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At least 19 recordsLinked to original sources
PubMed1995

Complete congruence between gene diversity estimates derived from genotypic data at enzyme and random amplified polymorphic DNA loci in black spruce.

Controversy still exists over the adaptive nature of variation of enzyme loci. In conifers, random amplified polymorphic DNAs (RAPDs) represent a class of marker loci that is unlikely to fall within or be strongly linked to coding DNA. We have compared the genetic diversity in natural populations of black spruce [Picea mariana (Mill.) B.S.P.] using genotypic data at allozyme loci and RAPD loci as well as phenotypic data from inferred RAPD fingerprints. The genotypic data for both allozymes and RAPDs were obtained from at least six haploid megagametophytes for each of 75 sexually mature individuals distributed in five populations. Heterozygosities and population fixation indices were in complete agreement between allozyme loci and RAPD loci. In black spruce, it is more likely that the similar levels of variation detected at both enzyme and RAPD loci are due to such evolutionary forces as migration and the mating system, rather than to balancing selection and overdominance. Furthermore, we show that biased estimates of expected heterozygosity and among-population differentiation are obtained when using allele frequencies derived from dominant RAPD phenotypes.

Alleles↗
PubMed1976

Diatom diversity as a function of insecticidal treatment with a controlled-release formulation of chlorpyrifos.

Following treatment with a controlled-release formulation of chlorpyrifos, no substantial differences between diversity estimates were evident for 6 post-treatment weeks for both treated and control plots. By post-treatment week 12, significant decreases in diversity estimates occurred in treated plots, suggesting that a directly proportional relationship exists between chlorpyrifos concentrations and reduced diatom colonization through time. Comparatively, diatom colonization progress "normally" and populations proceeded toward "maturity" in the control plots as indicated by the increase in the diversity estimates between post-treatment weeks 6 and 12. Any adverse effects due to the insecticidal treatment, however, were not considered to be environmentally deleterious in light of the restricted type of habitat (rice culture) in which the chlorpyrifos was used.

Biodegradation, Environmental↗
PubMed1994

Estimation of diversity and community structure through restriction fragment length polymorphism distribution analysis of bacterial 16S rRNA genes from a microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii.

PCR was used to amplify (eu)bacterial small-subunit (16S) rRNA genes from total-community genomic DNA. The source of total-community genomic DNA used for this culture-independent analysis was the microbial mats from a deep-sea, hydrothermal vent system, Pele's Vents, located at Loihi Seamount, Hawaii. Oligonucleotides complementary to conserved regions in the 16S rRNA-encoding DNA (rDNA) of bacteria were used to direct the synthesis of PCR products, which were then subcloned by blunt-end ligation into phagemid vector pBluescript II. Restriction fragment length polymorphism patterns, created by using tandem tetrameric restriction endonucleases, revealed the presence of 12 groups of 16S rRNA genes representing discrete operational taxonomic units (OTUs). The rank order abundance of these putative OTUs was measured, and the two most abundant OTUs accounted for 72.9% of all of the 16S rDNA clones. Among the remaining 27.1% of the 16S rDNA clones, none of the 10 OTUs was represented by more than three individual clones. The cumulative OTU distribution for 48 bacterial 16S rDNA clones demonstrated that the majority of taxa represented in the clone library were detected, a result which we assume to be an estimate of the diversity of bacteria in the native hydrothermal vent habitat. 16S rDNA fingerprinting of individual clones belonging to particular OTUs by using an oligonucleotide probe that binds to a universally conserved region of the 16S rDNA fragments was conducted to confirm OTU specificity and 16S rDNA identity.

Bacteria↗
PubMedDate not supplied

Gene diversity and estimation of genetic admixture among Mexican-Americans of Starr County, Texas.

The Mexican-Americans of Starr County, Texas, classified by sex and birthplace, were studied to determine the extent of genetic variation and contributions from ancestral populations such as Spanish, Amerindian and West African. Using 21 genetic marker systems, genetic distance and diversity analyses indicate that subpopulations of Mexican-Americans in Starr County are similar, and that more than 99% of the total gene diversity (HT) can be attributed to individual variation within the population. Genetic admixture analysis shows the predominant influence comes from the Spanish, a lesser contribution from Amerindians and a slight one from the West Africans. The contribution of the ancestral population to various subpopulations of the Mexican-Americans of Starr County is similar. The Mexican-Americans of Starr County are similar to the Mexican population from northeastern Mexico. The history of admixture is apparently old enough to have brought the entire Mexican-American gene pool to Hardy-Weinberg equilibrium. There is no non-random association of alleles among the genetic marker systems considered in the present study, in spite of the fact that this population is of admixed origin. These results, in aggregate, suggest genetic homogeneity of the Mexican-Americans of Starr County, Texas, and point towards the utility of this population for genetic and epidemiological studies.

Africa↗
PubMed1994

Paternally inherited chloroplast polymorphism in Pinus: estimation of diversity and population subdivision, and tests of disequilibrium with a maternally inherited mitochondrial polymorphism.

We have surveyed a chloroplast DNA restriction fragment length polymorphism in 745 individuals, distributed rangewide in eight allopatric natural populations of jack pine (Pinus banksiana Lamb.) and eight allopatric natural populations of lodgepole pine (Pinus contorta Dougl.). The polymorphic region of the chloroplast genome is located near duplicated psbA genes. Fourteen length variants were found in the survey, and these variants distinguished the two species qualitatively. Variant diversities were high in both species (hes = 0.43 in jack pine; hes = 0.44 in lodgepole pine). Population subdivision was weak within and among lodgepole pine subspecies and in jack pine (i.e., theta values were less than 0.05). This weak subdivision is compatible with theoretical predictions for paternally inherited markers in wind-pollinated outcrossers, as well as for polymorphisms with high length mutation rates. If these populations are at a drift-migration equilibrium, the chloroplast DNA restriction fragment data and previous mitochondrial frequency data from the same individuals are consistent with gene flow that is differential through seeds and pollen. The new data have permitted the first empirical tests of disequilibrium between maternally and paternally inherited factors. As expected, these tests failed to detect convincing evidence of nonrandom association between chloroplast and mitochondrial variants.

Chloroplasts↗
PubMed1990

DNA variation of the mammalian major histocompatibility complex reflects genomic diversity and population history.

The major histocompatibility complex (MHC) is a multigene complex of tightly linked homologous genes that encode cell surface antigens that play a key role in immune regulation and response to foreign antigens. In most species, MHC gene products display extreme antigenic polymorphism, and their variability has been interpreted to reflect an adaptive strategy for accommodating rapidly evolving infectious agents that periodically afflict natural populations. Determination of the extent of MHC variation has been limited to populations in which skin grafting is feasible or for which serological reagents have been developed. We present here a quantitative analysis of restriction fragment length polymorphism of MHC class I genes in several mammalian species (cats, rodents, humans) known to have very different levels of genetic diversity based on functional MHC assays and on allozyme surveys. When homologous class I probes were employed, a notable concordance was observed between the extent of MHC restriction fragment variation and functional MHC variation detected by skin grafts or genome-wide diversity estimated by allozyme screens. These results confirm the genetically depauperate character of the African cheetah, Acinonyx jubatus, and the Asiatic lion, Panthera leo persica; further, they support the use of class I MHC molecular reagents in estimating the extent and character of genetic diversity in natural populations.

Animals↗
PubMed2026

Genetic differentiation of the supralittoral gastropod Tectarius striatus (North Atlantic Archipelagos) and development of new microsatellite resources.

Microsatellite markers are invaluable tools for assessing genetic diversity and elucidating population structure across any species. This study reports the development and application of ten novel polymorphic microsatellite loci for Tectarius striatus, a littorinid species native to the shores of Macaronesia, a geographical region that includes the archipelagos of the Azores, Madeira, Selvagens, Canary Islands, and Cabo Verde. These markers together with a portion of the COI gene were used to genotype 65 individuals, using Illumina amplicon -sequencing across five geographically distinct populations. Our analysis shows moderate to high levels of allelic diversity across all populations. Furthermore, microsatellite markers supported genetic structure between a distant population of Cabo Verde Archipelago and the northern Macaronesian archipelagos. Conversely variation of the COI showed high levels of homogeneity across the sampled populations. While the presence of null alleles and moderate levels of missing data at several loci represent challenges to this study, the overall consistency of our results with earlier research underscores the reliability of microsatellite markers for population genetic inference in this marine gastropod. Nevertheless, our findings highlight the need for cautious interpretation of diversity estimates and population structure metrics, particularly when null alleles are frequent, and underscore the value of expanding the panel of available microsatellite markers for Tectarius striatus and related taxa to improve resolution and accuracy for future studies.

Animals↗
PubMed1997

Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA.

The community structure of bacterioplankton in meromictic Lake Saelenvannet was examined by PCR amplification of the V3 region of 16S rRNA from microbial communities recovered from various depths in the water column. Two different primer sets were used, one for amplification of DNA from the domain Bacteria and another specific for DNA from the domain Archaea. Amplified DNA fragments were resolved by denaturing gradient gel electrophoresis (DGGE), and the resulting profiles were reproducible and specific for the communities from different depths. Bacterial diversity estimated from the number and intensity of specific fragments in DGGE profiles decreased with depth. The reverse was true for the Archaea, with the diversity increasing with depth. Hybridization of DGGE profiles with oligonucleotide probes specific for phylogenetic groups of microorganisms showed the presence of both sulfate-reducing bacteria and methanogens throughout the water column, but they appeared to be most abundant below the chemocline. Several dominant fragments in the DGGE profiles were excised and sequenced. Among the dominant populations were representatives related to Chlorobium phaeovibrioides, chloroplasts from eukaryotic algae, and unidentified Archaea.

Animals↗
PubMed1997

A Shannon entropy analysis of immunoglobulin and T cell receptor.

In 1970, before any antigen-bound immunoglobulin structure had been solved, Elvin Kabat proposed that regions of high amino acid diversity would be the antigen binding sites of immunoglobulin (Kabat, 1970). Conversely, sites of low variability were proposed to be structural, framework regions. This variability was defined by Wu and Kabat as the number of different amino acids found at a site divided by the relative frequency of the most common amino acid at that site (Wu and Kabat, 1970). Several groups have subsequently devised improvements of Kabat-Wu variability analysis (Litwin and Jores, 1992). While these methods are somewhat better than Kabat-Wu, they still suffer from Kabat-Wu's basic limitation: they account for only the most common one or two amino acids in estimating diversity. This leads to underestimates of low diversities and exaggerations of high diversities. Shannon information analysis eliminates serious bias and is more stable than Kabat-Wu and second generation measures of diversity (Jores et al. 1990; Wu and Kabat, 1970). Statistical reliability can be measured using Shannon analysis, and Shannon measurements can be provided with error estimates. Here we use Shannon's method to analyze the amino acid diversity at each site of T cell receptor Valpha and Vbeta to identify complementarity determining regions and framework sites. Our results reveal that the T cell receptor is significantly more diverse than immunoglobulin-suggesting T cell receptor has more than the previously-discovered four complementarity determining regions. These new complementarity determining regions may represent a larger antigen combining site, additional combining sites, or an evolutionary strategy to avoid inappropriate interaction with other molecules.

Animals↗
PubMed2026

One-time duplication and ongoing loss of mitochondrial tRNA genes in Cryptocercus cockroaches.

Mitochondrial genome is a popular marker in phylogenetics and species diversity estimations. Mitogenome is relatively compact and conserved, while gene rearrangements were found in some species across various organisms. Models to explain the origin and evolution of gene rearrangement have been proposed but seldom demonstrated; empirical evidence from closely related species is particularly scarce. Here, through an intensive case study of the cockroach genus Cryptocercus Scudder, 1862, we elucidate the evolution of mitochondrial gene order. This study utilized 51 new samples and re-assembled raw reads of 26 published samples. A diversity of rearrangement patterns is recovered, especially in the tRNA gene cluster between ND3 and ND5, which is effectively explained by the duplication - random loss model. Specifically, the entire tRNA gene cluster was duplicated; this duplication is potentially facilitated by chance binding between the 3' end of ND5 gene and the ND3-trnA region during DNA replication. Furthermore, we reveal that one of the gene copies degenerated stochastically across lineages, directly contributing to the observed diversity in gene arrangement. Gene rearrangement patterns are apomorphies for certain clades, providing additional evidence for the inferred phylogeny and serving as potential indicators of species. This study underscores the importance of intensive sampling and rigorous data curation for deciphering the evolutionary mechanisms.

Duplication–random loss model↗
PubMed1995

[Blood group polymorphism in bison (Bison bonasus)].

Polymorphism of nine blood group systems was studied in three reproductive lines of auroch (European bison Bison bonasus), Belovezhskaya, Caucasian-Belovezhskaya, and Gornaya. All blood group systems analyzed were polymorphic; 50 out of the 57 antigens tested were detected. The number of detected blood group antigens in aurochs is comparable to that in breeds of domestic cattle. However, intrapopulation diversity, estimated with the mu test, is significantly higher in cattle than in aurochs. The lowest mu values were observed in line Belovezhskaya, which was founded by a small number of animals and has a high level of inbreeding. For the FV system, the amount by which heterozygotes exceeded the Hardy-Weinberg proportions was shown; this deviation was significant in all lines except Caucasian-Belovezhskaya. The excess of heterozygotes may be due to population processes that prevent the loss of genetic diversity in populations. The level of differentiation in the auroch lines was low. Similarity coefficients between the lines were higher than those between different stocks within a cattle breed.

Animals↗
PubMed1987

The molecular organization of the H-2K region of two t-haplotypes: implications for the evolution of genetic diversity.

The genetic diversity between the t12 and tw5 haplotype chromosomes was studied by analyzing the molecular organization of the H-2K region. Twenty-one cosmid clones spanning over 150 kb of the H-2K region of both t-haplotypes were defined, and high resolution restriction maps were determined. Detailed comparison of the t12 and tw5 restriction maps revealed the following. (i) The H-2K regions of both t-haplotypes retain a very similar molecular organization to that reported for B10, BALB/c and AKR. The nucleotide sequence diversity estimated from restriction site polymorphism is 0.68% between the t12 and tw5 haplotypes; these two t-haplotypes are no more similar to one another than BALB/c is to AKR. (ii) Genetic recombination is strongly implicated in generating H-2 polymorphism. (iii) Genetic polymorphisms, defined as small restriction fragment size differences, are observed at multiple sites along the H-2K region. An Alu-like B2 sequence and BAM5-R homologous sequence were identified as the inserted/deleted DNA segments of two of these sites, suggesting that insertion/deletion of mobile elements is a general mechanism for generating genetic diversity.

Animals↗
PubMed1997

Extent of heterogeneity in mitochondrial DNA of sub-Saharan African populations.

Variation in the mitochondrial DNA (mtDNA) control region as detected by sequence-specific oligonucleotide (SSO) probes is described for 381 individuals from nine sub-Saharan African populations. Population diversity estimates for SSO types ranged from 0.23 to 0.97, while 102 SSO types were detected, none of these types was shared by more than four populations. Eighteen types occurred in > or = 10% of individuals in some populations; of these, 11 were population-specific. One type occurred in 15% of the total sample, but was shared among only three populations. African SSO types were characterized by high frequencies of blank variants, indicating that there was additional variation present at the nucleotide sequence level in regions where SSO probes hybridize. Analyses of molecular variance (AMOVA) incorporating genetic distances between SSO types showed that 30% of the total variation was due to differences among populations, indicating that there is statistically significant heterogeneity (p < 0.001). An AMOVA on mtDNA control region nucleotide sequence data from 12 populations showed that including all additional variation present at the sequence level increased the variance due to population subdivision to 34% (p < 0.001). Overall, when considering both the low diversity within some populations and high heterogeneity among populations, SSO typing of mtDNA may not be a desirable forensic DNA typing method for continental African populations. Further mtDNA sampling of African-derived populations of North America should be carried out to determine how much of the continental African mtDNA variation is of forensic significance. However, the existence of extensive mtDNA control region nucleotide sequence variation in African populations means that control region sequencing is still appropriate in forensic cases requiring mtDNA analysis.

Africa, Central↗
PubMed1991

A conserved core structure in the 18-25S rRNA intergenic region from tobacco, Nicotiana rustica.

To identify conserved and functionally important features in the intergenic sequences of ribosomal DNAs, the nucleotide sequence of the 18-25S rRNA intergene region in tobacco rDNA was determined and compared to that of other higher plants. Unlike previous comparisons of more diverse organisms, sufficient sequence homology is retained in the higher plants to examine the evolutionary changes which make these regions diverse. Estimates of the secondary structure permit the identification of a 'core-like' structure which appears to maintain the processed sites in close proximity and can be identified in the more divergent sequences.

Base Sequence↗
PubMed1997

Reproduction and host-location among the parasitic platyhelminthes.

This review examines briefly the reproductive capacity of representatives of the 4 principal groups of platyhelminths, the "Turbellaria", Monogenea, Digenea and Cestoda. Of the flatworms, 3 main groups are wholly parasitic (monogeneans; digeneans; cestodes). Among the largely free-living "Turbellaria", there are several parasitic representatives in some families (Umagillidae; Graffillidae; Pterastericolidae; Fecampiidae; Acholadidae). Endoparasitic platyhelminths with complex life-cycles produce large numbers of eggs and numbers of offspring are increased further in the digeneans and a few cestodes by asexual multiplication. Like their free-living relatives, most ectosymbiotic and ento- and ectoparasitic flatworms ("turbellarians" and monogeneans) produce, on the whole, far fewer eggs and progeny but are still successful organisms in terms of their numbers of species and diversity. Estimates of parasite fecundity from in vivo experiments are needed for representatives from all flatworm groups. For those parasites that are host-specific, the particular species of host provides a predictable target to be located. Adaptations displayed by the eggs and infective stages of some flatworms increase their chances of finding and recognising their specific host and these are reviewed: attachment of eggs to their "host"; egg hatching in response to host chemicals; rhythmical emergence; special behaviours of infective stages; host recognition.

Animals↗
PubMed1983

Multilocus genetic structure in natural populations of Escherichia coli.

A survey of allozyme variation at 12 enzyme loci in 1,705 clones of the genetic species Escherichia coli (including four species of Shigella) from natural populations revealed 302 unique allele combinations (electrophoretic types). Single-locus diversity estimates fall within the range predicted by the neutral allele theory of molecular evolution, but the combination of alleles in electrophoretic types are highly nonrandom, as indicated by a test of association over all loci and by evidence of complex linkage disequilibria in several four-locus combinations. These linkage disequilibria reflect genetic differentiation of E. coli into three groups of strains. Because of restricted recombination, both the stochastic extinction of lines and selective differences between particular genetic combinations may have contributed to the evolution of subspecific structure in E. coli.

Electrophoresis↗
PubMed1995

Population genetics of trinucleotide repeat polymorphisms.

Trinucleotide repeats at five disease loci (DM, DRPLA, HD, SBMA and SCA1) were surveyed in phenotypically normal individuals from three continental populations. This is the first analysis to examine the population dynamics of these five disease-related trinucleotide repeats in the same individuals from worldwide populations. Roughly half of all alleles observed at each locus are shared between all continental groups. For three loci, disease prevalence in each population corresponds with the number of alleles in the upper tail of the allele-size distribution. The allele-size distributions of African, Asian and Caucasian groups show a high degree of variation, and gene diversity estimates for trinucleotide repeat loci exceed estimates derived from dinucleotide or tetranucleotide repeats. Analyses that compared infinite alleles and stepwise mutation models suggest that normal variation at trinucleotide loci is not generated by stepwise mutation alone. Trees constructed for subpopulations using trinucleotide repeat loci show accurate continental clustering. Interpopulation genetic distance estimates show remarkable similarity to distance estimates produced from tetranucleotide repeats or nuclear restriction site polymorphisms. This finding is especially noteworthy in light of the fact that trinucleotide repeat polymorphisms at these loci can cause disease, while restriction site and tetranucleotide polymorphisms appear to be selectively neutral. In contrast, genetic distance estimates from trinucleotide loci are poorly correlated with genetic distance estimates from mitochondrial sequence data.

Alleles↗
PubMedDate not supplied

Substantial genetic variation in southern African black rhinoceros (Diceros bicornis).

Thirty protein-coding loci of southern African black rhinoceros (Diceros bicornis) from four isolated populations were studied using starch gel electrophoresis and polyacrylamide gel electrophoresis. Gene diversity estimates varied between 0.036 and 0.058, with the Zambezi Valley population having the largest amount of protein variation. These levels are higher than those in other studies of genetic variation in black rhinoceros and are similar to the amount of genetic variation observed for outbred natural populations that are not genetically depauperate. Because the observed levels of genetic variation vastly exceed the expectations for current effective population sizes, the current levels apparently reflect large black rhinoceros populations which have existed until recently. Observed levels of genetic variation within populations are consistent with the expectations when recent demographic events are taken into account.

Africa, Southern↗