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At least 1,387 records · Page 77Linked to original sources
PubMed1999

Patterns of allozymic variation within calluna vulgaris populations at seed bank and adult stages

We investigated the spatial genetic structure within and between two plots of Calluna vulgaris and the extent to which the soil seed bank differed genetically from adults at seven allozyme loci. Averaged over the two plots, the seed bank and adult populations contained very similar levels of genetic diversity. Moreover, seeds contained in a single soil core (100 cm3) exhibited similar mean allozyme diversity to the surrounding adult population, indicating that the seed bank preserves genetic diversity at a very local scale. Few differences in allelic frequencies were found between the seed bank and its surrounding adult population in each plot. Mean GST indicated a lack of differentiation between the two plots at adult (GST = 0.008) and seed bank (GST = 0.002) stages. Low interplot differentiation is consistent with the outcrossing mating system of the population (tm = 0.91 in one plot) and its history of human disturbance. In contrast, spatial autocorrelation analysis of adults indicated a genetic structure at a very local scale, with positive autocorrelation for all alleles below 2 m in one plot and with a pattern of positive autocorrelation below 8 m in the two plots. Current limitation to seed dispersal rather than spatial extension of clones is thought to be responsible for local genetic structure.

Journal Article↗
PubMed1988

Diversity of some gene frequencies in European and Asian populations. IV. Genetic population structure assessed by the variogram.

Isolation-by-distance models of population structure predict an exponential decrease of genetic relatedness with distance. Under the Kimura-Weiss (1964) model the plots of gene frequency variance versus distance (variograms), computed at various loci, are expected to have equal slope and reach a common asymptote. The gene frequency distributions at eight loci in 192 European and Asian populations have been summarized by variograms. On the average, the Kimura-Weiss model seems to describe adequately allele frequency change up to 900 km, but gradients are apparent at greater distances for most markers studied. These patterns may result form either differential selection or long-range gene flow; however, the extensive clinal variation observed for glyoxalase, esterase D and 6-PGD cannot be entirely accounted for by the Neolithic radiation of early farmers in the Middle East and Europe.

Alleles↗
PubMed1990

Genetic population structure, clonal phylogeny, and pathogenicity of Salmonella paratyphi B.

Genetic diversity and relationships among 123 strains of Salmonella paratyphi B (serotype 1,4,[5],12:b:[1,2]) were estimated from an assessment of electrophoretically demonstrable allelic variation at 24 chromosomal enzyme gene loci. Fourteen electrophoretic types, marking clones, were distinguished, the phylogeny of the clonal lineages was reconstructed, and biotype and other phenotypic characters were mapped onto this structure. Most d-tartrate-negative strains are members of an abundant, globally distributed clone (Pb 1) that is polymorphic for many biotype characters (including d-tartrate utilization), bacteriophage type, rRNA pattern, and colicin M and phage ES18 sensitivity. This clone is largely responsible for S. paratyphi B enteric fever in humans. In contrast, d-tartrate-positive strains (formerly known as S. java) occurred in all seven of the clonal lineages identified by population genetic analysis, although most d-tartrate-positive isolates belong to only two clones (Pb 3 and Pb 4), which vary in frequency geographically. Monophasic strains represent four closely related clones forming a distinctive phylogenetic lineage. The Kauffmann hypothesis of convergence in serotype among distantly related cell lineages through recombination (via phage transduction or other means) may account for the considerable genotypic diversity among clones of S. paratyphi B. Pb 4, Pb 6, and Pb 7 are more closely allied with clones of S. typhimurium and S. saintpaul than with other clones of S. paratyphi B. Sensitivity or resistance to colicin M and phage ES18 and the electrophoretic pattern of the rRNA, which were incorporated into a recently proposed scheme for the identification of types of S. paratyphi B, individually or in combination fail to mark clones or other meaningful phylogenetic subdivisions.

Colicins↗
PubMed1999

Variation in short tandem repeats is deeply structured by genetic background on the human Y chromosome.

Eleven biallelic polymorphisms and seven short-tandem-repeat (STR) loci mapping on the nonrecombining portion of the human Y chromosome have been typed in men from northwestern Africa. Analysis of the biallelic markers, which represent probable unique events in human evolution, allowed us to characterize the stable backgrounds or haplogroups of Y chromosomes that prevail in this geographic region. Variation in the more rapidly mutating genetic markers (STRs) has been used both to estimate the time to the most recent common ancestor for STR variability within these stable backgrounds and to explore whether STR differentiation among haplogroups still retains information about their phylogeny. When analysis of molecular variance was used to study the apportionment of STR variation among both genetic backgrounds (i.e., those defined by haplogroups) and population backgrounds, we found STR variability to be clearly structured by haplogroups. More than 80% of the genetic variance was found among haplogroups, whereas only 3.72% of the genetic variation could be attributed to differences among populations-that is, genetic variability appears to be much more structured by lineage than by population. This was confirmed when two population samples from the Iberian Peninsula were added to the analysis. The deep structure of the genetic variation in old genealogical units (haplogroups) challenges a population-based perspective in the comprehension of human genome diversity. A population may be better understood as an association of lineages from a deep and population-independent gene genealogy, rather than as a complete evolutionary unit.

Africa, Northern↗
PubMed2002

A single mitochondrial lineage is shared by morphologically and allozymatically distinct freshwater Corbicula clones.

Despite that the exotic invasion and rapid range expansion of Asian freshwater Corbicula into new environments have been of intensive research topic in freshwater ecology, the genetic structures of freshwater Corbicula in its native range remain poorly understood. In this study, the genetic structures of two Korean freshwater Corbicula clonal lineages were characterized by cross-referencing the nuclear genomic structures with mtDNA sequence analysis. In spite of substantial genetic differences (Nei's D = 0.363-0.372) and a pronounced level of fixed allelic distinctions (in six of 20 allozyme loci) between Corbicula lineages, no lineage-specific mtDNA differentiation was observed. The evident disjunction between mtDNA sequences and nuclear genomes is a compelling evidence for the existence of interspecific nuclear hybrid genome structures, comprising different combinations of paternal and maternal contributions. This unusual novel finding is the first case demonstrating that morphologically and allozymatically distinct, yet mitochondrially identical clonal lineages exist in the genus Corbicula. However, we could not find the ancestral species for these two clonal lineages in the present study, and the answer for this question must wait until the genetic structure of Asian Corbicula taxa is fully characterized.

Animals↗
PubMed2004

Differential population structuring of two closely related fish species, the mackerel (Scomber scombrus) and the chub mackerel (Scomber japonicus), in the Mediterranean Sea.

Population genetic structures of the mackerel (Scomber scombrus) and chub mackerel (Scomber japonicus) were studied in the Mediterranean Sea. Fragments of 272 bp (S. scomber) and 387 bp (S. japonicus) of the 5'-end of the mitochondrial control region were sequenced from spawning individuals collected off the coasts of Greece, Italy, Spain, and Portugal. High levels of mitochondrial control region haplotypic diversity (> 0.98) were found for both Scomber species. Nucleotide diversity was higher in the mackerel (0.022) than in the chub mackerel (0.017). Global F(ST) values were also higher and significant in the mackerel (0.024, P < 0.0001) as opposed to the chub mackerel (0.003, P > 0.05). Molecular variance analyses showed differential genetic structuring for these two closely related species. There is extensive gene flow between Mediterranean Sea and Atlantic Ocean populations of chub mackerel, which are organized into a larger panmictic unit. In contrast, Mediterranean Sea populations of mackerel show some degree of genetic differentiation and are structured along an east-west axis. The analysed eastern Mediterranean Sea mackerel populations (Greece, Italy) are clearly separated from that of the western Mediterranean Sea (Barcelona), which forms a panmictic unit with eastern Atlantic Ocean populations. The genetic structures of both species showed asymmetric migration patterns and indicated population expansion.

Analysis of Variance↗
PubMed1998

[Diversity of hereditary pathology in the population of Marii El Republic and its differentiation with respect to gene frequencies for hereditary diseases].

The diversity of Mendelian hereditary pathology was studied in Marii El Republic. In total, 276,900 subjects, including 171,151 Maris and 88,714 Russians, living in seven raions (districts) were studied. Fifty-five autosomal dominant disease entities were found, with more than ten diseases having a frequency of 1:50,000 people or higher. In Maris, autosomal recessive hypotrichosis was observed at a relatively high frequency (1:15,337); this disease was not revealed in the Russian population studied earlier. Conversely, no phenylketonuria (PKU) was found in Maris, while it was a relatively common autosomal recessive disease in Russians. Regarding autosomal dominant pathology, 76 disease entities were revealed, with 21 diseases being observed at a frequency of at least 1:50,000. Ten X-linked diseases were found. The numbers of both autosomal recessive and autosomal dominant diseases exhibited a linear relationship with the number of subjects examined. The genetic structure of the Mari population was studied on the basis of data on the genes of recessive diseases. A matrix of Nei's genetic distances was calculated from the frequencies of 45 recessive diseases found in the seven districts studied. The average genetic distance calculated for the 45 loci of autosomal recessive diseases was 0.006175 x 10(-3). Similarly, matrix of genetic distances for five Mari populations was obtained (Medvedevskii and Zvenigovskii raions were not included) based on a total of 32 allelic frequencies for ten polymorphic immune and biochemical loci. The average genetic distance calculated from the ten polymorphic loci was 0.001930, i.e., 2.5 orders of magnitude greater than the average genetic distance for recessive diseases. The matrices of genetic distances for the five Mari populations calculated from the gene frequencies for recessive diseases and for the ten polymorphic systems were largely similar to each other. Thus, the main elements of the genetic structure of the Mari population can be estimated on the basis of gene frequencies for hereditary diseases. In this case, the characteristics of individual populations, which are more or less isolated, and of their interaction are the same as in the case of studying genetic structure with the use of polymorphic biological markers.

Female↗
PubMed1975

Structural and genetic basis of the in vivo immune response to TNP-LPS.

TNP-lipopolysaccharide (TNP-LPS) is a potent T-independent antigen in vivo, inducing a TNP-PFC response in T-depleted animals. The structural integrity of the lipid A-KDO portion of the LPS carrier molecule appears to be required since the haptenated LPS from Salmonella minnesota Re595 is immunogenic whereas the haptenated derivative of base hydrolyzed LPS is not. The immune response is not associated with any of the common histocompatiblity types, but does depend on the ability of the host strain to respond to LPS. C3H/HeJ mice are not killed by low doses of LPS and give a poor PFC response to TNP-LPS. Lethality and immunogenicity are dominant responses in hybrids of C3H/HeJ and responder mice. The structural and genetic requirements for the response to TNP-LPS suggest an active role for the carrier in the immunogenicity of this T-independent antigen.

Animals↗
PubMed2005

Genetics of brain structure and intelligence.

Genetic influences on brain morphology and IQ are well studied. A variety of sophisticated brain-mapping approaches relating genetic influences on brain structure and intelligence establishes a regional distribution for this relationship that is consistent with behavioral studies. We highlight those studies that illustrate the complex cortical patterns associated with measures of cognitive ability. A measure of cognitive ability, known as g, has been shown highly heritable across many studies. We argue that these genetic links are partly mediated by brain structure that is likewise under strong genetic control. Other factors, such as the environment, obviously play a role, but the predominant determinant appears to be genetic.

Animals↗
PubMed2002

[Gene structure and genetic diversity of immunoglobulins in fish].

The current knowledge concerning the structure of fish immunoglobulin (Ig) genes and the genetic mechanisms in generating fish antibody diversities is reviewed. The heavy (H-) and light (L-) chains of the immunoglobulin are encoded by multigenic loci on separate chromosomes. In different taxa of fish, the Ig genes are organized in different patterns. Fish antibody can recognize various foreign antigens,and the antibody diversity is generated by the following genetic mechanisms:the sequence diversity within the segments encoding the variable domain, the combinatorial diversity of V (D) J segments, the imprecision of rearrangements,gene conversion,somatic hypermutation,and the combination of H- and L-chain.

English Abstract↗
PubMed2001

Interspecific and geographical variation in the sequence of rDNA expansion segment D3 of Ixodes ticks (Acari: Ixodidae).

The base sequence of the rDNA D3 expansion segment and flanking H14 stem varies between six species of Ixodes ticks (Acari: Ixodidae) where only 33 invariant sites occur among sequences of 123-203 bases in length. Multiple copies of D3 were sequenced from localities across the geographical ranges of four species to investigate deep population genetic structure. Two species, I. pacificus, from western North America, and I. ricinus, from Europe, have no sequence variation indicating a lack of deep genetic structure. One species, I. scapularis, from eastern North America has two forms of the D3 sequence that are distributed differently among northern vs. southern populations, suggesting recent divergence and hybridization. I. persulcatus, from Eurasia, has sequence variation between localities of the order of that observed between other species, suggesting a long history of population isolation and deep genetic structure. With the exception of I. scapularis, sequence variation was not observed within localities. This indicates that cellular processes underpinning concerted evolution have homogenized populations and species for particular rDNA sequence variants.

Animals↗
PubMed2004

Population structure of California coyotes corresponds to habitat-specific breaks and illuminates species history.

Little is known about the relationship between animal movements and the emergent structure of populations, especially for species occupying large continuous distributions. Some such mammals disperse disproportionately into habitat similar to their natal habitat, a behavioural bias that might be expected to lead to habitat-conforming genetic structure. We hypothesized that coyotes (Canis latrans) would exhibit such natal-biased dispersal, and used 13 microsatellite loci to test, correspondingly, whether genetic structure conformed to major habitat breaks. First, we used a model-based approach to assign coyote genotypes to distinct genetic clusters irrespective of geographical location. Visualization on a geographical information system revealed a strong concordance between the locations of cluster assignments and habitat bioregions, not explainable in terms of physical dispersal barriers or intervening low-quality habitat. Next, we used a multiple Mantel test, which controlled for effects of geographical distance (itself, marginally significant; P = 0.06), to statistically determine that genetic distance was indeed higher between than within bioregions (P < 0.001). Whereas previously published examples of landscape effects on gene flow have typically been explainable in terms of species-wide habitat affinities or dispersal barriers, our finding that genetic subdivisions were associated with unobstructed boundaries between contiguous habitats suggests a role for intraspecific variability in habitat affinities as a factor underlying genetic structure. In addition, our data combined with previously published data suggest a pattern of genetic isolation-by-distance throughout western North America, consistent with independent evidence that the western half of the coyote range predates European settlement.

Animals↗
PubMed1998

Consequences of a catadromous life-strategy for levels of mitochondrial DNA differentiation among populations of the Australian bass, Macquaria novemaculeata.

The influence of a catadromous life-strategy on levels of spatial genetic structuring in fish is poorly understood. In an effort to gain a better appreciation of how this specialized life-strategy determines population genetic structuring, we assessed variation in the mitochondrial DNA (mtDNA) control region in a catadromous perciform, the Australian bass Macquaria novemaculeata. Nineteen putative haplotypes were resolved using temperature gradient gel electrophoresis from 10 geographically distinct populations. Significant heterogeneity was revealed in haplotype frequencies and their spatial distributions among many locales. Gene partitioning statistics (AMOVA) for both raw haplotype frequency data and frequency data with sequence divergences were concordant, indicating that M. novemaculeata populations were moderately genetically structured (phi ST = 0.05, 0.06; P < 0.001, respectively). Isolation by distance seems to be a strong structuring force in M. novemaculeata, culminating in no detectable phylogeographic structuring among haplotypes. Low sequence divergences were observed among many haplotypes and it is suggested that these are the result of pruning of maternal lineages by cyclical variations in female reproductive success. This study highlights the importance of life-history patterns and, in particular, spawning locality, in determining spatial structuring of mtDNA variation in catadromous species.

Animals↗
PubMed1982

Genetic fine structure of the Y chromosome of Drosophila hydei.

A genetic map of the Y chromosome of Drosophila hydei has been constructed from deletion/complementation experiments, with the aid of male sterile mutants of the Y chromosome. A central conclusion of our experiments is that not more than a single complementation group can be detected in each of the lampbrush loop forming sites. Additional complementation groups, functionally independent of lampbrush loops, reside between these loci. Six complementation groups have been defined by several methods of mapping. An additional ten complementation groups are indicated, but their exact definition requires further investigation. The "synthetic sterility" of mutations in these ten loci contributes to the difficulty in unequivocally establishing their individual boundaries. Mapping problems also arise from the instability of certain mutants.

Animals↗
PubMed1983

Primary structure and genetic organization of phage T4 DNA ligase.

The primary structure of phage T4 DNA ligase has been determined by DNA sequencing of a cloned restriction fragment containing its gene, and partial amino acid sequence analysis of the protein. The molecule has a Mr of 55,230, and contains 487 amino acids. The DNA sequence may also encode all of one and parts of two other, hitherto unidentified, T4 proteins. The four genes are closely packed, with overlaps between terminator and initiator codons of adjacent genes. Potential terminator and promoter sites for transcription are located within the coding sequence of one of the genes.

Amino Acid Sequence↗
PubMed2000

Genetic diversity and dynamics of Sinorhizobium meliloti populations nodulating different alfalfa cultivars in Italian soils.

We analyzed the genetic diversity of 531 Sinorhizobium meliloti strains isolated from nodules of Medicago sativa cultivars in two different Italian soils during 4 years of plant growth. The isolates were analyzed for DNA polymorphism with the random amplified polymorphic DNA method. The populations showed a high level of genetic polymorphism distributed throughout all the isolates, with 440 different haplotypes. Analysis of molecular variance allowed us to relate the genetic structure of the symbiotic population to various factors, including soil type, alfalfa cultivar, individual plants within a cultivar, and time. Some of these factors significantly affected the genetic structure of the population, and their relative influence changed with time. At the beginning of the experiment, the soil of origin and, even more, the cultivar significantly influenced the distribution of genetic variability of S. meliloti. After 3 years, the rhizobium population was altered; it showed a genetic structure based mainly on differences among plants, while the effects of soil and cultivar were not significant.

DNA, Bacterial↗
PubMed2005

Structural and genetic characterization of the Shigella boydii type 18 O antigen.

Shigella strains are important human pathogens and are normally identified by their O antigens. O antigen is an essential part of the lipopolysaccharide present in the outer membrane of Gram-negative bacteria and plays a role in pathogenicity. Structural and genetic organization of the Shigella boydii type 18 O antigen was investigated. As judged by sugar and methylation analyses and NMR spectroscopy data, the O antigen has a linear pentasaccharide repeating unit (O unit), which consists of three L-rhamnose residues, and one residue each of D-galacturonic acid (D-GalA) and N-acetylgalactosamine (D-GalNAc), and the following structure of the O unit was established. -->3)-beta-L-Rhap-(1-->4)-alpha-L-Rhap-(1-->2)-alpha-L-Rhap-(1-->2)-alpha-D-GalpA-(1-->3)-alpha-D-GalpNAc-(1--> The O antigen gene cluster of S. boydii type 18, which contains nine open reading frames (ORFs), was found between galF and gnd. Based on homology, all of the ORFs were identified as O antigen synthesis genes, involved in the synthesis of rhamnose, transfer of sugars, and processing of O unit. Genes specific for S. boydii type 18 were identified, which can be potentially used for the development of a PCR-based assay for the identification and detection of this strain.

Acetylation↗
PubMed2000

Estimation of gene flow in the tropical-rainforest tree Neobalanocarpus heimii (Dipterocarpaceae), inferred from paternity analysis.

Pollen flow and population genetic structure among 30 potentially flowering individuals of Neobalanocarpus heimii, a tropical emergent tree, were investigated in a lowland tropical rainforest of Malaysia using microsatellite polymorphism. The 248 offspring in the vicinity of five reproductive trees of the 30 potentially flowering trees were used in paternity analysis for pollen-flow study. Four primer pairs, developed in different species of dipterocarps, were adopted to detect microsatellite polymorphism. Based upon microsatellite polymorphism, pollen flow and seed migration were detected. Pollen-flow events of more than 400 m were observed directly, based on paternity analysis in the study plot. The estimated average mating distance of the five reproductive trees was 524 m. This result suggests that reproduction of this species is mediated by a long-distance pollinator. The haplotypes of some offspring were not compatible with the nearest reproductive tree. Thus, the results suggest that some seeds are dispersed by a seed dispersal vector. Investigation of genetic structure showed significant and negative correlation of genetic relatedness and spatial distances between the 30 potentially flowering trees, but this correlation was weak. We suggest that long-distance gene flow and seed migration are responsible for the poorly developed genetic structure of this species.

Ecosystem↗