Estimating null allele frequencies at a microsatellite locus in the oystercatcher (Haematopus ostralegus)

A significant heterozygote deficiency was found for microsatellite locus 20H7 among adult breeding birds in four populations of the oystercatcher ( Haematopus ostralegus ). Genotype frequencies at seven other loci were according to Hardy–Weinberg equilibria. Deviations between observed and expected genotype numbers decreased substantially when the data were corrected based on the estimated frequency of a putative null allele at locus 20H7 . However, no null homozygotes were observed in the total sample of 378 individuals. The probability that, because of chance effects, null homozygotes were not represented in the sample ( n =230) from the most intensively studied population (Schiermonnikoog) was estimated to be less than 1%. Parent–offspring comparisons from Schiermonnikoog showed that observed genotype numbers in the offspring were in accordance with expected values based on the estimated frequency of the putative null allele in the population. Moreover, a null homozygote was observed among the nestlings. The combined results indicated that a null allele is present at locus 20H7 in oystercatchers and that the inheritance is according to normal Mendelian segregation. If the absence of null homozygotes among adult animals cannot be ascribed to statistical effects, null homozygotes may suffer a selective disadvantage during the juvenile stage.     

Unequal allelic frequencies at the self‐incompatibility locus within local populations of Prunus avium L.: an effect of population structure?

In this paper, we investigated the genetic structure and distribution of allelic frequencies at the gametophytic self-incompatibility locus in three populations of Prunus avium L. In line with theoretical predictions under balancing selection, genetic structure at the self-incompatibility locus was almost three times lower than at seven unlinked microsatellites. Furthermore, we found that S-allele frequencies in wild cherry populations departed significantly from the expected isoplethic distribution towards which balancing selection is expected to drive allelic frequencies (i.e. identical frequency equal to the inverse of the number of alleles in the population). To assess whether this departure could be caused either by drift alone or by population structure, we used numerical simulations to compare our observations with allelic frequency distributions expected : (1) within a single deme from a subdivided population with various levels of differentiation; and (2) within a finite panmictic population with identical allelic diversity. We also investigated the effects of sample size and degree of population structure on tests of departure from isoplethic equilibrium. Overall, our results showed that the observed allele frequency distributions were consistent with a model of subdivided population with demes linked by moderate migration rate.     

PROBLEMS WITH TESTING INBREEDING AVOIDANCE: THE CASE OF THE COLLARED FLYCATCHER

Four year's data on collared flycatchers, Ficedula albicollis, breeding in a nestbox plot on the island of Gotland, Sweden, was used to investigate whether individuals avoid mating with close kin (i.e., parents or sibs). Only one case of close inbreeding (0.5% of all pairs) was observed during the years of study. The observed frequency of close inbreeding was compared to expected frequencies based on two different null models. Assuming no inbreeding avoidance behaviors (e.g., dispersal or kin recognition), but taking into account the fact that mortality, and different arrival and pairing times of individuals reduce the probability of mating with close kin, the expected frequency of close inbreeding is 10% and 15% for female and male recruits (i.e., born in the study plot), respectively. However, assuming mating to be random within the study plot reduced the expected frequency of close inbreeding to 1% or less for both males and females. Consequently, conclusions drawn concerning inbreeding avoidance depend on the null model used. Contrasting estimated costs of tolerating close inbreeding with those of avoiding it (by dispersal to other plots), however, suggests that the costs of avoiding close inbreeding are substantially greater than those of tolerating it. Therefore, although inbreeding avoidance cannot be rejected as a cause of dispersal of this species, it is not the primary cause, and particularly not for sex-biased dispersal. The general problems of investigating inbreeding avoidance are discussed. It is argued that all previous null models based on random mating in finite populations produce expected frequencies of close inbreeding that in fact include inbreeding avoidance, since they implicitly assume random dispersal within a finite population. Thus, comparisons between observed and expected frequencies of close inbreeding based on random mating are inadequate. The most promising method of investigating inbreeding avoidance is to experimentally study individual movements and mating preferences in the presence and absence of close kin.     

On the distribution of allele frequencies in a diffusion model

An expression is derived and values tabulated for the expected allele frequencies and their variances, arranged in decreasing order in a population, from the finite and infinite alleles diffusion model in Watterson (1976). The neutral model and also a model with heterozygote selection are considered. Some observed ABO blood group allele frequencies are compared with the tabulated expected frequencies in the neutral three allele model. This extends the results of Watterson and Guess (1977) who tabulate the expected value of the most common allele. One test of neutrality previously advocated is to consider the distribution of F, the population homozygosity, conditional on G, the product of allele frequencies. However it is shown here that for a large number of alleles, F and G are asymptotically independent, the test would not be a good one in this case. A limit theorem is derived for the distribution of allele frequencies in the neutral model when the mutation rate is large. In this case F is shown to be asymptotically normal. An inequality is derived for the probability that the oldest allele in a population is amongst the r most frequent types. An inequality is also found for the probability that a sample will only contain representatives of the r most frequent allele types in the population.     

Characteristics of evoked potentials and single neuron responses in the cat sensorimotor cortex to sound stimuli with different frequencies.

The characteristics of the averaged evoked potentials (AEP) (experiments with awake non-paralysed animals), of the evoked potentials (EP) and of the responses of single sensorimotor cortical neurons (acute experiments) of cats to tone-bursts with frequencies within 0.1-6.0 kHz were studied. Response selectivity to the tone-burst frequencies which are energetically pronounced in some biologically significant sounds for the cat was observed. The averaged curve of the dependence of the amplitude of AEP in the somatosensory cortical region (S1) on the tone-burst frequency has reliable maximum values at the frequencies of 0.8, 1.6 and 2.0-3.0 kHz. Most pronounced changes in the heart rhythm were observed within the tone-burst frequency ranges in which the AEP of the highest amplitudes were recorded. The amplitude of the AEP was found to increase during the conditioned reflex elaboration. The curve of the dependence of the probability of the EP occurrence on the frequency at equal sound pressure levels had maximum values at the frequencies of 1.6 and 3.2 kHz. The highest amplitude values of EP were found at frequencies of 0.8, 1.6 and 3.2 kHz. More than half of the recorded neurons revealed the lowest values of the response thresholds and the maximum values of the occurrence probability under suprathreshold stimulation at frequencies close to 0.8, 1.6, and 3.2 kHz. It is supposed that the above mentioned feature of the input frequency organization in sensorimotor cortex is connected with the selectivity as to the biological significance of acoustic stimuli.     

Nearest-neighbor tree species combinations in tropical forest: the role of chance, and some consequences of high diversity

In three permanent inventory plots comprising 12.4 ha of undisturbed forest at La Selva, Costa Rica, all stems ≥10 cm dbh were mapped and identified to species. There were 1628, 1478 and 1954 trees in the plots, representing 168, 166 and 171 species respectively. We determined the species of each nearest-neighbor pair of trees, and asked whether the occurrence of species pairs conforms to a simple random mixing model. If trees are randomly mixed in terms of species, the expected frequency of any nearest neighbor species combination is a function of the relative abundance of the two species. Departures from random mixing could arise from species interactions, differential responses to habitat, or both. The number of possible ij species combinations increases approximately as the square of the number of species. For the 168 species in plot 1, for example, there are 14 196 possible combinations. We compared the expected frequency of each species combination in the three plots (42 736 combinations in all) with observed frequencies. Over 98% of the combinations had observed frequencies of zero and expected frequencies close to zero. A consequence of high diversity is low density of most individual species, and exceedingly low frequencies of the vast majority of species combinations. For each of the 805 combinations with observed frequencies >0, we used simulation to generate a distribution of expected frequencies. We used a t-test to compare the observed frequency with the mean of the simulated distribution for each combination. Only 40 combinations (0.09% of the possible species combinations in the plots) departed from expected frequencies; 39 combinations were more common, and one less common than expected. The overwhelming majority of nearest neighbor species combinations occur at frequencies predictable from their individual abundances.     

Ion pairs in alpha helices

A survey of 47 globular proteins was made to determine the probability of occurrence of ion pairs separated by 1,2,3,... and 8 residues in the alpha helices. As a control, the probability of occurrence of like charged pairs was also determined. The survey showed that ion pairs of the type i,i +/- 3 and i, i +/- 4 are the most predominant. Such a preference was not observed for like charged pairs. The observed frequency of ion pairs is significantly greater than their expected frequency. The normalized frequencies of occurrence of the ion pairs were also found to increase generally with the helix length. These results indicate that the ion pairs may contribute to the stability of solvent-exposed alpha helices. Since the stabilization of protein secondary structure enhances the stability of protein tertiary structure, these results may throw light on the mechanism of protein folding.     

TRAB: testing whether mutation frequencies are above an unknown background

To rigorously determine whether a gene or a set of genes have alterations that are involved in carcinogenesis requires a comparison of the prevalence of identified changes to a control mutation frequency present in tumor DNA. To facilitate this task, we develop a testing approach and the associated R library, called TRAB, that evaluates whether the frequency of somatic mutation in a given gene is higher than that observed in a control group of genes. Specifically, we test the null hypothesis that the frequency belongs to a control population of frequencies, against the alternative hypothesis that the frequency is higher. Mutation frequencies in the control group are themselves allowed to be variable. TRAB computes the a posteriori probability and the Bayes factor for the hypothesis using a hierarchical Bayesian approach.     

Rates of cultural change and patterns of cultural accumulation in stochastic models of social transmission

Cultural variation in a population is affected by the rate of occurrence of cultural innovations, whether such innovations are preferred or eschewed, how they are transmitted between individuals in the population, and the size of the population. An innovation, such as a modification in an attribute of a handaxe, may be lost or may become a property of all handaxes, which we call “fixation of the innovation.” Alternatively, several innovations may attain appreciable frequencies, in which case properties of the frequency distribution—for example, of handaxe measurements—is important. Here we apply the Moran model from the stochastic theory of population genetics to study the evolution of cultural innovations. We obtain the probability that an initially rare innovation becomes fixed, and the expected time this takes. When variation in cultural traits is due to recurrent innovation, copy error, and sampling from generation to generation, we describe properties of this variation, such as the level of heterogeneity expected in the population. For all of these, we determine the effect of the mode of social transmission: conformist, where there is a tendency for each naïve newborn to copy the most popular variant; pro-novelty bias, where the newborn prefers a specific variant if it exists among those it samples; one-to-many transmission, where the variant one individual carries is copied by all newborns while that individual remains alive. We compare our findings with those predicted by prevailing theories for rates of cultural change and the distribution of cultural variation.     

The effect of recurrent mutation on the frequency spectrum of a segregating site and the age of an allele

The sample frequency spectrum of a segregating site is the probability distribution of a sample of alleles from a genetic locus, conditional on observing the sample to be polymorphic. This distribution is widely used in population genetic inferences, including statistical tests of neutrality in which a skew in the observed frequency spectrum across independent sites is taken as a signature of departure from neutral evolution. Theoretical aspects of the frequency spectrum have been well studied and several interesting results are available, but they are usually under the assumption that a site has undergone at most one mutation event in the history of the sample. Here, we extend previous theoretical results by allowing for at most two mutation events per site, under a general finite allele model in which the mutation rate is independent of current allelic state but the transition matrix is otherwise completely arbitrary. Our results apply to both nested and nonnested mutations. Only the former has been addressed previously, whereas here we show it is the latter that is more likely to be observed except for very small sample sizes. Further, for any mutation transition matrix, we obtain the joint sample frequency spectrum of the two mutant alleles at a triallelic site, and derive a closed-form formula for the expected age of the younger of the two mutations given their frequencies in the population. Several large-scale resequencing projects for various species are presently under way and the resulting data will include some triallelic polymorphisms. The theoretical results described in this paper should prove useful in population genomic analyses of such data.     

Changing environmental spectra influence age-structured populations: increasing ENSO frequency could diminish variance and extinction risk in long-lived seabirds

As global climate changes, there is increasing need to understand how changes in the frequencies of environmental variability affect populations. Age-structured populations have recently been shown to filter specific frequencies of environmental variability, favoring generational frequencies, and very low frequencies, a phenomenon known as cohort resonance. However, there has been little exploration of how changes in the spectra of environmental signals will affect the stability and persistence of age-structured populations. To examine this issue, we analyzed a likely example to show how changes in the frequency of an influential climate phenomenon, the El Niño-Southern Oscillation (ENSO), could affect a marine bird population. We used a density-dependent, age-structured population model to calculate the transfer function (i.e., the frequency-dependent sensitivity) of Brandt’s cormorant (Phalacrocorax penicillatus), a representative marine bird species known to be influenced by ENSO. We then assessed how the population would be affected by ENSO forcing that was doubled and halved in frequency. The transfer function indicated this population is most sensitive to variance at low frequencies, but does not exhibit the sensitivity to generational frequencies (cohort resonance) observed in shorter-lived species. Doubling the frequency of ENSO unexpectedly resulted in higher mean adult population abundance, lower variance, and lower probability of extinction, compared to forcing with the historical or reduced ENSO frequency. Our results illustrate how long-lived species with environmentally driven variability in recruitment, including many species of marine birds and fish, may respond in counterintuitive ways to anticipated changes in environmental variability.     

Frequencies of attached and free ear lobes in Lagos (Nigeria)

A sample of 1,600 unrelated individuals in Lagos (Nigeria) were examined for attached or free ear lobes. Pedigree data were obtained for 11 families by questionnaire. The corrected proportion of attached among the progeny of free X free was 0.27 compared to an expected value of 0.25. The observed frequencies of the three types of marriages were not significantly different from the expected values derived from the frequencies of the traits in the population. Males and females in the population were equally affected by the traits. Thus, the population frequency of attached is 25.37%, a value within the range for Caucasoids but lower than for Mongoloids.     

A null model for randomization tests of nestedness in species assemblages

Analysis of the degree of order in species assemblages in terms of nested subsets has received increased interest during the last decade. However, recently a series of papers have questioned the validity of methods employed for testing whether observed patterns deviate from random expectations. The current view seems to be that the randomization procedure should control for both number of species per site and species frequencies. The randomization procedures used also choose to keep the total number of observations constant in each resample. In this paper I question some of these assumptions when analyzing species-by-site matrices for detecting whether the biota is significantly nested or not. My basic assumption is that the observed species frequency is only an estimate of the probability of occurrence for the particular species. For a test of degree of nestedness all sites should be regarded as being equal. To what extent size, isolation or habitat quality may influence species distribution is a secondary question if nestedness can be statistically proven. This implies that generation of random matrices should only consider the frequency of the species (as an estimate of their probability of occurring in any patch). Such matrices are computationally simple and besides providing a test of nestedness also open the possibility of testing whether the range in species richness is smaller or larger than expected under random expectations. The choice of null model for the test should always be viewed in relation to the question asked. If nestedness is concerned the methods proposed here should be used. However, if other questions are at hand the restrictions of previous approaches may be valid. This is for instance the case if pairwise species co-occurrences are analyzed. In this case, the richness of each site should obviously be incorporated in the randomization to control for the higher probability of co-occurrence at species-rich sites.     

Frequency of resistance to Bacillus thuringiensis toxin CrylAb in Greek and Spanish population of Sesamia nonagrioides (Lepidoptera: Noctuidae)

The high-dose/refuge strategy is considered as the main strategy for delaying resistance in target pests to genetically modified crops that produce insecticidal proteins derived from Bacillus thuringiensis Berliner. This strategy is based on a key assumption that resistance alleles are initially rare (<10(-3)). To test this assumption, we used an F2 screen on natural populations of Sesamia nonagrioides Lefebvre (Lepidoptera: Noctuidae) from Greece and Spain. In total, 75 lines from Greece and 85 lines from Spain were screened for survival of F2 larvae on Cry1Ab corn, Zea mays L., leaves. No major resistance alleles were found. The frequency of resistance alleles in the Greek population was <9.7 x 10(-3) with 95% probability, which was very similar to that of the Spanish population (<8.6 x 10(-3) with 95% probability), and the expected frequencies were 3.2 x 10(-3) (0-0.0097) and 2.9 x 10(-3) (0-0.0086) in Greece and Spain (pooled 1.5 x 10(-3)). The experiment-wise detection probability of resistance was 94.0 and 97.5% for the Greek and the Spanish population, respectively. Evidence of alleles conferring partial resistance to Cry1Ab was found only for the Greek population. The frequency of alleles for partial resistance was estimated as 6.5 x 10(-3) with a 95% credibility interval between 8 x 10(-4) and 17.8 x 10(-3) and a detection probability of 94%. Our results suggest that the frequency of alleles conferring resistance to CrylAb, regarding the population of S. nonagrioides, may be rare enough so that the high-dose/refuge strategy could be applied with success for resistance management.     

Sixth and seventh cusp on lower molar teeth of Icelanders

The occurrence of lower molar accessory cusps c6 and c7 is studied in three local populations of known Caucasoid origin in the Northeast of Iceland. The sample comprises 1,010 school-children, 506 boys and 504 girls. The scoring is made from dental stone casts with reference to standard plaques. Only the frequency of c6 on the second deciduous molar is relatively low as expected in a Caucasoid population. Otherwise both c6 and c7 are more common than expected, the frequencies are in fact comparable to those predicted by the Mongoloid dental complex for Mongoloid populations.     

Host Genetic Analysis by Using Puccinia recondita tritici Induced Mutants for Increased Virulence

Monogenic lines derived by recombination from Buck Manantial wheat, a cultivar which has durable resistance, were used as hosts to detect Puccinia recondita tritici induced mutants for increased virulence. After treatments with ethyl methane sulphonate on clone 66 of P. recondita 9 types of mutants were obtained at approximate frequencies of 1 × 10^?4 and host lines were grouped in 6 classes, No increase virulence was obtained against B. Manantial after 2 cycles of treatments, but different combinations of virulences were observed on monogenic lines derived from it. Simultaneity of occurrence of some mutational events suggests complexity of virulence genes in the pathogen. At least 4 genes for incompatibility are present in B. Manantial when confronted with clone 66 and 4 to 7 mutational points are recognized in the pathogen. The specific relationships tending to equate the number of genes in both organisms would not be a general rule. Durable resistance can be explained by a combination of several specific disease reaction genes for which the pathogen population has not been able to accumulate all the corresponding alleles for virulence.     

Evolution of Microsatellites in the Yeast Saccharomyces cerevisiae: Role of Length and Number of Repeated Units

The observed and expected frequencies of occurrence of microsatellites in the yeast Saccharomyces cerevisiae were investigated. In all cases, the observed frequencies exceeded the expected ones. In contrast to predictions by Messier et al. (1996), there is no critical number of repeats beyond which the observed frequencies of microsatellites significantly exceed the frequencies expected in a random DNA sequence of the same size. Rather, the degree of deviation from expectation was found to be dependent on the length of the microsatellite. That is, a fourfold concatemeric repeat of 3 bp was found to deviate from expectation as much as threefold concatemeric repeat of 4 bp, unlike the deviation of a fourfold concatemeric repeat of 4 bp. These findings suggest that microsatellites evolve through strand-slippage events, rather than recombination events. This, in turn, suggests that the chances of erroneous hybridizations leading to strand-slippage are length dependent. Received: 1 June 1998 / Accepted: 16 September 1998     

Genetic variation of new 21 autosomal short tandem repeat loci in a Chinese Salar ethnic group

In the present study, we reported the allele frequencies for new 21 autosomal short tandem repeat (STR) loci, including D6S474, D12ATA63, D22S1045, D10S1248, D1S1677, D11S4463, D1S1627, D3S4529, D2S441, D6S1017, D4S2408, D19S433, D17S1301, D1GATA113, D18S853, D20S482, D14S1434, D9S1122, D2S1776, D10S1435 and D5S2500 loci. Forensic statistical parameters were estimated from a sample set of 120 unrelated healthy individuals from the Salar ethnic group in Xunhua Salar Autonomous County of Qinghai province, China. A total of 151 alleles were observed at 21 STR loci in the population, and their allele frequencies were in the range of 0.004–0.554. All STR loci showed a high degree of genetic polymorphisms, and the combined probability of exclusion, combined power of discrimination and combined probability of matching for all 21 STR loci were 0.9999993134, 0.99999999999999999991739 and 8.2607 × 10⁻²⁰, respectively. For all the 21 STR loci in the Salar ethnic group, the observed genotypic data showed no significant deviation from those expected under the Hardy-Weinberg equilibrium. The allele frequency distributions for the 21 autosomal STR loci were compared between the Salar group and its neighboring populations and significant differences were detected among these populations at D1S1677, D2S441, D3S4529, D4S2408, D6S1017, D11S4463, D12ATA63, D14S14343, D18S853, D19S433 and D22S1045 loci.     

Namesakes or relatives? Approaches to investigating the relationship between Y chromosome haplogroups and surnames

Population genetics successfully applies surnames as quasi-genetic markers when estimating similarity between populations and calculating the level of random inbreeding. These calculations are based on the isonymy coefficient, which assumes that every surname is monophyletic, i.e., it originated from a single common ancestor and all namesakes are therefore relatives. On the other hand, there is a general opinion that a typical Russian surname is polyphyletic: it originated multiple times and most namesakes are, therefore, not related to each other. Combined studies of Y chromosomes and surnames now allow us to address this issue. This study discusses approaches to statistical evaluation of Y chromosome haplogroup frequencies in groups of people bearing the same surname (namesakes). The proposed index of accumulated haplogroup frequency eliminates the artifactual effect of a randomly increased haplogroup frequency in namesakes by subtracting its population (expected) frequency from the observed value, while the expected frequency is calculated as the weighted average of the frequencies of this haplogroup in the populations where the surname carriers come from. From the total sample (comprising 1244 persons from 13 populations of the historical Russian area), 123 individuals carrying 14 most frequent surnames were chosen. A comparison of the haplogroup frequencies in these 14 namesake groups and in 14 respective population control groups compiled from the total sample showed that accumulation of certain Y chromosome haplogroups was nonrandom even in carriers of widespread surnames. An analysis of Y-STR haplotypes rather than Y-SNP haplogroups could provide a better insight into relationships between namesakes and will be the subject of further research.     

Theoretical exclusion percentages obtainable by blood grouping of pigs

On the basis of the frequency of blood group alleles in Danish Landrace pigs, the theoretical probability of excluding incorrectly alleged paternity and parentage by means of the various blood group systems are calculated. The probability of excluding incorrect paternity of 1 and 4 pigs, will be 85 and 97%, respectively. In 96% of the cases, the parentage of an accidentally interchanged pig can be excluded.
A study of the progeny groups actually excluded during the period 1960-1968, showed good agreement between the observed and theoretically expected frequencies of exclusions in the various blood group systems, except for the G-system.