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PubMed2004

Spatial structure and genetic diversity of two tropical tree species with contrasting breeding systems and different ploidy levels.

Analyses of the spatial distribution pattern, spatial genetic structure and of genetic diversity were carried out in two tropical tree species with contrasting breeding systems and different ploidy levels using a 50-ha demographic plot in a lowland dipterocarp forest in Peninsular Malaysia. Shorea leprosula is a diploid and predominantly outcrossed species, whereas S. ovalis ssp. sericea is an autotetraploid species with apomictic mode of reproduction. Genetic diversity parameters estimated for S. leprosula using microsatellite were consistently higher than using allozyme. In comparisons with S. leprosula and other tropical tree species, S. ovalis ssp. sericea also displayed relatively high levels of genetic diversity. This might be explained by the lower pressure of genetic drift due to tetrasomic inheritance, and for autotetraploids each locus can accommodate up to four different alleles and this allows maintenance of more alleles at individual loci. The observed high levels of genetic diversity in S. ovalis ssp. sericea can also be due to a random retention of more heterogeneous individuals in the past, and the apomictic mode of reproduction might be an evolutionary strategy, which allows the species to maintain high levels of genetic diversity. The spatial distribution pattern analyses of both species showed significant levels of aggregation at small and medium but random distribution at the big diameter-class. The decrease in magnitude of spatial aggregation from small- to large-diameter classes might be due to compensatory mortality during recruitment and survival under competitive thinning process. Spatial genetic structure analyses for both species revealed significant spatial genetic structure for short distances in all the three diameter-classes. The magnitude of spatial genetic structure in both species was observed to be decreasing from smaller- to larger-diameter classes. The high spatial genetic structuring observed in S. ovalis ssp. sericea at the small-diameter class is due primarily to limited seed dispersal and apomictic mode of reproduction. The similar observation in S. leprosula, however, can be explained by limited seed and pollen dispersal, which supports further the fact that the species is pollinated by weak fliers, mainly of Thrips and Megalurothrips in the lowland dipterocarp forest.

Age Factors↗
PubMed1999

Impacts of seed and pollen flow on population genetic structure for plant genomes with three contrasting modes of inheritance.

The classical island and one-dimensional stepping-stone models of population genetic structure developed for animal populations are extended to hermaphrodite plant populations to study the behavior of biparentally inherited nuclear genes and organelle genes with paternal and maternal inheritance. By substituting appropriate values for effective population sizes and migration rates of the genes concerned into the classical models, expressions for genetic differentiation and correlation in gene frequency between populations can be derived. For both models, differentiation for maternally inherited genes at migration-drift equilibrium is greater than that for paternally inherited genes, which in turn is greater than that for biparentally inherited nuclear genes. In the stepping-stone model, the change of genetic correlation with distance is influenced by the mode of inheritance of the gene and the relative values of long- and short-distance migration by seed and pollen. In situations where it is possible to measure simultaneously Fst for genes with all three types of inheritance, estimates of the relative rates of pollen to seed flow can be made for both the short- and long-distance components of migration in the stepping-stone model.

Diploidy↗
PubMedDate not supplied

[Comparative analysis of the genetic structure of hybrid populations of European toads of the genus Bombina (Oken, 1816) from Ukraine and Croatia].

The comparative analysis of hybrid populations of toads Bombina bombina and B. variegata from Ukraine and Croatia revealed the essential differences in their genetic structure. The population composition and the direction of genetic introgression are determined initially by the ecological factors (the locality type, the country relief). The clear predominance of the red-bellied toad Bombina bombina was found in two cases: in the lowland populations and in the big samples. The second parental species, B. variegata, predominates in the highlands and in the small samples, respectively.

Alleles↗
PubMed1988

[Relative role of selective migration and pathology in the formation of genetic structure].

It is shown that elective migration, with respect to polymorphic loci genotypes, and their association with pathology affect unequally formation of genetic structure features of the population analysed. The correlative role of two processes mentioned is more or less specific, with respect to every concrete locus: the elective migration and the pathology have unidirectional impact in all groups, which leads to maximum dynamics of genotypes in groups with different duration of dwelling under extreme conditions (AcP, Pp loci). These processes act as antagonists, preserving constant genotype frequency (AK locus). Genotype frequency dynamics is mainly determined by the elective migration (Rh locus) or the pathology (PGD locus). The correlative role of the elective migration and the pathology is often unequal in groups with different duration of dwelling under the North-East conditions, as applied to concrete locus (GLO-1, PGM1), though the elective migration participates in groups with comparatively small dwelling-term in the North and the pathology has more influence as this term increases. The problem of genetic aspects of human adaptation is under discussion.

Adaptation, Physiological↗
PubMed2000

The use of molecular markers to investigate the genetic structure of an oil palm breeding programme.

RFLP markers (40 probes covering 60% of the oil palm genome) have been used to assess genetic diversity within 54 palms of a specific oil palm breeding programme. A further 10 palms encompassing a broader range of origins were also included to provide a wider framework for comparative analysis. These palms represent a majority of the parents in a crossing programme which aims to combine the best features of African tenera germplasm with South-east Asian Deli dura material. Progeny from these crosses are planted in up to six sites on three continents, where the palms are being assessed in detail for yield components. A total of 157 RFLP bands were scored and the data analysed by calculating genetic distances according to Nei & Li, and by correspondence and cluster analysis. The relationships that emerge through this molecular analysis correspond well with known pedigree and provenance. For example, south-east Asian Deli dura material forms a cluster clearly distinct from AVROS pisifera gene pools, and a selection of African breeding material forms a further and broader grouping. The potential ability of markers to assist in oil palm breeding through examination of the genetic structure of crossing programmes is discussed, as is their value in parental selection to maintain residual diversity within specific breeding pools and use in evaluating the fidelity of breeding lineages.

Chromosome Mapping↗
PubMed2001

Genetic structure of Siberian lemmings (Lemmus sibiricus) in a continuous habitat: large patches rather than isolation by distance.

In a continuous habitat, restricted dispersal and local genetic drift are likely to create a pattern of increasing genetic differentiation with distance. Here, we describe the genetic structure of Siberian lemming (Lemmus sibiricus) populations in a continuous tundra habitat on the western coast of the Taimyr Peninsula, in order to determine the spatial scale at which genetic differentiation and isolation by distance occur. Sampling was carried out at three different geographical scales: (1) a continuous 11 km transect; (2) localities 10-30 km apart; and (3) two localities at 300 and 600 km from the main study area. Two types of genetic markers were used: partial sequences of the mitochondrial DNA control region and four microsatellite loci. On this basis the study populations were genetically quite homogeneous within patches extending over 8 km or more. Contrary to theoretical predictions, no pattern of isolation by distance among patches could be identified. This observation was interpreted as representing populations in migration-drift disequilibrium after a recent major mixing event. The lack of concordance between mtDNA haplotype phylogeny and the geographical distribution of haplotypes supported this interpretation. Spatial autocorrelation among individual genotypes on a local scale was weak and observed only in females, indicating a considerable amount of mostly male-mediated gene flow. Average gene flow per generation was estimated to be in the range of several hundred metres.

Alleles↗
PubMed2003

[Genetic structure of the Iranian-speaking population of Azerbaijan from data on frequencies of immunologic and biochemical gene markers].

The data on the genetic studies of Iranian-speaking populations from Azerbaijan (Talyshs and Tats) are presented. In these populations gene frequency distributions for the immunological (AB0, MN, Rhesus-D, -C, -E, P, Lewis, and Kell-Chellano) and biochemical (HP, GC, C'3, TF, 6PGD, GLO1, ESD, ACP1, and PGM1) gene markers were determined. Comparison of the genetic structure of the populations examined with the other Iranian-speaking populations (Persians and Kurds from Iran, Ossetins and Tajiks) and Azerbaijanis showed that Iranian-speaking populations from Azerbaijan were more close to Azerbaijanis, than to Iranian-speaking populations inhabiting other world regions.

Azerbaijan↗
PubMed1981

Periodic selection, infectious gene exchange and the genetic structure of E. coli populations.

As a consequence of sequential replacements by clones of higher fitness (periodic selection), bacterial populations would be continually purged of genetic variability, and the fate of selectively neutral alleles in very large populations of bacteria would be similar to that in demes of sexually reproducing organisms with small genetically effective population sizes. The significance of periodic selection in reducing genetic variability in these clonally reproducing species is dependent on the amount of genetic exchange between clones (recombination). In an effort to determine the relationship between the rates of periodic selection, recombination and the genetically effective sizes of bacterial populations, a model for periodic selection and infectious gene exchange has been developed and its properties analyzed. It shows that, for a given periodic selection regime, genetically effective population size increases exponentially with the rate of recombination.--With the parameters of this model in the range anticipated for natural populations of E. coli, the purging effects of periodic selection on genetic variability are significant; individual populations or lineages of this bacterial species would have very small genetically effective population sizes.--Based on this result, some other a priori considerations and a review of the results of epidemiological and genetic variability studies, it is postulated that E. coli is composed of a relatively limited number of geographically widespread and genetically nearly isolated and monomorphic lineages. The implications of these considerations of the genetic structure of E. coli populations on the interpretation of protein variation and the neutral gene hypothesis are discussed.

Escherichia coli↗
PubMed1982

The genetic structure of Iceland.

Gene frequencies and parent-offspring migration data from nine geographic subdivisions in Iceland are analyzed. Estimated values of FST show high genetic homogeneity. Genetic maps are studied and the results are interpreted in the light of social and historical patterns. Actual road distances between subdivisions provide a slightly better indication of geographic isolation by distance than do straight-line distances. A high correlation between genetic structure predicted by migration data and the structure estimated from gene frequencies is obtained.

Aged↗
PubMed2001

Hierarchical genetic structure of the introduced wasp Vespula germanica in Australia.

The wasp Vespula germanica is a highly successful invasive pest. This study examined the population genetic structure of V. germanica in its introduced range in Australia. We sampled 1320 workers and 376 males from 141 nests obtained from three widely separated geographical areas on the Australian mainland and one on the island of Tasmania. The genotypes of all wasps were assayed at three polymorphic DNA microsatellite markers. Our analyses uncovered significant allelic differentiation among all four V. germanica populations. Pairwise estimates of genetic divergence between populations agreed with the results of a model-based clustering algorithm which indicated that the Tasmanian population was particularly distinct from the other populations. Within-population analyses revealed that genetic similarity declined with spatial distance, indicating that wasps from nests separated by more than approximately 25 km belonged to separate mating pools. We suggest that the observed genetic patterns resulted from frequent bottlenecks experienced by the V. germanica populations during their colonization of Australia.

Animals↗
PubMedDate not supplied

Genetic structure, mating system, and long-distance gene flow in heart of palm (Euterpe edulis Mart.).

We report a detailed analysis of the population genetic structure, mating system, and gene flow of heart of palm (Euterpe edulis Mart.-Arecaceae) in central Brazil. This palm is considered a keystone species because it supplies fruits for birds and rodents all year and is intensively harvested for culinary purposes. Two populations of this palm tree were examined, using 18 microsatellite loci. The species displays a predominantly outcrossed mating system (tm = 0.94), with a probability of full sibship greater than 70% within open-pollinated families. The following estimates of interpopulation genetic variation were calculated and found significant: FIT = 0.17, FIS = 0.12, FST = 0.06, and RST = 0.07. This low but significant level of interpopulation genetic variation indicates high levels of gene flow. Two adult trees were identified as likely seed parents (P > 99.9%) of juveniles located at a distance of 22 km. Gene flow over such distances has not been reported before for tropical tree species. The establishment and management of in situ genetic reserves or ex situ conservation and breeding populations for E. edulis should contemplate the collection of several hundreds open-pollinated maternal families from relatively few distant populations to maximize the genetic sampling of a larger number of pollen parents.

Arecaceae↗
PubMed1974

The genetic structure of natural populations of Drosophila melanogaster. XI. Genetic variability in a local population.

Six hundred and ninety-one second chromosomes were extracted from a Raleigh, North Carolina population, and the following experimental results were obtained: (1) Salivary gland chromosomes of all lines were observed and the number of inversion-carrying chromosomes was 130, among which 76 carried In(2R)NS, 36 carried In(2L)t, 4 carried In(2L)t and In(2R)NS, and 14 carried different kinds of rare inversions. (2) Viabilities of homozygotes and heterozygotes were examined. The frequency of lethal-carrying chromosomes was 275/691 (or 0.398):70/130 (or 0.538) in inversion-carrying chromosomes and 205/561 (or 0.365) in inversion-free chromosomes. The former is significantly higher than the latter. The average homozygote viability was 0.4342 including lethal lines and 0.7163 excluding those, the average heterozygote viability being 1.0000. The detrimental load to lethal load ratio (D:L ratio) was 0.334/0.501 = 0.67. The average viability of lethal heterozygotes was less than that of lethal-free heterozygotes, significantly in inversion-free individuals but not significantly so in inversion-carrying individuals. Inversion heterozygotes seem to have slightly better viability than the inversion-free heterozygotes on the average, but not significantly so. (3) The average degree of dominance of viability polygenes was estimated to be 0.293 +/- 0.071 for all heterozygotes whose component chromosomes had better viabilities than 0.6 of the average heterozygote viability, 0.177 +/- 0.077 for inversion-free heterozygotes and 0.489 +/- 0.082 for inversion heterozygotes. (4) Mutation rates of viability polygenes and lethal genes were estimated on the basis of genetic loads and average degrees of dominance of lethal genes and viability polygenes. Estimates were very close to those obtained by direct estimation. (5) Possible overdominance and epistasis were detected, but the magnitude must be very small. (6) The effective size of the population was estimated to be much greater than 10,000 by using the allelism rate of lethal-carrying chromosomes (0.0040) and their frequency.-On the basis of these findings and the comparison with the predicted result (Mukai and Maruyama 1971), the mechanisms of the maintenance of genetic variability in the population are discussed.

Adaptation, Biological↗
PubMed2000

Genetic structure of avian populations--allozymes revisited.

Selection on allozymes has sometimes been advanced as one explanation for the low levels of population differentiation detected in avian populations by the use of enzymatic markers. Comparisons of the amount of population subdivision (estimated by FST values or analogous indices) measured by enzymatic and mitochondrial DNA (mtDNA) markers in birds were seen as evidence for this because mtDNA typically produces a more structured picture of population subdivisions. In fact, when taking into account the smaller effective population size of mtDNA, nuclear and mitochondrial markers give concordant results. Some discrepancies still exist, but I suggest that some might originate from different amounts of nuclear vs. mitochondrial gene flow due to partial reproductive isolation. Variable number of tandem repeat (VNTR) loci do not provide a dramatically different picture of population structures in birds compared to allozymes. Although more tests are needed, such as comparing the amount of genetic structure detected in the same populations with allozymes and microsatellites, the low levels of population subdivision measured with allozymes in birds seem to reflect historical and demographic processes and would not appear to result from any peculiarities of bird enzymatic loci.

Animals↗
PubMed1988

Fine-structure genetics of ama-1, an essential gene encoding the amanitin-binding subunit of RNA polymerase II in Caenorhabditis elegans.

A fine-structure genetic map has been constructed for ama-1 IV, an essential gene in Caenorhabditis elegans encoding the amanitin-binding subunit of RNA polymerase II. Sixteen EMS-induced recessive-lethal mutations have been positioned in the gene by determining their intragenic recombination frequencies with m118, a mutation that confers dominant resistance to alpha-amanitin. The 16 mutants, all isolated in the ama-1(m118) background, include 13 that are early larval lethals, and three that are mid-larval lethals, at 25 degrees. Six of the mutants exhibit temperature-dependence in the severity of their phenotype. Intragenic recombination between the lethal site and the parental resistance mutation was detected by means of resistance to amanitin. Recombinants were detected at frequencies as low as 2 X 10(-6). The segregation of the closely linked flanking markers, unc-17 and unc-5, revealed whether the lethal mutation was to the left or the right of m118. By adding the distances between the extreme left and right mutations, the ama-1 gene is estimated to be 0.011 map unit long, with m118 positioned 0.004 map unit from the left-most lethal mutation. To order the lethal mutations with respect to each other, viable heteroallelic strains were constructed using the free duplication, mDp1[unc-17(e113) dpy-13(+) ama-1(+)]. The heteroallelic strains were sensitive to amanitin, and recombination events between the lethal mutations were specifically selected by means of the dominant amanitin resistance encoded on the recombinant chromosome. The segregation of outside markers revealed the left-right order of the lethal mutations. The position of mutations within the gene is nonrandom. Functional domains of the ama-1 gene indicated by the various lethal phenotypes are discussed.

Alleles↗
PubMed2004

Population genetic structure of the polypore Datronia caperata in fragmented mangrove forests.

Datronia caperata, a basidiomycete fungus, is one of the dominant polypore species found in neotropical mangrove forest fragments, where it is locally specialized on Laguncularia racemosa. We examined the genetic structure of D. caperata populations from four Panamanian mangrove forests using AFLP markers. Using five primer pair combinations, 145 loci were detected, 98.6% of which were polymorphic. Each of the populations showed a high degree of genetic diversity (Nei's h ranging from 0.146 to 0.223). Results from minimum spanning trees and Mantel tests showed little evidence for small-scale spatial structure within sites. A significant amount of total genetic variation was partitioned among populations (phi(ST) = 0.21) separated by 10s to 100s of km, a considerably greater amount than has been detected in other mushroom and wood-decaying fungi sampled at equal or greater geographic distances. These results suggest that despite production of copious basidiospores capable of long distance dispersal, some homobasidiomycete fungi may be susceptible to genetic isolation due to habitat fragmentation.

Base Sequence↗
PubMed2001

Population genetic structure of the malaria mosquito Anopheles arabiensis across Nigeria suggests range expansion.

Ten microsatellite loci, four located within and six outside chromosome inversions, were employed to study the genetic structure of Anopheles arabiensis across the ecological zones of Nigeria (arid savannah in the north gradually turns into humid forest in the south). Regardless of location within or outside inversions, genetic variability at all loci was characterized by a reduction in both the number of alleles per locus and heterozygosity from savannah to forest. Across all loci, all but one allele in the forest also occurred in the savannah, whereas at least 78 alleles in the savannah were missing in the forest. Genetic differentiation increased with geographical distance; consequently, genetic distances between zones exceeded those within zones. The largest genetic distances were between localities at the extremes of the transect (range F(ST) = 0.196-0.258 and R(ST) = 0.183-0.468) and were as large as those between A. arabiensis and Anopheles gambiae s.s. Gene flow across the country was very low, so that Nm between the extremes of the transect was < 1. These data suggest that A. arabiensis has extended its range from the savannah into the forest during which it experienced a reduction in effective population size due to sequential founder effects. Gene flow post range expansion appears too restricted by geographical distance to homogenize the gene pool of A. arabiensis across Nigeria.

Alleles↗
PubMedDate not supplied

Population genetic structure and colonization sequence of Drosophila subobscura in the Canaries and Madeira Atlantic Islands as inferred by autosomal, sex-linked and mtDNA traits.

The genetic structure in Atlantic Islands and continental populations of Drosophila subobscura has been studied using autosomal and sex-linked allozymes and mitochondrial DNA (mtDNA) haplotypes. From the data it is deduced that whereas the Canary islands have long been isolated, the neighboring island of Madeira has been subjected to continuous migration from the mainland. In addition, sex-linked allozymes and mtDNA data show a large divergence between the geologically younger western islands of the Canarian Archipelago and the older central ones, finding strong founder effects in the former. Divergence rates of sex-linked and mitochondrial genes relative to autosomic loci several times higher than expected under neutrality have been explained by differential migration between sexes. The Canarian Archipelago colonization fits in well with a stepping-stone model of a directional east-west migration that parallels the geological origin of these Islands.

Animals↗