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PubMed2003

Genetic structure of age classes in Camellia japonica (Theaceae).

Camellia japonica L. (Theaceae), an insect- and bird-pollinated, broad-leaved evergreen tree, is widely distributed in Japan and the southern Korean peninsula. The species has a relatively even age distribution within populations, which may influence the spatial genetic structure of different age classes relative to species with typical L-shaped age distributions. To determine whether the internal spatial genetic structure found in seedlings and young individuals carries over into adults, we used allozyme loci, F-statistics, spatial autocorrelation statistics (Moran's I), and coancestry measures to examine changes in genetic structure among seven age classes in a population (60-m x 100-m area) in southern Korea. In seedlings, weak but significant positive values of Moran's I-statistics and coancestry measures were found for distances less than 14 m, which is consistent with a mechanism of limited seed dispersal combined with overlapping seed shadows. This spatial structure, however, dissipates in older age classes, and in adults genetic variation has an essentially random spatial distribution. Morisita's index of dispersion of individuals in each age class showed that seedlings and juveniles are more highly clustered than are older individuals. These results suggest that self-thinning changes the spatial relationships of individuals, and thus genotypes. A multilocus estimate of FST (0.008) shows a small but statistically significant difference in allele frequencies among age classes. In summary, intrapopulation genetic structure within and among age classes of C. japonica was significant but weak. Despite presumably limited seed dispersal, weak spatial genetic structure in juveniles suggests overlapping seed shadows followed by self-thinning during recruitment. The present study also demonstrates that studies of spatial genetic structure focusing on limited numbers of generations may not be sufficient to reveal the entire picture of genetic structure in populations with overlapping generations.

Electrophoresis↗
PubMed2005

Microsatellite analyses reveal fine-scale genetic structure in grey mouse lemurs (Microcebus murinus).

Information on genetic structure can be used to complement direct inferences on social systems and behaviour. We studied the genetic structure of the solitary grey mouse lemur (Microcebus murinus), a small, nocturnal primate endemic to western Madagascar, with the aim of getting further insight on its breeding structure. Tissue samples from 167 grey mouse lemurs in an area covering 12.3 km2 in Kirindy Forest were obtained from trapping. The capture data indicated a noncontinuous distribution of individuals in the study area. Using 10 microsatellite markers, significant genetic differentiation in the study area was demonstrated and dispersal was found to be significantly male biased. Furthermore, we observed an overall excess of homozygotes in the total population (F(IT) = 0.131), which we interpret as caused by fine-scale structure with breeding occurring in small units. Evidence for a clumped distribution of identical homozygotes was found, supporting the notion that dispersal distance for breeding was shorter than that for foraging, i.e. the breeding neighbourhood size is smaller than the foraging neighbourhood size. In conclusion, we found a more complex population structure than what has been previously reported in studies performed on smaller spatial scales. The noncontinuous distribution of individuals and the effects of social variables on the genetic structure have implications for the interpretation of social organization and the planning of conservation activities that may apply to other solitary and endangered mammals as well.

Animals↗
PubMed2002

Size-class differences in genetic structure and individual distribution of Camellia japonica L. in a Japanese old-growth evergreen forest.

Size-class differences in genetic structure and individual spatial distribution were investigated for Camellia japonica within a 1-ha plot in a Japanese old-growth evergreen forest using microsatellite markers. Three size-classes were considered containing plants that were: 30-32.5 cm tall, 103.8 cm-200 cm tall and those that had a diameter at breast height > or =5 cm, designated JV1, JV2, and ADL, respectively. Each size-class contained 174 individuals. Morisita's index of dispersion indicated clumping of individuals was present within all size-classes, with JV2 displaying the highest level. The clumped distribution of JV1 individuals may be a result of limited seed dispersal, while that of JV2 may be attributed to heterogenieties of favourable microsites, such as canopy gaps. There were no significant differences in allele frequencies among size-classes. There were, however, some differences in spatial genetic structure among them. Moran's I spatial autocorrelation analysis revealed clear spatial genetic structure in class JV1 probably due to limited seed dispersal. In class JV2, genetic structure was not observed. Overlapping seed shadows, probably in canopy gaps, may lead to blurred genetic structure in JV2.

Camellia↗
PubMed2001

Analysis of six prophages in Lactococcus lactis IL1403: different genetic structure of temperate and virulent phage populations.

We report the genetic organisation of six prophages present in the genome of Lactococcus lactis IL1403. The three larger prophages (36-42 kb), belong to the already described P335 group of temperate phages, whereas the three smaller ones (13-15 kb) are most probably satellites relying on helper phage(s) for multiplication. These data give a new insight into the genetic structure of lactococcal phage populations. P335 temperate phages have variable genomes, sharing homology over only 10-33% of their length. In contrast, virulent phages have highly similar genomes sharing homology over >90% of their length. Further analysis of genetic structure in all known groups of phages active on other bacterial hosts such as Escherichia coli, Bacillus subtilis, MYCOBACTERIUM: and Streptococcus thermophilus confirmed the existence of two types of genetic structure related to the phage way of life. This might reflect different intensities of horizontal DNA exchange: low among purely virulent phages and high among temperate phages and their lytic homologues. We suggest that the constraints on genetic exchange among purely virulent phages reflect their optimal genetic organisation, adapted to a more specialised and extreme form of parasitism than temperate/lytic phages.

Bacteriophages↗
PubMed1999

Population genetic structure and the effect of founder events on the genetic variability of moose, Alces alces, in Canada.

Moose, Alces alces, occur naturally throughout most of Canada but successful introductions of known numbers of animals have been made to the islands of Newfoundland and Cape Breton. Five microsatellite loci were used to investigate the population genetic structure and any change in genetic variability due to founder events of moose in Canada. Comparisons of allele frequencies for moose from 11 regions of the country suggested that there are at least seven genetically distinct populations (P < 0.05) in North America, namely Alberta, eastern Ontario, New Brunswick, Cape Breton, Labrador, western Newfoundland, and the Avalon Peninsula of Newfoundland. The average population heterozygosity was approximately 33% (range from 22 to 41%). UPGMA analysis of Nei's genetic distances produced phenograms similar to what would be expected when geographical location and population history are considered. The loss of heterozygosity due to a single founder event (n = 3; two introductions and a natural colonization) ranged from 14 to 30%, and the cumulative loss of heterozygosity due to two successive founder events (an introduction followed by a natural colonization) was 46%. In these examples loss of genetic variability has not been associated with any known phenotypic deviances, suggesting that populations may be established from a small number of founders. However, the viability of these founded populations over evolutionary timescales cannot be determined and is highly dependent upon chance.

Alleles↗
PubMed1999

Systematics and genetic structure of Ponderosae taxa (Pinaceae) inhabiting the mountain islands of the Southwest.

The systematics and genetic structure of taxa representing the Ponderosae subsection of genus Pinus were assessed for disjunct, isolated, and peripheral populations occupying the mountain islands of the Southwest. Wind-pollinated progenies of 290 trees were compared in common gardens according to ten variables reflecting allometric, needle, and phenologic characteristics of 2-yr-old trees. The tests also included populations of similar taxa from the Rocky Mountains to the north and the Sierra Madre to the south. Principal component and canonical discriminant analyses demonstrated that the taxa segregated into three distinct groups, one of which contained two subgroups. These groupings collectively accounted for all of the many and confusing taxonomic descriptions that exist for the Ponderosae of the southwest United States and northern Mexico. The results suggested that intertaxa hybrids or hybrid derivatives may have been segregating within the progenies of only three of the parental trees. Hybridization, therefore, appears to be infrequent and inconsequential to the interrelationships among taxa and to contemporary genetic structures of taxa. Univariate analyses showed that the three distinct groups displayed different genetic structures despite similarities in their geographic distributions. While genetic variation within populations of all groups was abundant, a group labeled "quinquefoliata" displayed little variation among populations; one labeled "engelmannii" had abundant interpopulation variation that was largely randomly distributed across the landscape; and in a group containing the subgroups called "scopulorum" and "taxon X," abundant interpopulation variability was arranged systematically along moderately steep clines. These disparate genetic structures showed no apparent effects of the isolated, disjunct, and peripheral conditions under which populations of these taxa exist.

Journal Article↗
PubMedDate not supplied

Population genetic structure of Anopheles arabiensis mosquitoes in Ethiopia and Eritrea.

This study examined the population genetic structure of the major malaria vector, Anopheles arabiensis mosquitoes, in Ethiopia and Eritrea. Ethiopia and Eritrea have great geographical diversity, with high mountains, rugged plateaus, deep gorges, and rolling plains. The plateau is bisected diagonally by the Great Rift Valley into the Northwestern Highlands and the Southeastern Highlands. Five A. arabiensis populations from the Northwestern Highlands region and two populations from high-altitude sites in the Great Rift Valley were genotyped using six microsatellite markers to estimate the genetic diversity and population genetic structure of A. arabiensis. We found that A. arabiensis populations from the Northwestern Highlands and the Great Rift Valley region showed a similar level of genetic diversity. The genetic differentiation (F(ST)) of the five mosquito populations within the Northwestern Highlands region was 0.038 (P <.001), while the two populations within the Great Rift Valley showed little genetic differentiation (F(ST) = 0.007, P <.01). The degree of genetic differentiation between the Northwestern Highlands region and the Great Rift Valley region was small but statistically significant (F(ST) = 0.017, P <.001). The population genetic structure of A. arabiensis in the study area did not follow the isolation-by-distance model (r(2) = 0.014, P >.05). The low F(ST) estimates for A. arabiensis populations in Ethiopia and Eritrea are consistent with the general population genetic structure of this species in East Africa based on other molecular markers.

Animals↗
PubMed2004

Population genetic structure of a colonising, triploid weed, Hieracium lepidulum.

Understanding the breeding system and population genetic structure of invasive weed species is important for biocontrol, and contributes to our understanding of the evolutionary processes associated with invasions. Hieracium lepidulum is an invasive weed in New Zealand, colonising a diverse range of habitats including native Nothofagus forest, pine plantations, scrubland and tussock grassland. It is competing with native subalpine and alpine grassland and herbfield vegetation. H. lepidulum is a triploid, diplosporous apomict, so theoretically all seed is clonal, and there is limited potential for the creation of variation through recombination. We used intersimple sequence repeats (ISSRs) to determine the population genetic structure of New Zealand populations of H. lepidulum. ISSR analysis of five populations from two regions in the South Island demonstrated high intrapopulation genotypic diversity, and high interpopulation genetic structuring; PhiST = 0.54 over all five populations. No private alleles were found in any of the five populations, and allelic differentiation was correlated to geographic distance. Cladistic compatibility analysis indicated that both recombination and mutation were important in the creation of genotypic diversity. Our data will contribute to any biocontrol program developed for H. lepidulum. It will also be a baseline data set for future comparisons of genetic structure during the course of H. lepidulum invasions.

Alleles↗
PubMedDate not supplied

[The genetic structure of Kulunda sheep].

The analysis of the genetic structure of the Kulunda sheep in eight polymorphous genetic-biochemical systems was carried out. While comparing with the genetic structures of number of sheep breeds, differentiated by the origin history, productivity traits and the breeding regions, the locus-specificity particularities of the Kulunda sheep were described. The importance of creating of the "genetic portrait" for disappearing breeds was discussed.

Alleles↗
PubMed2005

Spatial genetic structure among and within populations of Primula sieboldii growing beside separate streams.

We investigated the hierarchical genetic structure of SSR (simple sequence repeats) and cpDNA (chloroplast DNA) polymorphisms among and within populations of Primula sieboldii, a heterostylous clonal herb. Seven out of eight populations at the study site, located in a mountainous region of Nagano Prefecture, had each developed alongside a different stream, and the other occurred on a flat area 70 m from the nearest stream. The magnitude of genetic differentiation among streamside populations in maternally inherited cpDNA (Phi = 0.341) was much higher than that in biparentally inherited SSRs (Phi = 0.011). This result suggests that seed dispersal among streams was restricted, and pollen was the primary agent of gene flow among streamside populations. In contrast, genetic differentiation among subpopulations within streams were low at both markers (Phi = 0.053 for cpDNA, Phi = 0.025 for SSR). This low differentiation among subpopulations in cpDNA compared with that among streamside populations suggest that seed dispersal occur along the stream probably during flooding. This hypothesis was supported by the fact that in cpDNA haplotypes, no clear genetic structure was detected within the streamside population, while a significant genetic structure was found within 20 m in the nonstreamside population. Furthermore, within the streamside populations, two pairs of ramets with identical multilocus genotypes for eight SSR loci were distantly (> 50 m) distributed along the same streamside, suggesting dispersal of clonal propagule. Our study showed that the heterogeneity of the landscape can influence gene flow and hence spatial genetic structure.

Chloroplasts↗
PubMed1985

Genetic structure of populations of Legionella pneumophila.

The genetic structure of populations of Legionella pneumophila was defined by an analysis of electrophoretically demonstrable allelic variation at structural genes encoding 22 enzymes in 292 isolates from clinical and environmental sources. Nineteen of the loci were polymorphic, and 62 distinctive electrophoretic types (ETs), representing multilocus genotypes, were identified. Principal coordinates and clustering analyses demonstrated that isolates received as L. pneumophila were a heterogeneous array of genotypes that included two previously undescribed species. For 50 ETs of L. pneumophila (strict sense), mean genetic diversity per locus was 0.312, and diversity was equivalent in ETs represented by isolates recovered from clinical sources and those collected from environmental sources. Cluster analysis revealed four major groups or lineages of ETs in L. pneumophila. Genetic diversity among ETs of the same serotype was, on average, 93% of that in the total sample of ETs. Isolates marked by particular patterns of reactivity to a panel of nine monoclonal antibodies were also genetically heterogeneous, mean diversity within patterns being about 75% of the total. Both Pontiac fever and the pneumonic form of legionellosis may be caused by isolates of the same ET. The genetic structure of L. pneumophila is clonal, and many clones apparently are worldwide in distribution. The fact that L. pneumophila is only 60% as variable as Escherichia coli raises the possibility that isolates recovered from clinical cases and man-made environments are a restricted subset of all clones in the species as a whole.

Alleles↗
PubMed2004

Genetic structure among closely spaced leks in a peripheral population of lesser prairie-chickens.

We evaluated the genetic structure of birds from four closely spaced leks in a peripheral population of lesser prairie-chickens (Tympanuchus pallidicinctus). Analyses of molecular variance revealed significant genetic structuring among birds from different leks for six microsatellite loci (FST = 0.036; P = 0.002), but we found no genetic differentiation at the mtDNA control region. Significant deviations from Hardy-Weinberg revealed an excess of homozygote genotypes within each of the leks studied (FIS = 0.190-0.307), indicative of increased inbreeding. Estimates of relatedness using microsatellite data suggest that the genetic structuring among lesser prairie-chicken leks occurs in part because of a lek mating system in which males at some leks are related. Structuring may also be caused by stochastic effects associated with a historical decline in population size leading to small, semi-isolated leks and high site fidelity by reproductive males. Results from this study suggest that microspatial genetic structuring may occur in lek-mating bird species with low levels of dispersal.

Analysis of Variance↗
PubMed2000

Genetic structure of Camellia japonica L. in an old-growth evergreen forest, Tsushima, Japan.

The spatial genetic structure of Camellia japonica was investigated, using microsatellite markers, in a 4-ha permanent plot within an old-growth forest. Spatial distribution of individuals was also assessed to obtain an insight into spatial relationships between individuals and alleles. Morisita's index of dispersion showed that 518 C. japonica individuals in the plot were clumped, and Moran's I spatial autocorrelation coefficient revealed weak genetic structure, indicating a low level of allele clustering. Average I correlograms showed that there was stronger genetic structure over short-distance classes. The clumped distribution of individuals and the positive autocorrelation over short-distance classes may result from the limited seed dispersal and microsite heterogeneity of the stand, while the genetic structure may be weakened by overlapping seed shadow and extensive pollen flow, mediated by animal vectors, and the high outcrossing rate found in C. japonica.

Ericales↗
PubMed2004

Size distribution and genetic structure in relation to clonal growth within a population of Magnolia tomentosa Thunb. (Magnoliaceae).

To establish a baseline for conservation of a threatened clonal tree, Magnolia tomentosa, we investigated size distribution and genetic structure within a population, using six microsatellite markers. Within the study site, 1044 living ramets (stems) were distinguished into 175 genets (individuals). The mean number of ramets per genet was 5.97, and 76% of all genets had multiple ramets. Genets, which apparently produced new ramets through sprouting and layering, were generally composed of several large ramets and many small ramets. Spatial autocorrelation analysis of microsatellite alleles revealed positive autocorrelation over short distances for both ramets and genets. The Moran's I-value of ramets in the shortest distance class was 3.8 times larger than that of genets, reflecting the effect of clonal growth. To analyse the size-class differences in genetic structure, the 175 genets were separated into two size classes, small and large. The correlogram for the small genets exhibited positive spatial autocorrelation in the shortest distance class, but this was not the case for the correlogram for the large genets, indicating that genetic structure is weakened or lost through self-thinning as the genets grow. The FIS value over all loci for the small genets was positive and deviated significantly from zero, while the corresponding value for the large genets was close to zero. The excess homozygotes in the small genets may be the result of genetic substructuring and/or inbreeding, and the reduction in homozygote frequency from the small to large genets may be because of loss of genetic structure and/or inbreeding depression.

Alleles↗
PubMed2005

Clonal and spatial genetic structures of aspen (Populus tremuloides Michx.).

To portray aspen clonal and spatial genetic structures, we mapped and genotyped trees in two 1-ha plots, each containing three aspen cohorts originating from fire or subsequent secondary disturbances. We used four microsatellite loci to identify aspen clones and increment core analysis to determine tree age. Clonal dimensions were measured by the maximum distance between two ramets and the number of ramets per genet. Standard normal deviate (SND) was used to assess the spatial distribution of aspen genets and cohorts, and multivariate spatial genetic autocorrelations to assess the spatial distribution of aspen genetic variation. Most aspen genets consisted of only one ramet (> 75%). Median clonal dimensions were 19 and 29 m (maxima: 104 and 72 m in the two plots). No segregation was observed between clones. Aspen cohorts were spatially segregated but trees were spatially aggregated within old and medium-aged cohorts. In contrast, trees were more randomly distributed within the youngest cohorts. This coincided with a spatial genetic autocorrelation at small scales (up to 30 m) in the older cohorts and a more random genetic distribution in the youngest ones. Our results suggest that aspen spatial genetic structuring reflects the spatial patterns produced by the regeneration of discrete cohorts at different stages of succession. Vegetative reproduction leads to aspen genetic spatial structuring at small scales (few metres) until midsuccession. However, as the stand gets older, the spatial distribution of aspen trees and genetic structure evolve from a structured pattern to a more random one under a gap disturbances regime.

Clone Cells↗
PubMed1994

Population genetic structure of the schistosome-vector snail Bulinus globosus: examining the role of genetic drift, migration and human activities.

Bulinus globosus, one of the intermediate hosts of the genus Schistosoma, is an hermaphrodite freshwater snail species. This species occupies different kinds of environments in Africa, which are generally subjected to large variations in water availability. The mating system of this species is outcrossing, although selfing has been suggested for one population. Here we investigate the genetic structure of populations of B. globosus in natural and human-modified environments from Niger and Ivory Coast using protein electrophoresis. Our goal is to analyse the respective role of the environment (genetic drift and gene flow), the mating system and human activities. Our results indicate a low intrapopulation polymorphism. A large differentiation among populations occurs on the scale of the whole study area whereas neighbouring populations can show little differentiation. These results point to the role of genetic drift and gene flow as the main factors shaping the genetic structure, with human activities playing a role occasionally.

Alleles↗
PubMed2005

[Genetic structure and phylogeny status of Chaidamu goat population].

Genetic structure and character of Chaidamu goats were studied through simple random sampling. Genetic structure was analysed from five aspects, and phylogeny status was also investigated. The results indicated that: (1) the average phenotypic heterogeneity degree of coat color and morphological character were 0.3419 and 0.5207, respectively; (2) polymorphous blood albumen existed in 6 loci and the average loci heterozygosity was 0.2584; and (3) polymorphism existed in marked genes by DND-RAPD with diversity of 0.4085 approximately 0.5318. Phylogeny status was investigated through clustering by Ward's method on Chaidamu Goats and other domestic goats. All these indicated that Chaidamu Goats was a domestic goat with less intensively selected breed.

Albumins↗
PubMed1999

Fine-scale genetic structuring in a natural population of European wild rabbits (Oryctolagus cuniculus).

The genetic structure of a free-living tagged population of European wild rabbits (Oryctolagus cuniculus) was investigated for two consecutive years (1990 and 1991) using 10 polymorphic microsatellite loci. A specific social behaviour, the formation of stable breeding groups, influenced the genetic structure of the population. These breeding groups were shown to constitute genetically differentiated units with low levels of gene flow between them. The average relatedness among members of a social group was higher than within the population as a whole. As a result of female philopatry coupled with male-biased natal dispersal, the relatedness of females was higher than that of males, both within social groups and in the whole population. Furthermore, the average relatedness of females within groups was twice the relatedness of females between groups. This study reveals marked fine-scale, intrapopulation genetic structure, which is attributable to the social behaviour of the European wild rabbit.

Age Factors↗