bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microsatellite DNA analysis of genetic effects of harvesting in old‐growth eastern white pine (Pinus strobus) in Ontario, Canada
Authors: Rajora O. P. , Rahman M. H. , Buchert G. P. , Dancik B. P. 
Published: March 2003

AbstractMicrosatellite DNA markers from 13 simple sequence repeat (SSR) loci were used to compare genetic diversity between preharvest pristine and postharvest residual gene pools of two adjacent virgin, old‐growth (≈ 250 years) stands of eastern white pine (Pinus strobus L.) in Ontario. There was concurrence in genetic diversity changes in the postharvest gene pools of the two stands. The total and mean numbers of alleles detected in each stand were reduced by ≈ 26% after tree density reductions of ≈ 75%. Approximately 18 and 21% of the low‐frequency (0.25 > P ≥ 0.01) alleles and 76 and 92% of the rare (P < 0.01) alleles were lost from residual stands A and B, respectively, after harvesting. Multilocus gametic diversity was reduced by 38 and 85% and genotype additivity by ≈ 50% in the residual stands after harvesting. Latent genetic potential of each stand was reduced by ≈ 40%. Although heterozygosity was reduced (1–5%) in the postharvest residual stands, the reductions were not substantial and not comparable to those using other genetic diversity measures. The reductions in genetic diversity measures were slightly higher than those theoretically expected in postbottleneck populations according to drift theory. In the absence of substantial gene migration that could ameliorate the genetic losses, the ability of the postharvest white pine gene pools to adapt to changing environmental and disease conditions may have been compromised. The microsatellite DNA results for genetic effects of harvesting in old‐growth eastern white pine stands were similar to those that we reported earlier from allozyme analysis (
Buchert et al. 1997
). The results indicate that silvicultural practices should ensure that the gene pools of remaining pristine old‐growth stands are reconstituted in the regenerating stands.
Phylogeographical pattern correlates with Pliocene mountain building in the alpine scree weta (Orthoptera, Anostostomatidae)
Authors: Trewick S. A. , Wallis G. P. , Morgan‐Richards M. 
Published: March 2003

AbstractMost research on the biological effects of Pleistocene glaciation and refugia has been undertaken in the northern hemisphere and focuses on lowland taxa. Using single‐strand conformation polymorphism (SSCP) analysis and sequencing of mitochondrial cytochrome oxidase I, we explored the intraspecific phylogeography of a flightless orthopteran (the alpine scree weta, Deinacrida connectens) that is adapted to the alpine zone of South Island, New Zealand. We found that several mountain ranges and regions had their own reciprocally monophyletic, deeply differentiated lineages. Corrected genetic distance among lineages was 8.4% (Kimura 2‐parameter [K2P]) / 13% (GTR + I + Γ), whereas within‐lineage distances were only 2.8% (K2P) / 3.2% (GTR + I + Γ). We propose a model to explain this phylogeographical structure, which links the radiation of D. connectens to Pliocene mountain building, and maintenance of this structure through the combined effects of mountain‐top isolation during Pleistocene interglacials and ice barriers to dispersal during glacials.
Molecular phylogeography and cryptic speciation in the mosses, Mielichhoferia elongata and M. mielichhoferiana (Bryaceae)
Authors: Shaw A. J. 
Published: March 2003

AbstractNucleotide sequence variation in the ITS1–5.8S–ITS2 region of nuclear ribosomal DNA (nrDNA) from 70 populations of Mielichhoferia elongata and M. mielichhoferiana, plus two outgroup species, was analysed using maximum parsimony and maximum likelihood methods. High levels of nucleotide substitution and numerous insertion–deletion events were detected within and between the two species. M. elongata is monophyletic with regard to nrDNA variation, but M. mielichhoferiana is paraphyletic. (M. elongata is nested within it.) A clade within M. mielichhoferiana provides evidence of vicariance, with North American and Scandinavian sister groups of populations. Two major clades are resolved in M. elongata by sequence data that are completely congruent with previous isozyme work. One clade includes populations from both North America and Europe whereas the other is strictly North American. These two clades, resolved by multiple independent loci, clearly represent cryptic species within the morphologically uniform M. elongata. Certain geographical areas, most notably southwestern Colorado in Ouray and San Juan Counties, harbour diverse populations of M. elongata with distinct phylogenetic and phylogeographical histories. Morphologically indistinguishable but phylogenetically distant populations were detected a few metres apart at one site. In contrast, all populations collected over hundreds of kilometres in California belong to a single clade. Arctic North American populations belong to a clade that includes disjunct populations in Alaska, northern Ellesmere Island, and the northeastern USA, but not subarctic Swedish populations, which are more closely related to plants from the Rocky Mountains. Morphological uniformity belies complex infraspecific phylogenetic patterns within M. elongata and M. mielichhoferiana.
Accurate gene diversity estimates from amplified fragment length polymorphism (AFLP) markers
Authors: Krauss Siegfried L. 
Published: March 2003

AbstractThree procedures for the estimation of null allele frequencies and gene diversity from dominant multilocus data were empirically tested in natural populations of the outcrossing angiosperm Persoonia mollis (Proteaceae). The three procedures were the square root transform of the null homozygote frequency, the Lynch & Milligan procedure, and the Bayesian method. Genotypes for each of 116 polymorphic loci generated by amplified fragment length polymorphism (AFLP) were inferred from segregation patterns in progeny arrays. Therefore, for the plus phenotype (band present), heterozygotes were distinguished from homozygotes. In contrast to previous studies, all three procedures produced very similar mean estimates of heterozygosity, which were in turn accurate estimators of the direct value (HO = 0.28). A second population of P. mollis displayed markedly lower levels of heterozygosity (HO = 0.20) but approximately twice as many polymorphic loci (284). These AFLP results show that biases in estimates of average null allele frequency and heterozygosity are largely eliminated in highly polymorphic dominant marker data sets displaying a J‐shaped beta distribution with a high percentage of loci containing more than three null homozygotes and relatively few loci with no null homozygotes. This distribution may be typical of outcrossing angiosperms.
RAPD variation and population genetic structure inPrunus mahaleb(Rosaceae), an animal‐dispersed tree
Authors: Jordano Pedro , Godoy José A. 
Published: March 2003

AbstractWe examined the patterns of random amplified polymorphic DNA (RAPD) variation among sevenPrunus mahaleb(Rosaceae) populations extending over ≈ 100 km2to examine local differentiation in relation to spatial isolation due to both geographical distance and differences in elevation. No less than 51.4% of the RAPD loci were polymorphic, but very few were fixed and among‐population variation accounted for 16.46% of variation in RAPD patterns. Mean gene diversity was 0.1441, with mean Nei’s genetic diversity for individual populations ranging between 0.089 and 0.149. MeanGSTvalue across loci was 0.1935 (range, 0.0162–0.4685), giving an average estimate forNmof 1.191. These results suggest extensive gene flow among populations, but higherGSTand lowerNmvalues relative to other outcrossing, woody species with endozoochorous dispersal, also suggest a process of isolation by distance. The combined effect of both geographical and elevation distances and nonoverlapping flowering and fruiting phenophases on theGSTmatrix was partially significant, revealing only marginal isolation of theP. mahalebpopulations. The matrix correlation between estimatedNmvalues among populations and the geographical + elevation distance matrices (r = −0.4623,P = 0.07), suggests a marginal trend for more isolated populations to exchange less immigrants. Long‐distance seed dispersal by efficient medium‐sized frugivorous birds and mammals is most likely associated to the high levels of within‐population genetic diversity. However, vicariance factors and demographic bottlenecks (high postdispersal seed and seedling mortality) explain comparatively high levels of local differentiation.
High genetic variation in leopards indicates large and long‐term stable effective population size
Authors: Spong G. , Johansson M. , Björklund M. 
Published: March 2003

AbstractIn this paper we employ recently developed statistical and molecular tools to analyse the population history of the Tanzanian leopard (Panthera pardus), a large solitary felid. Because of their solitary lifestyle little is known of their past or present population dynamics. Eighty‐one individuals were scored at 18 microsatellite loci. Overall, levels of heterozygosity were high (0.77 ± 0.03), with a small heterozygote deficiency (0.06 ± 0.03). Effective population size (Ne) was calculated to be 38 000–48 000. A Ne:N ratio of 0.42 (average from four cat studies) gives a present population size of about 100 000 leopards in Tanzania. Four different bottleneck tests indicated that this population has been large and stable for a minimum of several thousand years. FST values were low and no significant genetic structuring of the population could be detected. This concurs well with the large migration values (Nm) obtained (>3.3 individuals/generation). Our analysis reveals that ecological factors (e.g. disease), which are known to have had major impact on other carnivore populations, are unlikely to have impacted strongly on the population dynamics of Tanzanian leopards. The explanation may be found in their solitary life‐style, their often nonconfrontational behaviour toward interspecific competitors, or that any bottlenecks have been of limited size, localized, or too short to have affected genetic variation to any measurable degree. Since the genetic structuring is weak, gene flow is not restricted to within protected areas. Local loss of genetic variation is therefore not of immediate concern.
Molecular analysis of orchid pollinaria and pollinaria‐remains found on insects
Authors: Widmer A. , Cozzolino S. , Pellegrino G. , Soliva M. , Dafni A. 
Published: March 2003

AbstractDirect observations of pollinator visits to orchids are often difficult and time consuming, especially in orchids with a deceptive pollination system where seed set is typically pollinator‐limited. This lack of direct observations greatly inhibits our understanding of orchid–pollinator relationships and especially the degree of pollinator‐specificity. Here we describe a molecular approach to the study of orchid–pollinator relationships based on the analysis of DNA recovered from pollinaria found on insects. The insects were collected from nectar‐rich plants flowering near natural orchid populations, or taken from museum collections. Sequence analysis of the nuclear ribosomal ITS region allowed the identification of the orchid species or species‐group from which the pollinaria originated. Four out of eight orchid–pollinator relationships established with this approach have not been reported previously, which highlights the value of molecular tools for the study of orchid pollination biology.
Patterns and levels of gene flow in Rhododendron metternichii var. hondoense revealed by microsatellite analysis
Authors: Kameyama Yoshiaki , Isagi Yuji , Nakagoshi Nobukazu 
Published: March 2003

AbstractParentage analysis was conducted to elucidate the patterns and levels of gene flow in Rhododendron metternichii Sieb. et Zucc. var. hondoense Nakai in a 150 × 70 m quadrat in Hiroshima Prefecture, western Japan. The population of R. metternichii occurred as three subpopulations at the study site. Seventy seedlings were randomly collected from each of three 10 × 10 m plots (S1, S2, and S3) on the forest floor of each subpopulation (A1, A2, and A3). Almost all parents (93.8%) of the 70 seedlings were unambiguously identified by using 12 pairs of microsatellite markers. Within the quadrat, adult trees less than 5 m from the centre of the seedling bank (plots S1, S2, and S3) produced large numbers of seedlings. The effects of tree height and distance from the seedling bank on the relative fertilities of adult trees were highly variable among subpopulations because of the differences in population structure near the seedling bank: neither distance nor tree height had any significant effect in subpopulation A1; distance from the seedling bank had a significant effect in subpopulation A2; and tree height had a significant effect in subpopulation A3. Although gene flow within each subpopulation was highly restricted to less than 25 m and gene flow among the three subpopulations was extremely small (0–2%), long‐distance gene flow from outside the quadrat reached 50%. This long‐distance gene flow may be caused by a combination of topographical and vegetational heterogeneity, differences in flowering phenology, and genetic substructuring within subpopulations.
Spatio‐temporal dynamics of theAllonemobius fasciatus–A. sociusmosaic hybrid zone: a 14‐year perspective
Authors: Britch S. C. , Cain M. L. , Howard D. J. 
Published: March 2003

AbstractLong‐term studies of hybrid zones can provide valuable insight into a number of questions that have long attracted the attention of evolutionists. These questions range from the stability and fate of hybrid zones to the relative fitness of hybrids. In this paper we report the results of a 14‐year survey of theAllonemobius fasciatus–Allonemobius sociushybrid zone. Populations were collected intensively in 1986 and 1987 and then more sporadically through the end of the 1980s and throughout the 1990s. By documenting changes in the genetic composition of populations near and within the zone during this period of time we assessed: the strength of the reproductive isolation between the two species; the relative growth rates (which can be considered a surrogate of relative fitness) of genotype classes corresponding to hybrids and to pure species individuals; and, the power of single‐year and multi‐year measurements of relative growth rates to predict changes in the genetic composition of mixed populations through time. In brief, we found very large year‐to‐year variation in the relative growth rates of pure species and hybrid individuals. This variation may reflect the fact that both species are at the edge of their range and perhaps at the limits of their ability to deal with environmental perturbations. As a consequence of the variation, even multi‐year estimates of relative growth rates often provided imprecise predictions regarding the future genotypic composition of mixed populations. Despite our limited ability to predict the dynamics of individual populations, some trends are apparent.A. socius, the southern species, has clearly increased in frequency along a transect through the Appalachian Mountains, indicating that the zone is moving north in this region. In contrast, the zone appeared to be more stable along the East Coast transect. Within mixed populations, character‐index profiles are often bimodal and stable through time, indicating relatively strong reproductive isolation between the two species that is not being reinforced, nor is it breaking down.
Genetic differentiation in Eurasian populations of the postfire ascomycete Daldinia loculata
Authors: Johannesson H. , Vasiliauskas R. , Dahlberg A. , Penttilä R. , Stenlid J. 
Published: March 2003

AbstractThe genetic population structure of the postfire ascomycete Daldinia loculata was studied to test for differentiation on a continental scale. Ninety‐six samples of spore families, each comprising mycelia from six to 10 spores originating from single perithecia, were sampled from one Russian and six Fennoscandian forest sites. Allelic distribution was assayed for six nuclear gene loci by restriction enzyme analyses of polymerase chain reaction (PCR)‐amplified gene fragments. In addition, the full sequence of the gene fragment was analysed for a subset of haploid single‐ascospore isolates in a multiallelic approach. A third data set was generated by using arbitrary‐primed PCR with the core sequence of the phage M13 as primer. Although there was a reduction in heterozygosity in the total population from what would have been expected at random mating, the levels of genetic differentiation among the Eurasian subpopulations of D. loculata were low. All subpopulations were found to be in Hardy–Weinberg equilibrium and gametic equilibrium was observed between all investigated nuclear gene loci. The results obtained by the different markers were consistent; we confirmed low levels of genetic differentiation among the Eurasian subpopulations of D. loculata. The differentiation did not increase with distance; the Russian subpopulation, sampled more than 7000 km from the Fennoscandian subpopulations, was only moderately differentiated from the others (FST = 0.00–0.14). In contrast, one of the Swedish populations was the most highly differentiated from the others, with FST and GST values of 0.10–0.16. The results suggest that D. loculata consists of a long‐lived backround Eurasian population of latent mycelia in nonburned forests, established by sexual ascospores dispersed from scattered burned forest sites. Local differentiation is probably due to founder effects of populations in areas with low fire frequency. A tentative life cycle of D. loculata is presented.
Relatedness structure in Rhododendron metternichii var. hondoense revealed by microsatellite analysis
Authors: Kameyama Yoshiaki , Isagi Yuji , Nakagoshi Nobukazu 
Published: March 2003

AbstractThe relatedness structure of Rhododendron metternichii Sieb. et Zucc. var. hondoense Nakai was analysed in a 150 × 70‐m quadrat in Hiroshima Prefecture, western Japan. The population of R. metternichii occurred as three subpopulations at the study site (A1–A3). Pairwise relatedness based on microsatellite genotypes at eight loci and Mantel tests revealed a hierarchical structure of relatedness within and among subpopulations: (i) relatedness between individuals within 10 m of one another was significantly positive; (ii) relatedness between individuals in the same subpopulation was significantly positive, but negative between individuals in distant subpopulations; and (iii) relatedness was not significantly different from zero among neighbouring subpopulations. In detail, however, relatedness within each subpopulation was significantly positive in subpopulation A1, relatively weak but significantly positive in subpopulation A2, and not significantly different from zero in subpopulation A3. Relatedness within each subpopulation was inversely related to correlations between interindividual distance and relatedness. The aggregation of related individuals at short distances from one another may lead to decreasing relatedness within subpopulations as a whole. Moreover, negative correlations between interindividual distance and relatedness corresponded to high flowering densities at less than 10‐m distance, implying that high flowering densities reduce pollinator foraging distance and lead to stronger genetic structure within subpopulations. Small individuals (< 2.0 m in height) showed stronger genetic structure compared with that of large individuals (≥ 2.0 m in height). The different relatedness structure within and among subpopulations may be caused by various degrees of gene flow affected by distribution patterns of individuals and population density.
Genetic variation of symbiotic fungi cultivated by the macrotermitine termite Odontotermes formosanus (Isoptera: Termitidae) in the Ryukyu Archipelago
Authors: Katoh H. , Miura T. , Maekawa K. , Shinzato N. , Matsumoto T. 
Published: March 2003

AbstractFungus‐growing termites have a mutualistic relationship with their cultivated fungi. To improve understanding of genetic aspects of this relationship, we examined molecular markers in the fungus‐growing termite Odontotermes formosanus and its fungi Termitomyces spp. from the Ryukyu Archipelago. Based on the polymorphic band patterns obtained from arbitrarily primed polymerase chain reaction methods, we constructed cladograms for related colonies of the termites and fungi. The resulting trees indicated that the termites display little genetic variation among the colonies, while the symbiotic fungi consist of two major genetic types. In addition, molecular phylogenetic trees of the symbiotic fungi based on internal transcribed spacer and 18S rDNA suggested that these two types of fungi are different species. We also demonstrated that the fungi comprising the fruiting bodies and fungus combs are identical, and that fungus combs are probably a monoculture within a single termite colony. Our results indicate that horizontal transmission of symbiotic fungi among termite colonies occurred during the evolutionary history of this symbiosis.
Molecular genecology of temperature response in Lolium perenne: 1. preliminary analysis to reduce false positives
Authors: Hamilton N. R. Sackville , Skøt L. , Chorlton K. H. , Thomas I. D. , Mizen S. 
Published: March 2003

AbstractMolecular genecology is the study of geographical clines in frequencies of molecular markers and their relationship to ecological clines in environmental conditions. This study outlines the principles underlying the selection of populations, focusing on avoiding ‘false positives’— noncausal correlations between allele frequency and the environment. The principles are illustrated by identifying a set of populations of Lolium perenne for the study of temperature responses. The selected set of populations encompasses a 20 °C range in mean January temperature. Their freezing tolerance shows a linear trend with winter temperature, LT50 decreasing by 0.25 °C for each 1 °C reduction in mean January temperature.