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At least 541 records · Page 30Linked to original sources
PubMed2005

Is variation in susceptibility to Phytophthora ramorum correlated with population genetic structure in coast live oak (Quercus agrifolia)?

California coastal woodlands are suffering severe disease and mortality as a result of infection from Phytophthora ramorum. Quercus agrifolia is one of the major woodland species at risk. This study investigated within- and among-population variation in host susceptibility to inoculation with P. ramorum and compared this with population genetic structure using molecular markers. Susceptibility was assessed using a branch-cutting inoculation test. Trees were selected from seven natural populations in California. Amplified fragment length polymorphism molecular markers were analysed for all trees used in the trials. Lesion sizes varied quantitatively among individuals within populations, with up to an eightfold difference. There was little support for population differences in susceptibility. Molecular structure also showed a strong within-population, and weaker among-population, pattern of variation. Our data suggest that susceptibility of Q. agrifolia to P. ramorum is variable and is under the control of several gene loci. This variation exists within populations, so that less susceptible local genotypes may provide the gene pool for regeneration of woodlands where mortality is high.

California↗
PubMed2006

Fine-scale genetic structure and gene dispersal inferences in 10 neotropical tree species.

The extent of gene dispersal is a fundamental factor of the population and evolutionary dynamics of tropical tree species, but directly monitoring seed and pollen movement is a difficult task. However, indirect estimates of historical gene dispersal can be obtained from the fine-scale spatial genetic structure of populations at drift-dispersal equilibrium. Using an approach that is based on the slope of the regression of pairwise kinship coefficients on spatial distance and estimates of the effective population density, we compare indirect gene dispersal estimates of sympatric populations of 10 tropical tree species. We re-analysed 26 data sets consisting of mapped allozyme, SSR (simple sequence repeat), RAPD (random amplified polymorphic DNA) or AFLP (amplified fragment length polymorphism) genotypes from two rainforest sites in French Guiana. Gene dispersal estimates were obtained for at least one marker in each species, although the estimation procedure failed under insufficient marker polymorphism, limited sample size, or inappropriate sampling area. Estimates generally suffered low precision and were affected by assumptions regarding the effective population density. Averaging estimates over data sets, the extent of gene dispersal ranged from 150 m to 1200 m according to species. Smaller gene dispersal estimates were obtained in species with heavy diaspores, which are presumably not well dispersed, and in populations with high local adult density. We suggest that limited seed dispersal could indirectly limit effective pollen dispersal by creating higher local tree densities, thereby increasing the positive correlation between pollen and seed dispersal distances. We discuss the potential and limitations of our indirect estimation procedure and suggest guidelines for future studies.

French Guiana↗
PubMed2022

Genetic structure correlates with ethnolinguistic diversity in eastern and southern Africa.

African populations are the most diverse in the world yet are sorely underrepresented in medical genetics research. Here, we examine the structure of African populations using genetic and comprehensive multi-generational ethnolinguistic data from the Neuropsychiatric Genetics of African Populations-Psychosis study (NeuroGAP-Psychosis) consisting of 900 individuals from Ethiopia, Kenya, South Africa, and Uganda. We find that self-reported language classifications meaningfully tag underlying genetic variation that would be missed with consideration of geography alone, highlighting the importance of culture in shaping genetic diversity. Leveraging our uniquely rich multi-generational ethnolinguistic metadata, we track language transmission through the pedigree, observing the disappearance of several languages in our cohort as well as notable shifts in frequency over three generations. We find suggestive evidence for the rate of language transmission in matrilineal groups having been higher than that for patrilineal ones. We highlight both the diversity of variation within Africa as well as how within-Africa variation can be informative for broader variant interpretation; many variants that are rare elsewhere are common in parts of Africa. The work presented here improves the understanding of the spectrum of genetic variation in African populations and highlights the enormous and complex genetic and ethnolinguistic diversity across Africa.

Africa, Southern↗
PubMed2006

Life on the edge: the long-term persistence and contrasting spatial genetic structure of distinct brown trout life histories at their ecological limits.

The Atlantic Iberian brown trout is at the southwestern limit of its distribution. At this ecological edge, which was once a glacial refugia, anadromy becomes less common as increased water temperatures restricted populations closer to the headwaters. We examined 847 individuals from 20 populations from throughout this region and assessed spatial genetic structure using 11 protein and four microsatellite loci. The higher levels of heterozygosity and allelic diversity north of the southernmost limit of anadromy (SLA), as well as an isolation-by-distance model of population structure, likely influenced by the anadromous forms, suggest that more stable demographic conditions existed over time in this region. Populations south of the SLA were highly differentiated given the restricted size of the area (protein F(ST) = 0.16 in the north and 0.63 in the south of the SLA; microsatellite F(ST) = 0.18 in the north and 0.70 in the south of the SLA). The low levels of heterozygosity and the pattern of southward allele depletion in resident populations is indicative of fragmentation, caused by stressful ecological conditions that reduced the anadromy (restricting gene flow) and the effective population sizes (higher genetic drift), which, in combination, dramatically decreased within-population genetic variation and increased among-population genetic variation. The higher gene diversity north of the SLA does not reflect ancestry but rather the signature of a population size expansion, as evidence suggest the persistence of older populations (with several private alleles) south of the SLA. These data support a scenario that demonstrates how contemporary events (critical ecological conditions) can moderate historical influences, suggesting that careful interpretation of the evolutionary history of glacial refugia is necessary, especially where populations persisted for a long time but not always with optimal ecological conditions. These peripheral populations are of high conservation value and should be preserved to help conserve the future potential of the species.

Animals↗
PubMed2004

Genetic structure of nest aggregations and drone congregations of the southeast Asian stingless bee Trigona collina.

In stingless bees, sex is determined by a single complementary sex-determining locus. This method of sex determination imposes a severe cost of inbreeding because an egg fertilized by sperm carrying the same sex allele as the egg results in a sterile diploid male. To explore how reproductive strategies may be used to avoid inbreeding in stingless bees, we studied the genetic structure of a population of 27 colonies and three drone congregations of Trigona collina in Chanthaburi, Thailand. The colonies were distributed across six nest aggregations, each aggregation located in the base of a different fig tree. Genetic analysis at eight microsatellite loci showed that colonies within aggregations were not related. Samples taken from three drone congregations showed that the males were drawn from a large number of colonies (estimated to be 132 different colonies in our largest swarm). No drone had a genotype indicating that it could have originated from the colony that it was directly outside. Combined, these results suggest that movements of drones and possibly movements of reproductive swarms among colony aggregations provide two mechanisms of inbreeding avoidance.

Animals↗
PubMed2002

The genetic structure of natural and reintroduced roe deer (Capreolus capreolus) populations in the Alps and central Italy, with reference to the mitochondrial DNA phylogeography of Europe.

The first hypervariable fragment (HVI) of the mitochondrial DNA control region was sequenced in 90 individuals of the European roe deer (Capreolus capreolus) from the Alps, central Italy and Spain. Pooling these data with 70 published sequences from several European regions, we were able to identify patterns of divergence within the Italian peninsula, and in Europe in general. The results we obtained can be summarized as follows. First, the genetic structure of European roe deer populations is substantial (PhiST values around 0.6). Second, the divergence between some central Italian populations, the Alpine group (which is genetically close to the French, the Spanish and the Norwegian samples) and the Eastern European populations seems to reflect Upper Pleistocene subdivisions, possibly related to three southern European refugia. Third, a different group of central Italian individuals probably diverged more recently from the Alpine group, and their attribution to the subspecies C. c. italicus does not appear justified. Fourth, the analysis of mitochondrial DNA in the roe deer can be used to identify recently reintroduced animals in the western Alps which clearly cluster within the Eastern European group, thus providing an important tool for conservation and management strategies for this species.

Animals↗
PubMed2003

Genetic structure of Mediterranean populations revealed by Y-chromosome haplotype analysis.

The allelic variability at six Y-chromosome-specific polymorphisms (YAP, DYS19, DYS389-I, DYS390, DYS391, and DYS392) was used to generate male-specific haplotypes in 333 males representing 12 population samples from the region around the Mediterranean sea. Extreme interindividual variation was observed, as more than 160 distinct Y-chromosome variants could be defined as six-locus haplotypes. Concomitant with this high variability, low levels of population genetic structure were observed. In particular, a "core" of populations directly facing the north and the east of the Mediterranean basin, from the Middle East to the Italian Peninsula, was found to be genetically undifferentiated. This observation, supported by a reanalysis of Y-specific binary polymorphisms in the same populations, suggests that at least part of the male-specific gene pools of these populations has either a very recent common origin (that could be related with the Neolithic demic diffusion hypothesis), and/or that gene flow has played a significant role in shaping the patterns of genetic variability in this region. In agreement with both hypotheses, we found that the spatial distribution of DYS392 alleles revealed a marked differentiation between the East and the West of the Mediterranean area. Through the analysis of microsatellite variation, the time to the most recent common ancestor (TMRCA) of the YAP(+) sublineage 4 has been estimated. The estimations, based on two different data sets, turn out to be quite recent (7,000-11,000 YBP), suggesting that this lineage may have been first introduced into Southern Europe through Neolithic migrations from the Middle East.

Chromosomes, Human, Y↗
PubMed2006

Genetic structure of wild and cultivated olives in the central Mediterranean basin.

BACKGROUND AND AIMS: Olive cultivars and their wild relatives (oleasters) represent two botanical varieties of Olea europaea subsp. europaea (respectively europaea and sylvestris). Olive cultivars have undergone human selection and their area of diffusion overlaps that of oleasters. Populations of genuine wild olives seem restricted to isolated areas of Mediterranean forests, while most other wild-looking forms of olive may include feral forms that escaped cultivation. METHODS: The genetic structure of wild and cultivated olive tree populations was evaluated by amplified fragment length polymorphism (AFLP) markers at a microscale level in one continental and two insular Italian regions. KEY RESULTS: The observed patterns of genetic variation were able to distinguish wild from cultivated populations and continental from insular regions. Island oleasters were highly similar to each other and were clearly distinguishable from those of continental regions. Ancient cultivated material from one island clustered with the wild plants, while the old plants from the continental region clustered with the cultivated group. CONCLUSIONS: On the basis of these results, we can assume that olive trees have undergone a different selection/domestication process in the insular and mainland regions. The degree of differentiation between oleasters and cultivated trees on the islands suggests that all cultivars have been introduced into these regions from the outside, while the Umbrian cultivars have originated either by selection from local oleasters or by direct introduction from other regions.

Genes, Plant↗
PubMed1999

Population genetic structure of the African elephant in Uganda based on variation at mitochondrial and nuclear loci: evidence for male-biased gene flow.

A drastic decline has occurred in the size of the Uganda elephant population in the last 40 years, exacerbated by two main factors; an increase in the size of the human population and poaching for ivory. One of the attendant consequences of such a decline is a reduction in the amount of genetic diversity in the surviving populations due to increased effects of random genetic drift. Information about the amount of genetic variation within and between the remaining populations is vital for their future conservation and management. The genetic structure of the African elephant in Uganda was examined using nucleotide variation of mitochondrial control region sequences and four nuclear microsatellite loci in 72 individuals from three localities. Eleven mitochondrial DNA (mtDNA) haplotypes were observed, nine of which were geographically localized. We found significant genetic differentiation between the three populations at the mitochondrial locus while three out of the four microsatellite loci differentiated KV and QE, one locus differentiated KV and MF and no loci differentiated MF and QE. Expected heterozygosity at the four loci varied between 0.51 and 0.84 while nucleotide diversity at the mitochondrial locus was 1.4%. Incongruent patterns of genetic variation within and between populations were revealed by the two genetic systems, and we have explained these in terms of the differences in the effective population sizes of the two genomes and male-biased gene flow between populations.

Animals↗
PubMed2001

Phylogeography of the yucca moth Tegeticula maculata: the role of historical biogeography in reconciling high genetic structure with limited speciation.

Tegeticula maculata is one of the most ancient and morphologically variable lineages within the yucca moths, yet has apparently undergone little diversification in comparison with much younger yucca moth lineages that have rapidly diversified. A phylogeographic approach was used to determine the number of independent lineages within T. maculata and to examine whether these patterns corresponded with morphological differences between its subspecies maculata and extranea. Phylogenetic analysis of mitochondrial DNA sequence variation indicated that the two subspecies are in separate clades, but there was also an equally deep split within subspecies maculata. There was no evidence for gene flow among regions and there was considerable substructure within clades. The phylogeographic structure of moth populations among and within subspecies can be explained in part by historical biogeographic boundaries and increasingly patchy postglacial distribution of the exclusive host plant, Hesperoyucca whipplei. Local specialization and co-adaptation would be possible in the absence of apparent gene flow, yet gross morphological divergence is limited to the very old split between the subspecies. Sorting of ancient mitochondrial lineages followed by local genetic differentiation may explain the pattern of high genetic structure with limited speciation.

Animals↗
PubMed2005

Clonal diversity and population genetic structure of arbuscular mycorrhizal fungi (Glomus spp.) studied by multilocus genotyping of single spores.

A nested multiplex PCR (polymerase chain reaction) approach was used for multilocus genotyping of arbuscular mycorrhizal fungal populations. This method allowed us to amplify multiple loci from Glomus single spores in a single PCR amplification. Variable introns in the two protein coding genes GmFOX2 and GmTOR2 were applied as codominant genetic markers together with the LSU rDNA. Genetic structure of Glomus spp. populations from an organically and a conventionally cultured field were compared by hierarchical sampling of spores from four plots in each field. Multilocus genotypes were characterized by SSCP (single stranded conformation polymorphism) and sequencing. All spore genotypes were unique suggesting that no recombination was taking place in the populations. There were no overall differences in the distribution of genotypes in the two fields and identical genotypes could be sampled from both fields. Analysis of gene diversity indicated that Glomus populations are subdivided between plots within each field. There were however, no subdivision between the fields.

Base Sequence↗
PubMed2006

Genetic structure and assignment tests demonstrate illegal translocation of red deer (Cervus elaphus) into a continuous population.

Molecular forensic methods are being increasingly used to help enforce wildlife conservation laws. Using multilocus genotyping, illegal translocation of an animal can be demonstrated by excluding all potential source populations as an individual's population of origin. Here, we illustrate how this approach can be applied to a large continuous population by defining the population genetic structure and excluding suspect animals from each identified cluster. We aimed to test the hypothesis that recreational hunters had illegally introduced a group of red deer into a hunting area in Luxembourg. Reference samples were collected over a large area in order to test the possibility that the suspect individuals might be recent immigrants. Due to isolation-by-distance relationships in the data set, inferring the number of genetic clusters using Bayesian methods was not straightforward. Biologically meaningful clusters were only obtained by simultaneously analysing spatial and genetic information using the program baps 4.1. We inferred the presence of three genetic clusters in the study region. Using partial Mantel tests, we detected barriers to gene flow other than distance, probably created by a combination of urban areas, motorways and a river valley used for viticulture. The four focal animals could be excluded with a high certainty from the three genetic subpopulations and it was therefore likely that they had been released illegally.

Animal Migration↗
PubMed2004

Population genetic structure of Titanotrichum oldhamii (Gesneriaceae), a subtropical bulbiliferous plant with mixed sexual and asexual reproduction.

BACKGROUND AND AIMS: Titanotrichum oldhamii is a monotypic genus distributed in Taiwan, adjacent regions of China and the Ryukyu Isands of Japan. Its conservation status is vulnerable as most populations are small and widely scattered. Titanotrichum has a mixed system of reproduction with vegetative bulbils and seeds. The aim of this study was to understand the population genetic structure of Titanotrichum in relation to its specific reproductive behaviour and to determine possible implications for conservation strategies. METHODS: After an extensive inventory of most wild populations of Titanotrichum in East Asia, samples from 25 populations within its major distribution were carried out utilizing RAPD and inter-SSR molecular fingerprinting analysis. KEY RESULTS: The findings support the conclusion that many populations reproduce predominantly asexually but that some genetic variation still exists within populations. However, significant amounts of variation exist between populations, perhaps reflecting population differentiation by drift. This partitioning of genetic diversity indicates that the level of inter-population gene exchange is extremely low. These findings are consistent with field observations of very limited seed production. The Chinese populations are similar to those of Northern Taiwan, while the Ryukyu populations fall within the range of variation of the north-central Taiwan populations. The Taiwanese populations are relatively variable and differentiation between north, east and south Taiwan is evident. CONCLUSIONS: The distribution of Titanotrichum seems to be consistent with a former land connection between China, Taiwan and the Ryukyu Islands at a glacial maximum during the Quaternary, followed by progressive fragmentation of the populations. North-central Taiwan is the centre of genetic diversity, possibly due to the proximity of the former land bridge between the regions, together with the variety of suitable habitats in north Taiwan. The significance of these findings for conservation is discussed.

Base Sequence↗
PubMed1993

Genetic structures of the B2 and B1 Escherichia coli strains responsible for extra-intestinal infections.

Escherichia coli strains causing human extra-intestinal infections may be divided into two groups, B1 and B2 according to the electrophoretic patterns of carboxylesterase B. This study compares the restriction fragment length polymorphism (RFLP) of ribosomal DNA (rDNA) for 45 B1 strains and 45 B2 strains to examine the genetic structure of B2 strains and to distinguish them from B1 strains. The isolates were chosen for diversity in their allozymes of esterases, B, A, C and I, their production of virulence factors (alpha-haemolysin, mannose resistant haemagglutinin and cytotoxic necrotizing factor) and certain O antigens, and their pathological and geographical origins. DNA was digested with HindIII and BamHI restriction enzymes and analysed by Southern blotting. The resulting rDNA RFLP patterns of B2 strains were distinct from those of the B1 strains. Moreover, the B2 strains appeared to be less heterogeneous than the B1 strains. The B2 strains gave 13 ribotypes (resulting from the combination of the rDNA RFLP patterns obtained with HindIII and BamHI digestions) while the B1 strains gave 32 ribotypes. Correspondence analysis of the data showed that several clusters of strains were identified in the B2 strains by particular ribotypes, certain associations of esterase B and A electrophoretic variants, O serotypes and virulence factor production. In contrast, these parameters appeared to be unrelated in the B1 strains, reflecting their heterogeneity. These findings, which differentiate two levels of genetic heterogeneity within E. coli pathogenic isolates, indicate that the B2 strains constitute a phylogenetically distinct group within the species.

Carboxylesterase↗
PubMed2007

Genetic structure and reproductive strategy of the ant Cardiocondyla elegans: strictly monogynous nests invaded by unrelated sexuals.

Cardiocondyla elegans is a Mediterranean ant that nests on river banks. It rears only wingless (ergatoid) males that live peacefully in the same nest as opposed to other species of the same genus, which have both peaceful, winged and mutually aggressive 'ergatoid' males. Using microsatellite analysis, we investigated the genetic structure of 21 colonies from three different locations as well as the parentage of sexuals of two colonies of C. elegans. We show that C. elegans is strictly monogynous, and that its nests can contain foreign sexuals. The presence of alien sexuals inside ant nests is described for the first time and probably counteracts inbreeding resulting from matings between siblings. In the laboratory, aggression tests showed that workers only allow alien males to enter their nests, while all winged female sexuals attempting to enter were attacked. Nevertheless, the presence of alien female sexuals in nests in the field seems to result from active carrying behaviour by workers during the reproductive period.

Animals↗
PubMed1985

Physical and genetic structure of the IncN plasmid R15.

Restriction sites for seven hexanucleotide-specific endonucleases were located on the map of the conjugative IncN plasmid R15 (SmrSurHgr, 62.3 kb). The distribution of the cleavage sites is strongly asymmetric. Twenty-eight of thirty-four sites for BamHI, EcoRI, HindIII, SalI, SmaI, and PstI were located close to or within the sequences of an IS5-like element and the transposons Tn2353 and Tn2354. By analysis of R15::Tn1756 deletion derivatives and recombinant plasmids harboring R15 fragments, the genetic determinants for the streptomycin, sulfonamide, and mercury resistances were mapped, as well as the regions necessary for EcoRII restriction-modification and for plasmid replication and conjugation. The features of physical and genetic structures of the plasmid R15 and other IncN plasmids are discussed.

Bacteriophage lambda↗
PubMed1995

Structural, genetic and pharmacological identity of the rat alpha 2-adrenergic receptor subtype cA2-47 and its molecular characterization in rat adrenal, adrenocortical carcinoma and bovine retina.

Subsequent to the first alpha 2-adrenergic receptor (alpha 2-AR) gene cloning of alpha 2-C10 from human platelet, cloning of the first rodent alpha 2-AR cDNA, cA2-47, was reported. Based on the structural and limited pharmacological comparison, it was concluded that the rodent receptor is a molecular and pharmacological analog of the human receptor, which is pharmacologically classified as the alpha 2A-AR. A later study slightly revised the structure of the human receptor. Thus, the precise structural comparison of the rat receptor to the human platelet receptor is no longer valid. Another rat alpha 2-AR gene, RG20, was then cloned and was also found to be a structural analog of the human alpha 2-C10. It, however, varied slightly from the alpha 2A subtype pharmacology, but matched the newly defined alpha 2D subtype pharmacology. It was, therefore, concluded that RG20 encodes the alpha 2D subtype. The structural and pharmacological relationship of RG20 with cA2-47 is not known, although it has been tacitly assumed that both are the identical alpha 2D receptor subtypes. The present study addresses this and other issues relating to the precise structural, genetic and pharmacological relationship of cA2-47 with the human platelet alpha 2-C10 receptor, and also the localization of cA2-47 transcript in certain rat tissues. The results show that the cA2-47 receptor shows a high degree of sequence identity to the alpha 2-C10 receptor, yet important differences exist between them. The sequence identity of cA2-47 receptor to the RG20 receptor is almost, but not quite complete. The cA2-47 gene is not present in the human and the human gene is not present in the rat; that cA2-47 receptor subtype is pharmacologically similar to the RG20 receptor subtype, both being of the alpha 2D subtype. The cA2-47 receptor transcript in addition to being found in the rat brain is present in the rat adrenal gland, testes, adrenocortical carcinoma and the bovine retina.

Adrenal Cortex Neoplasms↗
PubMed1999

History can be more important than 'pollination syndrome' in determining the genetic structure of plant populations: the case of aconitum lycoctonum (Ranunculaceae)

The Aconitum lycoctonum complex is a widespread yellow-flowered group of species found in central and southern Europe. Because of extreme morphological variability, the systematics of this group is confusing, and hybridizations among taxa are often hypothesized. To determine whether hybridization, realized mating system within populations or colonization from different Pleistocene refugia might explain some of the morphological variation, the genetic structure of 19 populations from central and southern Europe was studied using starch gel electrophoresis and 10 enzyme loci, of which eight were polymorphic. A pattern typical of an outcrossing species was expected because A. lycoctonum flowers are adapted to pollination by long-tongued bumblebees. However, heterozygosity was very low (between 0.031 and 0.150), which is atypical of either widespread or outcrossing species. The inbreeding coefficient, FIS, also suggested inbreeding in more than half the populations. Analysis of molecular variance showed that 31% of the genetic variation is found among populations, again suggesting inbreeding. A neighbour-joining tree based on Reynolds's genetic distance showed a clear separation between the central/eastern European populations and the samples from the Iberian peninsula and Alpes Maritimes. These data are consistent with the hypothesized refugia and the phylogeographical histories of several European forest trees. The genetic identity of all populations was very high, suggesting that all investigated populations belong to the same species despite high morphological variability. Hybridization was not supported by the data.

Journal Article↗