bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mitochondrial control region and protein coding genes sequence variation among phenotypic forms of brown trout Salmo trutta from northern Italy
Authors: GIUFFRA E. , BERNATCHEZ L. , GUYOMARD R. 
Published: April 2008

AbstractThe Pô River basin of northern Italy is the home of distinctive and endemic morphological forms of brown trout Salmo trutta. We used PCR‐direct sequencing and RFLP techniques to study variation in the mitochondrial control region of 225 trout in order to assess genetic relatedness among 18 populations from that region. The distribution analysis of these genotypes among north Italian populations confirmed the phylogenetic differentiation of marbled trout Salmo trutta marmoratus populations and the postglacial origin of S. t. fario. Extensive genetic heterogeneity was observed among morphologically identical S. t. fario populations. Introgression with domestic strains of Atlantic basin origin was detected in all forms. In order to assess the phylogenetic congruence detected in coding and noncoding regions of the mitochondrial genome, we also analysed sequence variation in segments of the cytochrome b and ATPase subunit VI genes among representatives of all variants detected in the analysis of the control region. Variation in protein coding genes was only slightly less than that observed in the control region of the same individuals, both in terms of number of variants detected and of pairwise sequence divergence estimates among variants. Phylogenetic analysis based on protein coding genes sequences identified the same phylogenetic groupings defined by the control region analysis and also allowed a partial resolution of their phyletic relationships that was previously unresolved. However, coding and noncoding segments differed substantially in the transition‐transversion ratio (17:0 in coding segments vs. 17:6 in control region segments).
Molecular phylogeny of the actinorhizal Hamamelidae and relationships with host promiscuity towards Frankia
Authors: MAGGIA L. , BOUSQUET J. 
Published: April 2008

AbstractSeveral of the most studied actinorhizal symbioses involve associations between host plants in the subclass Hamamelidae of the dicots and actinomycetes of the genus Frankia. These actinorhizal plants comprise eight genera distributed among three families of ‘higher’ Hamamelidae, the Betulaceae, Myricaceae, and Casuarinaceae. Contrasting promiscuity towards Frankia is encountered among the different actinorhizal members of these families, and a better assessment of the evolutionary history of these actinorhizal taxa could help to understand the observed contrasts and their implications for the ecology and evolution of the actinorhizal symbiosis. Complete DNA sequences of the chloroplast gene coding for the large subunit of ribulose 1,5‐bisphosphate carboxylase (rbcL) were obtained from taxa representative of these families and the Fagaceae. The phylogenetic relationships among and within these families were estimated using parsimony and distance‐matrix approaches. All families appeared monophyletic. The Myricaceae appeared to derive first before the Betulaceae and the Casuarinaceae. In the Casuarinaceae, the genus Gymnostoma derived before the genera Casuarina and Allocasuarina, which were found closely related. The analysis of character‐state changes in promiscuity along the consensus tree topology suggested a strong relationship between the evolutionary history of host plants and their promiscuity toward Frankia. Indeed, the actinorhizal taxa that diverged more recently in this group of plants were shown to be susceptible to a narrower spectrum of Frankia strains. The results also suggest that the ancestor of this group of plant was highly promiscuous, and that evolution has proceeded toward narrower promiscuity and greater specialization. These results imply that a tight relationship between the phytogenies of both symbiotic partners should not be expected, and that host promiscuity is likely to be a key determinant in the establishment of an effective symbiosis.
Paternity exclusion in a community of wild chimpanzees using hypervariable simple sequence repeats
Authors: MORIN P. A. , WALLIS J. , MOORE J. J. , WOODRUFF DAVID S. 
Published: April 2008

AbstractWe report the use of hypervariable simple sequence repeat (SSR) nuclear loci to study paternity in a community of wild chimpanzees (Pan troglodytes schweinfurthii) in Gombe National Park, Tanzania. All 43 living members of a habituated community were sampled and 35 were genotyped at 8 SSR loci using DNA amplified from hair. Paternity exclusions were performed for 25 chimpanzees including 10 for whom the mother was also genotyped. In each case 12–20 males were potential fathers based on their age and/ or direct observation of sexual behaviour. 179 tests involving potential father/offspring combinations were performed. In four cases the data permit the probable identification of the previously undetermined father; these are the first such determinations for free‐ranging chimpanzees, and the first based on non‐invasive sampling. In another four cases we were able to exclude all but two to five potential fathers, and in the remaining cases we were able to exclude all living males. For molecular ecologists SSR genotype databases offer important advantages over currently popular minisatellite DNA fingerprinting: they can be analysed unequivocally using traditional population genetics techniques and they can be expanded through time and space by other researchers.
Microsatellite analysis of genetic variation in black bear populations
Authors: PAETKAU D. , STROBECK C. 
Published: April 2008

AbstractMeasuring levels of genetic variation is an important aspect of conservation genetics The informativeness of such measurements is related to the variability of the genetic markers used; a particular concern in species, such as bears, which are characterized by low levels of genetic variation resulting from low population densities and small effective population sizes We describe the development of microsatellite analysis in bears and its use in assessing interpopulation differences in genetic variation in black bears from three Canadian National Parks These markers are highly variable and allowed identification of dramatic differences in both distribution and amount of variation between populations Low levels of variation were observed in a population from the Island of Newfoundland The significance of interpopulation differences in variability was tested using a likelihood ratio test of estimates of θ= 4Neu.
Molecular separation of genera in Cassiinae (Leguminosae), and analysis of variation in the nodulating species of Chamaecrista
Authors: WHITTY P. W. , POWELL W. , SPRENT J. I. 
Published: April 2008

AbstractRandomly Amplified Polymorphic DNA (RAPD) methods have been adapted for use as a phenetic tool on the legume tribe Cassiinae. RAPD‐generated polymorphism within local populations was lower than between populations from different geographic regions, between species and genera. Examination of three Cassia species, 12 Chamaecrista species and 13 Senna species using eight primers showed the potential for separation of the nodulated/nitrogen fixing genus Chamaecrista from the previously congeneric groups Cassia and Semis. Similarly, RAPD analysis of two groups of nine Ch. rotundifolia and nine Ch. mimosoides samples using 11 primers has given separation according to both species and to geographical location. Analysis of a small sample of five Chamaecrista species from Brazil with eight primers gave separation consistent with known variations in nodule structure.
Charomid cloning vectors meet the pedipalpal chelae: single‐locus minisatellite DNA probes for paternity assignment in the harlequin beetle‐riding pseudoscorpion
Authors: ZEH D. W. , ZEH J. A. , MAY C. A. 
Published: April 2008

AbstractWe describe the first application of the charomid‐cloning method for developing single‐locus minisatellite DNA probes in a terrestrial arthropod. From a genomic library of the neotropical pseudoscorpion, Cordylochernes scorpioides, we have isolated two probes with heterozygosities exceeding 95%. These probes yielded single‐locus patterns after only low stringency washing and in the absence of genomic competitor DNA. Analysis of three pedigrees indicated germline stability and showed no evidence of linkage between the loci. Patterns of allelic transmission generally conformed closely to Mendelian expectations but large offspring numbers did enable detection of one example of significant bias in allele inheritance. Two test cases are presented to illustrate the clarity and power with which these probes can establish paternity: (i) a female mated to three unrelated males, and (ii) a female mated to two of her brothers. In both cases, a single probe could be used to assign the paternity of all offspring.
A phylogenetic analysis of micro‐organisms isolated from subsurface environments
Authors: Stim K. P. 
Published: April 2008

AbstractThree methods were used to provide information on the identity and phylogenetic relatedness of 19 aerobic, chemoheterotrophic bacteria isolated from topsoil and deep subsurface sediments at a site in South Carolina. These methods were (i) analysis of selected physiological traits, (ii) restriction endonuclease analysis (REA) of genomic DNA, and (iii) analysis of 16S ribosomal RNA sequences. When the 16S rRNA sequences were compared with those for 12 standard strains, two topsoil isolates and six subsurface strains formed a tight group with the high‐G+C Gram‐positive bacteria and appeared to be most closely related to Arthrobacter globiformis— a coryneform‐actinomycete bacterium with unusually effective survival capabilities. The rest of the subsurface isolates were scattered among the standard strains from the Proteobacteria— including the pseudomonads and Agrobacterium tumefaciens— or the low‐G+C Gram‐positive bacteria.
Effect of cellular physiology on PCR amplification efficiency
Authors: Silva M. C. , Batt C. A. 
Published: April 2008

AbstractCulture conditions, and other variables that modulate a cell's physiology, can bias a polymerase chain reaction (PCR) amplification against generating a representative population profile. Two Pseudomonas putida nahR alleles were constructed in pUC19 that differ solely in a 31‐bp internal segment whose sequence has been inverted. After PCR amplification, the products could be distinguished on the basis of a change in a unique restriction site. When an Escherichia coli strain carrying one nahR allele is submitted to different growth conditions, the consequences of such variations on the relative PCR amplification of whole cells can be ascertained through coamplification with a strain carrying the other allele and subsequent restriction analysis. Cells in stationary phase displayed improved amplifiability while cells grown at 42°C were equally amplifiable as compared to cells grown at 37°C. However, sublethal levels of tetracycline or growth in minimal medium made the PCR target in these cells relatively less amplifiable. When cells are completely lysed and the plasmid DNA is purified beforehand, the coamplification bias is eliminated. These results suggest that mixed populations containing cells in different physiological states may not be representatively amplified by PCR unless a DNA extraction step is included.
Molecular genetic analysis of the response of three soil microbial communities to the application of 2, 4‐D
Authors: Xia Xueqing , Bollinger John , Ogram Andrew 
Published: April 2008

AbstractThe responses of three different soil microbial communities to the experimental application of 2, 4‐dichlorophenoxyacetic acid (2, 4‐D) were evaluated with a variety of molecular genetic techniques. Two of the three soil communities had histories of prior direct exposure to 2, 4‐D, and one had no prior direct application of any herbicide. Dominant 2, 4‐D degrading strains isolated from these soils the previous year were screened for hybridization with three catabolic genes (tfdA, tfdAII, and tfdB) cloned from the well‐studied 2, 4‐D degradative plasmid, pJP4, revealing varying degrees of similarity with the three genes. Hybridization of total community DNA from the three soils with the tfd gene probes also indicated that pJP4‐like tfd genes were not harboured by a significant percentage of the community. Community level response was evaluated by the comparison of different treatments by Random Amplified Polymorphic DNA (RAPD) fingerprints and by community DNA cross‐hybridization. No differences between treatments within the same soil were detected in any of the RAPD fingerprints generated with 17 primers. Community DNA cross‐hybridization also indicated that the application of 2, 4‐D at the applied rates did not quantitatively affect the structure of the soil microbial communities present in the three soils during the time‐frame studied.
A new hypothesis for the origin of pentaploid Holcus from diploid Holcus lanatus L. and tetraploid Holcus mollis L. in France
Authors: Richard M. , Jubier M. F. , Bajon R. , Gouyon P. H. , Lejeune B. 
Published: April 2008

AbstractThe Holcus complex in France consists of two species, Holcus lanatus L. (Yorkshire fog; 2n= 2x= 14) and Holcus mollis L. (Creeping soft‐grass; 2n= 4x= 28) and an interspecific hybrid H.m.×H.l. (2n= 5x= 35), which is morphologically similar to Holcus mollis. A heterologous rDNA probe from wheat was used to detect the corresponding region in Holcus (s. l.) genomic DNA'fragments, for six to eight plants from 13 populations located south‐west of Paris. A restriction enzyme map of the ribosomal RNA genes (rDNA) in Holcus (s. l.) was also constructed. The length polymorphism detected in the IGS region was used as a DNA fingerprint for the identification of different cytotypes and species of the Holcus complex and for the typing and delimitation of individuals in populations. In the light of the results we reconsider the assumption that the pentaploid hybrid H.m.×H.l. is purely clonal. New hypotheses concerning the origin of the pentaploid hybrid and its reproduction are proposed, and the consequences for genetic diversity in natural populations discussed.
Clonal dispersal and spatial mixing in populations of the plant pathogenic fungus, Sclerotinia sclerotiorum
Authors: Kohli Y. , Brunner L. J. , YOELL H. , Milgroom M. G. , Anderson J. B. , Morrall R. A. A. , Kohn L. M. 
Published: April 2008

AbstractTwo thousand seven hundred and forty‐seven isolates of Sclerotinia sclerotiorum were sampled from four field populations of canola in western Canada. Each field was sampled in a grid of 128 50‐m 50‐m quadrats plus four intensive quadrats each sampled in a diagonal transect. Sampling was done at two phases of the disease cycle: (1) from ascospore inoculum on petals and (2) from disease lesions in stems. A total of 594 unique genotypes was identified by DNA fingerprinting. In each field, a small group of clones represented the majority of the sample, with a large group of clones or genotypes sampled once or twice. Clone frequencies were compared by χ2 tests. The difference in profiles of clone frequencies for the two fields sampled in 1991 was not significant, but in 1992 the difference in profiles was marginally significant, indicating some local population substructure. The difference in profiles of clone frequencies for petals and lesions was not significant in each of the two fields sampled in 1991. In each of the two fields sampled in 1992, however, the difference was highly significant, consistent either with selection for some clones or with waves of immigration during the disease cycle. Nine of the 30 most frequently sampled clones from this study were previously recovered in a macrogeographical sample from western Canada in 1990. For spatial analyses, randomization tests indicated no significant spatial aggregation of either clones on petals or clones from lesions. Also, isolates of a clone on petals were not closer to isolates of the same clone from lesions than could be predicted by chance. Both observations suggest spatial mixing of ascospore inoculum from resident or immigrant sources.
Mitochondrial DNA sequence variation and genetic stock structure of Atlantic cod (Gadus morhua) from bay and offshore locations on the Newfoundland continental shelf
Authors: Carr S. M. , Snellen A. J. , Howse K. A. , Wroblewski J. S. 
Published: April 2008

AbstractBay cod, Atlantic cod (Gadus morhua) that over‐winter in the deep‐water bays of northeastern Newfoundland, have historically been regarded as distinct in migration and spawning behaviour from offshore (Grand Bank) cod stocks. To investigate their genetic relationships, we determined the DNA sequence of a 307‐base‐pair portion of the mitochondrial cytochrome b gene for 236 adult cod taken from the waters off northeastern Newfoundland, including fish found over‐wintering and spawning in Trinity Bay. Although 17 genotypes were found, a single common genotype occurs at a frequency of greater than 80% in all samples, and no alternative genotype occurs at a frequency of greater than 3%. Genotype proportions did not differ significantly among samples. Measures of genetic subdivision among sampling locations are nil. Cod over‐wintering in Trinity Bay are not genetically distinct from offshore cod. In combination with tagging and physiological studies, these data suggest that there is sufficient movement of cod between bay and offshore locations to prevent the development or maintenance of independent inshore stocks. Adult cod that over‐winter in Trinity Bay appear to represent an assemblage of temporarily nonmigratory fish that have become physiologically acclimated to cold‐water inshore environments. The pattern of genetic variation in northern cod suggests a recent population structure characterized by extensive movement of contemporary individuals superimposed on an older structure characterized by a bottleneck in the population size of cod in the north‐western Atlantic.
Conservation genetics of the European brown bear ‐ a study using excremental PCR of nuclear and mitochondrial sequences
Authors: Kohn M. , Knauer F. , Stoffella A. , SCHRÖDER W. , PÄÄBO S. 
Published: April 2008

AbstractIn the Brenta area of northern Italy, a brown bear Ursus arctos population is rapidly going extinct. Restocking of the population is planned. In order to study the genetics of this highly vulnerable population with a minimum of stress to the animals we have developed a PCR‐based method that allows the study of mitochondrial and nuclear gene sequences from droppings collected in the field. This method is generally applicable to animals in the wild. Using excremental as well as hair samples, we show that the Brenta population is monomorphic for one mitochondrial lineage and that female as well as male bears exist in the area. In addition, 70 samples from other parts of Europe were studied. As others have previously reported, the mitochondrial gene pool of European bears is divided into two major clades, one with a western and the other with an eastern distribution. Whereas populations generally belong to either one or the other mitochondrial clade, the Romanian population contains both clades. The bears in the Brenta belong to the western clade. The implications for the management of brown bears in the Brenta and elsewhere in Europe are discussed.
Analysis of genetic structure in soil populations of Rhizobium leguminosarum recovered from the USA and the UK
Authors: STRAIN S. R. , WHITTAM T. S. , BOTTOMLEY P. J. 
Published: April 2008

AbstractAlthough many studies have shown that animal‐associated bacterial species exhibit linkage disequilibrium at chromosomal loci, recent studies indicate that both animal‐associated and soil‐borne bacterial species can display a nonclonal genetic structure in which alleles at chromosomal loci are in linkage equilibrium. To examine the situation in soil‐borne species further, we compared genetic structure in two soil populations of Rhizobium leguminosarum bv. trifolii and two populations of R. leguminosarum bv. viciae from two sites in Oregon, with genetic structure in R. leguminosarum bv. viciae populations recovered from peas grown at a site in Washington, USA, and at a site in Norfolk, UK. A total of 234 chromosomal types (ET) were identified among 682 strains analysed for allelic variation at 13 enzyme‐encoding chromosomal loci by multilocus enzyme electrophoresis (MLEE). Chi‐square tests for heterogeneity of allele frequencies showed that the populations were not genetically uniform. A comparison of the genetic diversity within combined and individual populations confirmed that the Washington population was the primary cause of genetic differentiation between the populations. Each individual population exhibited linkage disequilibrium, with the magnitude of the disequilibrium being greatest in the Washington population and least in the UK population of R. leguminosarum bv. viciae. Linkage disequilibrium in the UK population was created between two clusters of 9 and 23 ETs, which, individually, were in linkage equilibrium. Strong linkage disequilibrium between the two major clusters of 8 and 12 ETs in the Washington population was caused by the low genetic diversity of the ETs within each cluster relative to the inter‐cluster genetic distance. Because neither the magnitude of genetic diversity nor of linkage disequilibrium increased as hierarchical combinations of the six local populations were analysed, we conclude that the populations have not been isolated from each other for sufficient time, nor have they been exposed to enough selective pressure to develop unique multilocus genetic structure.
An unusual mitochondrial DNA polymorphism in the Chorthippus biguttulus species group (Orthoptera: Acrididae)
Authors: MASON D. J. , BUTLIN R. K. , GACESA P. 
Published: April 2008

AbstractMitochondrial DNA restriction fragment patterns have been used to investigate the Chorthippus biguttulus group: a group of morphologically similar grasshopper species with very distinct male calling songs. Ten haplotypes were identified in 21 populations, representing six species. Haplotype diversity was as great within species, and in some case within populations, as it was among species and no clear geographical patterns of haplotype distribution were revealed. In the light of grasshopper range changes since the last glaciation it is unlikely that these data can be explained entirely by the retention of ancestral polymorphism. This suggests that hybridization has occurred during periods of grasshopper range expansion since the last glacial maximum, allowing mtDNA transfer between populations that have previously diverged in allopatry.