bluuebunny/crossref_metadata_2025 huggingface dataset:
The phylogeographic pattern of mitochondrial DNA variation in the Dall's porpoise Phocoenoides dalli
Authors: MCMILLAN W. O. , BERMINGHAM E.
Published: April 2008

We used 11 restriction endonucleases to study mtDNA variation in 101 Dall's porpoises Phocoenoides dalli from the Bering Sea and western North Pacific. There was little phylogeographic patterning among the 34 mtDNA haplotypes identified in this analysis, suggesting a strong historical connection among populations across this region. Nonetheless, mtDNA variation does not appear to be randomly distributed in this species. Both GST and AMOVA uncovered significant differences in the distribution of mtDNA variation between the Bering Sea and western North Pacific populations. These mtDNA results, coupled with differences in allozyme variation and parasite infestation, support the demographic distinctiveness of Bering Sea and western North Pacific stocks of Dall's porpoise. The lack of a strong phylogeographic orientation of mtDNA haplotypes within the Dall's porpoise is similar to the pattern reported in other vertebrates such as coyotes, blackbirds, chickadees, marine catfish, and catadromous eels. Like Dall's porpoise, these species are broadly distributed, and have large populations linked by moderate to high levels of gene flow. However, the more complex, deeply branched phylogenetic network of mtDNA haplotypes within Dall's porpoise, relative to these other vertebrates, suggests important differences between these species in the forces shaping mtDNA variation. One such force is the effective size of female populations, which appears to have been comparatively large and stable in Dall's porpoise.
Founder effects and sex ratio in the gynodioecious Thymus vulgaris L.
Authors: MANICACCI D. , COUVET D. , BELHASSEN E. , GOUYON P. H. , ATLAN A.
Published: April 2008

Thymus vulgaris is a gynodioecious species (in which females and hermaphrodites coexist) with a highly variable frequency of females among natural populations (5–95%) and a high average female frequency (60%). Sex determination involves both cytoplasmic genes responsible for male sterility, i.e. the female phenotype, and specific nuclear factors responsible for the restoration of male fertility, and thus a hermaphrodite phenotype. In this study, molecular markers of the mitochondrial genome have been used to quantify the cytoplasmic diversity in 11 clumps of individuals observed in four recently founded populations. The very low diversity within patches in conjunction with the strong diversity among patches strongly suggests that clumps of individuals are the result of single matrilinear families. In clumps that contain mainly females, all the analysed females showed the same cytoplasmic pattern. This pattern differed from that shown by neighbouring hermaphrodites, indicating that the determination of sex is locally cytoplasmic. A comparison of genetic diversity before and after fire in one population showed that disturbances may cause a reduction in genetic diversity and a concurrent induction of local cytoplasmic determination of sex. Such cytoplasmic determination of sex in colonizing populations, together with the greater seed set of females, may largely improve the colonizing ability of the species.
Compatibility of systemic acquired resistance and microbial biocontrol for suppression of plant disease in a laboratory assay
Authors: CHEN J. , JACOBSON L. M. , HANDELSMAN J. , GOODMAN R. M.
Published: April 2008

Systemic acquired resistance (SAR) and microbial biocontrol each hold promise as alternatives to pesticides for control of plant diseases. SAR and Bacillus cereus UW85, a microbial biocontrol agent, separately suppress seedling damping‐off diseases caused by oomycete pathogens. The purposes of this study were to investigate how expression of SAR affected the efficacy of biocontrol by UW85 and if UW85 treatment of plants induced SAR. We devised a laboratory assay in which seedling damping‐off disease, induction of SAR, and growth of UW85 could be quantified. Seedlings of Nicotiana tabacum Xanthi nc were germinated on moist filter paper and transferred after 7 days to water agar plates (40 seedlings per plate). Zoospores of oomycete pathogens (Pythium torulosum, Pythium aphanidermatum, or Phytophthora parasitica) were applied at concentrations that caused 80% seedling mortality within 10 days. Seedling mortality was dependent on zoospore inoculum concentration. The level of disease suppression caused by treatment with UW85 depended on the UW85 dose applied. SAR was induced with 0.5‐mM salicylic acid or 0.1‐mM 2,6‐dichloroisonicotinic acid. Expression of an SAR‐related gene was confirmed by northern analysis with a probe prepared from a tobacco PR‐1a cDNA. Induction of SAR suppressed disease caused by each of the oomycete pathogens, but did not alter the growth of UW85 on roots. Treatment of seedlings with UW85 did not induce the expression of PR‐1a. The combination of induction of SAR and treatment with UW85 resulted in additive suppression of disease as measured by seedling survival.
Homology among RAPD fragments in interspecific comparisons
Authors: RIESEBERG L. H.
Published: April 2008

The use of RAPDs for comparative purposes relies on the assumption that similarity of fragment size is a dependable indicator of homology. To test the validity of this assumption, homology among 220 pairs of comigrating fragments from three wild sunflower species was determined. Ninety‐one per cent cross‐hybridized and/or displayed congruent restriction fragment profiles suggestive of homology. However, comparative linkage mapping data indicated that 13% of the homologous loci mapped to genomic locations that were incongruent with the majority of loci, suggestive of paralogous rather than orthologous relationships. Thus, of the 220 pairwise comparisons, only 174 (79.1%) identified loci that are useful for comparative genetic studies. These problems, as well as several other factors discussed in the text, will introduce noise into RAPD data sets and thereby reduce the probability of generating accurate estimates of genetic relationships. Recommended methods for reducing noise in RAPD data sets include increasing gel resolution and/or testing fragment homology. However, implementation of these approaches will not eliminate all uncertainties, and it is also recommended that RAPD data sets be tested for structure and reliability.
Molecular characterization of clonal population structure and biogeography of arctic apomictic Daphnia from Greenland and Iceland
Authors: WEIDER L. J. , HOBÆK A. , CREASE T. J. , STIBOR H.
Published: April 2008

As part of a continuing international project to characterize the population genetic (clonal) structure of arctic members of the Daphnia pulex complex, 34 populations from western Iceland (N= 1373), and 76 populations from western Greenland (N= 2917), were surveyed for allozymic variation at six polymorphic enzyme loci. Mean clonal richness (±SE) was 1.91±0.19 and 1.50±0.12 for Iceland and Greenland populations, respectively. Mean clonal diversity (±1 SE) was 1.20±0.07 and 1.13±0.04 for Iceland and Greenland populations, respectively. Four widely distributed clones constituted 92.2% of the total animals surveyed from Iceland, while three locally abundant clones constituted 80.1% of the total animals collected primarily from Disko Island, western Greenland. Selected populations were screened for mitochondrial (mt)DNA variation using PCR‐based RFLP analysis of a 2100 bp fragment containing part of the ND4 and ND5 genes. One mtDNA haplotype was very widespread in both western Greenland and western Iceland, although, a number of mutational derivatives were also detected. These data indicate the potential for long‐distance dispersal of mtDNA lineages, of the order of hundreds or thousands of kilometers across the arctic. Phylogenetic analysis of the sequence of a 254 base pair (bp) fragment of the control region of the mtDNA molecule revealed two major clades one of which consisted solely of non‐melanic lineages, and the other of which consisted almost exclusively of melanic lineages (i.e. one non‐melanic lineage also clustered in this clade). Sequence divergence between the two clades averaged 7.3%. Both mitochondrial analyses did not reveal any distinct intraregional clustering of lineages. We discuss our results in reference to previous molecular work done on this arctic Daphnia complex, and we attempt to infer phylogeographic patterning based on geological/glaciological historical events in this region of the arctic.
Molecular diversity of fungi from ericoid mycorrhizal roots
Authors: PEROTTO S. , ACTIS‐PERINO E. , PERUGINI J. , BONFANTE P.
Published: April 2008

In order to investigate the diversity of fungal endophytes in ericoid mycorrhizal roots, about 150 mycelia were isolated from surface‐sterilized roots of 10 plants of Calluna vulgaris. Each mycelium was reinoculated to C. vulgaris seedlings under axenic conditions, and the phenotype of the plant‐fungus association assessed by light and electron microscopy. Many isolates that were able in vitro to produce typical ericoid mycorrhizae did not form reproductive structures under our culture conditions, whereas others could be identified as belonging to the species Oidiodendron maius. Morphological and molecular analysis of the fungal isolates showed that the root system of a single plant of C. vulgaris is a complex mosaic of several populations of mycorrhizal and non mycorrhizal fungi. PCR‐RFLP techniques, used to investigate the mycorrhizal endophytes, revealed up to four groups of fungi with different PCR‐RFLP patterns of the ITS ribosomal region from a single plant. Some of the mycorrhizal fungi sharing the same PCR‐RFLP pattern showed high degree of genetic polymorphism when analysed with the more sensitive RAPD technique; this technique may prove a useful tool to trace the spread of individual mycorrhizal mycelia, as it has allowed us to identify isolates with identical RAPD fingerprints on different plants.
Dissemination of thestrA‐strBstreptomycin‐resistance genes among commensal and pathogenic bacteria from humans, animals, and plants
Authors: SUNDIN G. W. , BENDER C. L.
Published: April 2008

Gene transfer within bacterial communities has been recognized as a major contributor in the recent evolution of antibiotic resistance on a global scale. The linkedstrA‐strBgenes, which encode streptomycin‐inactivating enzymes, are distributed worldwide and confer streptomycin resistance in at least 17 genera of gram‐negative bacteria. Nucleotide sequence analyses suggest thatstrA‐strBhave been recently disseminated. In bacterial isolates from humans and animals,strA‐strBare often linked with thesulIIsulfonamide‐resistance gene and are encoded on broad‐host‐range nonconjugative plasmids. In bacterial isolates from plants,strA‐strBare encoded on the Tn3‐type transposon Tn5393 which is generally borne on conjugative plasmids. The wide distribution of thestrA‐strBgenes in the environment suggests that gene transfer events between human, animal, and plant‐associated bacteria have occurred. Although the usage of streptomycin in clinical medicine and animal husbandry has diminished, the persistence ofstrA‐strBin bacterial populations implies that factors other than direct antibiotic selection are involved in maintenance of these genes.
Low frequency of extra‐pair paternity in two colonies of the socially monogamous short‐tailed shearwater Puffinus tenuirostris
Authors: AUSTIN J. J. , PARKIN D. T.
Published: April 2008

The short‐tailed shearwater is a colonially nesting, socially monogamous seabird. Little is known about mate fidelity and breeding behaviour in this species because breeding birds are nocturnal on land and spend much of their time within subterranean nesting burrows. Colonial breeding and extended sperm storage create opportunities for extra‐pair copulations which may form a significant component of the mating strategy in this species. Multilocus DNA fingerprinting was used to examine the genetic relationship between nestlings and the male and female nest attendants in 83 burrows from two distinct breeding colonies. Genetic analyses identified nine nestlings, approximately equally distributed between the two colonies, that were not related to the attendant pair male in those burrows, implying extra‐pair paternity through extra‐pair copulations. These results are used retrospectively to discuss the characteristics of extra‐pair copulations and extra‐pair fertilizations and the implications for estimates of life‐time reproductive success in the short‐tailed shearwater.
Genetic exchange and recombination in populations of the root‐infecting fungus Armillaria gallica
Authors: SAVILLE B. J. , YOELL H. , ANDERSON J. B.
Published: April 2008

Genetic individuals, or genets, of Armillaria and other root‐infecting basidiomycetes are usually found in discrete patches that often include the root systems of several adjacent trees. Each diploid individual is thought to arise in an unique mating event and then grow vegetatively in an expanding territory over a long period of time. Our objective in this study was to describe the population from which such genetic individuals are drawn. In a sample including 274 collections representing 121 genetic individuals of A. gallica (synonym A. bulbosa) from two sites in each of four regions of eastern North America, genotype frequencies at seven nuclear loci were not significantly different from Hardy‐Weinberg expectations. Furthermore, allele frequencies at the seven loci were not significantly different between regions. Additional allelic data from four non‐contiguous regions of mitochondrial DNA showed little or no population subdivision over the four regions. Analysis of the distribution of multilocus mtDNA haplotypes revealed some clonal transmission of mtDNAs between genets and nonrandom mating within sites. Despite the sharing of mtDNA types by some individuals, the overall sample contained a high level of genotypic diversity. The apparent linkage equilibrium between some pairs of loci and the high level of phylogenetic inconsistency among all four loci suggest the occurrence heteroplasmy and recombination among mtDNAs of A. gallica in nature. In laboratory matings of two haploid strains with different mtDNA types, a low frequency of recombination in mtDNA was detected.
RAPD marker estimation of genetic structure among isolated northern leopard frog populations in the south‐western USA
Authors: KIMBERLING D. N. , FERREIRA A. R. , SHUSTER S. M. , KEIM P.
Published: April 2008

Amphibians in the south‐western United States are currently experiencing population declines. Causal explanations for these population changes as well as the implementation of sound management practices requires an understanding of the genetic structure of natural amphibian populations. To this end, we estimated genetic differences within and among seven isolated populations of northern leopard frogs, Rana pipiens, from Arizona and southern Utah using random amplified polymorphic DNA (RAPD) analyses. Fourteen arbitrarily designed primers detected 38 polymorphic loci in 85 individual frogs. Three types of population structure were observed in this study, (i) Two populations showed low genetic diversity (D= 0.10 and 0.04) and may have been established by relatively recent events, (ii) Two were not genetically distinct and exhibited a high degree of within‐population diversity (D= 0.35). The possibility of gene flow between these populations is high due to their geographical proximity and their shared genetic structure, (iii) Three populations were genetically distinct from each other and the other populations, and exhibited intermediate within‐population variation (D= 0.19, 0.17, 0.14). Genetic distances among the seven populations ranged from 0.00 to 0.20, suggesting that some of these leopard frog populations are genetically distinct. Although based on relatively small samples, these data suggest that leopard frog populations in the south‐west are likely to represent unique genetic entities worthy of conservation. The management implications of these results are that isolated leopard frog populations should be evaluated on an individual basis to best preserve them.
Indo‐Pacific population structure and evolutionary history of the coconut crab Birgus latro
Authors: LAVERY S. , MORITZ C. , FIELDER D. R.
Published: April 2008

Mitochondrial DNA variation was used to examine population structure in a widespread, marine‐dispersed species, Birgus latro. Crabs were collected from eight locations throughout the species' Indo‐Pacific distribution. Purified mtDNA from 160 individuals was cut with five restriction enzymes, revealing high haplotype diversity (0.96) and moderate nucleotide diversity (0.75%). Island populations from the Indian Ocean (Christmas I.) and Pacific Ocean were significantly different (GST= 0.37) and had distinct mtDNA lineages with a net sequence divergence of 1.4%. Pacific island populations had diverged in a manner consistent with isolation by distance, with only the most peripheral populations being significantly different. The results for mtDNA are largely concordant with those from allozymes, although estimates of gene flow between the Indian and Pacific Oceans were much lower when based on mtDNA. The mtDNA phylogeny also permitted a deeper examination of the evolutionary and demographic history of Birgus latro. Long‐term separation of populations is evident in the complete phylogenetic subdivision of mtDNA lineages between the Indian and Pacific Ocean populations sampled. The starlike phylogeny of alleles from the Pacific suggests a rapid population expansion in the Pacific during the Pleistocene. Including information about allele phylogeny, as well as distribution and frequency, obscured contemporary population structure, but provided unique insights into the evolutionary history of the species.
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

The 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

Genetic 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

Tuatara 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

DNA 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

The 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

A 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

Analysis 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

The 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

The 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

Erodium 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

Intraspecific 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

In 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

Pyrenean 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

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

Intrasexual 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

During 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

The 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.
Protein N‐glycosylation determines functionality of the Saccharomyces cerevisiae cell wall integrity sensor Mid2p
Authors: Hutzler Franziska , Gerstl Ronald , Lommel Mark , Strahl Sabine
Published: April 2008

The fungal cell wall is a highly dynamic structure that is essential to maintain cell shape and stability. Hence in yeasts and fungi cell wall integrity is tightly controlled. The Saccharomyces cerevisiae plasma membrane protein Mid2p is a putative mechanosensor that responds to cell wall stresses and morphological changes during pheromone induction. The extracellular domain of Mid2p, which is crucial to sensing, is highly O‐ and N‐glycosylated. We showed that O‐mannosylation is determining stability of Mid2p. If and how N‐glycosylation is linked to Mid2p function was unknown. Here we demonstrate that Mid2p contains a single high mannose N‐linked glycan at position Asn‐35. The N‐glycan is located close to the N‐terminus and is exposed from the plasma membrane towards the cell wall through a highly O‐mannosylated domain that is predicted to adopt a rod‐like conformation. In contrast to O‐mannosylation, lack of the N‐linked glycan affects neither, stability of Mid2p nor distribution at the plasma membrane during vegetative and sexual growth. However, non‐N‐glycosylated Mid2p fails to perceive cell wall challenges. Our data further demonstrate that both the extent of the N‐linked glycan and its distance from the plasma membrane affect Mid2p function, suggesting the N‐glycan to be directly involved in Mid2p sensing.
The role of laccase in prostaglandin production by Cryptococcus neoformans
Authors: Erb‐Downward John R. , Noggle Rachael M. , Williamson Peter R. , Huffnagle Gary B.
Published: April 2008

Recently, it has been demonstrated that the opportunistic fungal pathogen Cryptococcus neoformans can synthesize authentic immunomodulatory prostaglandins. The mechanism by which this takes place is unclear as there is no cyclooxygenase homologue in the cryptococcal genome. In this study, we show that cryptococcal production of both PGE2 and PGF2α can be chemically inhibited by caffeic acid, resveratrol and nordihydroguaiaretic acid. These polyphenolic molecules are frequently used as inhibitors of lipoxygenase enzymes; however, blast searches of the cryptococcal genome were unable to identify any homologues of mammalian, plant or fungal lipoxygenases. Next we investigated cryptococcal laccase, an enzyme known to bind polyphenols, and found that either antibody depletion or genetic deletion of the primary cryptococcal laccase (lac1Δ) resulted in a loss of cryptococcal prostaglandin production. To determine how laccase is involved, we tested recombinant laccase activity on the prostaglandin precursors, arachidonic acid (AA), PGG2 and PGH2. Using mass spectroscopy we determined that recombinant Lac1 does not modify AA or PGH2, but does have a marked activity toward PGG2 converting it to PGE2 and 15‐keto‐PGE2. These data demonstrate a critical role for laccase in cryptococcal prostaglandin production, and provides insight into a new and unique fungal prostaglandin pathway.
The role of somatosensory cortical regions in the processing of painful gastric fundic distension: an update of brain imaging findings
Authors: Van Oudenhove L. , Dupont P. , Vandenberghe J. , Geeraerts B. , Van Laere K. , Bormans G. , Demyttenaere K. , Tack J.
Published: April 2008

Abstract  Painful gastric distension is processed in a network consisting of brainstem, thalamus, insula, anterior cingulate cortex, (lateral) orbitofrontal and prefrontal cortex, superior temporal cortex and cerebellum. However, the role of primary and secondary somatosensory cortical regions (SI/SII) in the processing of visceral sensation or pain in general and gastric sensation in particular remains unclear. The aim of this study was to localize activations in the SI/SII area from our previously published functional brain imaging studies on gastric distension more precisely, using newly available cytoarchitectonic probability maps of SI/SII, implemented in the SPM Anatomy toolbox. In healthy volunteers, we found two clusters to be overlapping with SII (mainly the OP4 subregion) and, to a lesser extent, SI, although this overlap was small in size. In functional dyspepsia patients, we found two clusters to be overlapping with SII (mainly OP4), of which the cluster in the right hemisphere also overlapped with SI. These findings were confirmed in a conjunction analysis of both groups. Activation in right SI/SII was significantly higher in healthy volunteers when formally compared to patients. These results provide more detailed information on the brain processing of gastric sensation, supporting the hypothesis that SI/SII are involved. This is in line with some previously published studies on visceral sensation, but at variance with some other studies. Methodological differences between the brain imaging studies on gastric distension may account for these somewhat discrepant findings.
Association between changes in symptoms and gastric emptying in gastroparetic patients treated with gastric electrical stimulation
Authors: Lin Z. , Hou Q. , Sarosiek I. , Forster J. , Mccallum R. W.
Published: April 2008

Abstract  To investigate whether there is an association between gastric emptying rate and symptom improvement in gastroparetic patients treated with gastric electrical stimulation (GES), we retrospectively reviewed 63 gastroparetic patients who received GES therapy for at least 1 year. Patient characteristics, seven upper gastrointestinal (GI) symptoms and 4‐h standardized gastric emptying test (GET) were evaluated at baseline and at 1 year of GES. All symptoms were significantly reduced (P < 0.001). Mean gastric retention was reduced by 7% (P = 0.102) for measurement at 4 h. Of the 63 patients, 14 had their GET normalized and 49 remained delayed after 1 year. Normalized GET patients had a similar symptom improvement as those whose GET remained delayed. Of all upper GI symptoms, the improvements in vomiting (P = 0.04), nausea (P = 0.002) and epigastric pain (P = 0.001) were significantly correlated with reduction in 4‐h gastric retention between baseline and 12 months of GES therapy for patients with normalized gastric emptying but there were no correlations with any symptoms and change in gastric emptying for those patients who remained delayed. In summary, overall gastric emptying is not significantly accelerated at 4 h after successful symptomatic improvement with GES but nausea, vomiting and epigastric pain can be correlated with normalization of GET in a subset of patients.