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PubMed1997

Information provided by pairs of distantly affected relatives to search for genes involved in rare autosomal dominant diseases.

When dominant mutations of different genes may lead to the same disease, it is often difficult to detect in a particular patient which gene is involved. A strategy is to make genealogical extensions to find affected relatives that should have inherited the same mutation. In particular, for diseases with late age of onset or short survival time, only poor information may be obtained from close relatives of probands and it can be particularly efficient to make genealogical extensions to detect pairs of distantly related affected individuals. Such a pair of affecteds may provide information concerning the region of the genome where the mutated gene should map. Two situations may be encountered depending on whether or not prior information on the location of mutated genes involved in the disease are available. If we already know, from previous linkage studies, that a gene located in a given region R of the genome may be involved in the disease, the problem is then to confirm that it is indeed a mutation of this gene that is involved in the affected pair. Once the implication of a gene in region R has been confirmed the affected pair of relatives may give information to restrict the length of this region R. In this paper we discuss these two points by deriving analytically first the lod score expected and second the expected reduction of the length of the region where the mutation is suspected to map as a function of the number of meioses between the two affected individuals and of the polymorphism of the markers available in the region.

Chromosome Aberrations↗
PubMed2004

Affected sib pair tests in inbred populations.

The affected-sib-pair (ASP) method for detecting linkage between a disease locus and marker loci was first established 50 years ago, and since then numerous modifications have been made. We modify two identity-by-state (IBS) test statistics of Lange (Lange, 1986a, 1986b) to allow for inbreeding in the population. We evaluate the power and false positive rates of the modified tests under three disease models, using simulated data. Before estimating false positive rates, we demonstrate that IBS tests are tests of both linkage and linkage disequilibrium between marker and disease loci. Therefore, the null hypothesis of IBS tests should be no linkage and no LD. When the population inbreeding coefficient is large, the false positive rates of Lange's tests become much larger than the nominal value, while those of our modified tests remain close to the nominal value. To estimate power with a controlled false positive rate, we choose the cutoff values based on simulated datasets under the null hypothesis, so that both Lange's tests and the modified tests generate same false positive rate. The powers of Lange's z-test and our modified z-test are very close and do not change much with increasing inbreeding. The power of the modified chi-square test also stays stable when the inbreeding coefficient increases. However, the power of Lange's chi-square test increases with increasing inbreeding, and is larger than that of our modified chi-square test for large inbreeding coefficients. The power is high under a recessive disease model for both Lange's tests and the modified tests, though the power is low for additive and dominant disease models. Allowing for inbreeding is therefore appropriate, at least for diseases known to be recessive.

Chi-Square Distribution↗
PubMed2000

Thiopurine methyltransferase polymorphic tandem repeat: genotype-phenotype correlation analysis.

BACKGROUND: Thiopurine methyltransferase (TPMT) is a genetically polymorphic enzyme that catalyzes the S-methylation of thiopurine drugs such as 6-mercaptopurine. Recently, a variable number tandem repeat (VNTR) within the TPMT promoter has been reported to "modulate" levels of this enzyme activity. METHODS: We set out to perform genotype-phenotype correlation analysis for the polymorphic TPMT tandem repeat in 1211 clinical laboratory samples in which red blood cell (RBC) TPMT activity had been measured and to compare those results with data for 279 control DNA samples. RESULTS: TPMT VNTR length varied from three to nine repeats ( *V3 to *V9), but the most common alleles were *V4 and *V5, with frequencies in the control samples of 0.54 and 0.36, respectively. The clinical laboratory samples were then stratified into those with "low," "intermediate," or "high" levels of RBC TPMT activity; that is, samples presumed to be homozygous for open reading frame (ORF)-based variant alleles, heterozygous for those alleles, or homozygous for the "wild-type" ORF sequence, respectively. TPMT VNTR genotype *V4/*V5 was associated with significantly higher RBC TPMT activity than were *V4/*V4 or *V5/*V5. Lowest activity levels were associated with genotypes that included an allele with more than 5 repeat elements. However, all of these effects were quantitatively small. Finally, there was linkage disequilibrium between VNTR allele *V5 and TPMT*3A, the most common ORF-based polymorphism associated with very low TPMT activity in white persons. CONCLUSIONS: These observations suggest that, in addition to the striking effects of ORF-based single nucleotide polymorphisms on TPMT activity, the VNTR within the 5'-flanking region of the TPMT gene also may modulate levels of RBC TPMT activity.

Adolescent↗
PubMed2002

Glyburide and glimepiride pharmacokinetics in subjects with different CYP2C9 genotypes.

OBJECTIVES: Our objective was to investigate the effects of genetic polymorphisms of cytochrome P450 (CYP) 2C9 on the pharmacokinetics of glyburide (INN, glibenclamide) and glimepiride, two widely used sulfonylurea antidiabetic drugs. METHODS: We conducted CYP2C9 genotyping for 29 healthy volunteers who had participated in our previous pharmacokinetic studies on glyburide or glimepiride. RESULTS: There were 17 subjects (59%) with the CYP2C9*1/*1 (wild-type) genotype, 8 (28%) with the CYP2C9*1/*2 genotype, 3 (10%) with the CYP2C9*1/*3 genotype, and 1 (3%) with the CYP2C9*2/*3 genotype. The pharmacokinetics of glyburide or glimepiride were not significantly changed among subjects with the CYP2C9*1/*2 genotype. However, in individuals heterozygous for the CYP2C9*3 allele, the median total area under the plasma concentration-time curve of glyburide (n = 2) was 280% (P < or = .05) and that of glimepiride (n = 3) was 267% (P < or = .01) of the respective values in subjects with the CYP2C9*1/*1 genotype (n = 5 and n = 12, respectively). Blood glucose responses to glyburide and glimepiride were not significantly affected by the CYP2C9 genotype. CONCLUSIONS: Genetic polymorphisms of CYP2C9 markedly affect the pharmacokinetics of both glyburide and glimepiride. The influence of the CYP2C9*3 variant allele on glyburide and glimepiride pharmacokinetics may be clinically significant.

Adult↗
PubMed2004

Assigning African elephant DNA to geographic region of origin: applications to the ivory trade.

Resurgence of illicit trade in African elephant ivory is placing the elephant at renewed risk. Regulation of this trade could be vastly improved by the ability to verify the geographic origin of tusks. We address this need by developing a combined genetic and statistical method to determine the origin of poached ivory. Our statistical approach exploits a smoothing method to estimate geographic-specific allele frequencies over the entire African elephants' range for 16 microsatellite loci, using 315 tissue and 84 scat samples from forest (Loxodonta africana cyclotis) and savannah (Loxodonta africana africana) elephants at 28 locations. These geographic-specific allele frequency estimates are used to infer the geographic origin of DNA samples, such as could be obtained from tusks of unknown origin. We demonstrate that our method alleviates several problems associated with standard assignment methods in this context, and the absolute accuracy of our method is high. Continent-wide, 50% of samples were located within 500 km, and 80% within 932 km of their actual place of origin. Accuracy varied by region (median accuracies: West Africa, 135 km; Central Savannah, 286 km; Central Forest, 411 km; South, 535 km; and East, 697 km). In some cases, allele frequencies vary considerably over small geographic regions, making much finer discriminations possible and suggesting that resolution could be further improved by collection of samples from locations not represented in our study.

Africa↗
PubMed2005

The application of statistical physics to evolutionary biology.

A number of fundamental mathematical models of the evolutionary process exhibit dynamics that can be difficult to understand analytically. Here we show that a precise mathematical analogy can be drawn between certain evolutionary and thermodynamic systems, allowing application of the powerful machinery of statistical physics to analysis of a family of evolutionary models. Analytical results that follow directly from this approach include the steady-state distribution of fixed genotypes and the load in finite populations. The analogy with statistical physics also reveals that, contrary to a basic tenet of the nearly neutral theory of molecular evolution, the frequencies of adaptive and deleterious substitutions at steady state are equal. Finally, just as the free energy function quantitatively characterizes the balance between energy and entropy, a free fitness function provides an analytical expression for the balance between natural selection and stochastic drift.

Adaptation, Biological↗
PubMed1972

Is the gene the unit of selection? Evidence from two experimental plant populations.

The dynamics of gametic frequency change have been analyzed in two experimental plant populations. Individual plants were scored for their genotype at four enzyme loci, and four-locus joint gametic frequencies were estimated from the genotypic data over generations. Striking correlations developed in allelic state over loci, including correlations between nonlinked loci, as these populations evolved. Furthermore, the same pair of four-locus complementary gametic types came into marked excess in the late generations of both populations. The results demonstrate that natural selection acted to structure the genetic resources of these populations into sets of highly interacting, coadapted gene complexes. They also provide evidence, at the level of the gene, that selection operating on correlated multilocus units is an important determinant of population structure.

Alleles↗
PubMed1990

A simple genealogical structure of strongly balanced allelic lines and trans-species evolution of polymorphism.

Different alleles undergoing strong symmetric balancing selection show a simple genealogical structure (allelic genealogy), similar to the gene genealogy described by the coalescence process for a sample of neutral genes randomly drawn from a panmictic population at equilibrium. The only difference between the two genealogies lies in the different time scales. An approximate scaling factor for allelic genealogy relative to that of neutral gene genealogy is [square root of S/(2M)].[In[S/(16 pi M2)]]-3/2, where M = Nu and S = 2Ns (N, effective population size; u, mutation rate to selected alleles per locus per generation; s, selection coefficient). The larger the value of square root of S/M (greater than or equal to 100), the larger the scaling factor. These findings, supported by simulation results, allow one to apply the theoretical results of the coalescence process directly to the allelic genealogy. Combined with the trans-species evolution of the major histocompatibility complex polymorphism for which balancing selection is believed to be responsible, allelic genealogy predicts that the number of breeding individuals in the human population could not be as small as 50-100 at any time of its evolutionary history. The analysis appears to contradict the founder principle as being important in recent mammalian evolution.

Alleles↗
PubMed1991

Error bounds for the fundamental and secondary theorems of natural selection.

Error bounds are derived for the approximation delta Z approximately C/W, where delta Z, C, and W denote the rate of change of the mean of a character under selection, the genic (or additive genetic) covariance of the character and fitness (i.e., the covariance of the average effect on the character and the average excess for fitness of every allele that affects the character), and the mean fitness, respectively. Generations are discrete and nonoverlapping; the monoecious population mates at random. The character is determined by arbitrarily many multiallelic loci without epistasis; the linkage map is also arbitrary. The genotypic values of the character are constant. Rounds on the absolute error in the above approximation are deduced for an arbitrary character, and these are converted to bounds on the relative error when the character is fitness itself. In that case, C is the genic variance in fitness, and the relative error cannot exceed one half the greatest genotypic selection coefficient.

Alleles↗
PubMed1994

An evolutionary approach to folding small alpha-helical proteins that uses sequence information and an empirical guiding fitness function.

Three short protein sequences have been guided by computer to folds resembling their crystal structures. Initially, peptide fragment conformations ranging in size from 9 to 25 residues were selected from a database of known protein structures. A fragment was selected if it was compatible with a segment of the sequence to be folded, as judged by three-dimensional profile scores. By linking the selected fragment conformations together, hundreds of trial structures were generated of the same length and sequence as the protein to be folded. These starting trial structures were then improved by an evolutionary algorithm. Selection pressure for improving the structures was provided by an energy function that was designed to guide the conformational search procedure toward the correct structure. We find that by evolution of only 400 structures for fewer than 1400 generations, the overall fold of some small helical proteins can be computed from the sequence, with deviations from observed structures of 2.5-4.0 A for C alpha atoms.

Algorithms↗
PubMed1999

Evolutionary consequences of niche construction and their implications for ecology.

Organisms regularly modify local resource distributions, influencing both their ecosystems and the evolution of traits whose fitness depends on such alterable sources of natural selection in environments. We call these processes niche construction. We explore the evolutionary consequences of niche construction using a two-locus population genetic model, which extends earlier analyses by allowing resource distributions to be influenced both by niche construction and by independent processes of renewal and depletion. The analysis confirms that niche construction can be a potent evolutionary agent by generating selection that leads to the fixation of otherwise deleterious alleles, supporting stable polymorphisms where none are expected, eliminating what would otherwise be stable polymorphisms, and generating unusual evolutionary dynamics. Even small amounts of niche construction, or niche construction that only weakly affects resource dynamics, can significantly alter both ecological and evolutionary patterns.

Alleles↗
PubMedDate not supplied

Polymorphism and genetic evolution in an isolate in the Antilles: Saint-Barthélémy.

St Barthélémy, a small island near Guadaloupe, has been isolated since the eighteenth century. The population is made up of two geographical isolates, genetically separated. In each, the inbreeding level is increasing on account of random genetic drift, which is reinforced by village endogamy, equivalent to a kind of spouse selection. Consanguinity between spouses has been analysed to give an estimate of the contributions of random genetic drift and spouse choice to total inbreeding. A second estimate to inbreeding can be obtained from the variation in observed gene frequencies. The two estimates obtained are of the same order, 0.6-1.0%, and are comparable with those still observed in isolated villages of the French Pyrenees.

Alleles↗
PubMed1995

Linear dose-response relationship and no inverse dose-rate effect observed for low X-ray dose-induced mitotic recombination in Drosophila melanogaster.

Mitotic recombination has emerged lately as a surprisingly common cause of recessive functional gene loss in mammalian cells and has been implicated in tumour suppressor gene loss in human neoplasms. In an assay, primarily monitoring mitotic recombination in Drosophila melanogaster, the ability of low dose acute- and chronic X-ray irradiation to induce clonal expression of recessive mutations of formally heterozygous loci was investigated. Mosaic spots of recessive wing-hair misshape mutations (mwh and flr) and of hair-into-bristles transforming mutation (zw3tic) were enhanced by a factor of two over control level following irradiation of heterozygous larvae to doses as low as 0.01, 0.03 or 0.1 Gy X-rays. The frequencies of mosaic spots induced with eight doses in the interval 0.01-2.0 Gy was linearly related to the dose. The regression lines show no significant intercept at zero dose. During the entire larval developmental period exposure of the exponentially growing target cell population to conditions of chronic irradiation at dose-rate of 15.7 x 10(-5) Gy/min provided no evidence of an inverse dose-rate effect as reported in yeast. In Drosophila, the probability of mitotic recombination per induced DNA double-strand break appears to be at least one order of magnitude higher than in man.

Animals↗
PubMed2002

Delimiting species using DNA and morphological variation and discordant species limits in spiny lizards (Sceloporus).

Haplotype phylogenies based on DNA sequence data are increasingly being used to test traditional species-level taxonomies based on morphology. However, few studies have critically compared species limits based on morphological and DNA data, and the methods used to delimit species using either type of data are only rarely explained. In this paper, we review three approaches for species delimitation (tree-based with DNA data and tree-based and character-based with morphological data) and propose explicit protocols for each. We then compare species limits inferred from these approaches, using morphological and mtDNA data for the Yarrow's spiny lizard (Sceloporus jarrovii), a traditionally polytypic species from the southwestern United States and Mexico. All three approaches support division of S. jarrovii into five species, but only two species are the same among the three approaches. We find the greatest support for the five species that are delimited based on mtDNA data, and we argue that mtDNA data may have important (and previously unappreciated) advantages for species delimitation. Because different data and approaches can disagree so extensively, our results demonstrate that the methodology of species delimitation is a critical issue in systematics.

Animals↗
PubMed1979

Statistical design of toxicity assays: role of genetic structure of test animal population.

This paper concerns certain statistical aspects of the problem of among-strain differences in cancer susceptibility and how these differences may affect the design of toxicity assays. First, the data of Innes et al. (1969) were examined to investigate the magnitude of within-study, between-strain differences in tumor induction. Although there was a very high overall association between mouse strains with respect to the induction of hepatomas, evidence of strain-to-strain variability was found for several compounds. Next, a number of long-term carcinogenicity studies with DDT were considered, and among-strain differences in cancer susceptibility for this compound were noted. Finally, it was shown that if susceptible subgroups do exist, and certain simplifying assumptions are made, then in many cases tumor increases can be detected more readily by studying several inbred mouse strains rather than a single outbred stock.

Animals↗