bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular evidence of natural hybridization between Abies veitchii and A. homolepis (Pinaceae) revealed by chloroplast, mitochondrial and nuclear DNA markers
Authors: Isoda K. , Shiraishi S. , Watanabe S. , Kitamura K. 
Published: March 2003

AbstractSub‐alpine Abies veitchii and A. homolepis are distributed in the central part of Honshu Island, Japan, and their habitats are segregated vertically. These species sometimes form a mixed forest in the overlapping area of the two species, that is, in the upper limit of the A. homolepis habitat and the lower limit of A. veitchii. These species have been considered to be distantly related because they were classified into different sections by most conventional classifications. No natural hybridization has been reported between the two species. The aim of this study was to demonstrate, through the use of molecular markers, whether natural hybridization takes place between these two species at two experimental sites on Mt. Fuji, where the species occur naturally. DNA markers from paternally inherited chloroplast DNA (cpDNA), maternally inherited mitochondrial DNA (mtDNA) and biparentally inherited nuclear DNA (nDNA), were used for this study. As organelle DNA markers, polymerase chain reaction–single strand conformation polymorphism (PCR–SSCP) markers were developed to determine the maternal and paternal species for each individual. Two of 334 individuals possessed a cpDNA haplotype derived from A. homolepis and a mtDNA haplotype from A. veitchii. Furthermore, the nDNA of these two individuals was analysed using the random amplified polymorphic DNA (RAPD) assay to investigate their genomic composition. RAPD analysis indicated that the nuclear genomes of the two individuals were derived from both species. We conclude that A. veitchii and A. homolepis produce natural hybrids, and that their systematic relationship should be re‐evaluated.
Do Wolbachia infections play a role in unidirectional incompatibilities in a field cricket hybrid zone?
Authors: Mandel Mark J. , Ross Charles L. , Harrison Richard G. 
Published: March 2003

AbstractTwo closely related field crickets, Gryllus firmus and G. pennsylvanicus, hybridize along an extensive north–south zone in the eastern United States. Crosses between G. firmus males and G. pennsylvanicus females produce viable and fertile F1, but the reciprocal cross consistently fails to produce offspring. Wolbachia, a bacterial parasite of arthropods that causes unidirectional incompatibilities in a variety of insect species, has been suggested as the cause of the observed incompatibility between G. pennsylvanicus and G. firmus. We examine the presence/absence of Wolbachia strains, defined by sequencing the ftsZ gene, in four cricket populations from the north‐eastern United States. Most G. firmus individuals are infected (100% in Guilford, Connecticut; 65% in Seaside Park, New Jersey) and > 95% of those infected harbour a single strain of Wolbachia. All individuals in G. pennsylvanicus populations (Ithaca, New York; Sharon, Connecticut) are infected; the majority of individuals carry a second strain of Wolbachia, but a significant fraction carry the same strain found commonly in G. firmus. The presence of an apparently identical Wolbachia strain in crickets of both species means that some crosses between G. pennsylvanicus males and G. firmus females should be compatible. We have no evidence of such compatibility. Furthermore, if Wolbachia infections are responsible for the observed incompatibility between species, then incompatibilities must also exist within G. pennsylvanicus, because this species harbours both Wolbachia strains. Although some single pair crosses within G. pennsylvanicus do fail to produce offspring, the proportion is lower than expected if Wolbachia were responsible. Therefore, Wolbachia is unlikely to be involved in reproductive isolation between the two cricket species.
Genetic polymorphism in Gymnodinium galatheanum chloroplast DNA sequences and development of a molecular detection assay
Authors: Tengs Torstein , Bowers Holly A. , Ziman Andrew P. , Stoecker Diane K. , Oldach David W. 
Published: March 2003

AbstractNuclear and chloroplast‐encoded small subunit ribosomal DNA sequences were obtained from several strains of the toxic dinoflagellate Gymnodinium galatheanum. Phylogenetic analyses and comparison of sequences indicate that the chloroplast sequences show a higher degree of sequence divergence than the nuclear homologue. The chloroplast sequences were chosen as targets for the development of a 5′–3′ exonuclease assay for detection of the organism. The assay has a very high degree of specificity and has been used to screen environmental water samples from a fish farm where the presence of this dinoflagellate species has previously been associated with fish kills. Various hypotheses for the derived nature of the chloroplast sequences are discussed, as well as what is known about the toxicity of the species.
Spatial population structure in a patchily distributed beetle
Authors: Roslin Tomas 
Published: March 2003

AbstractThe dynamics and evolution of populations will critically depend on their spatial structure. Hence, a recent emphasis on one particular type of structure — the metapopulation concept of Levins — can only be justified by empirical assessment of spatial population structures in a wide range of organisms. This paper focuses onAphodius fossor, a dung beetle specialized on cattle pastures. An agricultural database was used to locate nearly 50 000 local populations ofA. fossorin Finland. Several independent methods were then used to quantify key processes in this vast population system. Allozyme markers and mitochondrial DNA (mtDNA) sequences were applied to examine genetic differentiation of local populations and to derive indirect estimates of gene flow. These estimates were compared to values expected on the basis of direct observations of dispersing individuals and assessments of local effective population size. Molecular markers revealed striking genetic homogeneity inA. fossor.Differentiation was only evident in mtDNA haplotype frequencies between the isolated Åland islands and the Finnish mainland. Thus, indirect estimates of gene flow agreed with direct observations that local effective population size inA. fossoris large (hundreds of individuals), and that in each generation, a substantial fraction (approximately one‐fifth) of the individuals move between populations. Large local population size, extreme haplotype diversity and a high regional incidence ofA. fossorall testify against recurrent population turnover. Taken together, these results provide strong evidence that the whole mainland population ofA. fossoris better described as one large ‘patchy population’, with substantial movement between relatively persistent local populations, than as a classical metapopulation.
A microbial population–species interface: nested cladistic and coalescent inference with multilocus data
Authors: Carbone I. , Kohn L. M. 
Published: March 2003

AbstractUsing sequence data from seven nuclear loci in 385 isolates of the haploid, plant parasitic, ascomycete fungus, Sclerotinia, divergence times of populations and of species were distinguished. The evolutionary history of haplotypes on both population and species scales was reconstructed using a combination of parsimony, maximum likelihood and coalescent methods, implemented in a specific order. Analysis of site compatibility revealed recombination blocks from which alternative (marginal) networks were inferred, reducing uncertainty in the network due to recombination. Our own modifications of Templeton and co‐workers’ cladistic inference method and a coalescent approach detected the same phylogeographic processes. Assuming neutrality and a molecular clock, the boundary between divergent populations and species is an interval of time between coalescence (to a common ancestor) of populations and coalescence of species.
Lack of molluscan host diversity and the transmission of an emerging parasitic disease in Bolivia
Authors: Meunier C. , Tirard, C. , Hurtrez‐Boussès S. , Durand P. , Bargues M. D. , Mas‐Coma S. , Pointier J. P. , Jourdane J. , Renaud F. 
Published: March 2003

AbstractFasciolosis is a re‐emerging parasitic disease that affects an increasing number of people in developing countries. The most severe endemic affects the Bolivian Altiplano, where the liver fluke (Fasciola hepatica) and its hermaphroditic snail host,Lymnaea truncatula,have been introduced from Europe. To achieve a better understanding of the epidemiological situation and the consequences of the colonization event of this invasive species, genetic analysis of Bolivian snail populations was needed. Here we compare the genetic diversity and population structure of snail samples from the Bolivian Altiplano with samples from the Old World at six polymorphic microsatellite loci. Whereas some variability exists in the snail populations from the Old World, we observe only a single genotype ofL. truncatulain the Bolivian Altiplano. We discuss the possible explanations for such a reduction in genetic variability, and, given the high natural parasitism pressures exerted on the snail populations, we discuss the relevance of this result for host–parasite interactions.
Microsatellite variation in the yellowhammer Emberiza citrinella: population structure of a declining farmland bird
Authors: Lee Patricia L. M. , Bradbury Richard B. , Wilson Jeremy D. , Flanagan Nicola S. , Richardson Lynne , Perkins Allan J. , Krebs John R. 
Published: March 2003

AbstractIn recent years, there has been much concern in the UK about population declines of widespread species in agricultural habitats. Conservation‐orientated research on declining birds has focused on vital rates of survival and productivity. However, the environmental factors which may influence movements between populations of widespread species is poorly understood. Population genetic structure is an indirect description of dispersal between groups of individuals. To attempt to develop an understanding of genetic structuring in a widespread, but declining, farmland bird, we therefore investigated the yellowhammer, Emberiza citrinella, population in England and Wales using microsatellite data. Our first aim was to investigate whether there was genetic substructuring in the population. A second aim was to investigate if there was a relationship between genetic distances and various environmental variables. Finally, we analysed the microsatellite data for evidence of loss of genetic variation due to population decline. Our data showed a slight but significant structure within the yellowhammer population. This therefore cannot be considered a panmictic population. Our example from South Cumbria implies that high‐altitude barriers may have a slight influence on population structure. However, on the whole, genetic distances between sample sites were not significantly correlated with geographical distances, degrees of population connectivity, high altitudes, or differences in precipitation between sites. Finally, we detected departures from mutation‐drift equilibrium (excess heterozygosity), which is indicative of a loss of genetic variation through recent decline.
Distribution of individual inbreeding coefficients, relatedness and influence of stocking on native anadromous brown trout (Salmo trutta) population structure
Authors: Ruzzante D. E. , Hansen M. M. , Meldrup D. 
Published: March 2003

AbstractWe examined polymorphism at seven microsatellite loci in 4023 brown trout (Salmo trutta) collected from 32 tributaries to the Limfjord, Denmark (~200 km) and from two hatcheries used for stocking. Populations differ in their estimated sizes and stocking histories. Mean individual inbreeding coefficients do not differ among locations within rivers. Relatedness varies between sites within rivers indicating varied local dynamics at a very small geographical scale. Relatedness is sometimes lower than expected among an equal number of simulated individuals with randomized genotypes, suggesting structure within locations. Five per cent of the genetic variance is distributed among rivers (FST = 0.049), but in the western, less heavily stocked, area of the Limfjord a higher proportion of the genetic variance is distributed among rivers than among locations within rivers. The reverse is true of the eastern, more heavily stocked, area of the Limfjord. Here, a higher proportion of the genetic variance is distributed among locations within rivers than among rivers. Assignment tests reveal that the majority of trout (mean 77% of all fish) are more probably of local origin than hatchery origin but this proportion varies regionally, with rivers in the western area of the Limfjord showing a relatively high (mean 88%) and those in the eastern area showing a relatively low (mean 72%) proportion of locally assigned trout. These results can be interpreted as reflecting stocking impact. Also, the proportion of locally assigned trout correlates with the populations’ stocking histories, with rivers presently subjected to stocking (hatchery trout) showing low (mean ~0.73), and rivers where stocking was discontinued showing high (mean ~0.84) proportions of local fish, probably reflecting lower survival of hatchery than of wild trout. There is evidence for isolation by distance at a large geographical scale when individual river populations are pooled into nine geographical regions but not at a small geographical scale when populations are considered individually. We reject the null hypothesis that stocking has had no impact on population structure but the relatively high proportion of locally assigned trout in populations where stocking with domestic fish no longer takes place suggests limited long‐term success of stocking.
Detection of genetically divergent clone mates in apomictic dandelions
Authors: Mes Ted H. M. , Kuperus P. , Kirschner J. , Štepánek J. , Štorchová H. , Oosterveld P. , Den Nijs J. C. M. 
Published: March 2003

AbstractThis study aims to identify genetically diverged clone mates in apomictic dandelions. Clone mates are defined as individuals that may have diverged as a result of mutation accumulation and that have undergone only clonal reproduction since their most recent common ancestor. Based on distinctive morphology and an aberrant and rare chloroplast haplotype, northwest European individuals of Taraxacum section Naevosa are well suited for the detection of clonal lineages in which mutation has occurred. In the case of strictly clonal reproduction, nuclear genetic variability was expected to be hierarchically organized. Nucleotide polymorphisms in internal transcribed spacer (ITS) sequences, however, were incompatible with a clonal structure of the Norwegian individuals, probably due to persistent ancestral polymorphisms that pre‐date the origin of the Naevosa clone. This interpretation is supported by the presence of ITS variants in section Naevosa that were also found in distantly related dandelions. In contrast to the ITS sequence data, amplified fragment length polymorphisms (AFLPs), isozymes and microsatellites strongly supported the contention of prolonged clonal reproduction and mutation accumulation in Norwegian Naevosa. Because these markers are generally considered to be more variable and more rapidly evolving than ITS sequences, mutations in these markers probably evolved after the origin of the clone. Within the Norwegian clone, a surprising number of markers distinguished the clone mates. As a consequence, incorporation of mutation in the detection of clone mates is anticipated to have a big impact on estimates of size, geographical range and age of clones as well as on experimental designs of studies of clonal plants.
Genetic variation in original and colonizing Drosophila buzzatii populations analysed by microsatellite loci isolated with a new PCR screening method
Authors: Frydenberg J. , Pertoldi C. , Dahlgaard J. , Loeschcke V. 
Published: March 2003

AbstractA new polymerase chain reaction‐based screening method for microsatellites is presented. Using this method, we isolated 12 microsatellite loci from Drosophila buzzatii, two of which were X‐linked. We applied the other 10 microsatellite loci to the analysis of genetic variation in five natural populations of D. buzzatii. Two populations were from the species’ original distribution in Argentina, whereas the other three were from Europe (two) and Australia that were colonized 200 and 65 years ago, respectively. Allelic variation was much larger in the original populations than in the colonizing ones and there was a tendency to decreased heterozygosity in the colonizing populations. We used three different statistical procedures for detecting population bottlenecks. All procedures suggested that the low variability in the populations in the Old World was not the result of the recent population decline, but was due to a founder effect followed by a population expansion. In fact, one procedure which detects population expansions and declines based on the genealogical history of microsatellite data suggested that an expansion had taken place in all the colonized populations.
Spatial autocorrelation and linkage of Mendelian RAPD markers in a population of Picea abies Karst
Authors: Bucci Gabriele , Menozzi Paolo 
Published: March 2003

AbstractThe spatial clustering of single‐ and di‐locus genotypes in a natural, continuous population of Norway spruce was investigated using 69 Mendelian Random Amplified Polymorphic DNA (RAPD) markers that covered about 15% of the species’ genome, and whose linkage relationships were known. Spatial autocorrelation techniques and randomization tests, applied to both single‐ and di‐locus genotypes, revealed a weak, though significant, spatial structure at the scale 0–200 m (5% of single‐locus and 7% of di‐locus genotypes). To assess the relative importance of isolation by distance and linkage between markers on their spatial genetic structuring, we grouped joins between sampled trees into ‘equivalence categories’ expected to show similar, specific patterns of spatial distribution under isolation by distance. Results from both single‐ and di‐locus analyses were consistent with the existence of patches of like homozygotes (about 8% and 11% of loci at the single‐ and di‐locus level, respectively) surrounded by a mix of like heterozygotes. Similar structuring has been predicted by simulation models under isolation by distance and selective neutrality. Overall, linkage between markers accounted for an increase of spatial clumping of di‐locus genotypes involving tightly linked loci with recombination fractions up to 0.1, a consequence of limited, stochastic spread of single‐locus genotypes in space. Our results support the hypothesis that isolation by distance and linkage have a small, though significant, effect even within continuous forest tree populations. In general, the spatial distribution of multilocus genotypes within populations should be interpreted with caution when linkage relationships among the markers used are unknown.
Molecular analysis of a 11 700‐year‐old rodent midden from the Atacama Desert, Chile
Authors: Kuch Melanie , Rohland Nadin , Betancourt Julio L. , Latorre Claudio , Steppan Scott , Poinar Hendrik N. 
Published: March 2003

AbstractDNA was extracted from an 11 700‐year‐old rodent midden from the Atacama Desert, Chile and the chloroplast and animal mitochondrial DNA (mtDNA) gene sequences were analysed to investigate the floral environment surrounding the midden, and the identity of the midden agent. The plant sequences, together with the macroscopic identifications, suggest the presence of 13 plant families and three orders that no longer exist today at the midden locality, and thus point to a much more diverse and humid climate 11 700 years ago. The mtDNA sequences suggest the presence of at least four different vertebrates, which have been putatively identified as a camelid (vicuna), two rodents (Phyllotis and Abrocoma), and a cardinal bird (Passeriformes). To identify the midden agent, DNA was extracted from pooled faecal pellets, three small overlapping fragments of the mitochondrial cytochrome b gene were ampli‐fied and multiple clones were sequenced. These results were analysed along with com‐plete cytochrome b sequences for several modern Phyllotis species to place the midden sequence phylogenetically. The results identified the midden agent as belonging to an ancestral P. limatus. Today, P. limatus is not found at the midden locality but it can be found 100 km to the north, indicating at least a small range shift. The more extensive sampling of modern Phyllotis reinforces the suggestion that P. limatus is recently derived from a peripheral isolate.
Complex patterns of mating revealed in a Eucalyptus regnans seed orchard using allozyme markers and the neighbourhood model
Authors: Burczyk J. , Adams W. T. , Moran G. F. , Griffin A. R. 
Published: March 2003

AbstractThe neighbourhood model apportions offspring of individual mother plants to self‐fertilization, outcrossing to males within a circumscribed area around the mother plant (the neighbourhood), and outcrossing to males outside the neighbourhood. Formerly the model was applied only to haploid pollen gametes in the offspring of conifers, but is extended so that it can be used with genotypic data from diploid offspring of both angiosperms and gymnosperms. In addition, it is shown that the mating parameters can be estimated without independent estimates of allele frequencies in the pollen pools outside the neighbourhood; thus the model might be applied effectively to natural populations exposed to unknown external pollen sources. Parameters of the neighbourhood mating model were estimated for a 10‐year‐old seed orchard population of the insect‐pollinated tree, Eucalyptus regnans, in southeast Australia, which contained a mixture of two geographical provenances (Victoria and Tasmania). The mating patterns revealed were complex. Crosses between trees of the same provenance occurred three times more often than crosses between trees of different provenances. Levels of self‐fertilization and patterns of mating within neighbourhoods were influenced by provenance origin, crop fecundity and orchard position (central vs. edge) of mother trees. Gene dispersal, however, was extensive, with approximately 50% of effective pollen gametes coming from males more than 40 m away from mother trees (average distance between neighbouring trees was 7.4 m). Thus, insect pollinators are efficient promoters of cross‐fertilization in this orchard, with the result that the effective number of males mating with each female is large.