bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microsatellites from the beluga whaleDelphinapterus leucas
Authors: BUCHANAN F. C. , FRIESEN M. K. , LITTLEJOHN R. P. , CLAYTON J. W. 
Published: April 2008

AbstractFifteen microsatellites were isolated from a beluga whaleDelphinapterus leucas, genomic library. The microsatellites were amplified in 100 beluga obtained from two widely separated locations. An average of 8.6 alleles per locus were detected and the average heterozygosity was 0.65 with a range of 0.27–0.86. All microsatellites were polymorphic and 13 of the genotype distributions observed were in Hardy‐Weinberg equilibrium. It was possible with these microsatellites to assign correctly individual whales to their stock‐of‐origin 98% of the time. Microsatellites were amplified in 15 other cetaceans with these beluga‐derived primers.
Identification of a hybrid zone between distinctive colour variants of the alpine wetaHemideina maori(Orthoptera: Stenopelmatidae) on the Rock and Pillar range, southern New Zealand
Authors: KING T. M. , WALLIS G. P. , HAMILTON S. A. , FRASER J. R. 
Published: April 2008

AbstractThe wetaHemideina maorioccurs as yellow (to the north), black (to the south) and intermediate colour variants on the Rock and Pillar range in New Zealand. Isozyme electrophoresis revealed little genetic variation, whereas RFLP analysis of an amplified mtDNA sequence uncovered two haplotypes correlating completely with colour in allopatry and nearly so in sympatry. Intermediates had one or other haplotype. The observed distribution of colour variation and mtDNA genotypes is characteristic of a hybrid zone, perhaps formed by secondary contact. Work is continuing to locate nuclear DNA markers and to study the genetic interactions of the colour variants.
Microsatellite analysis of seed dispersal and parentage of saplings in bur oak, Quercus macrocarpa
Authors: DOW B. D. , ASHLEY M. V. 
Published: April 2008

AbstractMicrosatellite analysis was used to examine parentage and spatial distributions of 62 adult bur oaks Quercus macrocarpa, and 100 saplings in a single stand. Using genotypes scored by PCR products at four microsatellite loci, we determined that 94 saplings matched at least one parent in the stand. Saplings often occur as dense clusters of half‐sibs around the presumed maternal parent, and only four adults were seed parents to a large proportion of the saplings sampled. A stump apparently was the seed parent of the largest cluster of half‐sibs, which occupied a sizeable light gap opened up by the death of their maternal tree. Approximately half of the saplings appeared to have grown from seeds that had not been removed after falling from the tree, and half from seeds that were dispersed beyond the crown of their maternal parent. Long‐distance seed dispersal may be more common than has been previously reported. Extremely high levels of long‐distance pollination were indicated, and pollen donors within the stand were generally distributed randomly around maternal trees. More than half of the saplings had paternal parents outside of the stand. This study demonstrates the utility of microsatellite analysis for studying mating systems, seed dispersal and seedling establishment in natural plant populations.
Population structure of the yellow‐footed rock‐wallaby Petrogale xanthopus (Gray, 1854) inferred from mtDNA sequences and microsatellite loci
Authors: POPE L. C. , SHARP A. , MORITZ C. 
Published: April 2008

AbstractThe yellow‐footed rock‐wallaby Petrogale xanthopus is considered to be potentially vulnerable to extinction. This wallaby inhabits naturally disjunct rocky outcrops which could restrict dispersal between populations, but the extent to which that occurs is unknown. Genetic differences between populations were assessed using mitochondrial DNA (control region) sequencing and analysis of variation at four microsatellite loci among three geographically close sites in south‐west Queensland (P. x. celeris) and, for mtDNA only, samples from South Australia (P. x. xanthopus) as well. Populations from South Australia and Queensland had phylogenetically distinct mtDNA, supporting the present classification of these two groups as evolutionarily distinct entities. Within Queensland, populations separated by 70 km of unsuitable habitat differed significantly for mtDNA and at microsatellite loci. Populations separated by 10 km of apparently suitable habitat had statistically homogeneous mtDNA, but a significant difference in allele frequency at one microsatellite locus. Tests for Hardy‐Weinberg equilibrium and micro‐geographical variation at microsatellite loci did not detect any substructuring between two wallaby aggregations within a colony encircling a single rock outcrop. Although the present study was limited by small sample sizes at two of the three Queensland locations examined, the genetic results suggest that dispersal between colonies is limited, consistent with an ecological study of dispersal at one of the sites. Considering both the genetic and ecological data, we suggest that management of yellow‐footed rock‐wallabies should treat each colony as an independent unit and that conservation of the Queensland and South Australian populations as separate entities is warranted.
Stability of transformed antagonistic Fusarium oxysporum strains in vitro and in soil microcosms
Authors: MIGHELI Q. , FRIARD O. , TEDESCO D. DEL , MUSSO M. R. , GULLINO M. L. 
Published: April 2008

AbstractThe stability of a genetically modified strain of Fusarium oxysporum used as antagonist against phytopathogenic formae speciales of F. oxysporum was evaluated both in vitro and in microcosm assays. The Escherichia coli hygromycin B phosphotransferase gene (hph), conferring hygromycin B resistance, was introduced by genetic transformation into a recipient strain marked by benomyl resistance and a dark red pigmentation. Hybridization with the complete plasmid suggested that the integration had generally occurred in a multiple‐tandem array at multiple sites. Among nine independent transformants tested, only three of them were mitotically stable after four rounds of vegetative growth with no selective pressure, while six showed various changes in the integration pattern. One transformant had lost the ability to grow in the presence of hygromycin B. In soil microcosms all the transformants maintained the hygromycin B resistant phenotype, but six of them showed rearrangement of transforming DNA. Only one strain (coded T26.40) underwent no obvious rearrangement both after in vitro growth and after recovery from the soil microcosm. The nine transformants were used in three biological control experiments against Fusarium wilt of carnation in comparison to two untransformed reference strains and to the recipient mutant. A high degree of variability in the biocontrol activity was observed throughout the experiments and only transformant T26.40 consistently controlled the incidence of disease. The results are discussed in relation to risk assessment of the release of transgenic antagonistic fungi.
Genetic variation in natural populations of the aphid Rhopalosiphum padi as revealed by maternally inherited markers
Authors: MARTINEZ‐TORRES D. , SIMON J. C. , FERERES A. , MOYA A. 
Published: April 2008

AbstractA survey on 148 clones of the aphid Rhopalosiphum padi from 11 widespread localities has been carried out to study the genetic structure of populations of this species as revealed by mitochondrial DNA restriction site and length polymorphisms as well as by restriction site analysis of a maternally inherited plasmid carried by the aphid eubacterial endosymbiont Buchnera aphidicola. Our results support the existence in the area under study of two main aphid maternal lineages strikingly coincidental with the two main reproductive categories displayed by this species. Those aphid clones possessing an incomplete life cycle that lacks the sexual phase (anholocyclic or androcyclic clones) show mitochondrial DNA (mtDNA) haplotype I and plasmid haplotype I, whereas those clones displaying the complete life cycle (holocyclic clones) posses some other distinct mtDNA haplotypes closely related to each other and plasmid haplotype II. While restriction‐site analysis of maternally inherited markers points to a relatively ancient origin of anholocycly/androcycly (between 460 000 and 1 400 000 years) followed by interrupted gene flow with respect to the ancestral holocyclic population, mtDNA size variation also suggests that historical stochastic processes have a different effect on the evolution of both main aphid lineages. Evidence of occasional nuclear gene flow between lineages and its consequences on the correspondence between maternally inherited haplotypes and life cycle are also presented and discussed.
Molecular genetic identification of whale and dolphin products from commercial markets in Korea and Japan
Authors: BAKER C. S. , CIPRIANO F. , PALUMBI S. R. 
Published: April 2008

AbstractWe report the methods and results of molecular genetic identification of the species and, in some cases, geographical origins of whale and dolphin products purchased from retail markets and restaurants in Japan and South Korea. As reported previously (Baker & Palumbi 1994), we used the polymerase chain reaction (PCR) and a portable laboratory to amplify, purify and later sequence a portion of the mitochondrial DNA control region from 16 commercial products purchased in Japan. This ‘spot check’ revealed a surprising variety of species for sale, including minke, fin and humpback whales and one or two species of dolphins sold as ‘kujira’ or whale. In the Korean survey, DNA amplifications were conducted by two of us (C.S.B. and F.C.) working with independent equipment and reagents. The two sets of DNA amplifications were returned to our respective laboratories and sequenced independently for cross‐validation. Among the total of 17 species‐specific sequences we found a dolphin, a beaked whale, 13 Northern Hemisphere minke whales (representing at least seven distinct individuals) and two whales which are closely related to the recognized sei and Bryde's whales but could not be identified as either using available type sequences. We suggest that these two specimens represent a currently unrecognized species or subspecies of Bryde's whale, possibly the so‐called ‘small‐form’ reported from the tropical waters of the Indo‐Pacific.We conclude that molecular systematic analyses of DNA sequences have tremendous utility for the identification of whale and dolphin products. However, there are certain constraints on the application of these techniques for monitoring whaling or trade in whale products. First, PCR and DNA sequencing can generate misleading artefacts. These can generally be recognized or eliminated through experimental controls. Second, phylogenetic reconstructions of DNA sequences can be misinterpreted if the database of type sequences is inadequate or the taxonomy of the group is incomplete. This constraint is, at present, a more serious obstacle to molecular monitoring of whaling. Our results highlight uncertainties about the taxonomic status of oceanic populations and morphological forms of two species (or species complexes) targeted by legal and illegal hunting, the minke and Bryde's whales. Despite these uncertainties, it is difficult to reconcile some of the species available in Japanese and Korean commercial markets with recent catch records made available to the International Whaling Commission. It is particularly disturbing that two specimens of an unrecognized species or subspecies of baleen whale were for sale in a restaurant in South Korea in October, 1994, 8 years after the acceptance of an international moratorium on commercial whaling.
Molecular genetic variation following a population crash in the endangered Mauna Kea silversword,Argyroxiphium sandwicensessp.sandwicense(Asteraceae)
Authors: FRIAR E. A. , ROBICHAUX R. H. , MOUNT D. W. 
Published: April 2008

AbstractThe endangered Mauna Kea silversword,Argyroxiphium sandwicensessp.sandwicense(Asteraceae), has experienced a severe decline in distribution and abundance because of predation by alien ungulates. The small remnant natural population on the Mauna Kea volcano contains only 46 individuals. By contrast, the Haleakala silversword,A. sandwicensessp.macrocephalum, consists of a large, vigorous population exceeding 60 000 individuals. Molecular genetic variation in the two populations was assessed using random amplified polymorphic DNA (RAPD) loci. Despite its severe crash in size, the Mauna Kea population did not differ significantly from the Haleakala population in the number of detectably polymorphic loci or in heterozygosity. The lack of substantial reduction in genetic variation, at least as measured with RAPD loci, suggests that the Mauna Kea population may not yet have gone through multiple generations at very small size.
Estimation of genomic variation between British populations of the potato cyst nematode Globodera pallida using RAPD‐PCR
Authors: BURROWS P. R. , HALFORD P. D. , EVANS K. 
Published: April 2008

AbstractRandom amplified polymorphic DNA (RAPD) has been used to investigate the interrelationships of 20 populations of Globodera pallida collected originally from field soils around the UK. RAPD analysis revealed a high level of relative genomic diversity within British G. pallida but there was no general correlation of genomic similarity with geographic distribution. Two populations of pathotype Pa1 were clearly divergent from the bulk of G. pallida and might represent a distinct introduction. Two other populations, from Scotland and Wales, were also dissimilar from each other and from the rest of the G. pallida populations.
Mitochondrial cytochrome b DNA sequence variation of Atlantic cod Gadus morhua, from Norway
Authors: ARNASON E. , PÁLSSON S. 
Published: April 2008

AbstractWe studied sequence variation of a fragment of the mitochondrial cytochrome b gene using polymerase chain reaction (PCR) and direct sequencing among 85 Norwegian Atlantic cod Gadus morhua, from nine sampling localities representing three overall areas: arctic, coastal and middle. In the analysis we include an additional 15 cod studied by Carr & Marshall (1991a). Nine base changes were found among the 100 sequences defining 11 haplotypes which differ from each other by one to five mutations. Two sites have been hit twice. All but one mutation are at third position silent sites. The variation passes several neutral‐theory tests and is thus suitable as marker for studying population differentiation. Coefficients of coancestry or intraclass correlation coefficient are negative both at the level of individuals within localities and localities within areas. This implies greater differences among individuals within populations than between populations. Intralocality nucleotide diversity is high and masks interlocality nucleotide divergence such that the net interlocality nucleotide divergence is nil. Similarly the net interarea nucleotide divergence is nil.
Genetic and ecotypic structure of a fluorescent Pseudomonas population
Authors: HAUBOLD B. , RAINEY B. 
Published: April 2008

AbstractFluorescent pseudomonads are among the most numerous bacteria found on plant surfaces and the activity of certain isolates can affect plant growth. In 1993, 108 fluorescent Pseudomonas isolates were collected on a single sampling occasion from the leaves of sugar beet plants grown at the Oxford University Field Station, Wytham. Isolates were obtained from 54 different leaves, from nine plants, and characterized using 10 allozyme and 23 biotype markers. Statistical analysis of the combined data revealed five biotypic traits which permitted a rational classification of the sample. Analysis of the allozyme data showed that the population was in overall linkage disequilibrium. Clonality was also observed after subdivision of allozyme data along spatial and habitat levels. However, two genetically defined subgroups were in linkage equilibrium which suggests the possibility of frequent large‐scale recombination among certain isolates. A significant correlation between isolate distribution and habitat (leaf type and plot) indicates that the population has ecotypic structure.
Molecular genetic examination of the polymorphic Arctic charr Salvelinus alpinus of Thingvallavatn, Iceland
Authors: VOLPE J. P. , FERGUSON M. M. 
Published: April 2008

AbstractThingvallavatn, Iceland contains two sympatric morphotypes (benthic and limnetic) of Arctic charr Salvelinus alpinus. Each morphotype is composed of two morphs and these differ markedly in ecology, behaviour and life history. We used molecular genetic approaches to test whether (i) genetic heterogeneity exists among morphs and (ii) if morphs arose in allopatry and came into secondary contact or arose sympatrically within the lake through genetic segregation and/or phenotypic plasticity. Direct sequencing of 275 bp of the mitochondrial DNA (mtDNA) control region, mtDNA restriction fragment length polymorphisms and single locus minisatellite analyses detected insufficient variation to test our hypotheses. Analysis of multilocus minisatellite band sharing detected no significant differences between morphs within the same morphotype. However, significant differences among morphs belonging to different morphotypes suggest some genetic heterogeneity in Thingvallavatn charr. Limnetic charr from Thingvallavatn were more similar to sympatric benthic charr than to allopatric limnetics from two other Icelandic lakes. This suggests that the Thingvallavatn morphs arose sympatrically within the lake rather than in allopatry followed by secondary contact.
Population differentiation and evolution in the common guillemot Uria aalge
Authors: FRIESEN V. L. , MONTEVECCHI W. A. , BAKER A. J. , BARRETT R. T. , DAVIDSON W. S. 
Published: April 2008

AbstractCommon (Uria aalge) and Brünnich's guillemots (U. Iomvia) are colonial seabirds that nest in temperate to arctic oceans throughout the Northern hemisphere. They are very similar in the characteristics of ecology, demography and life history that are thought to determine the extent of differentiation among populations, yet geographic variation in morphology is notably greater in common guillemots. Despite evidence of strong natal philopatry, previous analyses of allozymes and the mitochondrial cytochrome b gene revealed little genetic differentiation among North Atlantic colonies of Brünnich's guillemots. To determine if the more extensive morphological variability in common guillemots reflects greater genetic variability, we sequenced part of the cytochrome b gene for 160 common guillemots from 10 colonies distributed throughout the Northern hemisphere. Genotype frequencies and phylogenetic relationships among genotypes both indicated that Atlantic and Pacific populations are genetically distinct. Genetic divergence among genotypes suggested that differentiation of these populations has resulted from separation by Pleistocene glaciers and the Bering Landbridge, as well as by currently unsuitable breeding habitat in the Arctic Ocean. Cytochrome b genotype frequencies also differed among Atlantic colonies, and appeared to define a cline similar to that described for morphological characters. Analyses of sequence variation suggested that this variation probably results from secondary contact between two refugial populations from the Pleistocene glaciations, rather than from isolation by distance or selection. In contrast, the Atlantic population of Brünnich's guillemots appears to have arisen through recent expansion of a single homogeneous refugial population.
Conservation genetics of the plain pigeon Columba inornata in Puerto Rico and the Dominican Republic
Authors: YOUNG D. L. , ALLARD M. W. 
Published: April 2008

AbstractGenetic sequence variation in the mitochondrial D‐loop was assessed for 42 individuals of the plain pigeon Columba inornata from Puerto Rico and the Dominican Republic. While overall genetic diversity was low in these populations, five haplotypes were observed, with one unique to Puerto Rico and three haplotypes unique to the Dominican Republic sample (with haplotype diversity of hPR= 0.479 and hDR= 0.591, and nucleotide diversity of πPR= 0.2% and πDR= 0.4% where the subscripts correspond to Puerto Rico and the Dominican Republic, respectively). A G‐test of haplotype frequencies between these two populations suggest that these two subspecies (C. i. wetmorei and C. i. inornata) are genetically distinct and should be managed separately. With little apparent gene flow between these two islands (estimates of migration Nm= 1.18) it would appear that the endangered species C. i. wetmorei is endemic to the island of Puerto Rico and that these current populations were not founded by a recent extinction and recolonization event from the Dominican Republic.
The essentiality and involvement of Streptococcus intermedius histone‐like DNA‐binding protein in bacterial viability and normal growth
Authors: Liu Dali , Yumoto Hiromichi , Murakami Keiji , Hirota Katsuhiko , Ono Tsuneko , Nagamune Hideaki , Kayama Shizuo , Matsuo Takashi , Miyake Yoichiro 
Published: April 2008

Summary Streptococcus intermedius histone‐like DNA‐binding protein (Si‐HLP) is a homodimeric protein and, conserved with Escherichia coli HU, a well‐documented nucleoid‐associated protein (NAP). In E. coli, HU plays important roles as both structural and regulatory factors, but it is not essential for E. coli viability. Streptococcal HLP has been found to bind host cells and induce cytokine production, but its physiological role remains poorly defined. In the present study, using gene insertion knockout and tetracycline‐regulated antisense RNA expression techniques, we determined whether Si‐HLP is essential for bacterial viability and normal growth in S. intermedius. The Si‐HLP‐downregulated S. intermedius strain showed alterations in its morphology and surface properties. Downregulation of Si‐HLP led to an expanded nucleoid to fill the intracellular space. Transcription levels of several genes, including virulence‐associated factors, were found to be activated or repressed in the antisense Si‐hlp RNA‐expressing strain by real‐time PCR and reverse‐transcription PCR. Collectively, these data suggest that Si‐HLP serves as an essential NAP governing the nucleoid architecture and controlling the gene transcription profile in S. intermedius.
The Ustilago maydis Cys2His2‐type zinc finger transcription factor Mzr1 regulates fungal gene expression during the biotrophic growth stage
Authors: Zheng Yan , Kief Jan , Auffarth Kathrin , Farfsing Jan W. , Mahlert Michael , Nieto Fernanda , Basse Christoph W. 
Published: April 2008

SummaryThe smut fungus Ustilago maydis establishes a biotrophic relationship with its host plant maize to progress through sexual development. Here, we report the identification and characterization of the Cys2His2‐type zinc finger protein Mzr1 that functions as a transcriptional activator during host colonization. Expression of the U. maydis mig2 cluster genes is tightly linked to this phase. Upon conditional overexpression, Mzr1 confers induction of a subset of mig2 genes during vegetative growth and this requires the same promoter elements that confer inducible expression in planta. Furthermore, expression of the mig2‐4 and mig2‐5 genes during biotrophic growth is strongly reduced in cells deleted in mzr1. DNA‐array analysis led to the identification of additional Mzr1‐induced genes. Some of these genes show a mig2‐like plant‐specific expression pattern and Mzr1 is responsible for their high‐level expression during pathogenesis. Mzr1 function requires the b‐dependently regulated Cys2His2‐type cell cycle regulator Biz1, indicating that two stage‐specific regulators mediate gene expression during host colonization. In spite of a role as transcriptional activator during biotrophic growth, mzr1 is not essential for pathogenesis; however, conditional overexpression interfered with proliferation during vegetative growth and mating ability, caused a cell separation defect, and triggered filamentous growth. We discuss the implications of these findings.