bluuebunny/crossref_metadata_2025_split huggingface dataset:
High genome‐wide mutation rates in vegetatively propagated bermudagrass
Authors: Caetano‐anollés G. 
Published: March 2003

AbstractA cascade DNA amplification strategy that generates arbitrary signatures from amplification profiles (ASAP) was used to measure genome‐wide mutation rates in bermudagrass (Cynodon). ASAP quantified nucleotide changes that were induced by irradiation, genetic instabilities and normal vegetative growth of cultivars and accessions of sterile interspecific hybrids. DNA sequence divergence between cultivar ‘Tifway’ and its γ radiation‐induced mutant ‘Tifway II’ (0.70 ± 0.66%) was comparable to estimates in radiation‐induced mutants and spontaneous sports of chrysanthemum (Chrysanthemum morifolium Ramat.). A similar divergence in sequence (0.95 ± 0.20%) was observed in the pairwise comparison of 17 nondisjunctive ‘Tifgreen’ and ‘Tifdwarf’ accessions. Mutation during normal Tifdwarf vegetative growth was evaluated by planting sprigs and sampling their offspring. Somatic sequence divergence levels (0.004 ± 0.007%) resulted in a mutation rate of 1.05 × 10−8 per nucleotide per generation, assuming that a bermudagrass sprig constitutes a generation of growth. These rates were comparable to those found in germinal cells and individuals of either human or Drosophila melanogaster, supporting the notion that eukaryotic evolution is generation rather than time dependent. The high accumulation of somatic mutations (10 per triploid genome) is consistent with a model whereby mutation load in a population exhibiting obligate vegetative reproduction is substantially higher than in a population under sexual or asexual reproduction. These constraints could be the cause of reported genetic instabilities in the Tifgreen–Tifdwarf complex. Finally, a long‐term rate measured across accessions and indicative of the accumulation of mutations in 17 Tifgreen–Tifdwarf populations (µ = 1.02 × 10−8 per nucleotide per generation) was strikingly congruent with the bermudagrass vegetative mutation rate, suggesting absence of evolutionary constraints in the sampled genomic regions. Mutation rates calculated from across‐accesions divergence estimates (5.18 ± 0.53%) indicated that plant material was evolving 100 times faster (3.8 × 10−7 changes per nucleotide per year) than a molecular clock rate estimate for grasses, probably resulting from the compound effect of clonal growth and life span of the hybrid plant material.
Divergence in the chloroplast genome and nuclear rDNA of the rare Western Australian plantLambertia orbifoliaGardner (Proteaceae)
Authors: Byrne M. , Macdonald B. , Coates D. 
Published: March 2003

AbstractThe population genetic structure of the Australian plantLambertia orbifoliawas investigated for chloroplast DNA (cpDNA) and rDNA based on restriction fragment length polymorphism. Variation was assessed in 14–20 individuals from six populations with probes covering the majority of the chloroplast genome and the whole rRNA gene unit. For cpDNA, eight mutations were detected which were distributed over five haplotypes. Nucleotide diversity in the species was high and the majority of this diversity was distributed between populations with diversity within populations restricted to a single population. There was significant differentiation between the two regions in the species distribution with the Narrikup region being distinguished by a single haplotype that was characterized by six unique mutations. Variation in rDNA was detected with three gene length variants present in most individuals. However, the Narrikup region was characterized by homogenization of the gene unit to a single length variant in all individuals. The divergence of the Narrikup region suggests that the disjunction in the species distribution has been present for a long time and the two regions represent separate evolutionary lineages.
Genetic variation in an apomictic grass, Heteropogon contortus, in the Hawaiian Islands
Authors: Carino Debbie A. , Daehler Curtis C. 
Published: March 2003

AbstractRandom amplified polymorphic DNA (RAPD) markers were used to assess genetic variation within and among Hawaiian populations of an apomictic grass, Heterogopon contortus (pili grass). From among 56 individuals sampled from six populations on O’ahu and Hawai’i, 55 unique genotypes were detected using 33 polymorphic markers. This lack of uniformity among individuals may indicate frequent sexual reproduction in these populations. Analysis of molecular variance (amova) revealed significant variation among populations (30.2%), but higher levels of variation within populations (68.1%). Cluster analysis revealed a high degree of clustering for most populations, but populations from different islands did not cluster together. The presence of among‐population differentiation but lack of between‐island differentiation may suggest that H. contortus was an early Polynesian introduction to the Hawaiian Islands.
Genetic characterization of heather (Calluna vulgaris (L.) Hull) subject to different management regimes across Great Britain
Authors: Meikle A. , Paterson S. , Finch R. P. , Marshall G. , Waterhouse A. 
Published: March 2003

AbstractHeather plants were collected from 34 populations in Great Britain, which differed according to their geographical location and associated management histories. Comparisons of differential grazing regimes were made across 10 sites in the first year of study, whereas the influence of differential burning regimes was considered at four sites during the second year. The extent of genetic variation, both within and between the selected heather populations, was examined using polymerase chain reaction (PCR)‐based DNA fingerprinting methodologies. Initially, high genetic variation within populations obscured differences between populations. Heather stands that were geographically close proved to be genetically similar. Site latitude and longitude were strongly associated with genetic differences between heather populations; however, a range of grazing and burning management treatments had no consistent effect upon genetic diversity. The results represent the first national survey of genetic variation at the DNA level within UK populations of this important heathland species. They provided insights into the genetic structure of heather‐dominated heathlands, revealing a lack of clonal dominance within populations, but rather a much more varied genetic makeup than might have been expected given the species’ ability to propagate vegetatively. The processes that influence genetic diversity in heather populations are discussed, and the potential role of molecular techniques in heathland conservation is considered.
Hypothesis testing with the similarity index
Authors: Leonard A. C. , Franson S. E. , Hertzberg V. S. , Smith M. K. , Toth G. P. 
Published: March 2003

AbstractMultilocus DNA fingerprinting methods have been used extensively to address genetic issues in wildlife populations. Hypotheses concerning population subdivision and differing levels of diversity can be addressed through the use of the similarity index (S), a band‐sharing coefficient, and many researchers construct hypothesis tests with S based on the work of Lynch. It is shown in the present study, through mathematical analysis and through simulations, that estimates of the variance of a mean S based on Lynch’s work are downwardly biased. An unbiased alternative is presented and mathematically justified. It is shown further, however, that even when the bias in Lynch’s estimator is corrected, the estimator is highly imprecise compared with estimates based on an alternative approach such as ‘parametric bootstrapping’ of allele frequencies. Also discussed are permutation tests and their construction given the interdependence of Ss which share individuals. A simulation illustrates how some published misuses of these tests can lead to incorrect conclusions in hypothesis testing.
Molecular evidence for multiple infections of a new subgroup ofWolbachiain the European raspberry beetleByturus tomentosus
Authors: Malloch G. , Fenton B. , Butcher R. D. J. 
Published: March 2003

AbstractWolbachia, a group of maternally inherited intracellular parasitic bacteria, alter host reproduction, including the induction of thelytokous parthenogenesis, feminization of genetic males, son killing and, most commonly, the induction of cytoplasmic incompatibility (CI), in a diverse array of arthropods. CI can result in infertility and has attracted attention because of its potential in biological control and as an agent in speciation. Although there has been some analysis of overall infection rates in arthropods and within individual insect orders, there has been little exploration of within‐species variation. In this study, primers specific for theftsZgene ofWolbachiawere used to amplify it from different geographical samples of the European raspberry beetle (Byturus tomentosus), confirming the presence ofWolbachia. More than 99% of UK individuals were found to be infected withWolbachiaand 97% of theseB. tomentosusbeetles harboured multiple infections. Preliminary analysis ofB. tomentosusbeetles from continental European populations revealed a lower level of infection (24%) than those from the UK. Phylogenetic analysis using theftsZDNA sequences placesWolbachiafromB. tomentosusinto a new clade (Abt) within the A division, with some revisions to the existingWolbachiaphylogeny.
Mitochondrial DNA sequences support allozyme evidence for cryptic radiation of New Zealand Peripatoides (Onychophora)
Authors: Trewick S. A. 
Published: March 2003

AbstractA combination of single‐strand conformation polymorphism analysis (SSCP) and sequencing were used to survey cytochrome oxidase I (COI) mitochondrial DNA (mtDNA) diversity among New Zealand ovoviviparous Onychophora. Most of the sites and individuals had previously been analysed using allozyme electrophoresis. A total of 157 peripatus collected at 54 sites throughout New Zealand were screened yielding 62 different haplotypes. Comparison of 540‐bp COI sequences from Peripatoides revealed mean among‐clade genetic distances of up to 11.4% using Kimura 2‐parameter (K2P) analysis or 17.5% using general time‐reversible (GTR + I + Γ) analysis. Phylogenetic analysis revealed eight well‐supported clades that were consistent with the allozyme analysis. Five of the six cryptic peripatus species distinguished by allozymes were confirmed by mtDNA analysis. The sixth taxon appeared to be paraphyletic, but genetic and geographical evidence suggested recent speciation. Two additional taxa were evident from the mtDNA data but neither occurred within the areas surveyed using allozymes. Among the peripatus surveyed with both mtDNA and allozymes, only one clear instance of recent introgression was evident, even though several taxa occurred in sympatry. This suggests well‐developed mate recognition despite minimal morphological variation and low overall genetic diversity.
Genetic subdivision, glacial refugia and postglacial recolonization in the golden‐striped salamander, Chioglossa lusitanica (Amphibia: Urodela)
Authors: Alexandrino J. , Froufe E. , Arntzen J. W. , Ferrand N. 
Published: March 2003

AbstractThe golden‐striped salamander (Chioglossa lusitanica) is an ecologically specialized species, endemic to north‐western Iberia. Patterns of genetic variation were assessed at seven polymorphic enzyme loci and one mitochondrial DNA (mtDNA) marker (cytochrome b) in 17 populations across its range. Estimates of enzyme genetic diversity revealed a high degree of genetic subdivision (FST = 0.68), mainly attributable to the existence of two groups of populations. The groups were located, respectively, north and south of the Mondego River, indicating that this river coincided with a major historical barrier to gene flow. A significant decrease in genetic variability from the Mondego northwards was associated with the Douro and Minho rivers. mtDNA sequence variation revealed a congruent pattern of two haplotype groups (d = 2.2%), with a geographical distribution resembling that of allozymes. The pattern and depth of genetic variation is consistent with the following hypotheses: (i) subdivision of an ancestral range of the species prior to the middle Pleistocene; (ii) secondary contact between populations representing historical refugia; (iii) relatively recent range expansion giving rise to the northern part of the species range; and (iv) loss of genetic variation through founder effects during range expansion across major rivers.
Clonal structure in a dwarf bamboo (Sasa senanensis) population inferred from amplified fragment length polymorphism (AFLP) fingerprints
Authors: Suyama Y. , Obayashi K. , Hayashi I. 
Published: March 2003

AbstractAmplified fragment length polymorphism (AFLP) fingerprints were used to reveal clonal structure of a dense population of dwarf bamboo, Sasa senanensis, in a 10‐ha study plot at Sugadaira Montane Research Center, University of Tsukuba, Nagano, Japan. We generated AFLP fingerprints for 51 leaf samples, collected at 50 m intervals, using three selective primer pairs. A total of 135–166 fragments were detected per sample, and 22 different fingerprints were identified based on 24–83 differing fragments. Our results demonstrate that the S. senanensis population in our plot consists of at least 22 clones and that the largest single clone occurs over a distance of about 300 m. Furthermore, the clone distribution pattern implies a relationship between site quality and clonal structure.
Phylogeography and population structure of an ecotonal marsupial,Bettongia tropica, determined using mtDNA and microsatellites
Authors: Pope L. C. , Estoup A. , Moritz C. 
Published: March 2003

AbstractThe northern bettong,Bettongia tropica, is an endangered species of Potoroidae with a restricted distribution in the wet tropics of north Queensland, Australia. The species is only found within a thin strip of sclerophyll forest along the western margin of rainforest. This tight association with rainforest boundaries is predicted to have resulted in population isolation as rainforest contracted during the Pleistocene, though some have proposed that the northern bettong was not present in the wet tropics until the late Pleistocene. The dispersal ability of the species, and of the family, is not known. This study examined gene flow among populations within areas of continuous habitat complemented by a broader analysis of phylogeography. Individuals trapped at each of the four known regions (one region was subsampled at three different sites), were sequenced for 547 base pairs of the mitochondrial DNA (mtDNA) control region and typed for seven microsatellite loci. The mtDNA phylogeny showed congruence with a biogeographical hypothesis, a relatively deep split suggesting historical isolation in separate northern and southern refugia. The two divergent clades were both present within the Lamb Range, indicating an expansion from these refuges and subsequent admixture at one site. mtDNA allele frequencies indicated relatively limited gene flow within the Lamb Range over distances as short as nine km. Tests of population divergence using microsatellites (FSTand assignment tests) strongly supported this result. A molecular signal indicative of a recent bottleneck was unexpectedly detected in one of the Lamb Range subpopulations. This lead us to examine the behaviour of the statistics used in this bottleneck test under a linear stepping‐stone model with varying migration rates. We found that it may be more difficult to detect molecular signatures for recent bottlenecks under conditions of very low migration rates than for isolated populations and, conversely, that ‘false’ bottleneck signatures may be observed at higher migration rates. The Lamb RangeFSTestimate clearly fell within the category of potentially ‘false’ bottleneck signals. Despite relatively limited gene flow, evidence for asymmetric dispersal suggests more complicated population dynamics than a simple linear stepping‐stone model.
Colonization, extinction, and phylogeographic patterning in a freshwater crustacean
Authors: Cox Andrea J. , Hebert Paul D. N. 
Published: March 2003

AbstractPhylogeographic analyses have revealed the importance of Pleistocene vicariance events in shaping the distribution of genetic diversity in freshwater fishes. However, few studies have examined the patterning of variation in freshwater organisms with differing dispersal syndromes and life histories. The present investigation addresses this gap, examining the phylogeography of Sida crystallina, a species whose production of diapausing eggs capable of passive dispersal was thought to constrain its regional genetic differentiation. By contrast, the present analysis has revealed deep allozyme and cytochrome oxidase I mitochondrial DNA divergence between populations from North America and Europe. Moreover, North American populations are separated into four allopatric assemblages, whose distribution suggests their derivation from different Pleistocene refugia. These lineages show higher haplotype diversity and deeper sequence divergence than those of any fish from temperate North America. Its distinctive life history traits have evidently sheltered lineages of Sida from extinction, contributing to a remarkably comprehensive and high resolution phylogeographic record.
Molecular ecology of social behaviour: analyses of breeding systems and genetic structure
Authors: Ross Kenneth G. 
Published: March 2003

AbstractMolecular genetic studies of group kin composition and local genetic structure in social organisms are becoming increasingly common. A conceptual and mathematical framework that links attributes of the breeding system to group composition and genetic structure is presented here, and recent empirical studies are reviewed in the context of this framework. Breeding system properties, including the number of breeders in a social group, their genetic relatedness, and skew in their parentage, determine group composition and the distribution of genetic variation within and between social units. This group genetic structure in turn influences the opportunities for conflict and cooperation to evolve within groups and for selection to occur among groups or clusters of groups. Thus, molecular studies of social groups provide the starting point for analyses of the selective forces involved in social evolution, as well as for analyses of other fundamental evolutionary problems related to sex allocation, reproductive skew, life history evolution, and the nature of selection in hierarchically structured populations. The framework presented here provides a standard system for interpreting and integrating genetic and natural history data from social organisms for application to a broad range of evolutionary questions.
Using phylogeographic analyses of gene trees to test species status and processes
Authors: Templeton Alan R. 
Published: March 2003

AbstractA gene tree is an evolutionary reconstruction of the genealogical history of the genetic variation found in a sample of homologous genes or DNA regions that have experienced little or no recombination. Gene trees have the potential of straddling the interface between intra‐ and interspecific evolution. It is precisely at this interface that the process of speciation occurs, and gene trees can therefore be used as a powerful tool to probe this interface. One application is to infer species status. The cohesion species is defined as an evolutionary lineage or set of lineages with genetic exchangeability and/or ecological interchangeability. This species concept can be phrased in terms of null hypotheses that can be tested rigorously and objectively by using gene trees. First, an overlay of geography upon the gene tree is used to test the null hypothesis that the sample is from a single evolutionary lineage. This phase of testing can indicate that the sampled organisms are indeed from a single lineage and therefore a single cohesion species. In other cases, this null hypothesis is not rejected due to a lack of power or inadequate sampling. Alternatively, this null hypothesis can be rejected because two or more lineages are in the sample. The test can identify lineages even when hybridization and lineage sorting occur. Only when this null hypothesis is rejected is there the potential for more than one cohesion species. Although all cohesion species are evolutionary lineages, not all evolutionary lineages are cohesion species. Therefore, if the first null hypothesis is rejected, a second null hypothesis is tested that all lineages are genetically exchangeable and/or ecologically interchangeable. This second test is accomplished by direct contrasts of previously identified lineages or by overlaying reproductive and/or ecological data upon the gene tree and testing for significant transitions that are concordant with the previously identified lineages. Only when this second null hypothesis is rejected is a lineage elevated to the status of cohesion species. By using gene trees in this manner, species can be identified with objective, a priori criteria with an inference procedure that automatically yields much insight into the process of speciation. When one or more of the null hypotheses cannot be rejected, this procedure also provides specific guidance for future work that will be needed to judge species status.
Mitochondrial DNA variation and GIS analysis confirm a secondary origin of geographical variation in the bushcricketEphippiger ephippiger(Orthoptera: Tettigonioidea), and resurrect two subspecies
Authors: Ritchie Michael G. , Kidd David M. , Gleason Jennifer M. 
Published: March 2003

AbstractGeographic variation within species can originate through selection and driftin situ(primary variation) or from vicariant episodes (secondary variation). Most patterns of subspecific variation within European flora and fauna are thought to have secondary origins, reflecting isolation in refugia during Quaternary ice ages. The bushcricketEphippiger ephippigerhas an unusual pattern of geographical variability in morphology, behaviour and allozymes in southern France, which has been interpreted as reflecting recent primary origins rather than historical isolation. Re‐analysis of this variation using Geographical Information Systems (GIS) suggests a possible zone of hybridization within a complex pattern of geographical variation. Here we produce a genetic distance matrix from restriction fragment length polymorphism (RFLP) bandsharing of an approximately 4.5 kb fragment of mitochondrial DNA (mtDNA), and compare this with predictions resulting from the GIS analysis. The mtDNA variation supports a postglacial origin of geographical variation. Partial Mantel test comparisons of genetic distances with matrices of geographical distance, relevant environmental characteristics and possible refugia show refugia to be the best predictors of genetic distance. There is no evidence to support isolation by distance. However, environmental contrasts do explain significant variation in genetic distance after allowing for the effect of refugial origin. Also, a neighbour‐joining tree has a major division separating eastern and western forms. We conclude that the major source of variation within the species is historical isolation in glacial refugia, but that dispersal, hybridization and selection associated with environmental features has influenced patterns of mtDNA introgression. At least two valid subspecies can be defined.