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At least 433 records · Page 24Linked to original sources
PubMed1998

Geographic analysis of nucleotide diversity and song sparrow (Aves: Emberizidae) population history.

Mitochondrial DNA (mtDNA) control-region (CR) sequences were analysed to address three questions regarding the evolution of geographical variation in song sparrows. (i) Are mtDNA sequences more informative about phylogenetic relationships and population history than previously published restriction fragment (RFLP) data? (ii) Are song sparrow CR sequences evolving in a selectively neutral manner? (iii) What do the haplotype cladogram and geographical pattern of nucleotide diversity (pi) suggest about the recent evolutionary history of song sparrow populations? Results from phylogenetic analyses of CR sequences corroborate RFLP results and reveal instances in which haplotypes do not group by locality. Neutrality tests (Tajima 1989a) suggest that song sparrow mtDNA is evolving in a selectively neutral manner, although exceptions are noted. A novel geographical pattern of pi suggests a model of song sparrow population history involving multiple Pleistocene refugia and colonization of some formerly glaciated regions from multiple sources. Moreover, application of coalescence theory to the haplotype cladogram suggests that two different haplotypes (48NF and 151HA) may have predominated in different parts of the song sparrow's range. This model provides insight into the current distribution of song sparrow mtDNA haplotypes and may explain the discordance between evolutionary history inferred from mtDNA and morphology in this species.

Animals↗
PubMed1998

Analysis of clonal diversity of the peach-potato aphid, Myzus persicae (Sulzer), in Scotland, UK and evidence for the existence of a predominant clone.

Clones of the peach-potato aphid, Myzus persicae (Sulzer), mostly from Scotland, UK were examined using an rDNA fingerprinting technique. Eighty patterns (genotypes) were found amongst the 276 clones. A large number of clones (30%) from all sample areas in Scotland exhibited the same simple pattern, suggesting the presence of a single M. persicae clone. There was no difference in genotype distributions between M. persicae collected from brassica or potato crops, suggesting that host-adapted genotypes have no advantage in the field. Different fingerprints were randomly distributed in the environment, although clones taken from the same leaf were more often the same fingerprint. Highly distinctive fingerprints, which were more widely distributed, suggest that this technique could be used to follow individual clones. In addition to the common clonal type, multiple fingerprint bands were found over successive years, implying that, in Scotland, local overwintering asexual populations are the most common source of M. persicae in the following year.

Animals↗
PubMed2000

Microsatellite analysis of genetic diversity in African buffalo (Syncerus caffer) populations throughout Africa.

Genetic diversity in nine African buffalo (Syncerus caffer) populations throughout Africa was analysed with 14 microsatellites to study the effects of rinderpest epidemics and habitat fragmentation during the 20th century. A gradient of declining expected heterozygosity was observed among populations in Save Valley Conservancy (Zimbabwe), and northern and southern Kruger National Park (South Africa). This was explained by a high mortality in northern Kruger National Park during the rinderpest pandemic at the end of the 19th century followed by recolonization from neighbouring populations, resulting in intermediate heterozygosity levels in northern Kruger National Park. In other populations expected heterozygosity was very high, indicating that rinderpest and recent habitat fragmentation had a limited effect on genetic diversity. From expected heterozygosity, estimates of long-term effective population size were derived. Migration rates among populations in eastern and southern Africa were very high, as shown by a weak isolation by distance and significant correlation in allele frequencies between populations. However, there were indications that dry habitats could limit migration. Genetic distances within buffalo in central Africa were relatively large, supporting their status as distinct subspecies. Finally, it was observed that the higher polymorphic microsatellites were less sensitive at detecting isolation by distance and differences in Ne, which may be a result of the high mutation pressure at these loci.

Africa↗
PubMed2001

A molecular analysis of dietary diversity for three archaic Native Americans.

DNA was extracted from three fecal samples, more than 2,000 years old, from Hinds Cave, Texas. Amplification of human mtDNA sequences showed their affiliation with contemporary Native Americans, while sequences from pronghorn antelope, bighorn sheep, and cottontail rabbit allowed these animals to be identified as part of the diet of these individuals. Furthermore, amplification of chloroplast DNA sequences identified eight different plants as dietary elements. These archaic humans consumed 2-4 different animal species and 4-8 different plant species during a short time period. The success rate for retrieval of DNA from paleofeces is in strong contrast to that from skeletal remains where the success rate is generally low. Thus, human paleofecal remains represent a source of ancient DNA that significantly complements and may in some cases be superior to that from skeletal tissue.

Animals↗
PubMed1973

Analysis of gene diversity in subdivided populations.

A method is presented by which the gene diversity (heterozygosity) of a subdivided population can be analyzed into its components, i.e., the gene diversities within and between subpopulations. This method is applicable to any population without regard to the number of alleles per locus, the pattern of evolutionary forces such as mutation, selection, and migration, and the reproductive method of the organism used. Measures of the absolute and relative magnitudes of gene differentiation among subpopulations are also proposed.

Alleles↗
PubMed1998

Analysis of variable (diversity) joining recombination in DNAdependent protein kinase (DNA-PK)-deficient mice reveals DNA-PK-independent pathways for both signal and coding joint formation.

Previous studies have suggested that ionizing radiation causes irreparable DNA double-strand breaks in mice and cell lines harboring mutations in any of the three subunits of DNA-dependent protein kinase (DNA-PK) (the catalytic subunit, DNA-PKcs, or one of the DNA-binding subunits, Ku70 or Ku86). In actuality, these mutants vary in their ability to resolve double-strand breaks generated during variable (diversity) joining [V(D)J] recombination. Mutant cell lines and mice with targeted deletions in Ku70 or Ku86 are severely compromised in their ability to form coding and signal joints, the products of V(D)J recombination. It is noteworthy, however, that severe combined immunodeficient (SCID) mice, which bear a nonnull mutation in DNA-PKcs, are substantially less impaired in forming signal joints than coding joints. The current view holds that the defective protein encoded by the murine SCID allele retains enough residual function to support signal joint formation. An alternative hypothesis proposes that DNA-PKcs and Ku perform different roles in V(D)J recombination, with DNA-PKcs required only for coding joint formation. To resolve this issue, we examined V(D)J recombination in DNA-PKcs-deficient (SLIP) mice. We found that the effects of this mutation on coding and signal joint formation are identical to the effects of the SCID mutation. Signal joints are formed at levels 10-fold lower than in wild type, and one-half of these joints are aberrant. These data are incompatible with the notion that signal joint formation in SCID mice results from residual DNA-PKcs function, and suggest a third possibility: that DNA-PKcs normally plays an important but nonessential role in signal joint formation.

Animals↗
PubMed1983

Quantitative studies on T cell diversity. IV. Mathematical analysis of multiple limiting populations of effector and suppressor T cells.

Limiting dilution (LD) analyses of polyclonally activated T cells yielded results suggesting the existence of multiple paired populations of effector and suppressor precursors for a number of different T cell functions and specificities analyzed. These populations occur at graded frequencies and suppression occurs within a pair but not between pairs. In this paper, we establish the mathematical basis for the interpretation of these multi-component limiting dilution results. First, we derive equations for a number of mathematical models and identify one model that both makes biological sense and can be used to reproduce experimental data. Second, within this model, we identify parameters such as the frequency of suppressive cells and the number of suppressive cells required for suppression. The results suggest that within each paired population, suppressor precursors are 20 times more frequent that effector precursors. Furthermore, a similar but variable excess of suppressor cells is required for suppression to become effective. Together with the high frequency (1/50-1/500) of most effector T cell precursors previously reported, the results suggest that up to 40% of the T cells can become involved in suppression of an antigen-specific effector T cell population. These studies may provide exact estimates for predictions to be tested in experiments on immune regulation.

Cell Count↗
PubMed2001

Genetic diversity and phylogenetic analysis of human immunodeficiency virus type 1 subtypes circulating in French Guiana.

We investigated the characterization of different HIV-1 subtypes present in French Guiana by use of three different methods. Serological methods were used for the initial screening, which were then confirmed by the heteroduplex mobility assay (HMA). The V3 env region was subsequently sequenced for phylogenetic analysis, to confirm the subtype of the samples, and to assign a subtype to samples that gave results that were difficult to interpret or discordant by serology or HMA. A total of 221 HIV-1 seropositive samples were typed; 110 of them were confirmed by HMA and 16 were sequenced. Of the 221 samples tested 210 patients (95%) were found to be infected with subtype B, 10 (4.5%) were infected with subtype A, and one patient was infected with subtype F. Phylogenetic analysis demonstrated that the strains from French Guiana were closely related to the subtype A and B subtypes, and that one strain was closely related to an F subtype (100% bootstrap value). Four strains from French Guiana clustered in the subtype A (99% bootstrap value) and the other strains were associated with subtype B (100% bootstrap value). The geographic position of French Guiana suggested that HIV-1 was probably introduced into the country via several routes, and thus the pattern of the HIV-1 epidemic might evolve in the near future.

AIDS Serodiagnosis↗
PubMed1999

Global sequence diversity of BRCA2: analysis of 71 breast cancer families and 95 control individuals of worldwide populations.

The aim of this study was to evaluate the prevalence of simple sequence variation in the BRCA2 gene. To this end, 71 breast and breast-ovarian cancer (HBC/HBOC) families along with 95 control individuals from a wide range of ethnicities were analyzed by means of denaturing high-performance liquid chromatography (DHPLC) and direct sequence analysis. In the coding (10 257 bp) and non-coding (2799 bp) sequences of BRCA2, 82 sequence variants were identified. Three different, apparently disease-associated BRCA2 mutations were found in six HBC/HBOC families (8%): two splice site mutations in introns 5 and 21, and one frameshift mutation in exon 11. In the coding region, 53 simple sequence variants were found: 35 missense mutations, one 2 bp deletion (CT) resulting in a stop at codon 3364, one nonsense mutation with a stop at codon 3326, one deletion of a complete codon (AAA) resulting in the loss of leucine, and 15 silent mutations. In the non-coding region, 26 polymorphisms were detected. Of the 79 sequence variants that were not obviously disease-associated, eight were detected only in HBC/HBOC families. The remaining 71 variants were identified in both HBC/HBOC families and control individuals. Sixty three sequence variants (80%) were specific for a continent. Forty two percent (33 out of 79) of the sequence variants were detected exclusively in Africa, though only 13% of the 332 chromosomes screened were of African origin. Our data indicate that, in BRCA2, simple sequence variation is frequent [in the coding region 1 in 194 bp (straight theta = 2.2 x 10(-4)), and in the non-coding region 1 in 108 bp (straight theta = 4.4 x 10(-4)), respectively].

Africa↗
PubMedDate not supplied

Microsatellite analysis of genetic diversity in wild and farmed Emus (Dromaius novaehollandiae).

The emu (Dromaius novaehollandiae) occupies most regions of the Australian continent and in recent times has been farmed for meat, oil, and leather. Very little is known about the genetic structure of natural or farmed populations of these birds. We report a preliminary study of genetic variation in emus undertaken by typing birds from five farms and two natural populations at five polymorphic microsatellite loci. Genetic diversity was high for all populations and there was little evidence of inbreeding, with most populations conforming to Hardy-Weinberg equilibrium for most loci. Significant heterozygote deficiencies at one locus in a number of populations were detected and may indicate the presence of null alleles. Comparisons of allele frequencies showed little evidence of genetic differentiation either among farmed populations or between farmed and natural populations.

Animals↗
PubMedDate not supplied

Microsatellite analysis of genetic diversity of the Vietnamese sika deer (Cervus nippon pseudaxis).

The Vietnamese sika deer (Cervus nippon pseudaxis) is an endangered subspecies of economic and traditional value in Vietnam. Most living individuals are held in traditional farms in central Vietnam, others being found in zoos around the world. Here we study the neutral genetic diversity and population structure of this subspecies using nine microsatellite loci in order to evaluate the consequences of the limited number of individuals from which this population was initiated and of the breeding practices (i.e., possible inbreeding). Two hundred individuals were sampled from several villages. Our data show both evidence for limited local inbreeding and isolation by distance with a mean F(ST) value of 0.02 between villages. This suggests that exchange of animals occurs at a local scale, at a rate such that highly inbred mating is avoided. However, the genetic diversity, with an expected heterozygosity (H(e)) of 0.60 and mean number of alleles (k) of 5.7, was not significantly larger than that estimated from zoo populations of much smaller census size (17 animals sampled; H(e) = 0.65, k = 4.11). Our results also suggest that the Vietnamese population might have experienced a slight bottleneck. However, this population is sufficiently variable to constitute a source of individuals for reintroduction in the wild in Vietnam.

Animals↗
PubMed2004

Sensing and responding to diverse extracellular signals? Analysis of the sensor kinases and response regulators of Streptomyces coelicolor A3(2).

Streptomyces coelicolor is a Gram-positive soil bacterium that undergoes a complex developmental life cycle. The genome sequence of this organism was recently completed and has revealed the presence of over 60 sigma factors and a multitude of other transcriptional regulators, with a significant number of these being putative two-component signal transduction proteins. The authors have used the criteria established by Hoch and co-workers (Fabret et al., 1999, J Bacteriol 181, 1975-1983) to identify sensor kinase and response regulator genes encoded within the S. coelicolor genome. This analysis has revealed the presence of 84 sensor kinase genes, 67 of which lie adjacent to genes encoding response regulators. This strongly suggests that these paired genes encode two-component systems. In addition there are 13 orphan response regulators encoded in the genome, several of which have already been characterized and are implicated in development and antibiotic production, and 17 unpaired and as yet uncharacterized sensor kinases. This article attempts to infer useful information from sequence analysis and reviews what is currently known about the two-component systems, unpaired sensor kinases and orphan response regulators of S. coelicolor from both published reports and the authors' own unpublished data.

Adaptation, Physiological↗
PubMed2003

Genetic diversity and phylogenetic analysis of glycoprotein 5 of European-type porcine reproductive and respiratory virus strains in Spain.

The gene encoding glycoprotein 5 (ORF5) of 21 porcine reproductive and respiratory syndrome virus (PRRSV) isolates from Spain and two European-type vaccines currently available in that country were analysed using RT-PCR and sequencing. Sequences were then compared with other European-type sequences available through GenBank. Results showed percentages of similarity to Lelystad virus (LV), which, in most cases, were below 90 %. In contrast, two strains were very similar (>99 %) to a PRRSV variant from the Czech Republic. Evolutionary trees showed three types of strains: one grouped old Spanish sequences; a second grouped isolates from this study together with two Czech variant strains; and the third comprised other GenBank sequences. Regarding the predicted protein sequences, some isolates from this study showed a low degree of similarity to LV (below 50 %) and most of the strains examined had additional N-linked glycosylation sites compared to LV. These results provide evidence of the existence of variant PRRSV strains in Spain with characteristics that may be advantageous for immune evasion.

Animals↗
PubMed2004

Molecular diversity and phylogenetic analysis of mariner-like transposons in the genome of the silkworm Bombyx mori.

Genome-wide screening of mariner-like elements (MLEs) in the silkworm Bombyx mori has revealed the presence of five different types of MLEs (Bmmar1, Bmmar2, Bmmar3, Bmmar4 and Bmmar5). We isolated and characterized sixty copies of the MLEs representing the five Bmmar types. Their nucleotide sequences, nucleotide compositions, deduced transposase sequences, codon preferences, and the copy numbers showed extensive variations. Phylogenetic analysis of the sequences revealed that Bmmar1, Bmmar2, and Bmmar3 have been in the B. mori genome for a long time, while Bmmar4 is probably a recent invader of the genome. Because of the long-term association of Bmmar1 and Bmmar2 with the genome, highly mutated miniature Bmmar1 and Bmmar2 are widespread in the genome, and the footprints of these elements are also present in different silkworm genes. However, miniature copies of Bmmar4 were not detected. This recently acquired element has very few mutations. None of the characterized copies had functional transposase open reading frames. They essentially exist as fossils in the genome.

Amino Acid Sequence↗
PubMedDate not supplied

Analysis of genetic diversity at the arom locus in isolates of Pneumocystis carinii.

The DNA sequences of a portion of the 5-enolpyruvyl shikimate phosphate synthase domain of the arom gene, encoding the pentafunctional AROM protein, were determined from isolates of Pneumocystis carinii from five mammalian host species (rat, human, ferret, rabbit and mouse). High levels of genetic divergence were found among P. carinii derived from different host species, 7-22% at the DNA sequence level, and 7-26% at the derived amino acid sequence level. Two separate and distinct sequences were isolated from infected ferret lungs. Low levels of divergence were seen in human-derived organisms.

3-Phosphoshikimate 1-Carboxyvinyltransferase↗
PubMed1993

16S rDNA analysis reveals phylogenetic diversity among the polysaccharolytic clostridia.

Small subunit rDNA sequences were determined for 13 mesophilic, polysaccharolytic, mainly cellulolytic species of the genus Clostridium and one cellulolytic Eubacterium species. Sequences were compared to those of 36 representatives of mesophilic and thermophilic clostridia, including those of nine thermophilic polysaccharolytic species published previously. The majority of strains group with 23S rRNA clusters I and III, while the others group with the thermophilic polysaccharolytic clostridia, i.e. C. stercorarium, C. thermolacticum and C. thermocellum. Lack of close genetic relationships between the various polysaccharolytic species is unexpected and may indicate that these biotechnologically important organisms differ with respect to the enzymology of polysaccharolytic degradation as well.

Clostridium↗