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PubMed2004

Genetic variability and drift load in populations of an aquatic snail.

Population genetic theory predicts that in small populations, random genetic drift will fix and accumulate slightly deleterious mutations, resulting in reduced reproductive output. This genetic load due to random drift (i.e., drift load) can increase the extinction risk of small populations. We studied the relationship between genetic variability (indicator of past population size) and reproductive output in eight isolated, natural populations of the hermaphroditic snail Lymnaea stagnalis. In a common laboratory environment, snails from populations with the lowest genetic variability mature slower and have lower fecundity than snails from genetically more variable populations. This result suggests that past small population size has resulted in increased drift load, as predicted. The relationship between genetic variability and reproductive output is independent of the amount of nonrandom mating within populations. However, reproductive output and the current density of snails in the populations were not correlated. Instead, data from the natural populations suggest that trematode parasites may determine, at least in part, population densities of the snails.

Animals↗

PubMed2025

Bayesian Modeling of Cancer Outcomes Using Genetic Variables Assisted by Pathological Imaging Data.

With the increasing maturity of genetic profiling, an essential and routine task in cancer research is to model disease outcomes/phenotypes using genetic variables. Many methods have been successfully developed. However, oftentimes, empirical performance is unsatisfactory because of a "lack of information." In cancer research and clinical practice, a source of information that is broadly available and highly cost-effective comes from pathological images, which are routinely collected for definitive diagnosis and staging. In this article, we consider a Bayesian approach for selecting relevant genetic variables and modeling their relationships with a cancer outcome/phenotype. We propose borrowing information from (manually curated, low-dimensional) pathological imaging features via reinforcing the same selection results for the cancer outcome and imaging features. We further develop a weighting strategy to accommodate the scenario where information borrowing may not be equally effective for all subjects. Computation is carefully examined. Simulations demonstrate competitive performance of the proposed approach. We analyze TCGA (The Cancer Genome Atlas) LUAD (lung adenocarcinoma) data, with overall survival and gene expressions being the outcome and genetic variables, respectively. Findings different from the alternatives and with sound properties are made.

Humans↗

PubMed2004

The effects of mating system and genetic variability on susceptibility to trematode parasites in a freshwater snail, Lymnaea stagnalis.

The amount and distribution of genetic variability in host populations can have significant effects on the outcome of host-parasite interactions. We studied the effect of mating system and genetic variability on susceptibility of Lymnaea stagnalis snails to trematode parasites. Mating system of snails from eight populations differing in the amount of genetic variability was manipulated, and self- and cross-fertilized offspring were exposed to naturally occurring trematode parasites in a controlled lake experiment. Susceptibility of snails varied between populations, but mating-system treatment did not have a significant effect. Heterozygosity of snails was negatively correlated with the probability of trematode infection, however, suggesting that parasitic diseases may pose a serious threat to populations lacking genetic variability.

Analysis of Variance↗

PubMed1999

Epidemiology and genetic variability of two species of nematodes (Heligmosomoides polygyrus and Syphacia stroma) of Apodemus spp.

The epidemiology and genetic variability of 2 parasitic nematodes Heligmosomoides polygyrus and Syphacia stroma of Apodemus spp. were investigated. Both are parasites of the same host, exhibit a direct life-cycle and are dioecious. However, H. polygyrus has a diploid and S. stroma a haplodiploid mode of reproduction. Haplodiploidy may lead to a more female biased sex ratio and reduced genetic variability. Levels of genetic diversity were analysed using both isoenzyme electrophoresis and RAPDs (random amplified polymorphic DNA). Both parasites showed a female biased sex ratio with a stronger bias for the haplodiploid parasite. Results showed significantly fewer genetic polymorphisms as measured by RAPDs for the haplodiploid parasite S. stroma in comparison with H. polygyrus. Despite the observed female biased sex ratio this could not be explained by a significant amount of inbreeding. Heterozygote deficiency for individual allozyme loci--which could indicate inbreeding--was not found in either parasite species. Other features of the particular life-history of these species are likely to have an impact on the sex ratio and genetic variability too.

Animals↗

PubMed1991

Development of vivo of genetic variability of simian immunodeficiency virus.

Rapid development of genetic variability may contribute to the pathogenicity of lentiviruses as it may allow escape from immune surveillance and/or from suppression of virus replication. Although apathogenic in African green monkeys, simian immunodeficiency virus isolated from African green monkeys is shown to display extensive genetic variability and defectiveness in the V1- and V2-like variable domains of the external envelope protein comparable to that known for human immunodeficiency virus. However, in contrast to the situation in human immunodeficiency virus-infected individuals, a predominant major virus variant was detected neither in a monkey naturally infected for more than 10 years nor in two monkeys infected with a molecular virus clone for 15-20 months. Extensive variability evolves from a single genotype with a maximal rate of 7.7 mutations per 1000 nucleotides per year. A remarkable selection for nonsynonymous mutations that accounts for 92% of all changes indicates continuous selection of variants.

Amino Acid Sequence↗

PubMed2003

Analysis of 22 heterologous microsatellite markers for genetic variability in Indian goats.

The genetic variability of 22 heterologous microsatellite markers was analyzed in two Indian goat breeds, namely Bengal and Chegu. The heterozygosity, polymorphism information content (PIC), and probability of identity of two individuals were calculated for all microsatellite loci in both the breeds. The observed number of alleles varied between 4 and 13 at the studied microsatellite loci. The evaluated microsatellite loci exhibited high mean heterozygosity of 0.69 +/- 0.11 and 0.66 +/- 0.07 in Bengal and Chegu goats, respectively. The mean PIC values of the studied loci in these breeds were 0.79 +/- 0.08 and 0.78 +/- 0.05, respectively. The probability of identity of two random individuals from different breeds, taking into account, all the 22 microsatellite loci was as low as 5.523 x 10(-40). On the basis of these results, we propose that these microsatellite markers may be used with reliability for studying genetic diversity and for identification of individuals in Indian goat breeds.

Alleles↗

PubMed1979

Genetic variability maintained in a finite population under mutation and autocorrelated random fluctuation of selection intensity.

By using the diffusion equation method, the level of genetic variability maintained under mutation pressure in a finite population is investigated, assuming autocorrelated random fluctuation of selection intensity. An appropriate mathematical model was formulated to treat the change of gene frequencies, incorporating mutation pressure and fluctuating selection. Extensive Monte Carlo simulation experiments were also performed to supplement the theoretical treatments. Excellent agreement between the two results suggests the validity of the present diffusion model for the autocorrelated selection. One of the most important findings from the simulation studies is that mutations and random sampling drift largely determine the level of genetic variability, and that the presence of autocorrelated selection can significantly lower genetic variability only when its strength, as measured by the cumulative variance of selection intensity, is larger than about 10(3) times the mutation rate. It is pointed out that the effects of both mutations and random sampling drift have to be incorporated in order to assess the role of various factors for the maintenance of genetic variability in natural populations.

Journal Article↗

PubMed1987

Genetic variability in endoparasitic helminths.

Biochemical genetic studies have revealed high levels o f polymorphism and heterozygosity in natural populations of endoporasitic helminths. With few exceptions, these parasitic helminths appear just as genetically variable as free-living invertebrates. But this finding is not consistent with the idea that the internal environment o f the host represents a stable and homogeneous habitat which selects for parasite homozygosity. In this article, Steven Nadler examines alternative explanations drawn from the perennial 'selectionist-neutralist' debate-do all genes necessarily confer selective advantages or disadvantages, or are some effectively neutral?

Journal Article↗

PubMed2005

Effect of genetic variability on the inflammatory response to periodontal infection.

AIM: To review the association between genetic variability and the inflammatory response induced by periodontal infection. MATERIAL AND METHODS: A search of MEDLINE-PubMed was performed from January 2000 up to and including March 2005. The search included all types of publications, published in English without other limitations. The following search terms were used: "cytokine polymorphism", "gene polymorphism", "periodontitis", "gingivitis", "inflammation" and "host-response". The papers resulting from the above search were used as an additional source for relevant articles. RESULTS: Genetic variability was examined for the correlation to clinical indicators of inflammation such as bleeding on probing (BOP), gingival inflammation, cytokine in gingival crevicular fluid (GCF) and cytokine production by inflammatory cells. According to the current literature, most of the studies found no association between genetic variability and BOP, gingival inflammation or cytokine concentrations in the GCF. These studies were hampered by inappropriate study designs and the use of inflammatory parameters as secondary rather than primary outcome variables. The data suggest that the production of inflammatory mediators by inflammatory cells may be affected by different genetic traits but further studies are needed in order to establish this association. CONCLUSIONS: To date, there is no clear correlation between any of the gene polymorphisms and clinical indicators of inflammation. The powering of studies to reveal associations between single or multiple nucleotide polymorphisms and inflammatory parameters will need to involve a much larger number of subjects than were used in the past. The available data (including the interleukin-1 composite genotype) do not currently support the utility of such tests in the diagnosis and prognostic assessments of periodontal diseases.

Bacteria, Anaerobic↗

PubMed2002

Sheep as a mammalian model of genetic variability in melatonin.

Large inter-individual variability in plasma melatonin concentration at night is a common mammalian trait. In sheep, it varies from < 50 pg ml(-1) to > 800 pg ml(-1) but is very consistent within individuals. This inter-individual variability is under strong genetic control, which depends on melatonin secretion from the pineal gland, but not on melatonin catabolism. This genetic variability does not originate from differences in the synthetic enzymes or from a difference in melatonin secretion per mg of tissue, but from a difference in pineal size, which is highly variable among lambs of the same age and live weight. The genetic difference among lambs is already expressed at birth and is due to a difference in the number of pinealocytes rather than in their size. Pineal size and number of pinealocytes correlate strongly with plasma melatonin concentrations. The variability in pineal mass is not associated with the variability in any other organ (for example, the pituitary). The identification of genetic markers in the genome associated with the size of the pineal gland may lead to identification of genes involved in development of the mammalian pineal gland. Divergent selection of sheep on the basis of plasma melatonin concentrations could be used to constitute a mammalian model for extreme plasma concentrations.

Animals↗

PubMed2006

The effects of selective breeding against scrapie susceptibility on the genetic variability of the Latxa Black-Faced sheep breed.

Breeding sheep populations for scrapie resistance could result in a loss of genetic variability. In this study, the effect on genetic variability of selection for increasing the ARR allele frequency was estimated in the Latxa breed. Two sources of information were used, pedigree and genetic polymorphisms (fifteen microsatellites). The results based on the genealogical information were conditioned by a low pedigree completeness level that revealed the interest of also using the information provided by the molecular markers. The overall results suggest that no great negative effect on genetic variability can be expected in the short time in the population analysed by selection of only ARR/ARR males. The estimated average relationship of ARR/ARR males with reproductive females was similar to that of all available males whatever its genotype: 0.010 vs. 0.012 for a genealogical relationship and 0.257 vs. 0.296 for molecular coancestry, respectively. However, selection of only ARR/ARR males implied important losses in founder animals (87 percent) and low frequency alleles (30 percent) in the ram population. The evaluation of mild selection strategies against scrapie susceptibility based on the use of some ARR heterozygous males was difficult because the genetic relationships estimated among animals differed when pedigree or molecular information was used, and the use of more molecular markers should be evaluated.

Alleles↗

PubMed2003

Recent habitat fragmentation caused by major roads leads to reduction of gene flow and loss of genetic variability in ground beetles.

Although habitat fragmentation is suspected to jeopardize the long-term survival of many species, few data are available on its impact on the genetic variability of invertebrates. We assess the genetic population structure of the flightless ground beetle Carabus violaceus L., 1758 in a Swiss forest, which is divided into several fragments by a highway and two main roads. Eight samples were collected from different forest fragments and analysed at six microsatellite loci. The largest genetic differentiation was observed between samples separated by roads and in particular by the highway. The number of roads between sites explained 44% of the variance in pairwise F(ST) estimates, whereas the age of the road and the geographical distance between locations were not significant factors. Furthermore, a comparison of allelic richness showed that the genetic variability in a small forest fragment isolated by the highway was significantly lower than in the rest of the study area. These findings strongly support the hypothesis that large roads are absolute barriers to gene flow in C. violaceus, which may lead to a loss of genetic variability in fragmented populations.

Animals↗

PubMed2004

Effects of genetic variability and habitat of Qualea parviflora (Vochysiaceae) on herbivory by free-feeding and gall-forming insects.

BACKGROUND AND AIMS: Differences in the chemical and physical traits of plants caused by both genetic and habitat characteristics may influence attack by herbivores. Leaves of Qualea parviflora (Vochysiaceae), a common tree of different habitats in the Brazilian Neotropical savannas (cerrado), are susceptible to severe attack by herbivorous free-living and gall-forming insects. Attack by free-living and gall-forming insects within and between populations of Q. parviflora were examined and it was determined to what extent genetic variability (detected by RAPD markers), phenotypic characteristics of the plants and habit traits influence the number of free-living and gall-forming insect species and individuals attacking the plants, and the intensity of attack. METHODS: On four occasions in 2000, leaves were sampled from ten individual trees in each of three types of vegetation in the cerrado: campo sujo, cerrado sensu stricto and cerradão at the Ecological Station of Pirapitinga (ESP), in Três Marias, north-western Minas Gerais, Brazil. Genetic variability was detected by RAPD markers, and concentrations of nutrients, phenols and tannins, sclerophylly and pre-dawn water potential of leaves were measured. Water and nutrient contents in the soil below each tree characterized the habitat. The free-living and gall-forming herbivorous insects were determined. KEY RESULTS: Of 69 RAPD markers analysed, 41 were polymorphic and were used for analyses of genetic variability of Q. parviflora. Most of the variability occurred within habitats, accounting for 97.65 % of the genetic variability. Plants in the cerrado sensu stricto and campo sujo were the most similar. There were no significant associations between genetic similarity and the chemical and physical traits of Q. parviflora, or with habitat, nor was there significant correlation between phenotypic and habitat traits. Increasing concentrations of tannins and sulphur, C : N ratio and sclerophylly correlated with increasing percentage of leaf area damaged by herbivores. Decreased sclerophylly, concentration of tannins and C : N ratio, and increased concentration of nutrients in leaves correlated with increased severity of attack by gall-forming insects. CONCLUSIONS: Nutrient concentration in the soil had more influence, indirectly, on free-feeding insects than did composition of Q. parviflora leaves. However, gall-forming insects are affected more by leaf quality, attacking fewer sclerophyllous leaves, with larger nutrient but smaller tannin concentrations.

Animals↗

PubMed2002

Determining genetic variability in the distribution of sensitivities to toxic stress among and within field populations of Daphnia magna.

To extrapolate credibly from individuals in the laboratory to field populations, it is essential to account for genetic differences in susceptibility to toxic stress and thus incorporate genetic variability into ecological risk estimates. In this study, the distribution of sensitivities across two toxic chemicals among and within field populations of Daphnia magna were used to quantify genetic variability. The study employed 30 D. magna clones from three geographically separate European populations. The sensitivity of each population studied and its constituent clones was estimated in terms of the concentrations of lambda-cyhalothrin and cadmium impairing individual fitness by 10 and 50% (EC10-50). Results revealed that differences in tolerance among clones within populations were large when compared with differences between populations and that the genetic range of sensitivities to toxic stress within populations was log-normally distributed. Furthermore, reported variation in sensitivity values to toxic stress among different laboratory species, populations, and clones was similar to that observed among and within field populations of Daphnia. These results suggest that it is possible to estimate genetic variability by estimating the tolerance distribution of laboratory populations and clones and that extrapolation approaches currently used in ecological risk assessment should explicitly incorporate genetic variability in tolerance into risk estimates.

Adaptation, Physiological↗

PubMed1992

Genetic variability and rodent models of human aging.

Inbred strains, outbred strains, and natural populations of rodents differ greatly in the amount and nature of the genetic variability they possess. Consequently, as models of human aging they vary with respect to the areas of research to which they are best suited. Inbred strains, in which all individuals are genetically identical, are best suited as models of specific disease processes and for manipulations involving tissue transplantation. Their lack of genetic variability, however, and the disruption of genetic linkage groups that occurs during inbreeding limit their value as models of more general aging processes. Outbred strains exhibit large interindividual genetic variation--a result of ongoing random accumulation of deleterious alleles with late ages of action. This makes them ideal models for studying the diversity of pathologic lesions, connections between pathologies, and susceptibility to pathologic lesions that collectively produce the reductions in reproductive capacity, physiological efficiency, and viability that are characteristic of aging. Natural populations also may exhibit relatively large amounts of interindividual genetic variability. However, difficulties with husbandry, variable parasite loads, and complex population genetics can compromise their suitability as models of human aging. Ultimately, a consideration of the range of animal models available and a more careful matching of the goals of a study with the genetic system of the model will prove fruitful to gerontology.

Aging↗

PubMed2005

The catadromous European eel Anguilla anguilla (L.) as a model for freshwater evolutionary ecotoxicology: relationship between heavy metal bioaccumulation, condition and genetic variability.

Understanding the effects of pollutants on the genome is of crucial importance to preserve the evolutionary potential of endangered natural populations. The highly vagile European eel (Anguilla anguilla L.) has suffered a dramatic decline in recruitment since two decades, urging for a better understanding of the genetic impact of pollution. Its catadromous life history constitutes a model to assess local selection of pollutants on condition and genetic variability, as juveniles recruit in European rivers without appreciable pollution load or interfering genetic background. Because of its high fat content and local benthic feeding behaviour, the feeding stage is considered extremely prone to the bioaccumulation of pollutants. We studied the relationship between heavy metal bioaccumulation, fitness (condition) and genetic variability in the European eel. The muscle tissues of 78 sub-adult eels, originating from three Belgian river basins (Scheldt, Meuse and Yser), were examined for nine heavy metal pollutants (Hg, Cd, Pb, Cu, Zn, Ni, Cr, As and Se), while in total 123 individuals were genotyped at 12 allozyme and 8 microsatellite loci. A significant negative correlation between heavy metal pollution load and condition was observed, suggesting an impact of pollution on the health of sub-adult eels. In general, we observed a reduced genetic variability in strongly polluted eels, as well as a negative correlation between level of bioaccumulation and allozymatic multi-locus heterozygosity (MLH). Microsatellite genetic variability did not show any pollution related differences, suggesting a differential response at metabolic enzymes and possibly direct overdominance of heterozygous individuals.

Anguilla↗

PubMed1995

Genetic variability of carrot seed proteins analyzed by one- and two-dimensional electrophoresis with immobilized pH gradients.

The genetic variability of eight carrot populations representing commercially important morphological types was analyzed for seed protein polymorphism by one- and two-dimensional electrophoresis using immobilized pH gradients (IPG) in order to assess the potential of both techniques in carrot hybrid breeding as well as genetic quality testing of carrot trade seeds. The digitized silver-stained one- and two-dimensional gels of the urea/detergent-soluble seed proteins were subjected to computer analysis to estimate both the inter- and intrapopulation genetic variability. The results indicated that isoelectric focusing (IEF-IPG) of seed proteins is a powerful tool for quick screening of the genetic variability present between and within carrot populations, while two-dimensional polyacrylamide gel electrophoresis (IPG-DALT) can be employed to establish detailed genetic relationships of carrot populations selected by initial IEF-IPG screening in order to use genetic distant and homogeneous populations for successful carrot hybrid breeding. However, the applicability of IEF-IPG in genetic quality testing of carrot seeds seems to be restricted to hybrid purity testing. IPG-DALT is a far more powerful tool to profile unambiguously all carrot varieties commercially used in order to test the genetic quality of trade seeds, because this technique exhibits protein spots or spot combinations exclusively found in each of the eight varieties investigated.

Daucus carota↗

PubMed2001

Assessment of genetic variability of resistance to gastrointestinal nematode parasites in Creole goats in the humid tropics.

Goat production is widespread in the tropics. Goats are very susceptible to gastrointestinal nematode infection, but there is less evidence of their genetic resistance. Genetic resistance of Creole goats to gastrointestinal nematodes has been studied at Guadeloupe in the French West Indies since 1995. The objective of this research was to investigate genetic variation for resistance to gastrointestinal nematode infection, in order to introduce this trait into breeding schemes. Genetic variability was assessed within a Creole experimental flock. Forty-nine sire groups were characterized at weaning and 55 during fattening after weaning. Kids were naturally infected, mainly by Haemonchus contortus and Trichostrongylus colubriformis. Fecal egg counts were determined once at weaning and every 6 and 7 wk after drenching during fattening. Blood samples were collected every 7 wk during fattening for determination of packed cell volume. Live weights were recorded at weaning and at the beginning and middle of every infection period during fattening. Genetic parameters were estimated using the REML for multivariate animal models. The heritability estimate for transformed fecal egg count was 0.37+/-0.06 at weaning. During fattening, it increased from 0.14+/-0.05 at 4 mo to 0.33+/-0.06 at 10 mo. Heritabilities of packed cell volume ranged from 0.10 to 0.33. At weaning, maternal heritability of fecal egg count reached 0.26 and direct heritability 0.20. After 6 mo of age, maternal effects were found to be unimportant for fecal egg count and packed cell volume. Live weights presented significant genetic variability. Genetic relationships between fecal egg counts and live weight in infected pastures were never significant. Genetic correlations between packed cell volume and live weight decreased from 0.47 to 0.10 from weaning to 10 mo of age. These results demonstrated the feasibility of breeding for improved resistance to nematodes in Creole kids.

Animals↗