M. , FREDGA K. 
Published: April 2008

AbstractThe population genetic structure of wood lemmings (Myopus schisticolor) from Scandinavia, Finland and western Siberia was examined by restriction fragment length polymorphism of mitochondrial DNA (mtDNA) in 45 individuals from six localities. The 12 observed mtDNA haplotypes demonstrated a distinct phylogeographic pattern, suggesting that the postglacial colonization of Scandinavia by wood lemmings occurred from north‐east. However, a very low level of haplotype and nucleotide diversity and a lack of geographical structure were found within Scandinavia. The limited mtDNA diversity in the Scandinavian populations probably reflects recent divergence in situ after colonization by a limited number of founders. Allozyme data support this scenario.
Sensitive detection of transgenic plant marker gene persistence in soil microcosms
Authors: WIDMER F. , SEIDLER R. J. , WATRUD L. S. 
Published: April 2008

AbstractGenetic engineering offers the opportunity to generate plants with useful new traits conferred by genes originating from a variety of organisms. The objectives of this study were to establish methods for investigating persistence of recombinant plant marker DNA after introduction into soil and to collect data from controlled laboratory test systems. As a model system, we studied the stability of DNA encoding recombinant neomycin phosphotransferase II (rNPT‐II), a neomycin/kanamycin resistance marker, used in plant genetic engineering. The recombinant nature of the target (i.e. fusion of nopaline synthase promoter and NPT‐II coding region) allowed us to design a rNPT‐II‐specific PCR primer pair. DNA preparation and quantitative PCR protocols were established. Effects of temperature and moisture, on DNA persistence in soil were determined in two laboratory test systems. In the first system, purified plasmid DNA was added to soil and incubated under controlled conditions. Up to 0.08% of the rNPT‐II target sequences were detectable after 40 days. In the second system, fresh leaf tissue of transgenic tobacco was ground, added to soil, and incubated under controlled conditions. After 120 days, up to 0.14% of leaf tissue‐derived genomic rNPT‐II sequences were detectable. Under most experimental conditions, leaf tissue‐derived and plasmid DNA were initially degraded at a high rate. A small proportion of the added DNA resisted degradation and was detectable for several months. We hypothesize that this DNA may have been adsorbed to soil particles and was protected from complete degradation.
Kinship and genetic divergence among populations of tuatara Sphenodon punctatus as revealed by minisatellite DNA profiling
Authors: FINCH M. O. , LAMBERT D. M. 
Published: April 2008

AbstractTuatara represent the last surviving member of the order Rhynchocephalia, a group of reptiles the members of which first appeared in the fossil record 200 million years ago. We report the existence of extensive minisatellite DNA variation in island populations of tuatara, as revealed by the use of heterologous DNA probes and compare this variation to that found in other vertebrates. Patterns of minisatellite variation within and among populations of tuatara on the Taranga and Marotere Islands off the coast of New Zealand are detailed. Individuals from West Bay and South Cove on Motumuka Island show higher levels of bandsharing than that recorded between randomly sampled individuals from the same island. We suggest that these populations comprise a proportion of closely related individuals and that populations within islands are genetically structured. Moreover, we identified individuals which have high levels of bandsharing with substantial proportions of the sampled population, suggesting close kinship. A pairwise, inter‐island comparison of individuals from Motumuka, Whatupuke and Mauimua Islands, reveals significant differences in distribution of restriction fragments in minisatellite DNA profiles.
DNA fingerprinting supports notions of clonality in a rare mallee, Eucalyptus argutifolia
Authors: KENNINGTON W. J. , WAYCOTT M. , JAMES S. H. 
Published: April 2008

AbstractDNA fingerprinting was used to test for genetic variation within putative clones of Eucalyptus argutifolia, a rare multistemmed (mallee) species endemic to Western Australia. Hybridization of the M13 repeat sequence to HaeIII digested DNA samples was able to discriminate between seedlings from the same maternal plant, demonstrating the capability of this probe in detecting different individuals of this species. Each of the putative clones yielded a unique banding pattern, but no variation was found within clones. These results are consistent with the notion of clonality in E. argutifolia and reaffirm that populations are likely to contain considerably fewer individuals than originally anticipated.
Population level processes in Rhizobium leguminosarum bv. trifolii: the role of founder effects
Authors: HAGEN M. J. , HAMRICK J. L. 
Published: April 2008

AbstractThe importance of genotype‐specific selection between host and symbiont, founder effect, and clonal reproduction in Rhizobia leguminosarum biovar trifolii populations is relatively unknown. A field experiment was conducted to sample 1268 isolates of R. l. bv. trifolii from four genotypically distinct Trifolium pratense plants for allozyme variation at nine loci. Genetic and genotypic variation, population genetic substructure, and linkage disequilibrium were estimated. Of the 1268 isolates 188 genotypically distinct strains (electrophoretic types or ETs) were identified with an average of 11.04 different ETs per plant. Total genetic diversity in the plot was 0.346 and most of the variation was found within plants (= 80%). Our data suggests that genotype‐specific selection between the rhizobia and the four host‐plant genotypes tested does not influence local population structure, but evidence of founder effect was present. Significant linkage disequilibrium was observed and is most likely due to the clonal reproduction of R. l. bv. trifolii.
An analysis of genetic variation inAstragalus cremnophylaxvar.cremnophylax, a critically endangered plant, using AFLP markers
Authors: TRAVIS S. E. , MASCHINSKI J. , KEIM P. 
Published: April 2008

AbstractA recently developed molecular technique (amplified fragment length polymorphisms, AFLP) was used for characterizing genetic heterogeneity within and among populations of a critically endangered species of plant,Astragalus cremnophylaxvar.cremnophylax. Using AFLP, up to 50 polymorphic genetic markers per AFLP‐PCR amplification were generated, and a total of 220 variable markers overall. This information was used first to assess genetic diversity within each of the three known populations ofAstragalus cremnophylaxvar.cremnophylaxfrom Grand Canyon National Park in Arizona, USA: North Rim (NR;n= 970), South Rim Site 1 (SR1;n= 500), and South Rim Site 2 (SR2;n= 2). Diversity in the form of average heterozygosity (H) and the proportion of polymorphic genes (P) was greatest in the NR population ((H) = 0.13 and (P) = 0.38) and least in the SR2 population ((H) = 0.02 and (P) = 0.04). Diversity was also quite low for the SR1 population ((H) = 0.04 and (P) = 0.10). In addition, substantial genetic differentiation among populations was indicated by both phenetic (AMOVA) and genetic analyses (overall correctedFST= 0.41). This finding was corroborated by the results of several multivariate analyses which utilized the genetic data, including a UPGMA cluster analysis and a principal coordinate analysis which revealed the existence of discrete groups corresponding to the populations. Population structure was further revealed within the NR population which was known to consist of four spatially separated groups of plants. Several recommendations for the future management of the species are discussed.
Mitochondrial haplotypes in populations of the plant‐infecting fungus Sclerotinia sclerotiorum: wide distribution in agriculture, local distribution in the wild
Authors: KOHLI Y. , KOHN L. M. 
Published: April 2008

AbstractAnalysis of mitochondrial DNA (mtDNA) haplotypes of Sclerotinia sclerotiorum points to a common origin of some genotypes from agricultural populations, especially when compared with two wild populations that are sharply distinguished from the agricultural sample and from each other. Five agricultural population samples from canola (Alberta, Canada and Norway), cabbage (North Carolina, USA), sunflower (Manitoba, Canada and Queensland, Australia) and two Norwegian populations from a wild plant, Ranunculus ficaria were compared. Haplotypes were determined by Southern hybridization of purified organelle DNA from S. sclerotiorum and Neurospora crassa to total genomic DNA of S. sclerotiorum. Each isolate had one haplotype. Haplotypes of S. sclerotiorum from R. ficaria were different between the two wild populations and also from all haplotypes observed in the agricultural populations. Among the wild isolates, DNA fingerprint, mtDNA haplotype and location in the sampling transect were all associated. Among the agricultural isolates, four haplotypes were observed in at least two agricultural populations and one haplotype was observed in all agricultural populations. In the Canadian canola sample some clones had one mtDNA haplotype, indicating association with DNA fingerprint, some clones had more than one haplotype, and some groups of clones shared haplotypes. Some of the haplotype diversity may be due to the presence of extra‐chromosomal elements associated with the mitochondria of S. sclerotiorum.
Population and colony structure of the carpenter ant Camponotus floridanus
Authors: GADAU J. , HEINZE J. , HÖLLDOBLER B. , SCHMID M. 
Published: April 2008

AbstractThe colony and population structure of the carpenter ant, Camponotus floridanus, were investigated by multilocus DNA fingerprinting using simple repeat motifs as probes [e.g. (GATA)4]. The mating frequency of 15 queens was determined by comparing the fingerprint patterns of the queen and 17–33 of her progeny workers. C. floridanus queens are most probably singly mated, i.e. this species is monandrous and monogynous (one queen per colony). C. floridanus occurs in all counties of mainland Florida and also inhabits most of the Key islands in the southern part of Florida. We tested whether the two mainland populations and the island populations are genetically isolated. Wright's FST and Nei's D‐value of genetic distance were calculated from intercolonial bandsharing‐coefficients. The population of C. floridanus is substructured (FST= 0.19 ± 0.09) and the highest degree of genetic distance was found between one of the mainland populations and the island populations (D= 0.35). Our fingerprinting technique could successfully be transferred to 12 other Camponotus species and here also revealed sufficient variability to analyse the genetic structure. In three of these species (C. ligniperdus, C. herculeanus and C. gigas) we could determine the mating frequency of the queen in one or two colonies, respectively.
Nonrandom mating in pikas Ochotona princeps: evidence for inbreeding between individuals of intermediate relatedness
Authors: PEACOCK M. M. , SMITH A. T. 
Published: April 2008

AbstractThe extent and effect of inbreeding in natural populations remain largely undetermined. Pikas Ochotona princeps have been considered a likely candidate for close inbreeding in natural populations due to observations of frequent juvenile philopatry (colonization of natal home range or neighbouring home range) and high levels of spatial overlap and social tolerance between neighbouring individuals of the opposite sex. A 4‐year investigation of inbreeding in pikas, however, has revealed that dispersal and mating patterns are uncoupled in this species, i.e. explained by different hypotheses. DNA fingerprinting analysis revealed that band‐sharing scores between mated pairs, identified via parentage analysis, were not commensurate with band‐sharing among known first‐order relatives, but were similar to scores for a small sample of known second‐order relatives (i.e. half‐siblings, grandparent‐grandchild pairs). Band‐sharing scores between mated pairs were then compared with those between potential mated pairs within the population to assess whether mating was random or nonrandom with respect to genetic similarity. The results of Monte Carlo randomization tests show that pikas mated with individuals with intermediate genetic similarity in greater proportion than would be expected by chance. These data suggest mate choice in pikas may be based upon intermediate levels of relatedness.
Genetic diversity within and among populations of a threatened species: Erodium paularense Fern. Gonz. & Izco
Authors: MARTÍN C. , GONZÁLEZ‐BENITO M. E. , IRIONDO J.M. 
Published: April 2008

AbstractErodium paularenseFern. Gonz. & Izco (Geraniaceae) is a perennial, endemic species of central Spain. The restricted distribution of its three populations has made it necessary to consider measures for conservation. Random amplified polymorphic DNA markers were used to determine genetic variation among and within populations. Sixty‐three per cent of the bands were polymorphic. No population‐specific marker was identified. Cluster analysis based on Jaccard's coefficient of all the individuals grouped most of them according to the present populations. Within‐population variability was of a similar order in the three populations. Highly significant genetic differences between populations were detected through AMOVA. Within population diversity contributed 80–85% to the species diversity, a value typical of an outbreeding plant.
Development of multiple genetic markers for studies of genetic variation in arbuscular mycorrhizal fungi using AFLP™
Authors: ROSENDAHL S. , TAyLOR J. W. 
Published: April 2008

AbstractIntraspecific and interspecific genetic variation was studied among arbuscular mycorrhizal fungi. DNA was extracted from single spores and variation was analysed by AFLP (Amplified Fragment Length Polymorphism). The patterns of amplified fragments revealed substantial genetic variation between spores from the same isolates. Possible recombination in the fungi was studied by comparing the obtained data with data generated by artificial recombination of the data sets. No evidence for recombination was found by the analysis, suggesting that the fungi reproduce clonally. The AFLP technique generated a large number of fragments, and the potential for using the technique in population genetic studies of these important unculturable biotrophic fungi is discussed.
Microsatellite scoring errors associated with noninvasive genotyping based on nuclear DNA amplified from shed hair
Authors: GAGNEUX P. , BOESCH C. , WOODRUFF D. S. 
Published: April 2008

AbstractIn the context of a study of wild chimpanzees,Pan troglodytes verus, we found that genotypes based on single PCR amplifications of microsatellite loci from single shed hair have a high error rate. We quantified error rates using the comparable results of 791 single shed hair PCR amplifications of 11 microsatellite loci of 18 known individuals. The most frequent error was the amplification of only one of the two alleles present at a heterozygous locus. This phenomenon, called allelic dropout, produced false homozygotes in 31% of single‐hair amplifications. There was no difference in the probability of preferential amplification between longer and shorter alleles. The probability of scoring false homozygotes can be reduced to below 0.05 by three separate amplifications from single hairs of the same individual or by pooling hair samples from the same individual. In this study an additional 5.6% of the amplifications gave wrong genotypes because of contamination, labelling and loading errors, and possibly amplification artefacts. In contrast, amplifications from plucked hair taken from four dead individuals gave consistent results (error rate < 0.01%,n= 120). Allelic dropout becomes a problem when the DNA concentration falls below 0.05 ng/10 μL in the template as it can with shed hair, and extracts from faeces and masticated plant matter.
Noninvasive genetic tracking of the endangered Pyrenean brown bear population
Authors: TABERLET P. , CAMARRA J.‐J. , GRIFFIN S. , UHRÈS E. , HANOTTE O. , WAITS L. P. , DUBOIS‐PAGANON C. , BURKE T. , BOUVET J. 
Published: April 2008

AbstractPyrenean brown bears Ursus arctos are threatened with extinction. Management efforts to preserve this population require a comprehensive knowledge of the number and sex of the remaining individuals and their respective home ranges. This goal has been achieved using a combination of noninvasive genetic sampling of hair and faeces collected in the field and corresponding track size data. Genotypic data were collected at 24 micrdsatellite loci using a rigorous multiple‐tubes approach to avoid genotyping errors associated with low quantities of DNA. Based on field and genetic data, the Pyrenean population was shown to be composed at least of one yearling, three adult males, and one adult female. These data indicate that extinction of the Pyrenean brown bear population is imminent without population augmentation. To preserve the remaining Pyrenean gene pool and increase genetic diversity, we suggest that managers consider population augmentation using only females. This study demonstrates that comprehensive knowledge of endangered small populations of mammals can be obtained using noninvasive genetic sampling.
RST Calc: a collection of computer programs for calculating estimates of genetic differentiation from microsatellite data and determining their significance
Authors: GOODMAN S. J. 
Published: April 2008

Abstract R
ST, an analogue of FST, provides a convenient approach for estimating levels of genetic differentiation from microsatellite data. This paper examines current approaches for calculating estimates of RST and suggests a weighting scheme based on the transformation of allele sizes at loci across data sets. Combined within an analysis of variance framework this scheme yields an estimator of RST analogous to the θ estimator of FST. Software for the IBM‐PC is described which carries out such calculations and assesses the significance of RST or Nm estimates using bootstrap and permutation tests.
A molecular genetic examination of the mating system of pumpkinseed sunfish reveals high pay‐offs for specialized sneakers
Authors: RIOS‐CARDENAS OSCAR , WEBSTER MICHAEL S. 
Published: April 2008

AbstractIntrasexual variation in reproductive behaviour and morphology are common in nature. Often, such variation appears to result from conditional strategies in which some individuals (e.g. younger males or those in poor condition) adopt a low pay‐off phenotype as a ‘best of a bad job’. Alternatively, reproductive polymorphisms can be maintained by balancing selection, with male phenotypes having equal fitnesses at equilibrium, but examples from nature are rare. Many species of sunfish (genusLepomis) are thought to have alternative male reproductive behaviours, but most empirical work has focused on the bluegill sunfish and the mating systems of other sunfish remain poorly understood. We studied a population of pumpkinseed sunfish (Lepomis gibbosus) in upstate New York. Field observations confirm the existence of two male reproductive strategies: ‘parentals’ were relatively old and large males that maintained nests, and ‘sneakers’ were relatively young and small males that fertilize eggs by darting into nests of parentals during spawning. The sneaker and parental male strategies appear to be distinct life‐history trajectories. Sneaker males represented 39% of the males observed spawning, and sneakers intruded on 43% of all mating attempts. Microsatellite analyses revealed that sneaker males fertilized an average of 15% of the eggs within a nest. This level of paternity by sneaker males appears to be higher than seen in most other fishes, and preliminary analyses suggest that the two male reproductive strategies are maintained as a balanced polymorphism.
The Maurer's cleft protein MAHRP1 is essential for trafficking of PfEMP1 to the surface of Plasmodium falciparum‐infected erythrocytes
Authors: Spycher Cornelia , Rug Melanie , Pachlatko Esther , Hanssen Eric , Ferguson David , Cowman Alan F. , Tilley Leann , Beck Hans‐Peter 
Published: April 2008

SummaryDuring the intra‐erythrocytic development of Plasmodium falciparum, the parasite modifies the host cell surface by exporting proteins that interact with or insert into the erythrocyte membrane. These proteins include the principal mediator of cytoadherence, P. falciparum erythrocyte membrane protein 1 (PfEMP1). To implement these changes, the parasite establishes a protein‐trafficking system beyond its confines. Membrane‐bound structures called Maurer's clefts are intermediate trafficking compartments for proteins destined for the host cell membrane. We disrupted the gene for the membrane‐associated histidine‐rich protein 1 (MAHRP1). MAHRP1 is not essential for parasite viability or Maurer's cleft formation; however, in its absence, these organelles become disorganized in permeabilized cells. Maurer's cleft‐resident proteins and transit cargo are exported normally in the absence of MAHRP1; however, the virulence determinant, PfEMP1, accumulates within the parasite, is depleted from the Maurer's clefts and is not presented at the red blood cell surface. Complementation of the mutant parasites with mahrp1 led to the reappearance of PfEMP1 on the infected red blood cell surface, and binding studies show that PfEMP1‐mediated binding to CD36 is restored. These data suggest an important role of MAHRP1 in the translocation of PfEMP1 from the parasite to the host cell membrane.
DNA dynamics vary according to macrodomain topography in the E. coli chromosome
Authors: Espeli Olivier , Mercier Romain , Boccard Frédéric 
Published: April 2008

SummaryThe organization of the Escherichia coli chromosome has been defined genetically as consisting of four insulated macrodomains and two less constrained regions. Here we have examined the movement of chromosomal loci by tracking fluorescent markers in time‐lapse microscopy during a complete cell cycle. Analysing the positioning, the segregation pattern and the motility of markers allowed us to show that the dynamic behaviour of loci belonging to various macrodomains and less constrained regions is radically different. In macrodomains constraints on mobility are apparent whereas in non‐structured regions, markers exhibited a greater motility that may explain their ability to interact with flanking macrodomains. Following replication, duplicated markers belonging to macrodomains show a colocalization step and this landmark is not apparent in non‐structured regions. Chromosome segregation occurs in three steps: first, the origin‐proximal half of the chromosome consisting of the Ori macrodomain and the two non‐structured region segregates concomitantly in a short period of time. Second, the Right and Left macrodomains segregate progressively following the genetic map. Third, the Ter macrodomain is rapidly segregated before division, after a significant period of colocalization. Macrodomain territories defined as cellular spaces occupied by the different macrodomains can be identified.