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At least 19 recordsLinked to original sources
PubMed2003

Genetic structure, conservation genetics and evidence of speciation by range expansion in shy and white-capped albatrosses.

Six variable microsatellite loci were used to examine genetic structuring in the closely related shy albatross (Thalassarche cauta) and white-capped albatross (T. steadi). First, levels of genetic differentiation between the species, and among three populations within each species, were analysed using amova, FST and RST. We found high levels of genetic structuring and detected many unshared alleles between the species, which provide strong evidence against any contemporary gene flow between them. Within each species, shy albatross populations were found to be genetically distinct whereas white-capped albatross populations were undifferentiated, which implies that dispersal events are much rarer in the former than in the latter. These results formed the basis for the recommendation that the three white-capped albatross populations (as a whole) and each shy albatross population be treated as separate units for conservation. Second, levels of genetic diversity and allelic patterns in shy and white-capped albatrosses were assessed for whether they support earlier mtDNA results suggesting that shy albatrosses arose through range expansion of white-capped albatrosses. All measures indicated lower genetic diversity within shy albatrosses than within white-capped albatrosses and upheld the hypothesis that shy albatrosses were founded by white-capped albatrosses.

Analysis of Variance↗
PubMed2006

Fine-scale genetic structure among genetic individuals of the clone-forming monotypic genus Echinosophora koreensis (Fabaceae).

BACKGROUND AND AIMS: For rare endemics or endangered plant species that reproduce both sexually and vegetatively it is critical to understand the extent of clonality because assessment of clonal extent and distribution has important ecological and evolutionary consequences with conservation implications. A survey was undertaken to understand clonal effects on fine-scale genetic structure (FSGS) in two populations (one from a disturbed and the other from an undisturbed locality) of Echinosophora koreensis, an endangered small shrub belonging to a monotypic genus in central Korea that reproduces both sexually and vegetatively via rhizomes. METHODS: Using inter-simple sequence repeats (ISSRs) as genetic markers, the spatial distribution of individuals was evaluated using Ripley's L(d)-statistics and quantified the spatial scale of clonal spread and spatial distribution of ISSR genotypes using spatial autocorrelation analysis techniques (join-count statistics and kinship coefficient, F(ij)) for total samples and samples excluding clones. KEY RESULTS: A high degree of differentiation between populations was observed (phi(ST(g)) = 0.184, P < 0.001). Ripley's L(d)-statistics revealed a near random distribution of individuals in a disturbed population, whereas significant aggregation of individuals was found in an undisturbed site. The join-count statistics revealed that most clones significantly aggregate at < or = 6-m interplant distance. The Sp statistic reflecting patterns of correlograms revealed a strong pattern of FSGS for all four data sets (Sp = 0.072-0.154), but these patterns were not significantly different from each other. At small interplant distances (< or = 2 m), however, jackknifed 95% CIs revealed that the total samples exhibited significantly higher F(ij) values than the same samples excluding clones. CONCLUSION: The strong FSGS from genets is consistent with two biological and ecological traits of E. koreensis: bee-pollination and limited seed dispersal. Furthermore, potential clone mates over repeated generations would contribute to the observed high F(ij) values among genets at short distance. To ensure long-term ex situ genetic variability of the endangered E. koreensis, individuals located at distances of 10-12 m should be collected across entire populations of E. koreensis.

Conservation of Natural Resources↗
PubMed2003

[Studies of genetic structure of genetic relationship of Boer goat and its upgrading offspring to Tangshan Diary goat].

The gentic structure and relationship of Boer goat and its upgrading offspring to Tangshan Dairy goat were studied using the RAPD maker and some statistical program, such as POPGENE, PHYLIP and SPSS. The results indicated that there were the similar percentage of polymorphic loci, observed and effective number of alleles, gene diversity between Boer goat and its upgrading offspring, especially higher upgrading offspring. With the increasing of upgrading, the difference of population structure decreased as well as the genetic distance and differentiation among higher upgrading offspring and their improving parental, but gene flow and genetic identity increased. There was a close genetic relationship between higher upgrading offspring and Boer goat.

English Abstract↗
PubMed1980

Genetic structure and genetic variation of influenza viruses.

The following contribution summarizes our most recent results concerning analysis of the influenza A, B and C virus genomes. In addition, we present data on the extent of genetic variation of H1N1 influenza viruses isolated during the months following the 1977 outbreak of H1N1 influenza in China and Russia. A detailed description of these results is published elsewhere.

Base Sequence↗
PubMed2005

The "Kriging" model of spatial genetic structure in human population genetics.

This paper presents the application of Kriging technique in the field of human population genetics for quantifying the spatial genetic heterogeneity of HLA-A locus in the area of China,and for mapping its spatial genetic structure using the measurement of synthetic genetic structure (SPC) and the principal components (PC). Both principles of the method and the basic equations are given. The Kriging model has several advantages over other interpolation and smoothing methods. Firstly, it relies on the structure of the spatial genetic semivariogram model, which can be used to quantify the spatial genetic heterogeneity of the locus (loci) before mapping its spatial genetic structure. Secondly, it is virtually unbiased in the interpolation situation,where the location to be estimated is surrounded by data on all sides and is influenced within the range of these data. Thirdly, it allows of estimative error of interpolation, which can be used to appraise the predicting effect for the spatial estimation,and the error maps can be used to decide where to introduce new sampling population genetic data. However, the "Kriging" model also has some disadvantages. Firstly,when the theoretical spatial genetic semivariogram can not be fitted by any models, the "Kriging" model can not be set up. Secondly, if the Kriging model was built by a poor spatial genetic semivariogram,the Kriging estimation standard deviation is remarkably high in the whole area, hence the Kriging model can not be suitable to estimating the distribution of spatial genetic structure. In these situations,the interpolation algorithm, whose assumption is spatial random rather than spatial autocorrelation,such as the Cavalli-Sforza method in Genography, inverse distance-weighted methods, splines, should be used to estimate or map the distribution of spatial genetic structure.

Genetics, Population↗
PubMed2001

Molecular ecology of social behaviour: analyses of breeding systems and genetic structure.

Molecular 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.

Animals↗
PubMed2026

Climate Gradients and Habitat Discontinuity Structure Genetic Variation in a Spring-Specialist Plant.

BACKGROUND AND AIMS: Groundwater-dependent ecosystems support disproportionate biodiversity in arid regions, yet the population genetics of spring-specialist plants remains poorly understood. Here, we present the first species-wide genetic dataset for crimson monkeyflower (Mimulus verbenaceus, Phrymaceae), a spring-specialist plant distributed in seeps, springs, and associated riparian areas across desert regions of North America. We aim to relate landscape features and climate gradients to the spatial genetic structuring within this system. METHODS: Using genome-wide reduced representation sequencing data consisting of 10,760 SNPs from 175 individuals across 17 populations, we characterized the patterns of genetic differentiation and diversity. Population structure was assessed using ADMIXTURE and Principal Component Analysis. We examined the contributions of climate to range-wide genetic variation in crimson monkeyflower using redundancy analysis. KEY RESULTS: Patterns of genetic differentiation were more consistent with those of spring-specialist animal taxa than those of upland plants or generalist riparian plants. We found strong population structure at both broad regional scales and at fine local scales. While geographic and spatial structuring was a primary driver of genetic structure across all scales, riparian connectivity influenced local patterns of diversity, and adaptation to local climatic variation was more influential at regional scales, with temperature, relative humidity, and a monsoon-driven climate gradient contributing to genetic differentiation. CONCLUSIONS: Our findings highlight the distinctive association with isolated perennial groundwater sources, as well as climate gradients, with genetic variation in this spring-specialist plant. These findings suggest that spring-specialist plants deserve special consideration in ecological theory, management, and conservation.

Mimulus↗
PubMed2004

Neighbour joining trees, dominant markers and population genetic structure.

Population genetic theory for 'traditional' codominant loci showing low levels of allelic diversity (eg allozymes) has been well characterised and evaluated. In contrast, appropriate methods for the analysis of data from more recently developed marker systems are still being refined. For multilocus dominant markers such as amplified fragment length polymorphisms (AFLPs) and randomly amplified polymorphic DNA (RAPDs), the methods of data analysis can be split into two main categories. In population-based approaches, population allele frequencies are compared to obtain some measure of the partitioning of genetic diversity into within- and between-population components. In contrast, individual-based approaches use individual multilocus genotypes as the unit of analysis. Inferences on population processes such as gene flow are based on inter-relationships among individual samples as visualised on phenetic diagrams such as neighbour joining trees. Using a simulation approach coupled with neighbour joining analyses, we show that while the underlying population genetic structure is an important determinant of tree shape in the analysis of dominant data, the number of loci examined also affects the topology. At low levels of population differentiation (eg FST=0.07), mutually exclusive clustering of individuals into their respective populations can occur when sufficiently large numbers of loci are scored (eg 250 loci, typical of many AFLP studies). In contrast, unresolved star-shaped topologies can be recovered at higher levels of population differentiation (FST= >0.15) when lower numbers of loci are employed (eg 50 loci, typical of many RAPD studies). Thus, the relationship between tree topology and the extent of genetic structuring of populations is contingent upon the number of dominant loci scored. The consequences of these findings for the biological interpretation of individual-based analysis of dominant data sets are discussed.

Alleles↗
PubMed2005

[The "horse-shoe effect"of correspondence analysis for human population genetic structure and its population genetic explanation].

At present study, the reasons of "horse-shoe effect" in correspondence analysis for analyzing human population genetic structure was explained. Based on the structure of gene frequency matrix, we displaye the different patterns of Scallergram of correspondent analysis from different types of loci (HLA-A locus, and STR- CSF1PO locus in Chinese Han populations). The results indicate that different types of loci showed different patterns of Scallergram of correspondent analysis. When some alleles have very low frequency in the gene frequency matrix, there would be "horse-shoe effect" in the Scallergram of correspondent analysis. The reason is that the c2 distance measurement in correspondent analysis usually overrates the effect of the genes with low frequencies. To carry out the correspondent analysis of human population genetic structure, when the Scallergram presents "horse-shoe effect", one should examine the structure of gene frequency matrix, and confirm whether the "horse-shoe effect" shows the real pattern of population genetic structure. Only in this way, one can explain the "horse-shoe effect" correctly.

Alleles↗
PubMed2006

Extremely low effective population sizes, genetic structuring and reduced genetic diversity in a threatened bumblebee species, Bombus sylvarum (Hymenoptera: Apidae).

Habitat fragmentation may severely affect survival of social insect populations as the number of nests per population, not the number of individuals, represents population size, hence they may be particularly prone to loss of genetic diversity. Erosion of genetic diversity may be particularly significant among social Hymenoptera such as bumblebees (Bombus spp.), as this group may be susceptible to diploid male production, a suggested direct cost of inbreeding. Here, for the first time, we assess genetic diversity and population structuring of a threatened bumblebee species (Bombus sylvarum) which exists in highly fragmented habitat (rather than oceanic) islands. Effective population sizes, estimated from identified sisterhoods, were very low (range 21-72) suggesting that isolated populations will be vulnerable to loss of genetic variation through drift. Evidence of significant genetic structuring between populations (theta = 0.084) was found, but evidence of a bottleneck was detected in only one population. Comparison across highly fragmented UK populations and a continental population (where this species is more widespread) revealed significant differences in allelic richness attributable to a high degree of genetic diversity in the continental population. While not directly related to population size, this is perhaps explained by the high degree of isolation between UK populations relative to continental populations. We suggest that populations now existing on isolated habitat islands were probably linked by stepping-stone populations prior to recent habitat loss.

Animals↗
PubMed2003

Spatially structured genetic variation in a broadcast spawning bivalve: quantitative vs. molecular traits.

Understanding the origin, maintenance and significance of phenotypic variation is one of the central issues in evolutionary biology. An ongoing discussion focuses on the relative roles of isolation and selection as being at the heart of genetically based spatial variation. We address this issue in a representative of a taxon group in which isolation is unlikely: a marine broadcast spawning invertebrate. During the free-swimming larval phase, dispersal is potentially very large. For such taxa, small-scale population genetic structuring in neutral molecular markers tends to be limited, conform expectations. Small-scale differentiation of selective traits is expected to be hindered by the putatively high gene flow. We determined the geographical distribution of molecular markers and of variation in a shell shape measure, globosity, for the bivalve Macoma balthica (L.) in the western Dutch Wadden Sea and adjacent North Sea in three subsequent years, and found that shells of this clam are more globose in the Wadden Sea. By rearing clams in a common garden in the laboratory starting from the gamete phase, we show that the ecotypes are genetically different; heritability is estimated at 23%. The proportion of total genetic variation that is between sites is much larger for the morphological additive genetic variation (QST = 0.416) than for allozyme (FST = 0.000-0.022) and mitochondrial DNA cytochrome-c-oxidase-1 sequence variation (phiST = 0.017). Divergent selection must be involved and intraspecific spatial genetic differentiation in marine broadcast spawners is apparently not constrained by low levels of isolation.

Analysis of Variance↗
PubMed2026

Differences in structural color and population genetic structure of Western and Central Palearctic Polyommatus icarus populations.

The blue structural coloration of male Polyommatus icarus butterflies functions as a sexual signaling trait and exhibits remarkable spectral stability within populations despite being generated by highly complex photonic nanoarchitectures. The correlation of the blue sexual signaling color and population genetic variation of the butterflies was investigated across the Western and Central Palearctic regions. Dorsal wing reflectance spectra was measured for 95 male specimens and compared with the population genetic structure revealed in 99 specimens by 18 recently developed microsatellites. Reflectance measurements indicated a clear separation between the European and Central Asian populations, consistent with our previous findings, while the intermediate populations near the Ural Mountains exhibited distinct European spectral characteristics. In contrast, genetic variation showed limited structuring and correlated primarily with geographic distance, as indicated by a significant isolation-by-distance pattern. Thus, although both reflectance and genetic variations are geographically structured, spectral properties are only weakly correlated with genetic differentiation. Populations near the Ural Mountains exhibited genetic ancestry linked to Central Palearctic groups, while displaying distinct Western Palearctic coloration, suggesting that the focal species' sexual signaling is strongly influenced by local factors. These findings suggest that sexual signaling coloration may evolve at least partially independently of the neutral genetic background, offering additional insight into evolutionary divergence across broad geographic scales.

Animals↗
PubMed2002

The genetic structure of tetraploid Avena: a comparison of isozyme and RAPD markers.

Isozymes were the first widely used molecular markers in plant population analysis. They yielded valuable information on the amount and the structure of genetic variability. DNA technology has provided new types of markers based on DNA sequence, which make it possible to study polymorphisms in a much greater proportion of the genome. This is the reason why the use of isozymes is less popular nowadays. This effect would be justified if all markers provided the same type of information on polymorphism and genetic relationships among populations; otherwise, it would be necessary to use different markers to obtain the complete picture of the genetic structure of populations and species. In this study, we compared data of isozyme and RAPD markers in the populations of two tetraploid species of wild oats: Avena barbata populations collected in Argentina, and Avena murphyi populations collected in Spain and Morocco. The samples were evaluated for 9 isozymatic systems and 10 primers. The structure of genetic variability was studied using Nei's method, and the relationships between populations were estimated using Hedrick and Jaccard's similarities for isozymes and RAPDs, respectively. As expected, RAPDs were more polymorphic than isozymes, but the information obtained from both markers was weakly correlated. The various reasons for this observation are discussed, but our conclusion is that in order to study the structure of genetic variability, several types of markers should be used.

Argentina↗
PubMed2001

[Genetic structure and intraspecific genetic polymorphisms in natural populations of Psathyrostachys huashanica].

Psathyrostachys huashanica Keng, which is endemic to China, only distributes in Mt. Hua of Shaanxi Province. 5 enzyme systems coding 13 loci were analyzed in 13 subpopulations of P. huashanica from Mt. Hua. Allozyme analysis showed that high genetic variability and clonal diversity existed in the species. Mean proportions of polymorphic loci (95% criterion), average number of alleles per locus, and mean expected heterozygosity were 69.2%, 1.8 and 0.344, respectively. Simpson index was 0.998. A negative species mean fixation indice (-0.252) indicates that there is a considerable excess of heterozygotes compared to the expected proportions of heterozygote loci. Mean genetic distance among populations was 0.049 (range: 0-0.139), and 91% of the genetic variation resided within populations. Gene flow estimated by indirect methods was 2.77, which was much lower than the Nm value (5.24) of anemophytes. This suggested that gene flow of P. huashanica might be in a critical level, and genetic differentiation might occur in natural population of this species.

Genetic Variation↗
PubMed2004

[The gene flow of population genetic structure].

The difference of population genetic structure is one of the important embodiments of genetic diversity. There is a long history of the study of population genetic structure, and the study of gene flow of population genetic structure is aroused more and more importance. It has an important effect on population genetics, evolution biology, conservation biology and ecology. Although the level of gene flow is estimated by traditional population genetics, there is a large restriction in its precision. With the development of biological technology, the methods of the research on gene flow reach the molecular level. Methods of protein electrophoresis and molecular markers (RAPD, RFLP, VNTR, ISSR and mitochondrial DNA) are used to research gene flow among populations. This paper introduces not only some models of population genetic structure: Continent-Island Model, Island Model, Stepping-Stone Model, Isolation-By-Distance Model and Hierarchical Model; but also the study methods, function and role of gene flow is based on models of population genetic structure, research achievements in recent years and the restriction of the methods.

Alleles↗
PubMed2004

Spatial genetic structure within a metallicolous population of Arabidopsis halleri, a clonal, self-incompatible and heavy-metal-tolerant species.

Arabidopsis halleri, a close wild relative of A. thaliana, is a clonal, insect-pollinated herb tolerant to heavy metals (Zn, Pd, Cd) and a hyperaccumulator of Zn and Cd. It is of particular interest in the study of evolutionary processes and phytoremediation. However, little is known about its population gene flow patterns and the structure of its genetic diversity. We used five microsatellite loci to investigate the genetic structure at a fine spatial scale (10 cm to 500 m) in a metallicolous population of A. halleri. We also studied the contributions made by clonal propagation and sexual reproduction (seed and pollen dispersal) to the genetic patterns. Clonal diversity was high (D(G) > 0.9). Clonal spread occurs only at short distances (< 1 m). Both clonal spread and limited dispersal, associated with sexual reproduction, contribute to the significant spatial genetic structure revealed by spatial autocorrelation analysis. The shape of the autocorrelogram suggests that seed dispersal is restricted and pollen flow extensive, which may be related to intense activity by insect pollinators. Clonal spread was more extensive in the lowly polluted zone than in the highly polluted zone. This cannot be interpreted as a strategy for promoting the propagation of adapted genotypes under the harshest ecological constraints (highest heavy metal concentrations). The higher fine-scale spatial genetic structure found in the lowly polluted zone can be ascribed to plant densities that were lower than in the highly polluted zone. No evidence of genetic divergence due to spatial heavy metal heterogeneity was found between lowly and highly polluted zones.

Analysis of Variance↗
PubMed1978

Variation in the genetic structure of Peromyscus populations. I. Genetic heterozygosity--its relationship to adaptive divergence.

The genetic structure of nine Peromyscus maniculatus nebrascensis demes from southeastern Wyoming was determined by analyzing allozymes encoded by 23 genetic loci with polyacrylamide gel electrophoresis. Genetic variability is extremely high for two genetic parameters; the proportion of loci polymorphic per deme averaged 0.41. Previous estimates of genetic heterozygosity for species within the genus Peromyscus have a mean of 0.06. The results of the present study suggest that genetic heterozygosity is considerably higher within P. maniculatus demes than within demes of other species in the genus. Geographic range is correlated with heterozygosity among Peromyscus species, as is adaptive divergence into broad-niched species. These correlates suggest that high heterozygosity may reflect an adaptation to a variable environment.

Adaptation, Physiological↗