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PubMed2006

Insights into recombination from population genetic variation.

Patterns of genetic variation in natural populations are shaped by, and hence carry valuable information about, the underlying recombination process. In the past five years, the increasing availability of large-scale population genetic data on dense sets of markers, coupled with advances in statistical methods for extracting information from these data, have led to several important advances in our understanding of the recombination process in humans. These advances include the identification of large numbers of 'hotspots', where recombination appears to take place considerably more frequently than in the surrounding sequence, and the identification of DNA sequence motifs that are associated with the locations of these hotspots.

Animals↗
PubMed1994

Immunological parameters of periparturient Holstein cattle: genetic variation.

The genetic variability of blood neutrophil functions, lymphocyte blastogenic responses to mitogens, serum Ig concentrations, and serum complement and conglutinin activities was investigated from 35 d prepartum to 35 d postpartum for 137 Holstein cows. Periparturient cows experience an immunosuppression of various immunologic parameters at calving. Heritability estimates were obtained before, during, and after the episodes of immunosuppression. Significant genetic variability occurred in the periparturient changes for total number of neutrophils, neutrophil chemokinesis, assays of the neutrophil respiratory burst associated with phagocytosis (cytochrome c reduction, chemiluminescence, and iodination), serum concentrations of IgG1, IgG2, and IgM, and serum homolytic complement activity. This variability implies that immune profiles could be used for the selection of cattle with improved innate immune response without adverse effects on milk productivity. These results should be considered tentative, however, because the number of observations included in the data were limited.

Animals↗
PubMed2001

Genetic variation in 16S-23S rDNA internal transcribed spacer regions and the possible use of this genetic variation for molecular diagnosis of Bacteroides species.

The structural variation in 16S-23S rDNA internal transcribed spacer regions (ITS) among Bacteroides species was assessed by PCR amplification and sequencing analysis, and its possible use for molecular diagnosis of these species was evaluated. Ninety strains of the genus Bacteroides, including the species B. distasonis, B. eggerthii, B. fragilis, B. ovatus, B. thetaiotaomicron, B. uniformis and B. vulgatus, produced one to three ITS amplification products with sizes ranging from 615 to 810 bp. Some Bacteroides strains could be differentiated at species level on the basis of ITS amplification patterns and restriction fragment length polymorphism (RFLP) analysis using a four-nucleotide-recognizing enzyme, Msp I. The results of sequence analysis of ITS amplification products revealed genes for Ile-tRNA and Ala-tRNA in all strains tested. The nucleotide sequence, except for that in tRNA-coding regions, was highly variable and characteristic for each species, but a common sequence among B. fragilis, B. thetaiotaomicron and B. ovatus was observed. A digoxigenin-labeled oligonucleotide probe (named FOT1), which was designed from this conserved sequence, specifically hybridized to the ITS amplification products from B. fragilis, B. thetaiotaomicron and B. ovatus. These results suggest that the ITS region is a useful target for the development of rapid and accurate techniques for identification of Bacteroides species.

Bacteroides↗
PubMed2002

A brief history of genetic variation analysis.

As the human genome sequence is determined, there is an emerging need for the analysis of human sequence variations as genetic markers in diagnosis, linkage and association studies, cancer research, and pharmacogenomics. There are several different techniques and approaches for detecting these genetic variations, and here we review some of these techniques and their application fields. However, all the techniques have advantages and disadvantages, andfactors such as laboratory instrumentation, personnel experience, required accuracy, required throughput, and cost often have to be taken into account before selecting a method.

Genetic Techniques↗
PubMed2004

Genetic variation, classification and 'race'.

New genetic data has enabled scientists to re-examine the relationship between human genetic variation and 'race'. We review the results of genetic analyses that show that human genetic variation is geographically structured, in accord with historical patterns of gene flow and genetic drift. Analysis of many loci now yields reasonably accurate estimates of genetic similarity among individuals, rather than populations. Clustering of individuals is correlated with geographic origin or ancestry. These clusters are also correlated with some traditional concepts of race, but the correlations are imperfect because genetic variation tends to be distributed in a continuous, overlapping fashion among populations. Therefore, ancestry, or even race, may in some cases prove useful in the biomedical setting, but direct assessment of disease-related genetic variation will ultimately yield more accurate and beneficial information.

Genetic Variation↗
PubMed1998

Virtues of being faithful: can we limit the genetic variation in human immunodeficiency virus?

Human immunodeficiency virus (HIV) infections are characterized by a high degree of viral variation. The genetic variation is thought to be a combined effect of a high error rate of reverse transcriptase (RT), viral genomic recombination, the selection forces of the human immune system, the requirement for growth in multiple cell types during pathogenesis, and persistent immune activation associated with HIV disease. This hypermutability gives the virus an ability to escape mechanisms of innate immune surveillance and therapeutic interventions. Indeed, HIV variants that are resistant to drugs that antagonize both the HIV protease and RT enzymes are well described. Furthermore, there are seemingly no procedures to restrict this disarming property of HIV to mutate rapidly. Recently we have shown that some of the drug-resistant RTs display an increased in vitro polymerase fidelity. The question is whether this finding will stimulate new approaches that will not only help the immune system to deal with the virus more efficiently but also to reduce or delay resistance to various classes of anti-HIV drugs. The pros and cons of this concept and the influence of viral replication rates and viral fitness on HIV variability are discussed.

Drug Resistance, Microbial↗
PubMed2000

Genetic variance in temperature dependent adult size deriving from physiological genetic variation at temperature boundaries.

An increase in genetic variation in body size has often been observed under stress; an increase in dominance variance and interaction variance as well as in additive genetic variance has been reported. The increase in genetic variation must be caused by physiological mechanisms that are specific to adverse environments. A model is proposed to explain the occurrence of an increase in genetic variation in body size in Drosophila at extreme temperatures. The model has parameters specific to the low- and high-temperature regions of the viable range. Additive genetic variation in the boundary temperatures leads to a marked increase in additive genetic variation in development rate and body size at extreme temperatures. Additive genetic variation in the temperature sensitivity in the low- and high-temperature regions adds non-additive genetic variation. Development rate shows patterns in additive genetic variation that differ from the patterns of genetic variation in body size; therefore, the genetic correlation between development rate and body size changes sign repeatedly as a function of temperature. The existence of dominance in the genetic variation in the boundary temperatures or in the low- and high-temperature sensitivities leads to a higher total genetic variance due to higher dominance and interaction variance, for both development rate and body size.

Animals↗
PubMed1991

The nature of genetic variation among viruses.

Genetic variation among viruses may seem unimportant and academic--related only to pedagogical classification of things--but accurate determination of genetic relationships can have important implications, from characterizing the molecular basis of attenuation of viral vaccines to furthering knowledge about origins of viruses and even of life itself. It can even help to establish priority in the discovery of viruses when properly applied. The purpose of this brief review is to demonstrate how viruses change and what implications these changes can have on the delicate balance between the viral parasite and its host. Examples will be drawn from the hepatitis viruses when possible.

Animals↗
PubMed2001

High-throughput methods for detection of genetic variation.

Understanding human genetic variation is currently believed to reveal the cause of individual susceptibility to disease and the large variation observed in response to treatment. In this review, we will focus on different approaches to identify and visualize genetic alterations. The various approaches for allele discrimination are formally systematically divided into (i) enzymatic approaches, in which the properties of different enzymes to discriminate between nucleotides are used (restriction enzymes type II, Cleavase and Resolvase, DNA polymerase, and ligase); (ii) electrophoretic methods, in which the allele discrimination is based on the difference in mobility in polymeric gels or capillaries (single- and double-stranded conformation assays, heteroduplex analysis, and DNA sequencing); (iii) solid-phase determination of allelic variants, including high-density oligonucleotide arrays for hybridization analysis, minisequencing primer extension analysis, and fiberoptic DNA sensor array; (iv) chromatographic methods such as denaturing high-performance liquid chromatography (DHPLC); (v) other physical methods of discrimination of allelic variants such as mass spectrometry (mass and charge) or fluorescence exchange-based techniques; and (vi) in silico methods such as high-throughput analysis of expressed sequence tag data. The most frequently used techniques and instrumental settings applied in different combinations are described, and other methods that are less broadly used but have interesting potentials are discussed.

Alleles↗
PubMed2000

Low levels of genetic variation within and high levels of genetic differentiation among populations of species of Abies from southern Mexico and Guatemala.

Populations of Abies in southern Mexico and Guatemala (A. flinckii, A. guatemalensis, A. hickeli, and A. religiosa) have a patchy distribution. This pattern is particularly clear in A. guatemalensis. Genetic diversity within populations, measured by average heterozygosity at 16 isozyme loci, is lower than the range reported for most conifers (mean H(o) ranging from 0.069 in A. guatemalensis to 0.113 in A. flinckii), while differentiation among populations is higher than that observed in most conifer species studied (θ = F(st) ranging from 0.073 in A. hickeli to 0.271 in A. flinckii). Estimated levels of gene flow are low (ranging from 0.672 in A. flinckii to 3.17 in A. hickeli). Populations in most cases had an excess of homozygosity over that expected under Hardy-Weinberg equilibrium, suggesting some inbreeding (F(is) ranging from 0.074 in A. flinckii to 0.235 in A. guatemalensis). A significant relationship between gene flow and geographic distance was observed in A. religiosa, but not in the other three taxa studied. The patterns of genetic variation appear to have been influenced by the distributions and histories of these species. Paleoclimatic evidence suggests that the ranges of these species retreated upwards during the Pleistocene glaciation and became fragmented during the warming period that followed. The populations could have passed through genetic bottlenecks that reduced genetic variation and led to interpopulation differentiation.

Journal Article↗
PubMed1995

Quantitative genetic variation photoinduced by 8-methoxypsoralen in yeast.

The variation in cell mass production within cultured populations of Saccharomyces cerevisiae derived from untreated cells and from cells treated with 8-methoxypsoralen plus near-UV light (8MOP-NUV) was determined. Spontaneous mutation was not significant source of variation, since no genetic component of variance was detected in the untreated population. Following mutagenesis significant levels of genetic variation were found, showing that 8MOP-NUV was effective in inducing quantitative genetic variation among clonal populations of the yeast. The magnitudes of the estimates of the heritability and of the genetic coefficient of variation, indicate that, in phenotypic selection, greater genetic progress can be expected after mutagenic treatment than with untreated populations. The highest estimate of genetic gain was obtained at the intermediate survival level.

Analysis of Variance↗
PubMed2004

Naturally occurring genetic variation in Arabidopsis thaliana.

Currently, genetic variation is probably the most important basic resource for plant biology. In addition to the variation artificially generated by mutants in model plants, naturally occurring genetic variation is extensively found for most species, including Arabidopsis. In many cases, natural variation present among accessions is multigenic, which has historically hampered its analysis. However, the exploitation of this resource down to the molecular level has now become feasible, especially in model species like Arabidopsis, where several genes accounting for natural variation have already been identified. Dissecting this variation requires first a quantitative trait locus (QTL) analysis, which in Arabidopsis has proven very effective by using recombinant inbred lines (RILs). Second, identifying the particular gene and the nucleotide polymorphism underlying QTL is the major challenge, and is now feasible by combining high-throughput genetics and functional genomic strategies. The analysis of Arabidopsis natural genetic variation is providing unique knowledge from functional, ecological, and evolutionary perspectives. This is illustrated by reviewing current research in two different biological fields: flowering time and plant growth. The analysis of Arabidopsis natural variation for flowering time revealed the identity of several genes, some of which correspond to genes with previously unknown function. In addition, for many other traits such as those related to primary metabolism and plant growth, Arabidopsis QTL analyses are detecting loci with small effects that are not easily amenable by mutant approaches, and which might provide new insights into the networks of gene regulation.

Arabidopsis↗
PubMed2002

Fluctuating environments and the role of mutation in maintaining quantitative genetic variation.

We study a class of genetic models in which a quantitative trait determined by several additive loci is subject to temporally fluctuating selection. Selection on the trait is assumed to be stabilizing but with an optimum that varies periodically and might be perturbed stochastically. The population mates at random, is infinitely large and has discrete generations. We pursue a statistical and numerical approach, covering a wide range of ecological and genetic parameters, to determine the potential of fluctuating environments to maintain quantitative genetic variation. Whereas, in contrast to some recent claims, this potential seems to be rather limited in the absence of recurrent mutation, fluctuating environments might, in combination with it, often generate high levels of additive genetic variation. We investigate how the genetic variation maintained depends on the ecological parameters and on the underlying genetics.

Genetic Variation↗
PubMed2005

Evolution in heterogeneous environments and the potential of maintenance of genetic variation in traits of adaptive significance.

The maintenance of genetic variation in traits of adaptive significance has been a major dilemma of evolutionary biology. Considering the pattern of increased genetic variation associated with environmental clines and heterogeneous environments, selection in heterogeneous environments has been proposed to facilitate the maintenance of genetic variation. Some models examining whether genetic variation can be maintained, in heterogeneous environments are reviewed. Genetic mechanisms that constrain evolution in quantitative genetic traits indicate that genetic variation can be maintained but when is not clear. Furthermore, no comprehensive models have been developed, likely due to the genetic and environmental complexity of this issue. Therefore, I have suggested two empirical approaches to provide insight for future theoretical and empirical research. Traditional path analysis has been a very powerful approach for understanding phenotypic selection. However, it requires substantial information on the biology of the study system to construct a causal model and alternatives. Exploratory path analysis is a data driven approach that uses the statistical relationships in the data to construct a set of models. For example, it can be used for understanding phenotypic selection in different environments, where there is no prior information to develop path models in the different environments. Data from Brassica rapa grown in different nutrients indicated that selection changed in the different environments. Experimental evolutionary studies will provide direct tests as to when genetic variation is maintained.

Adaptation, Biological↗
PubMed2004

Genetic variation increases during biological invasion by a Cuban lizard.

A genetic paradox exists in invasion biology: how do introduced populations, whose genetic variation has probably been depleted by population bottlenecks, persist and adapt to new conditions? Lessons from conservation genetics show that reduced genetic variation due to genetic drift and founder effects limits the ability of a population to adapt, and small population size increases the risk of extinction. Nonetheless, many introduced species experiencing these same conditions during initial introductions persist, expand their ranges, evolve rapidly and become invasive. To address this issue, we studied the brown anole, a worldwide invasive lizard. Genetic analyses indicate that at least eight introductions have occurred in Florida from across this lizard's native range, blending genetic variation from different geographic source populations and producing populations that contain substantially more, not less, genetic variation than native populations. Moreover, recently introduced brown anole populations around the world originate from Florida, and some have maintained these elevated levels of genetic variation. Here we show that one key to invasion success may be the occurrence of multiple introductions that transform among-population variation in native ranges to within-population variation in introduced areas. Furthermore, these genetically variable populations may be particularly potent sources for introductions elsewhere. The growing problem of invasive species introductions brings considerable economic and biological costs. If these costs are to be mitigated, a greater understanding of the causes, progression and consequences of biological invasions is needed.

Animal Migration↗
PubMed2006

Associations between environmental stress, selection history, and quantitative genetic variation in Drosophila melanogaster.

Stressful environments may increase quantitative genetic variation in populations by promoting the expression of genetic variation that has not previously been eliminated or canalized by natural selection. This "selection history" hypothesis predicts that novel stressors will increase quantitative genetic variation, and that the magnitude of this effect will decrease following continued stress exposure. We tested these predictions using Drosophila melanogaster and sternopleural bristle number as a model system. In particular, we examined the effect of high temperature stress (31 degrees Celsius) on quantitative genetic variation before and after our study population had been reared at 31 degrees Celsius for 15 generations. High temperature stress was found to increase both additive genetic variance and heritability, but contrary to the selection history hypothesis prediction, the magnitude of this effect significantly increased after the study population had been reared for 15 generations under high temperature stress. These results demonstrate that high temperature stress increases quantitative genetic variation for bristle number, but do not support the selection history hypothesis as an explanation for this effect.

Adaptation, Biological↗
PubMed2004

Beyond race: towards a whole-genome perspective on human populations and genetic variation.

The renewed emphasis on population-specific genetic variation, exemplified most prominently by the International HapMap Project, is complicated by a longstanding, uncritical reliance on existing population categories in genetic research. Race and other pre-existing population definitions (ethnicity, religion, language, nationality, culture and so on) tend to be contentious concepts that have polarized discussions about the ethics and science of research into population-specific human genetic variation. By contrast, a broader consideration of the multiple historical sources of genetic variation provides a whole-genome perspective on the ways i n which existing population definitions do, and do not, account for how genetic variation is distributed among individuals. Although genetics will continue to rely on analytical tools that make use of particular population histories, it is important to interpret findings in a broader genomic context.

Genetic Variation↗
PubMed2003

Fungus-specific microsatellite primers of lichens: application for the assessment of genetic variation on different spatial scales in Lobaria pulmonaria.

We isolated 12 microsatellite loci for the epiphytic lichen-forming ascomycete Lobaria pulmonaria and studied their patterns of variation within and among populations from Canada and Switzerland. Even though several microsatellites exhibited high levels of variability at different spatial scales, we did not find any evidence for intrathalline variation. Most of the genetic variation was attributed to differences among individuals within populations. High genetic variation was also detected among L. pulmonaria samples taken from individual trees, suggesting that either multiple colonization events had occurred or that local recombination is frequent. The geographically structured distribution of alleles from several microsatellites indicated that L. pulmonaria from Canada and Switzerland represent two distinct evolutionary lineages. The potential to identify multiple alleles, and their transferability to closely related species, make microsatellites an ideal tool to study dispersal, population differentiation, and microevolution in lichens.

Alleles↗