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At least 55 records · Page 3Linked to original sources
PubMed2006

Fine-scale genetic structure of life history stages in the food-deceptive orchid Orchis purpurea.

In natural plant populations, fine-scale spatial genetic structure can result from limited gene flow, selection pressures or historical events, but the role of each factor is in general hard to discern. One way to investigate the origination of spatial genetic structure within a plant population consists of comparing spatial genetic structure among different life history stages. In this study, spatial genetic structure of the food-deceptive orchid Orchis purpurea was determined across life history stages in two populations that were regenerating after many years of population decline. Based on demographic analyses (2001-2004), we distinguished between recruits and adult plants. For both sites, there was no difference in the proportion of polymorphic loci and expected heterozygosity between life history stages. However, spatial autocorrelation analyses showed that spatial genetic structure increased in magnitude with life history stage. Weak or no spatial genetic structure was observed for recruits, whereas adult plants showed a pattern that is consistent with that found in other species with a predominantly outcrossing mating system. The observed differences between seedlings and adults are probably a consequence of changes in management of the two study sites and associated demographic changes in both populations. Our results illustrate that recurrent population crashes and recovery may strongly affect genetic diversity and fine-scale spatial genetic structure of plant populations.

Flowers↗
PubMed1994

Long DNA palindromes, cruciform structures, genetic instability and secondary structure repair.

Long DNA palindromes pose a threat to genome stability. This instability is primarily mediated by slippage on the lagging strand of the replication fork between short directly repeated sequences close to the ends of the palindrome. The role of the palindrome is likely to be the juxtaposition of the directly repeated sequences by intra-strand base-pairing. This intra-strand base-pairing, if present on both strands, results in a cruciform structure. In bacteria, cruciform structures have proved difficult to detect in vivo, suggesting that if they form, they are either not replicated or are destroyed. SbcCD, a recently discovered exonuclease of Escherichia coli, is responsible for preventing the replication of long palindromes. These observations lead to the proposal that cells may have evolved a post-replicative mechanism for the elimination and/or repair of large DNA secondary structures.

Base Sequence↗
PubMed2004

Population Graphs: the graph theoretic shape of genetic structure.

Patterns of intraspecific genetic variation result from interactions among both historical and contemporary evolutionary processes. Traditionally, population geneticists have used methods such as F-statistics, pairwise isolation by distance models, spatial autocorrelation and coalescent models to analyse this variation and to gain insight about causal evolutionary processes. Here we introduce a novel approach (Population Graphs) that focuses on the analysis of marker-based population genetic data within a graph theoretic framework. This method can be used to estimate traditional population genetic summary statistics, but its primary focus is on characterizing the complex topology resulting from historical and contemporary genetic interactions among populations. We introduce the application of Population Graphs by examining the range-wide population genetic structure of a Sonoran Desert cactus (Lophocereus schottii). With this data set, we evaluate hypotheses regarding historical vicariance, isolation by distance, population-level assignment and the importance of specific populations to species-wide genetic connectivity. We close by discussing the applicability of Population Graphs for addressing a wide range of population genetic and phylogeographical problems.

Cactaceae↗
PubMed1994

Isonymy and the genetic structure of Sicily.

The genetic structure of Sicily was analysed through the distribution of surnames of 758,793 users registered in the Italian Telephone Company, corresponding to 371 communes of the island. Estimates of the coefficient of consanguinity due to random isonymy, of Fisher's a, an indicator of abundance of surnames, and of Karlin-McGregor's v, an indicator of immigration rates, were obtained for each commune. Four different estimates of genetic distance between all possible pairs of communes within each province were also obtained, and their relationship with geographic distance was studied. The logarithmic transformation of Lasker's coefficient of relationship showed correlations with the log of geographic distance which range between -0.78 and -0.40; the strongest, for the province of Catania, was attributed to the presence of Mount Etna, and the weakest, for Palermo, to the high population density of this province.

Bias↗
PubMed2005

Variogram analysis of the spatial genetic structure of continuous populations using multilocus microsatellite data.

A geostatistical perspective on spatial genetic structure may explain methodological issues of quantifying spatial genetic structure and suggest new approaches to addressing them. We use a variogram approach to (i) derive a spatial partitioning of molecular variance, gene diversity, and genotypic diversity for microsatellite data under the infinite allele model (IAM) and the stepwise mutation model (SMM), (ii) develop a weighting of sampling units to reflect ploidy levels or multiple sampling of genets, and (iii) show how variograms summarize the spatial genetic structure within a population under isolation-by-distance. The methods are illustrated with data from a population of the epiphytic lichen Lobaria pulmonaria, using six microsatellite markers. Variogram-based analysis not only avoids bias due to the underestimation of population variance in the presence of spatial autocorrelation, but also provides estimates of population genetic diversity and the degree and extent of spatial genetic structure accounting for autocorrelation.

Analysis of Variance↗
PubMed2006

Effects of canopy gaps on the genetic structure of Camellia japonica saplings in a Japanese old-growth evergreen forest.

The genetic structure of Camellia japonica saplings was investigated in relation to canopy conditions in an old-growth evergreen forest in Tsushima, Japan. To elucidate effects of canopy gaps on genetic structure, a 1 ha study site was divided into 20 x 20 m quadrats, which were classified into a gap quadrats (GAP), closed canopy quadrats (CLS) and mixed quadrats. Five GAP quadrats and six CLS quadrats were analyzed separately. Isolation-by-distance was tested by examining the correlation between genetic distance and geographic distance. A significant positive correlation was detected for GAP quadrats, whilst that for CLS quadrats was significantly smaller and not significantly different from zero. On the other hand, an analysis using Moran's I spatial autocorrelation coefficients indicates that the genetic structure is weaker in GAP quadrats than in CLS quadrats in short distance classes. The values were significantly positive for both types of quadrat. These results, along with our field observations on flowering, suggest that canopy gaps affect the genetic structure of C. japonica saplings in two distinct ways. First, canopy gaps may promote flowering and mating in an isolation-by-distance manner within canopy gaps. Second, canopy gaps may promote seed production and resulting overlap in seed shadows may weaken fine-scale genetic structures.

Camellia↗
PubMed1997

Gender-specific regional changes in genetic structure of muscularity in early adolescence.

Genetic and environmental influences on muscle circumference measurements of the extremities were estimated in 105 pairs of twins between 10 and 14 yr of age. Four circumferences, extended upper arm (EAC), forearm (FC), thigh (TC), and calf (CC), were measured. Univariate model fitting revealed that the largest part (87-95%) of the variance for all circumferences at most ages was explained by additive genetic factors. Sex differences were observed for some age categories. Multivariate analyses showed a different pattern evolving according to age and gender. In boys from 10 to 12 yr of age, one general genetic factor influenced all four circumferences. With increasing age, an arm-leg model emerged, one genetic factor influencing the arm and another genetic factor the leg circumferences. In young girls one genetic factor loaded on the proximal (EAC, TC) and another on the distal (FC, CC) circumferences. With subjects at age 14 yr, an arm-leg model was observed. High genetic correlations indicated that genetic factors related to EAC, FC, TC, and CC did not act independently. The age-and gender-specific changes in the genetic structure suggest pubertal influences. This study shows that muscle circumferences are highly heritable characteristics and are therefore a promising starting point at which to locate their genes. Gene mapping could validate the gender-specific change of the genetic structure with age and region.

Adolescent↗
PubMed2006

Identifying the environmental factors that determine the genetic structure of populations.

The study of population genetic structure is a fundamental problem in population biology because it helps us obtain a deeper understanding of the evolutionary process. One of the issues most assiduously studied in this context is the assessment of the relative importance of environmental factors (geographic distance, language, temperature, altitude, etc.) on the genetic structure of populations. The most widely used method to address this question is the multivariate Mantel test, a nonparametric method that calculates a correlation coefficient between a dependent matrix of pairwise population genetic distances and one or more independent matrices of environmental differences. Here we present a hierarchical Bayesian method that estimates F(ST) values for each local population and relates them to environmental factors using a generalized linear model. The method is demonstrated by applying it to two data sets, a data set for a population of the argan tree and a human data set comprising 51 populations distributed worldwide. We also carry out a simulation study to investigate the performance of the method and find that it can correctly identify the factors that play a role in the structuring of genetic diversity under a wide range of scenarios.

Africa, Eastern↗
PubMed2003

Estimating seed vs. pollen dispersal from spatial genetic structure in the common ash.

Spatial genetic structure was analysed with five highly polymorphic microsatellite loci in a Romanian population of common ash (Fraxinus excelsior L.), a wind-pollinated and wind-dispersed tree species occurring in mixed deciduous forests over almost all of Europe. Contributions of seed and pollen dispersal to total gene flow were investigated by analysing the pattern of decrease in kinship coefficients among pairs of individuals with geographical distance and comparing it with simulation results. Plots of kinship against the logarithm of distance were decomposed into a slope and a shape component. Simulations showed that the slope is informative about the global level of gene flow, in agreement with theoretical expectations, whereas the shape component was correlated with the relative importance of seed vs. pollen dispersal. Hence, our results indicate that insights into the relative contributions of seed and pollen dispersal to overall gene flow can be gained from details of the pattern of spatial genetic structure at biparentally inherited loci. In common ash, the slope provided an estimate of total gene dispersal in terms of Wright's neighbourhood size of Nb = 519 individuals. No precise estimate of seed vs. pollen flow could be obtained from the shape because of the stochasticity inherent to the data, but the parameter combinations that best fitted the data indicated restricted seed flow, sigmas pound 14 m, and moderate pollen flow, 70 m pound sigmap pound 140 m.

Computer Simulation↗
PubMed2006

Dynamic of the genetic structure of bacterial and fungal communities at different developmental stages of Medicago truncatula Gaertn. cv. Jemalong line J5.

The genetic structure of bacterial and fungal communities was characterized in the rhizosphere of Medicago truncatula Gaertn. cv. Jemalong line J5 at five developmental stages (three vegetative and two reproductive stages), and in three compartments (bulk soil, rhizosphere soil and root tissues). The genetic structure of microbial communities was determined by cultivation-independent methods using directly extracted DNA that was characterized by automated ribosomal intergenic spacer analysis (ARISA). Principal component analyses (PCA) indicate that, for all developmental stages, the genetic structure of microbial communities differed significantly by compartment, with a major shift in the community in root tissues corresponding to the most intimate compartment with the plant. Differences were also recorded during plant development, the most significant being observed during the transition between vegetative and reproductive stages. Throughout this period, plants were shown to establish the highest level of symbiotic association (mycorrhization, nodulation) with arbuscular mycorrhizal fungi and Rhizobia. During the reproductive stages, the dynamics of the genetic structure differed between bacterial and fungal communities. At the last reproductive stage, the genetic structure of bacterial communities became close to that recorded during the first vegetative stages, suggesting a resilience phenomenon, whereas the genetic structure of fungal communities remained different from the vegetative stages and also from the early reproductive stages, suggesting a persistence of the rhizosphere effect.

Bacteria↗
PubMed2002

Examining genetic structure in a bogus yucca moth: a sequential approach to phylogeography.

Understanding the phylogeography of a species requires not only elucidating patterns of genetic structure among populations, but also identifying the possible evolutionary events creating that structure. The use of a single phylogeographic test or analysis, however, usually provides a picture of genetic structure without revealing the possible underlying evolutionary causes. We used current analytical techniques in a sequential approach to examine genetic structure and its underlying causes in the bogus yucca moth Prodoxus decipiens (Lepidoptera: Prodoxidae). Both historical biogeography and recent human transplantations of the moth's host plants provided a priori expectations of the pattern of genetic structure and its underlying causes. We evaluated these expectations by using a progression of phylogenetic, demographic, and population genetic analyses of mtDNA sequence data from 476 individuals distributed across 25 populations that encompassed the range of P. decipiens. The combination of these analyses revealed that much of the genetic structure has evolved more recently than suggested by historical biogeography, has been influenced by changes in demography, and can be best explained by long distance dispersal and isolation by distance. We suggest that performing a suite of analyses that focus on different temporal scales may be an effective approach to investigating the patterns and causes of genetic structure within species.

Animals↗
PubMed2005

Spatial genetic structure of two sympatric neotropical palms with contrasting life histories.

The spatial genetic structure within sympatric populations of two neotropical dioecious palm species with contrasting life histories was characterized to evaluate the influence of life history traits on the extent of genetic isolation by distance. Chamaedorea tepejilote is a common wind-pollinated arboreal understory palm. Chamaedorea elatior is an uncommon climbing subcanopy palm with entomophilous pollination syndrome. A total of 59 allozyme alleles for C. tepejilote and 53 alleles for C. elatior was analyzed using both unweighted (Iu) and weighted (Iw) Moran's I spatial autocorrelation statistics. The spatial genetic structure detected within these populations is consistent with those reported for highly dispersed plants. A significance test for differences between mean Moran's I-coefficients revealed less spatial genetic structure within the C. tepejilote population than that in the C. elatior population. Adjacent individuals of C. elatior exhibited significant spatial genetic autocorrelation (Iu=0.039, Iw=0.034), indicating a Wright's neighborhood size of about 100 individuals. For C. tepejilote, nonrandom genetic distribution among nearest neighbors was detected, even from small spatial autocorrelation values (Iu=0.008, Iw=0.009), consistent with a neighborhood size of about 300 individuals. For both species, seed dispersal, mortality among life cycle stages, overlapping generations, and contrasting traits of mating and reproduction influence the standing spatial genetic structure within populations.

Arecaceae↗
PubMed2004

Effective population sizes and temporal stability of genetic structure in Rana pipiens, the northern leopard frog.

Although studies of population genetic structure are very common, whether genetic structure is stable over time has been assessed for very few taxa. The question of stability over time is particularly interesting for frogs because it is not clear to what extent frogs exist in dynamic metapopulations with frequent extinction and recolonization, or in stable patches at equilibrium between drift and gene flow. In this study we collected tissue samples from the same five populations of leopard frogs, Rana pipiens, over a 22-30 year time interval (11-15 generations). Genetic structure among the populations was very stable, suggesting that these populations were not undergoing frequent extinction and colonization. We also estimated the effective size of each population from the change in allele frequencies over time. There exist few estimates of effective size for frog populations, but the data available suggest that ranid frogs may have much larger ratios of effective size (Ne) to census size (Nc) than toads (bufonidae). Our results indicate that R. pipiens populations have effective sizes on the order of hundreds to at most a few thousand frogs, and Ne/Nc ratios in the range of 0.1-1.0. These estimates of Ne/Nc are consistent with those estimated for other Rana species. Finally, we compared the results of three temporal methods for estimating Ne. Moment and pseudolikelihood methods that assume a closed population gave the most similar point estimates, although the moment estimates were consistently two to four times larger. Wang and Whitlock's new method that jointly estimates Ne and the rate of immigration into a population (m) gave much smaller estimates of Ne and implausibly large estimates of m. This method requires knowing allele frequencies in the source of immigrants, but was thought to be insensitive to inexact estimates. In our case the method may have failed because we did not know the true source of immigrants for each population. The method may be more sensitive to choice of source frequencies than was previously appreciated, and so should be used with caution if the most likely source of immigrants cannot be identified clearly.

Animals↗
PubMed2002

Isolation by distance and vicariance drive genetic structure of a coral reef fish in the Pacific Ocean.

We studied the genetic diversity of a coral reef fish species to investigate the origin of the differentiation. A total of 727 Acanthurus triostegus collected from 15 locations throughout the Pacific were analyzed for 20 polymorphic loci. The genetic structure showed limited internal disequilibrium within each population; 3.7% of the loci showed significant Hardy-Weinberg disequilibrium, mostly associated with Adh*, and we subsequently removed this locus from further analysis of geographic pattern. The genetic structure of A. triostegus throughout the tropical Pacific Ocean revealed a strong geographic pattern. Overall, there was significant population differentiation (multilocus F(ST) = 0.199), which was geographically structured according to bootstraps of neighbor-joining analysis on Nei's unbiased genetic distances and AMOVA analysis. The genetic structure revealed five geographic groups in the Pacific Ocean: western Pacific (Guam, Philippines, Palau, and Great Barrier Reef); central Pacific (Solomons, New Caledonia, and Fiji); and three groups made up of the eastern populations, namely Hawaiian Archipelago (north), Marquesas (equatorial), and southern French Polynesia (south) that incorporates Clipperton Island located in the northeastern Pacific. In addition, heterozygosity values were found to be geographically structured with higher values grouped within Polynesian and Clipperton populations, which exhibited lower population size. Finally, the genetic differentiation (F(ST)) was significantly correlated with geographic distance when populations from the Hawaiian and Marquesas archipelagos were separated from all the other locations. These results show that patterns of differentiation vary within the same species according to the spatial scale, with one group probably issued from vicariance, whereas the other followed a pattern of isolation by distance. The geographic pattern for A. triostegus emphasizes the diversity of the evolutionary processes that lead to the present genetic structure with some being more influential in certain areas or according to a particular spatial scale.

Animals↗
PubMed2005

Gene flow and inbreeding depression inferred from fine-scale genetic structure in an endangered heterostylous perennial, Primula sieboldii.

We estimated the gene dispersal distance and the magnitude of inbreeding depression from the fine-scale genetic structure in the endangered heterostylous perennial Primula sieboldii. We indirectly estimated the neighbourhood size (Nb) and the standard deviation of gene dispersal distance (sigma(g)) from the detected genetic structure by using 10 microsatellite markers. We also estimated the fitness reduction in mating among neighbouring individuals caused by biparental inbreeding according to the genetic structure. We found clear fine-scale genetic structure (a significantly positive kinship coefficient within 42.3 m), and the indirect estimates of sigma(g) and Nb were 15.7 m and 50.9, respectively. These indirect estimates were similar to the direct estimates (18.4 m and 44.0). The slightly larger indirect estimate of Nb may reflect that inbreeding depression and genetic structure or rare long-distance dispersal that were overlooked in the direct estimate have elongated the long-term average of gene dispersal distance. P. sieboldii is also likely to suffer about 19% fitness reduction in progenies from mating among individuals 5 m apart. Our results suggest that biparental inbreeding and genetic structure can affect the range of gene dispersal and seed reproductive success in P. sieboldii.

DNA, Plant↗
PubMed2005

Genetic structure of the cyclic fossorial water vole (Arvicola terrestris): landscape and demographic influences.

Genetic structure can be strongly affected by landscape features and variation through time and space of demographic parameters such as population size and migration rate. The fossorial water vole (Arvicola terrestris) is a cyclic species characterized by large demographic fluctuations over short periods of time. The outbreaks do not occur everywhere at the same time but spread as a wave at a regional scale. This leads to a pattern of large areas (i.e. some hundreds of km2), each with different vole abundances, at any given time. Here, we describe the abundance and genetic structures in populations of the fossorial water vole. We use the data to try to understand how landscape and demographic features act to shape the genetic structure. The spatial variability of vole abundance was assessed from surface indices, collected in spring 2002 (April) in eastern central France. Genetic variability was analysed using eight microsatellite loci at 23 localities sampled between October 2001 and April 2002. We found some congruence between abundance and genetic structures. At a regional scale, the genetic disruptions were associated with both sharp relief and transition between an area of low abundance and another of high abundance. At a local scale, we observed a variation of the isolation-by-distance pattern according to the abundance level of vole populations. From these results we suggest that the dispersal pattern in cyclic rodent populations varies throughout the demographic cycle.

Animals↗
PubMed2004

Population genetic structure of Anopheles gambiae mosquitoes on Lake Victoria islands, west Kenya.

BACKGROUND: Understanding the genetic structure of island Anopheles gambiae populations is important for the current tactics in mosquito control and for the proposed strategy using genetically-modified mosquitoes (GMM). Genetically-isolated mosquito populations on islands are a potential site for testing GMM. The objective of this study was to determine the genetic structure of A. gambiae populations on the islands in Lake Victoria, western Kenya. METHODS: The genetic diversity and the population genetic structures of 13 A. gambiae populations from five islands on Lake Victoria and six villages from the surrounding mainland area in the Suba District were examined using six microsatellite markers. The distance range of sampling sites varied between 2.5 and 35.1 km. RESULTS: A similar level of genetic diversity between island mosquito populations and adjacent mainland populations was found. The average number of alleles per locus was 7.3 for the island populations and 6.8 for the mainland populations. The average observed heterozygosity was 0.32 and 0.28 for the island and mainland populations, respectively. A low but statistically significant genetic structure was detected among the island populations (FST = 0.019) and between the island and mainland populations (FST = 0.003). A total of 12 private alleles were found, and nine of them were from the island populations. CONCLUSION: A level of genetic differentiation between the island and mainland populations was found. Large extent of gene flow between the island and mainland mosquito populations may result from wind- or human-assisted dispersal. Should the islands on Lake Victoria be used as a trial site for the release program of GMM, mosquito dispersal between the islands and between the island and the mainland should be vigorously monitored.

Alleles↗
PubMed2006

Population genetic structure of Arabidopsis lyrata in Europe.

Population genetic theory predicts that the self-incompatible and perennial herb, Arabidopsis lyrata, will have a genetic structure that differs from the self-fertilizing, annual Arabidopsis thaliana. We quantified the genetic structure for eight populations of A. lyrata ssp. petraea in historically nonglaciated regions of central Europe. Analysis of 20 microsatellite loci for 344 individuals demonstrated that, in accordance with predictions, diploid populations had high genome-wide heterozygosity (H(O) = 0.48; H(E) = 0.52), high within-population diversity (83% of total) compatible with mutation-drift equilibrium, and moderate differentiation among populations (F(ST) = 0.17). Within a single population, the vast majority of genetic variability (92%) was found at the smallest spatial scale (< 3 m). Although there was no evidence of biparental inbreeding or clonal propagation at this scale (F(IS) = 0.003), significant fine-scale spatial autocorrelation indicated localized gene flow presumably due to gravity dispersed seeds (Sp = 0.018). Limited gene flow between isolated population clusters (regions) separated by hundreds of kilometres has given rise to an isolation by distance pattern of diversification, with low, but significant, differentiation among regions (F(ST) = 0.05). The maintenance of geographically widespread polymorphisms and uniformly high diversity throughout central Europe is consistent with periglacial survival of A. lyrata ssp. petraea north of the Alps in steppe-tundra habitats during the last glacial maximum. As expected of northern and previously glaciated localities, A. lyrata in Iceland was genetically less diverse and highly differentiated from central Europe (H(E) = 0.37; F(ST) = 0.27).

Arabidopsis↗